biology i ch.17 (2)
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7/24/2019 Biology I Ch.17 (2)
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Michael Ye (예병억)
Associate Professor
Division of Liberal Arts & Sciences
General Biology IWeek 14 (2015.06.02)
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Week Description Notes
1st Introduction (3.03 & 3.05)
2nd Chapters 1 & 2. Study of Life & Chemistry of Life (3.10 & 3.12)
3rd Chapters 3 & 4. Chemistry of Water and Carbon (3.17 & 3.19) Exam #1
4th Chapter 5. Biomolecules (3.24 & 3.26) Exam #2
5th Chapter 6. The Cell (3.31 & 4.02) Exam #3
6th Chapters 7 & 8. The Cell Membrane & Metabolism (4.07 & 4.09) Exam #4
7th Chapters 9. Cellular Respiration (4.14 & 4.16) Exam #5
8th Midterm Exam
9th Chapter 12. The Cell Cycle (4.28 & 4.30)
10th Chapter 13. Meiosis (05.05 어린이날 & 5.07)
11th Chapter 14. The Gene (5.12 & 5.14) Exam #6
12th Chapter 15. Chromosomal Basis of Inheritance (5.19 & 5.21) Exam #7
13
th
Chapter 16. Molecular Basis of Inheritance (5.26 & 5.28) Exam #8
14th Chapter 17. From Gene to Protein (6.02 & 6.04) Exam #9
15th Chapter 18. Regulation of Gene Expression (6.09 & 6.11) Exam #10
16th Final Exam
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What is a Gene?
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Gene Structure (ORF)
The generic structure of a eukaryotic mRNA, illustrating some post-transcriptionalregulatory elements that affect gene expression. Abbreviations (from 5' to 3'): UTR,
untranslated region; m7G, 7-methyl-guanosine cap; hairpin, hairpin-like secondary
structures; uORF , upstream open reading frame; IRES, internal ribosome entry site;
CPE , cytoplasmic polyadenylation element; AAUAAA, polyadenylation signal.
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The two functions of DNA comprise the Central Dogma of Molecular Biology :
1. DNA can reproduce itself (replication)
2. DNA can copy its information into RNA (transcription)
3. RNA can specify a sequence of amino acids in a polypeptide (translation)
The Central Dogma of Molecular Biology
Replication
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Basic Principles of Transcription and Translation
• RNA is the bridge between genes and the proteins for which they code
•Transcription is the synthesis of RNA (messenger RNA, mRNA) under the direction ofDNA
• Translation is the synthesis of a polypeptide, using information in the mRNA
• Ribosomes are the sites of translation
• In prokaryotes, translation of mRNA can begin before transcription has finished
• In a eukaryotic cell, the nuclear envelope separates transcription from translation; also,
RNA transcripts are modified through RNA processing to yield finished mRNA
• A primary transcript is the initial RNA transcript from any gene prior to processing
• The central dogma:
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Basic Principles of Transcription and Translation
Coupled Transcription & Translation Uncoupled Transcription & Translation
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The Genetic Code
Some Important Questions
1. How are the instructions for assembling amino acids into proteins encoded into DNA? (There are
20 amino acids, but there are only four nucleotide bases in DNA)
2. How many nucleotides correspond to an amino acid?
Mechanism
• The flow of information from gene to protein is based on a codon
• The gene is transcribed into complementary, non-overlapping codon of mRNA, which is then
translated into amino acids (to form a polypeptide)
• During transcription, one of the two DNA strands, called the template strand , provides a template
for ordering the sequence of complementary nucleotides in an RNA transcript
• The template strand is always the same strand for a given gene
• During translation, the mRNA base triplets or codons, are read in the 5 to 3 direction
• Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a
polypeptide
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The Genetic Code
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Cracking the Code
• All 64 codons were deciphered by the mid-1960s
• Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation
• The genetic code is redundant (more than one codon may specify a particular amino acid) but not
ambiguous; no codon specifies more than one amino acid
• Codons must be read in the correct reading frame (correct groupings) in order for the specified
polypeptide to be produced
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• Degenerate & Specific: 64 codons encode 61 amino acids & 3 “stop” signals
• Multiple codes for an amino acid tend to have two bases in common
• Codons are written in a 5' 3' sequence
The Genetic Code
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Marshall Warren Nirenberg
Nirenberg (1962)
• Nobel Prize in Medicine (1968)
• NIH (National Institutes of Health)
• With Har Gobind Khorana and Robert W. Holley
• For…… "breaking the genetic code" and describing how it
operates in protein synthesis
• In August 1961, at the International Congress of
Biochemistry in Moscow , Nirenberg presented a paper to a
small group of scientists
• Poly-URIDINE (UUU): phenylalanine
•Poly-ADENOSINE (AAA): lysine
• Poly-CYTOSTINE (CCC): proline
• Poly-GUANOSINE (GGG): glycine
Har Gobind Khorana
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Translation
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The sequence of a hypothetical gene and the RNA transcribed from it are shown.
By convention, the gene is said to be transcribed from the 5’ end to the 3’ end, but
the template strand of DNA is copied from the 3’ end to the 5’ end. Growth of the
ribonucleotide chain proceeds 5‘ 3’
Direction of Transcription
• RNA sequences are written 5’ 3’ (left to right)
•Translation occurs 5’ 3’ with ribosomes reading the message 5’ 3’
• Genes are written so that transcription proceeds in a left to right direction
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Evolution of the Genetic Code
• The genetic code is nearly universal, shared by the simplest bacteria to the most
complex animals
• Genes can be transcribed and translated after being transplanted from one species to
another
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Molecular Components of Transcription
• Transcription is the first stage of gene expression
•
RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart andhooks together the RNA nucleotides
• The RNA is complementary to the DNA template strand
• RNA synthesis follows the same base-pairing rules as DNA, except that uracil
substitutes for thymine
• The DNA sequence where RNA polymerase attaches is called the promoter ; in bacteria,
the sequence signaling the end of transcription is called the terminator• The stretch of DNA that is transcribed is called a transcription unit
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The three stages of transcription
1. Initiation2. Elongation
3. Termination
Synthesis of an RNA Transcript
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• Promoters signal the transcriptional start point and usually extend several dozen
nucleotide pairs upstream of the start point
• Transcription factors mediate the binding of RNA polymerase and the initiation of
transcription
• The completed assembly of transcription factors and RNA polymerase II bound to a
promoter is called a transcription initiation complex
• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes
Initiation of Transcription
A eukaryotic promoter1
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Transcription initiation
complex forms
3
DNA
PromoterNontemplate strand
5
3
5
3
5
3
Transcription
factors
RNA polymerase II
Transcription factors
5
3
5
3
5
3
RNA transcript
Transcription initiation complex
5
3
TATA box
T
T T T T T
A A A A A
A A
T
Several transcription
factors bind to DNA
2
A eukaryotic promoter1
Start point Template strand
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Elongation of the RNA Strand
• As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time
• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes (E.coli DNA
polymerase III incorporates about 1000 nucleotides per second)
• A gene can be transcribed simultaneously by several RNA polymerases
• Nucleotides are added to the 3 end of the growing RNA molecule
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Termination of Transcription
• The mechanisms of termination are different in bacteria and eukaryotes
•
In bacteria, the polymerase stops transcription at the end of the terminator and themRNA can be translated without further modification
• In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the
RNA transcript is released 10 –35 nucleotides past this polyadenylation sequence
• Eukaryotic cells modify RNA after transcription
• Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the
genetic messages are dispatched to the cytoplasm• During RNA processing, both ends of the primary transcript are usually altered
• Also, usually some interior parts of the molecule are cut out, and the other parts
spliced together
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Post-transcriptional Modification of mRNA
• Each end of a pre-mRNA molecule is modified in a particular way
1. The 5
end receives a modified nucleotide 5 cap
2. The 3 end gets a poly-A tail
• These modifications share several functions
1. They seem to facilitate the export of mRNA
2. They protect mRNA from hydrolytic enzymes
3. They help ribosomes attach to the 5 end
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Split Genes and RNA Splicing
• Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides
that lie between coding regions
• These noncoding regions are called intervening sequences, or introns
• The other regions are called exons because they are eventually expressed, usually translated into
amino acid sequences
• RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous
coding sequence
• In some cases, RNA splicing is carried out by spliceosomes
• Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins(snRNPs) that recognize the splice sites
d l
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snRNPs and Spliceosomes
h l d l f
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The Functional and Evolutionary Importance of Introns
• Alternative splicing: some genes can encode more than one kind of polypeptide,
depending on which segments are treated as exons during splicing
• Consequently, the number of different proteins an organism can produce is much
greater than its number of genes
• Proteins often have a modular architecture consisting of discrete regions called
domains…..different exons code for the different domains in a protein
M l l C t f T l ti
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Molecular Components of Translation
• A cell translates an mRNA message into protein with the help of transfer RNA (tRNA)
• tRNA transfer amino acids to the growing polypeptide in a ribosome
• Translation is a complex process in terms of its biochemistry and mechanics
Th St t d F ti f T f RNA
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The Structure and Function of Transfer RNA
• A tRNA molecule consists of a single RNA strand (80 nucleotides); tRNAs are not identical
1. Each carries a specific amino acid on one end
2. Each has an anticodon on the other end; the anticodon base-pairs with a complementary
codon on mRNA
• tRNA twists and folds into a 3-D molecule (due to hydrogen bonds) into “L-shaped ” structure; an
unfolded tRNA molecule looks like a “cloverleaf ”
• Accurate translation requires two steps
1. Correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA
synthetase
2. Correct match between the tRNA anticodon and an mRNA codon
• Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to
more than one codon
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Amino acid
attachment
site
3
5
Hydrogen
bonds
Anticodon
(a) Two-dimensional structure (b) Three-dimensional structure
Anticodon Anticodon
3 5
Hydrogen
bonds
Amino acid
attachment
site5
3
A A G
Aminoacyl-tRNA
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Aminoacyl-tRNA
synthetase (enzyme)
Amino acid
P P P Adenosine
ATP
P
P
P
PPi
i
i
Adenosine
tRNA
AdenosineP
tRNA
AMP
Computer model
Aminoacid
Aminoacyl-tRNA
synthetase
Aminoacyl tRNA
(“charged tRNA”)
Ribosomes
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Ribosomes
• Ribosomes facilitate joining of tRNA anticodons with mRNA codons in protein synthesis
• The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA
(rRNA)
• A ribosome has three binding sites for tRNA
1. The P site holds the tRNA that carries the growing polypeptide chain
2. The A site holds the tRNA that carries the next amino acid to be added to the chain
3. The E site is the exit site, where discharged tRNAs leave the ribosome
tRNA
Growing
polypeptide Exit tunnel
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tRNA
molecules
polypeptide
E P
A
Large
subunit
Small
subunit
mRNA5
3
(a) Computer model of functioning ribosome
Exit tunnel Amino end
A site (Aminoacyl-
tRNA binding site)
Small
subunit
Largesubunit
E P A mRNA
E
P site (Peptidyl-tRNA
binding site)
mRNA
binding site
(b) Schematic model showing binding sites
E site
(Exit site)
(c) Schematic model with mRNA and tRNA
5
Codons
3
tRNA
Growing polypeptide
Next amino
acid to be
added to
polypeptide
chain
Ribosome Association and Initiation of Translation
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Ribosome Association and Initiation of Translation
The three stages of translation (require proteins that aid in the translation process)
1. Initiation
2. Elongation
3. Termination
Initiation
• The initiation stage of translation brings together mRNA, a tRNA with the first amino
acid, and the two ribosomal subunits• First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
• Then the small subunit moves along the mRNA until it reaches the start codon (AUG)
• Proteins called initiation factors bring in the large subunit that completes the
translation initiation complex
Initiation of Translation
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Initiation of Translation
Elongation of the Polypeptide Chain
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Elongation of the Polypeptide Chain
• Elongation: amino acids are added to the preceding amino acid at the C-terminus of
the growing chain; translation proceeds along the mRNA in a 5′ to 3′ direction
• Addition of each amino acid involves proteins called elongation factors and occurs in
three steps: codon recognition, peptide bond formation, and translocation
Termination of Translation
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Termination of Translation
• Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome
• The A site accepts a protein called a release factor which causes the addition of a water
molecule instead of an amino acid
• This reaction releases the polypeptide, and the translation assembly then comes apart
Polyribosomes
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Polyribosomes
Ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or
polysome), which allows a cell to make many copies of a polypeptide very quickly
Targeting Polypeptides to Specific Locations
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Targeting Polypeptides to Specific Locations
• Two populations of ribosomes in cells
1. Free ribosomes mostly synthesize proteins that function in the cytosol
2. Bound ribosomes (attached to the ER) make proteins of the endomembrane system andproteins that are secreted from the cell
• Polypeptide synthesis always begins in the cytosol and finishes in the cytosol unless the
polypeptide signals the ribosome to attach to the ER
• Polypeptides destined for the ER or for secretion are marked by a signal peptide
• A signal-recognition particle (SRP) binds to the signal peptide and brings the signal peptide and its
ribosome to the ER
DNA Mutations
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• Mutations (changes in the genetic material) of one or a few nucleotides can affect protein
structure and function
• Point mutations are chemical changes in just one base pair of a gene; the change of a singlenucleotide in a DNA template strand can lead to the production of an abnormal protein; two types
of point mutations within a gene
1. Nucleotide-pair substitutions
2. One or more nucleotide-pair insertions or deletions
DNA Mutations
Nucleotide Substitutions
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Nucleotide Substitutions
Nucleotide-pair substitution: replace one nucleotide pair with another pair of nucleotides
1. Silent mutations have no effect on the amino acid produced by a codon because of
redundancy in the genetic code
2. Missense mutations still code for an amino acid, but not the correct amino acid
3. Non-sense mutations change an amino acid codon into a stop codon, nearly always
leading to a non-functional protein
Wild type
DNA template strand 5
T T T T TAAAACCA GC C3
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te p ate st a d
mRNA5
5
3
Protein
Amino end
A instead of G
(a) Nucleotide-pair substitution
3
3
Met Lys Phe Gly Stop
Carboxyl end
TTTTTA A A A A
C
C
A A A A A
G G G G
G GGU U U U UG
(b) Nucleotide-pair insertion or deletion
Extra A
3
5
5
3
Extra U
5 3
T T T T
T T T T
A
A A A
A
AT G G G G
GAAA
AC
CCCC A
T 3 5
5 3
5
T T T T TAAAACCA A C C
TTTTTA A A A AT G G G G
U instead of C
Stop
UA A A A AG GGU U U U UG
MetLys Phe Gly
Silent (no effect on amino acid sequence)
T instead of C
T T T T TAAAACCA GT C
T A T T TAAAACCA GC C
A instead of G
C A A A A AG A GU U U U UG U A A A AG GGU U U G AC
A A U U A AU UGU G G C UA
G A U A U AA UGU G U U CG
Met Lys Phe Ser
Stop
Stop Met Lys
missing
missing
Frameshift causing immediate nonsense
(1 nucleotide-pair insertion)
Frameshift causing extensive missense
(1 nucleotide-pair deletion)
missing
T T T T TTCAACCA AC G
AGTTTA A A A ATG G G C
Leu Ala
Missense
A instead of T
TTTTTA A A A ACG G A G
A
C A U A A AG GGU U U U UG
TTTTTA T A A ACG G G G
Met
Nonsense
Stop
U instead of A
3
5
3 5
5
3
3
5
5
3
3
5 3
Met Phe Gly
No frameshift, but one amino acid missing
(3 nucleotide-pair deletion)
missing
3
5
5
3
5 3
U
T CA AA CA TTAC GTA G T T T G G A ATC
T T C
A A G
Met
3
T
A
Stop
3
5
5
3
5
3
Insertions and Deletions
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Insertions and Deletions
• Insertions (additions) and deletions (losses) of nucleotide pairs in a gene have a
disastrous effect on the resulting protein more often than substitutions do
• Insertion or deletion of nucleotides may alter the reading frame, producing a
frameshift mutation
Wild type
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yp
DNA template strand
mRNA
5
Protein
Amino end
Stop
Carboxyl end
3
3
3
5
Met Lys Phe Gly
A
A
A A
A A A A
A AT
T T T T T
T T TT
C C C C
C
C
G G G G
G
G
A
A A A AG GGU U U U U
(b) Nucleotide-pair insertion or deletion: frameshift causing immediate nonsense
Extra A
Extra U
5
3
5
3
3
5
Met
1 nucleotide-pair insertion
Stop
A C A A GT T A TC T A C G
T A T AT G T CT GG A T GA
A G U A U AU GAU G U U C
A T
A
AG
5
Wild type
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DNA template strand
mRNA
5
Protein
Amino end
Stop
Carboxyl end
3
3
3
5
Met Lys Phe Gly
A
A
A A
A A A A
A AT
T T T T T
T T TT
C C C C
C
C
G G G G
G
G
A
A A A AG GGU U U U U
(b) Nucleotide-pair insertion or deletion: frameshift causing extensive missense
yp
missing
missing
A
U
A A AT T TC C A T TC C G
A AT T TG GA A ATCG G
A G A A GU U U C A AG G U 3
5
3
3
5
Met Lys Leu Ala
1 nucleotide-pair deletion
5
5
Wild type
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DNA template strand
mRNA
5
Protein
Amino end
Stop
Carboxyl end
3
3
3
5
Met Lys Phe Gly
A
A
A A
A A A A
A AT
T T T T T
T T TT
C C C C
C
C
G G G G
G
G
A
A A A AG GGU U U U U
(b) Nucleotide-pair insertion or deletion: no frameshift, but one amino acid missing
AT C A A A A T TC C G
T T C missing
missing
Stop
5
3
3
5
3
5
Met Phe Gly
3 nucleotide-pair deletion
A GU C A AG GU U U U
T GA A AT T TT CG G
A A G
5
Universality of the Gene
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Gene is Universal
• When comparing gene expression in bacteria, archaea, and eukarya gene expression
differs among the domains of life but the concept of a gene is universal• Archaea are prokaryotes, but share many features of gene expression with eukaryotes
• Bacteria and eukarya differ in their RNA polymerases, termination of transcription, and
ribosomes; archaea tend to resemble eukarya in these respects
Transcription and Translation
• Bacteria can simultaneously transcribe and translate the same gene
• In eukarya, transcription and translation are separated by the nuclear envelope
• In archaea, transcription and translation are likely coupled
y
Coupled Transcription and Translation
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p p
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Sample Problems
In-Class Problem #1
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CDNA Double Helix
T G A
C A U mRNA Codon
G C A tRNA Anticodon
Tryptophan Amino Acid
In-Class Problem #2
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A double-stranded DNA molecule with the sequence shown here produces, in
vivo, a polypeptide that is five amino acids long.
TAC ATG ATC ATT TCA CGG AAT TTC TAG CAT GTA
ATG TAC TAG TAA AGT GCC TTA AAG ATC GTA CAT
a. Which strand of DNA is transcribed and in which direction?
b. Label the 5’ and the 3’ ends of each strand.