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Chapter 7

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The Structure and Replication of Genomes

bull Genetics bull Study of inheritance and inheritable traits as expressed

in an organisms genetic material

bull Genome bull The entire genetic complement of an organism

bull Includes its genes and nucleotide sequences

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Figure 71 The structure of nucleic acids

Hydrogen bond

SugarAdenine (A)nucleoside

Thymine (T)nucleoside

AndashT base pair (DNA) AndashU base pair (RNA)

Adenine (A)nucleoside

Uracil (U)nucleoside

Guanine (G)nucleoside

Cytosine (G)nucleoside

Double-stranded DNA

3prime end

5prime end3prime end

Adenine Thymine

5 endprime

Thymine nucleoside

Guanine Cytosine

GndashC base pair (DNA and RNA)

5prime end 5prime end3prime end

Thymine nucleotide

T A

CG

A T

G

3prime end

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Prokaryotic chromosomes

bull Main portion of DNA along with associated proteins and

RNA

bull Prokaryotic cells are haploid (single chromosome copy)

bull Typical chromosome is circular molecule of DNA in

nucleoid

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Figure 72 Bacterial genome

Nucleoid

Bacterium

Chromosome

Plasmid

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull Genetics bull Study of inheritance and inheritable traits as expressed

in an organisms genetic material

bull Genome bull The entire genetic complement of an organism

bull Includes its genes and nucleotide sequences

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Figure 71 The structure of nucleic acids

Hydrogen bond

SugarAdenine (A)nucleoside

Thymine (T)nucleoside

AndashT base pair (DNA) AndashU base pair (RNA)

Adenine (A)nucleoside

Uracil (U)nucleoside

Guanine (G)nucleoside

Cytosine (G)nucleoside

Double-stranded DNA

3prime end

5prime end3prime end

Adenine Thymine

5 endprime

Thymine nucleoside

Guanine Cytosine

GndashC base pair (DNA and RNA)

5prime end 5prime end3prime end

Thymine nucleotide

T A

CG

A T

G

3prime end

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Prokaryotic chromosomes

bull Main portion of DNA along with associated proteins and

RNA

bull Prokaryotic cells are haploid (single chromosome copy)

bull Typical chromosome is circular molecule of DNA in

nucleoid

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Figure 72 Bacterial genome

Nucleoid

Bacterium

Chromosome

Plasmid

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 71 The structure of nucleic acids

Hydrogen bond

SugarAdenine (A)nucleoside

Thymine (T)nucleoside

AndashT base pair (DNA) AndashU base pair (RNA)

Adenine (A)nucleoside

Uracil (U)nucleoside

Guanine (G)nucleoside

Cytosine (G)nucleoside

Double-stranded DNA

3prime end

5prime end3prime end

Adenine Thymine

5 endprime

Thymine nucleoside

Guanine Cytosine

GndashC base pair (DNA and RNA)

5prime end 5prime end3prime end

Thymine nucleotide

T A

CG

A T

G

3prime end

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Prokaryotic chromosomes

bull Main portion of DNA along with associated proteins and

RNA

bull Prokaryotic cells are haploid (single chromosome copy)

bull Typical chromosome is circular molecule of DNA in

nucleoid

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Figure 72 Bacterial genome

Nucleoid

Bacterium

Chromosome

Plasmid

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Prokaryotic chromosomes

bull Main portion of DNA along with associated proteins and

RNA

bull Prokaryotic cells are haploid (single chromosome copy)

bull Typical chromosome is circular molecule of DNA in

nucleoid

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Figure 72 Bacterial genome

Nucleoid

Bacterium

Chromosome

Plasmid

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 72 Bacterial genome

Nucleoid

Bacterium

Chromosome

Plasmid

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull The Structure of Prokaryotic Genomesbull Plasmids

bull Small molecules of DNA that replicate independently

bull Not essential for normal metabolism growth or reproduction

bull Can confer survival advantages

bull Many types of plasmids

bull Fertility factors

bull Resistance factors

bull Bacteriocin factors

bull Virulence plasmids

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Nuclear chromosomes

bull Typically have more than one chromosome per cell

bull Chromosomes are linear and sequestered within nucleus

bull Eukaryotic cells are often diploid (two chromosome

copies)

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 73 Eukaryotic nuclear chromosomal packaging

10 nm

HistonesLinkerDNA

DNA

10 nm

Nucleosomes Chromatin fiber Euchromatin andheterochromatin

Highly condensedduplicated chromosome of dividing nucleus

Active(loosely packed)

Inactive(tightlypacked)

Nucleosome

30 nm 700 nm1400 nm

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull The Structure of Eukaryotic Genomesbull Extranuclear DNA of eukaryotes

bull DNA molecules of mitochondria and chloroplasts

bull Resemble chromosomes of prokaryotes

bull Code only for about 5 of RNA and proteins

bull Some fungi algae and protozoa carry plasmids

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull DNA Replicationbull Key to replication is complementary structure of the two

strands

bull Replication is semiconservative

bull New DNA composed of one original and one daughter

strand

bull Anabolic polymerization process that requires

monomers and energy

bull Triphosphate deoxyribonucleotides serve both functions

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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DNA Replication Overview

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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DNA Replication

>

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 74 Semiconservative model of DNA replication

OriginalDNA

Firstreplication

Secondreplication

Original strand

New strands

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Guanosine triphosphate deoxyribonucleotide (dGTP)

Guanine nucleotide (dGMP)

High-energybond

DeoxyriboseGuanine base

Guanosine (nucleoside)

Existing DNA strand Triphosphatenucleotide

Diphosphate releasedenergy used for synthesis

Longer DNA strand

OH

Figure 75 The dual role of triphosphate deoxyribonucleotides as building blocks and energy sources in DNA synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull DNA Replicationbull Initial processes in bacterial DNA replication

bull Replication begins at the origin

bull DNA polymerase replicates DNA only 5prime to 3prime

bull Because strands are antiparallel new strands are

synthesized differently

bull Leading strand synthesized continuously

bull Lagging strand synthesized discontinuously

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 76a DNA replication

Chromosomal proteins(histones in eukaryotes andarchaea) removed

DNA helicase

Replication fork

DNA polymerase III

Initial processesStabilizing proteins

3prime

5prime

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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DNA Replication Replication Proteins

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Primase

RNA primer

Leading strand

Triphosphatenucleotide

Replication fork

Synthesis of leading strand

Replication fork

Triphosphatenucleotide

Okazakifragment Lagging

strand

DNA ligaseDNA polymerase IDNA polymerase IIIPrimase

RNAprimer

Synthesis of lagging strand

98

76

10

2

3 1

P P+

3prime5prime

3prime5prime

Figure 76b-c DNA replication

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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DNA Replication Forming the Replication Fork

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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DNA Replication Synthesis

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull DNA Replicationbull Other characteristics of bacterial DNA replication

bull Bidirectional

bull Gyrases and topoisomerases remove supercoils in DNA

bull DNA is methylated

bull Control of genetic expression

bull Initiation of DNA replication

bull Protection against viral infection

bull Repair of DNA

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 77 The bidirectionality of DNA replication in prokaryotes

Origin Parentalstrand

Daughterstrand

Replication forks

Replicationproceeds in both directions Termination

of replication

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull DNA Replicationbull Replication of eukaryotic DNA

bull Similar to bacterial replication

bull Some differences

bull Uses four DNA polymerases

bull Thousands of replication origins

bull Shorter Okazaki fragments

bull Plant and animal cells methylate only cytosine bases

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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The Structure and Replication of Genomes

bull Tell Me Whybull DNA replication requires a large amount of energy yet

none of a cells ATP energy supply is used Why isnt it

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull The Relationship Between Genotype and

Phenotypebull Genotype

bull Set of genes in the genome

bull Phenotype

bull Physical features and functional traits of the organism

bull Genotype determines phenotype

bull Not all genes are active at all times

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull The Transfer of Genetic Informationbull Transcription

bull Information in DNA is copied as RNA

bull Translation

bull Polypeptides are synthesized from RNA

bull Central dogma of genetics

bull DNA is transcribed to RNA

bull RNA is translated to form polypeptides

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 78 The central dogma of genetics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Transcription Overview

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Translation Overview

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull The Events in Transcriptionbull Five types of RNA transcribed from DNA

bull RNA primersbull mRNAbull rRNAbull tRNAbull Regulatory RNA

bull Occur in nucleoid of prokaryotesbull Three steps

bull Initiation bull Elongation bull Termination

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 79a The events in the transcription of RNA in prokaryotes

RNA polymerase attachesnonspecifically to DNA andtravels down its length untilit recognizes a promotersequence Sigma factorenhances promoterrecognition in bacteria

Upon recognition of thepromoter RNA polymeraseunzips the DNA moleculebeginning at the promoter

Unzipping of DNA movement of RNA polymerase

Attachment of RNA polymerase

Sigma factorPromoter

RNA polymerase

Bubble

Terminator

TemplateDNA strand

DNA

Initiation of transcription

5prime

3prime

5prime

5prime 3prime

3prime5prime

3prime

1a

1b

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 79b The events in the transcription of RNA in prokaryotes

Triphosphate ribonucleotidesalign with their DNAcomplements and RNApolymerase links themtogether synthesizing RNANo primer is needed Thetriphosphate ribonucleotidesalso provide the energyrequired for RNA synthesis

Elongation of the RNA transcript

Growing RNA molecule(transcript)

Bubble

TemplateDNAstrand

2

5prime

3prime

3prime

5prime5prime

5prime3prime

3prime

3prime

5prime

PP P

PPP

CG A

T A C C A C CAG

GUGGU

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 710 Concurrent RNA transcription

3prime 3prime 3prime 3prime 3prime 3prime 3prime 3prime5prime

5prime

5prime5prime5prime

5prime

5prime

5prime

Promoter

RNA polymerases

Sigma factor

RNA

Template DNAstrand

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 79c The events in the transcription of RNA in prokaryotes

3prime5prime

5prime

3prime

3prime

3prime

5prime

Self-termination transcription of GC-rich terminatorregion produces a hairpin loop which creates tensionloosening the grip of the polymeraseon the DNA

Rho-dependant termination Rho pushes between polymeraseand DNA This causes release of polymerase RNA transcriptand Rho

GC-richhairpinloop

Termination of transcription release of RNA polymerase

Templatestrand

Rho protein movesalong RNA

Rho terminationprotein

RNA polymerase

RNA transcriptreleased

Terminator

CC CCCG GAAAAAAAAT

UUUUUUUUU

3b3a

TerminatorTerminator

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Transcription The Process

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull The Events in Transcriptionbull Transcriptional differences in eukaryotes

bull RNA transcription occurs in the nucleus

bull Transcription also occurs in mitochondria and chloroplasts

bull Three types of nuclear RNA polymerases

bull Numerous transcription factors

bull mRNA is processed before translation

bull Capping

bull Polyadenylation

bull Splicing

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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3prime

3prime

3prime 5prime

5prime

5prime

5prime

Introns (noncoding regions)

TemplateDNA strand

Exon 1

cap Intron 1 Intron 2 Intron 3

Exon 2 Exon 3Pre-mRNA

Poly-A tail

Exon 1

Spliceosomes

Exons (polypeptide coding regions)

Processing

mRNA splicing

mRNA (codes forone polypeptide)

Nuclear envelopeNucleoplasm

Cytosol

mRNA

Nuclear pore

Exon 2Exon 3

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

AAAAAAAAAAAAAA

A

Intron 1

AAAAA

AAAAAA AA

Transcription

Figure 711 Processing eukaryotic mRNA

AA A AA

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Translationbull Process in which ribosomes use genetic information of

nucleotide sequences to synthesize polypeptides

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 712 The genetic code

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Translation Genetic Code

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Translationbull Participants in translation

bull Messenger RNA

bull Transfer RNA

bull Ribosomes and ribosomal RNA

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 713 A single prokaryotic mRNA can code for several polypeptides

5prime

5prime3prime

3prime

Promoter Gene 1 Gene 2 Gene 3 TerminatorTemplateDNA strand

StartcodonAUG

StartcodonAUG

StartcodonAUGUAA UAG UAA

Ribosomebindingsite (RBS)

Stopcodon

RBS Stopcodon

RBS Stopcodon

UntranslatedmRNA

mRNA

Polypeptide 1 Polypeptide 2 Polypeptide 3

Translation

Transcription

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 714 Transfer RNA

Acceptorstem

Hydrogenbonds

Hairpinloops

tRNA icon

Anticodon

Anticodon

5prime5prime

3prime

3prime

A C C

OH

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 715 Ribosomal structures

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 716 Assembled ribosome and its tRNA-binding sites

Largesubunit

mRNA

Smallsubunit

Prokaryotic ribosome(angled view) attachedto mRNA

Largesubunit

Nucleotidebases

Prokaryotic ribosome(schematic view) showingtRNA-binding sites

Smallsubunit

tRNA-bindingsites

Esite

Psite

Asite

mRNA

5prime 3prime

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Translationbull Events in translation

bull Three stages of translation

bull Initiation

bull Elongation

bull Termination

bull All stages require additional protein factors

bull Initiation and elongation require energy (GTP)

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Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 717 The initiation of translation in prokaryotes

fMetInitiatortRNA

AnticodonmRNA Start codon

Smallribosomalsubunit

GTP GDP P

fMet

tRNA

fMet

Initiation complex

5prime 3prime

fMet

Largeribosomalsubunit

UU U U AU GGA CA C

AP

U U U AU GGA C

AP

U U U AU GGA CU A C

AP

U AC

1 2 3

E

+

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Protein Synthesis

>

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 718 The elongation stage of translation

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ribosomes and polypeptides

mRNA Ribosomes Polypeptides mRNA Ribosomes Polypeptides

Direction oftranscription

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Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Gene Function

bull Translationbull Events in translation

bull Termination

bull Release factors recognize stop codons

bull Modify ribosome to activate ribozymes

bull Ribosome dissociates into subunits

bull Polypeptides released at termination may function

alone or together

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Protein Synthesis

>

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

copy 2015 Pearson Education Inc

Operons Overview

copy 2015 Pearson Education Inc

Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

copy 2015 Pearson Education Inc

Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Translation The Process

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Translationbull Translation differences in eukaryotes

bull Initiation occurs when ribosomal subunit binds to 5prime

guanine cap

bull First amino acid is methionine rather than f-methionine

bull Ribosomes can synthesize polypeptides into the cavity of

the rough endoplasmic reticulum

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

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Protein Synthesis

>

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

copy 2015 Pearson Education Inc

Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Protein Synthesis

>

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Regulation of Genetic Expressionbull Most genes are expressed at all times

bull Other genes are transcribed and translated when cells

need them

bull Allows cell to conserve energy

bull Quorum sensing regulates production of some proteins

bull Detection of secreted quorum-sensing molecules can

signal bacteria to synthesize a certain protein

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Regulation of Genetic Expressionbull Regulation of polypeptide synthesis

bull Typically halts transcription

bull Can stop translation directly

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull An operon consists of a promoter and a series of genes

bull Controlled by a regulatory element called an operator

bull Typically polycistronic (code for several polypeptides)

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 720 An operon

OperonPromoter Operator Structural genes

Template DNA strandRegulatory gene

5prime43213prime

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Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull Nature of prokaryotic operons

bull Inducible operons must be activated by inducers

bull Lactose operon

bull Repressible operons are transcribed continually until

deactivated by repressors

bull Tryptophan operon

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Operons Overview

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Template DNAstrand

Template DNA strand

RNA polymerase

lac operon

Operator(blocked)PromoterPromoter and

regulatory gene

Continual transcription

Repressor mRNA

Repressor

lac operon repressed

Lactose catabolism genes

TranscriptionproceedsRepressor

cannot bind

Repressor

Inactivatedrepressor

Inducer (allolactosefrom lactose)

lac operon induced

mRNA forlactose catabolism

2 31

3prime

3prime 5prime

5prime

5prime

RNApolymerasecannotbind

1

2

3

4

2 31

Continual translation

Repressor mRNA

Figure 721 The lac operon an inducible operon

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 722 CAP-cAMP enhances lac transcription

CAP binding site

lac genes

RNA polymerase

Transcription proceeds

Promoter Operator

cAMP bound to CAP

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

copy 2015 Pearson Education Inc

Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Operons Induction

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Figure 723 The trp operon a repressible operon

Regulatory gene

mRNA

Inactive repressor

trp operon active

Promoter

trp operon with five genes

Transcription

Enzymes of tryptophan biosynthetic pathway

Template DNA strand

Tryptophan

Operator blocked

Inactiverepressor

trp operon repressed

Trp

3prime

Movement of RNA polymerase ceases

Trp

Tryptophan (corepressor) Activated

repressor

mRNA coding multiple polypeptides5prime 3prime

Operator

5prime

1 2 3 4 55prime

3prime

1 2 3 4 55prime

TrpTrp

Trp

Trp

3prime

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Operons Repression

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull microRNAs

bull Produced by eukaryotic cells

bull Bind regulatory proteins to form miRNA-induced

silencing complex (miRISC)

bull Bind complementary mRNA and inhibit its

translation

bull Regulates several cellular processes

copy 2015 Pearson Education Inc

Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

copy 2015 Pearson Education Inc

Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

copy 2015 Pearson Education Inc

Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

copy 2015 Pearson Education Inc

Mutations Types

copy 2015 Pearson Education Inc

Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Regulation of Genetic Expressionbull RNA molecules can control translation

bull Regulatory RNAs can regulate translation of polypeptides

bull Short interference RNA (siRNA)

bull RNA molecule complementary to a portion of mRNA tRNA or DNA

bull Binds RISC proteins to form siRISC

bull siRISC binds and cuts the target nucleic acid

bull Riboswitch

bull RNA molecule that changes shape to help regulate translation

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

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Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

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Gene Function

bull Tell Me Whybull In bacteria polypeptide translation can begin even

before mRNA transcription is complete Why cant this

happen in eukaryotes

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Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

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Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

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Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

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Mutagens

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Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

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Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

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Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

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Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

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Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

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Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

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Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutation bull Change in the nucleotide base sequence of a genome

bull Rare event

bull Almost always deleterious

bull Rarely leads to a protein that improves ability of

organism to survive

copy 2015 Pearson Education Inc

Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

copy 2015 Pearson Education Inc

Mutations Types

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Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Types of Mutationsbull Point mutations

bull One base pair is affected

bull Substitutions and frameshift mutations

bull Frameshift mutations

bull Nucleotide triplets after the mutation are displaced

bull Creates new sequence of codons

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Mutations Types

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Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

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Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

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Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

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Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

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Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

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Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations Types

copy 2015 Pearson Education Inc

Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

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copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

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Transposons Insertion Sequences

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Transposons Complex Transposons

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Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 724 The effects of the various types of point mutations

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

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Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

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Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

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Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

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Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

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Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

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Transformation

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

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Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

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Transduction Generalized Transduction

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Transduction Specialized Transduction

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

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Conjugation F Factor

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F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

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Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

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Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Mutagensbull Radiation

bull Ionizing radiationbull Nonionizing radiation

bull Chemical mutagensbull Nucleotide analogs

bull Disrupt DNA and RNA replicationbull Nucleotide-altering chemicals

bull Alter the structure of nucleotidesbull Result in base-pair substitutions and missense

mutationsbull Frameshift mutagens

bull Result in nonsense mutations

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

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Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

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Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

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Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

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Horizontal Gene Transfer Overview

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Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutagens

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 725 A pyrimidine (in this case thymine) dimer

Ultraviolet light

Thymine dimer

G

C

C T G T AGG

G A C A A C C A T

T T=

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 726 The structure and effects of a nucleotide analog

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 727 The action of a frameshift mutagen

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Frequency of Mutationbull Mutations are rare events

bull Otherwise organisms could not effectively reproduce

bull About 1 of every 10 million genes contains an error

bull Mutagens increase the mutation rate by a factor of 10 to

1000 times

bull Many mutations stop transcription or code for

nonfunctional proteins

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations Repair

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 728a-b DNA repair mechanisms

Visible light

Thymine dimer

Light-activated repair enzyme

Cut

Repairenzyme

Light repair

Dark repair

DNA polymerase Iand ligase repairthe gap

G A C A

C T G A A T

T

C T G A A T

G A C AT TT=

C T G A A T

G A C AT T

G

C

C T G A A T

GA C A

T T

G

C

C T G A A T

G A C AT T

G

C=

=

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 728c-d DNA repair mechanisms

Base excision repair enzymes remove incorrect nucleotide

DNA polymerase I and ligase repair gap

Mutated DNA(incorrect nucleotide pair)

Mismatch repair enzyme removes incorrect segment

DNA polymerase III correctly repairs the gap

Mismatch repair

Base-excision repair

C C G A A T

G G C AT T

A

T C G T

G C AC C G A A T

G G C AT T

A

C G T

G C AC C G A A T

G G C AT T

A

G C G T

G C A

G G A T

C AT T

C

G C G T

G C A G G A T

CAT T

C

G C G T

G C A G G A T

C AC T

C

G C G T

G C A

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Identifying Mutants Mutagens and Carcinogens

bull Mutants

bull Descendants of a cell that does not repair a mutation

bull Wild types

bull Cells normally found in nature

bull Methods to recognize mutants

bull Positive selection

bull Negative (indirect) selection

bull Ames test

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

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Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

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Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

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Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 729 Positive selection of mutants

Medium with penicillin (only penicillin-resistant cell grows into colony)

Medium without penicillin (both types of cells form colonies)

Penicillin-sensitive cells

Penicillin- resistant cell

Penicillin- resistantmutants indistinguishable from nonmutants

Medium with penicillin Medium withoutpenicillin

Mutagen induces mutations

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 730 The use of negative (indirect) selection to isolate a tryptophan auxotroph

Bacteria

Stamp replica plates with velvet

Complete medium containing tryptophan

Medium lacking tryptophan

IncubationIdentify auxotrophas colony growing on complete medium but not on lacking medium

Tryptophan auxotroph cannot grow

All colonies grow

Inoculate auxotroph colony into complete medium

X

X X

XX

4

5

6

Bacterial suspension

Bacterial colonies grow A few may be tryptophan auxotrophs Most are wild type

Incubation

Mutagen

Inoculate bacteria onto complete medium containing tryptophan

Stamp sterile velvet onto plate picking up cells from each colony

Sterile velvet surface

3

2

1

X

X

X

X

X

X

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 731 The Ames test

Colony of revertant (his+) Salmonella

No growth

Incubation

Medium lacking

histidine

Liver extract

Experimental tube

Suspected mutagen

Liver extract

Control tube

Culture of hisndash Salmonella

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Mutations of Genes

bull Tell Me Whybull Changes in RNA resulting from poor transcription of

RNA to DNA are not as deleterious to an organism as

changes to its DNA resulting from mutations Why is this

the case

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Exchange of nucleotide sequences often occurs

between homologous sequences

bull Recombinants

bull Cells with DNA molecules that contain new nucleotide

sequences

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 732 Genetic recombination

Homologous sequences

Enzyme nicks one strand of DNA at homologous sequence

Recombination enzyme inserts the cut strand into second molecule which is nicked in the process

Ligase anneals nicked ends in new combinations

Molecules resolve into recombinants

Recombinant A

Recombinant B

3prime DNA A

DNA B5prime3prime5prime

A

B

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotes

bull Vertical gene transfer

bull Passing of genes to the next generation

bull Horizontal gene transfer

bull Donor cell contributes part of genome to recipient cell

bull Three types

bull Transformation

bull Transduction

bull Bacterial conjugation

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Horizontal Gene Transfer Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transformation

bull Recipient cell takes up DNA from the environment

bull Provided evidence that DNA is genetic material

bull Cells that take up DNA are competent

bull Results from alterations in cell wall and cytoplasmic

membrane that allow DNA to enter cell

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 733 Transformation of Streptococcus pneumoniae

Observations of Streptococcus pneumoniae

Live cellsInjection

Capsule

Heat-treateddead cells ofstrain S Injection

Strain R live cells(no capsule)

Injection

Griffiths experimentLivingstrain R

Mouse dies

Mouse lives

Mouse lives

Heat-treateddead cellsof strain S

Injection

Mouse dies

Culture ofStreptococcusfrom deadmouse

Living cellswith capsule(strain S)

In vitro transformation

Heat-treateddead cells ofstrain S

DNA brokeninto pieces

DNA fragmentfrom strain S

Living strain R

Some cells takeup DNA from theenvironment andincorporate it intotheir chromosomes

Transformed cellsacquire ability tosynthesize capsules

+

XXXX

XXXX XXXX

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transformation

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

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Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

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Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Transfer of DNA from one cell to another via replicating

virus

bull Virus must be able to infect both donor and recipient cells

bull Virus that infects bacteria called a bacteriophage (phage)

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 734 Transduction

Phage injects its DNA

Phage enzymesdegrade host DNA

PhageDNA

Cell synthesizes newphages that incorporatephage DNA and mistakenlysome host DNA

Transducing phageinjects donor DNA

Donor DNA is incorporatedinto recipients chromosomeby recombination

InsertedDNA

Transduced cell

Recipient host cell

Transducing phage

Phage with donor DNA(transducing phage)

Bacterial chromosome

BacteriophageHost bacterial cell(donor cell)

1

2

3

4

5

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Transduction

bull Generalized transduction

bull Transducing phage carries random DNA segment

from donor to recipient

bull Specialized transduction

bull Only certain donor DNA sequences are transferred

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transduction Generalized Transduction

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transduction Specialized Transduction

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Horizontal Gene Transfer Among Prokaryotesbull Conjugation

bull Genetic transfer requires physical contact between the

donor and recipient cell

bull Donor cell remains alive

bull Mediated by conjugation (sex) pili

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Conjugation Overview

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Conjugation F Factor

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

F plasmid Origin oftransfer

Pilus Chromosome

F

Donor cell attaches to a recipient cell withits pilus

Pilus may draw cells together

One strand of F plasmid DNA transfersto the recipient

The recipient synthesizes a complementarystrand to become an F+ cell with a pilus thedonor synthesizes a complementary strandrestoring its complete plasmid

Pilus

1

+ cell

2

F+ cell

3

4

F_

cellF+ cell

Figure 735 Bacterial conjugation

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 736 Conjugation involving an Hfr cellDonor chromosome

Pilus

F+ cell

Hfr cell

Pilus

F+ cell (Hfr)

F plasmid Donor DNA Part of F plasmid

F recipient

Incomplete F plasmidcell remains Fminus

F plasmid integratesinto chromosome byrecombination

Cells join via a pilus

Portion of F plasmid partiallymoves into recipient celltrailing a strand of donorsDNA

Conjugation ends with piecesof F plasmid and donor DNAin recipient cell cells synthesizecomplementary DNA strands

Donor DNA and recipientDNA recombine making arecombinant F cell

Recombinant cell (still Fminus )

ndash

1

2

3

4

5ndash

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Conjugation Hfr Conjugation

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Conjugation Chromosome Mapping

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Transposons

bull Segments of DNA that move from one location to another

in the same or different molecule

bull Result is a kind of frameshift insertion (transpositions)

bull Transposons all contain palindromic sequences at each

end

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 737 Transposition

DNATransposon

Jumping transposons Transposons move from one place to another on a DNA molecule

Replicating transposons Transposons may replicate while moving resulting in more transposons in the cell

Transposons can move onto plasmidsTransposons moving onto plasmids can be transferred to another cell

Plasmid withtransposon

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transposons Overview

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Transposons and Transpositionbull Simplest transposons

bull Insertion sequences

bull Have no more than two inverted repeats and a gene for

transposase

bull Complex transposons

bull Contain one or more genes not connected with

transposition

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Figure 738 TransposonsTransposon Insertion sequence IS1

Inverted repeat (IR) Transposase gene Inverted repeat (IR)

Target site

DNAmolecule

IS1

Target IS1

Transposase

Target site Copy of IS1

Copy oftarget site

OriginalIS1

Complex transposon

IS1

Kanamycin-resistancegene IS1

IR

A C T GT A C T TAT G A A T G A C T A

TA A

A AAATT

TTTTAC G G

G C C

IRIRIR

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transposons Insertion Sequences

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Transposons Complex Transposons

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Genetic Recombination and Transfer

bull Tell Me Whybull Why is the genetic ancestry of microbes much more

difficult to ascertain than the ancestry of animals

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics

copy 2015 Pearson Education Inc

Important topics

bull Structure of chromosomendash DNAndash Histonndash Chromatidndash Nucleosome

bull Comparison between bacterial and eukaryotic chromosomebull Bacterial plasmid

ndash Structure ndash Function

bull Replication processbull Transcription processbull Translation processbull Different forms of mutation

ndash Frameshiftndash Silentndash Missensendash Nonsense

bull Transformation vs conjugation and transduction

• Chapter 7
• The Structure and Replication of Genomes
• Figure 71 The structure of nucleic acids
• The Structure and Replication of Genomes (2)
• Figure 72 Bacterial genome
• The Structure and Replication of Genomes (3)
• The Structure and Replication of Genomes (4)
• Figure 73 Eukaryotic nuclear chromosomal packaging
• The Structure and Replication of Genomes (5)
• Slide 10
• The Structure and Replication of Genomes (6)
• DNA Replication Overview
• DNA Replication
• Figure 74 Semiconservative model of DNA replication
• Figure 75 The dual role of triphosphate deoxyribonucleotides
• The Structure and Replication of Genomes (7)
• Figure 76a DNA replication
• DNA Replication Replication Proteins
• Figure 76b-c DNA replication
• DNA Replication Forming the Replication Fork
• DNA Replication Synthesis
• The Structure and Replication of Genomes (8)
• Figure 77 The bidirectionality of DNA replication in prokaryo
• The Structure and Replication of Genomes (9)
• The Structure and Replication of Genomes (10)
• Gene Function
• Gene Function (2)
• Figure 78 The central dogma of genetics
• Transcription Overview
• Translation Overview
• Gene Function (3)
• Figure 79a The events in the transcription of RNA in prokaryo
• Figure 79b The events in the transcription of RNA in prokaryo
• Figure 710 Concurrent RNA transcription
• Figure 79c The events in the transcription of RNA in prokaryo
• Transcription The Process
• Gene Function (4)
• Figure 711 Processing eukaryotic mRNA
• Gene Function (5)
• Figure 712 The genetic code
• Translation Genetic Code
• Slide 42
• Gene Function (6)
• Figure 713 A single prokaryotic mRNA can code for several pol
• Figure 714 Transfer RNA
• Figure 715 Ribosomal structures
• Figure 716 Assembled ribosome and its tRNA-binding sites
• Gene Function (7)
• Figure 717 The initiation of translation in prokaryotes
• Figure 718 The elongation stage of translation
• Figure 719 In prokaryotes a polyribosomemdashone mRNA and many ri
• Gene Function (8)
• Translation The Process
• Gene Function (9)
• Slide 55
• Protein Synthesis
• Gene Function (10)
• Gene Function (11)
• Gene Function (12)
• Figure 720 An operon
• Gene Function (13)
• Operons Overview
• Figure 721 The lac operon an inducible operon
• Figure 722 CAP-cAMP enhances lac transcription
• Operons Induction
• Figure 723 The trp operon a repressible operon
• Operons Repression
• Slide 68
• Gene Function (14)
• Gene Function (15)
• Gene Function (16)
• Mutations of Genes
• Mutations of Genes (2)
• Mutations Types
• Figure 724 The effects of the various types of point mutation
• Slide 76
• Mutations of Genes (3)
• Mutagens
• Figure 725 A pyrimidine (in this case thymine) dimer
• Figure 726 The structure and effects of a nucleotide analog
• Figure 727 The action of a frameshift mutagen
• Mutations of Genes (4)
• Mutations Repair
• Figure 728a-b DNA repair mechanisms
• Figure 728c-d DNA repair mechanisms
• Mutations of Genes (5)
• Figure 729 Positive selection of mutants
• Figure 730 The use of negative (indirect) selection to isolat
• Figure 731 The Ames test
• Mutations of Genes (6)
• Genetic Recombination and Transfer
• Figure 732 Genetic recombination
• Genetic Recombination and Transfer (2)
• Horizontal Gene Transfer Overview
• Genetic Recombination and Transfer (3)
• Figure 733 Transformation of Streptococcus pneumoniae
• Transformation
• Genetic Recombination and Transfer (4)
• Figure 734 Transduction
• Genetic Recombination and Transfer (5)
• Transduction Generalized Transduction
• Transduction Specialized Transduction
• Genetic Recombination and Transfer (6)
• Conjugation Overview
• Conjugation F Factor
• Figure 735 Bacterial conjugation
• Figure 736 Conjugation involving an Hfr cell
• Conjugation Hfr Conjugation
• Conjugation Chromosome Mapping
• Slide 110
• Genetic Recombination and Transfer (7)
• Figure 737 Transposition
• Transposons Overview
• Genetic Recombination and Transfer (8)
• Figure 738 Transposons
• Transposons Insertion Sequences
• Transposons Complex Transposons
• Genetic Recombination and Transfer (9)
• Important topics