Dr. Parvin Pasalar

Tehran University of Medical Sciences

دانشگاه علوم پزشكي وخدمات بهداشتي درماني تهران

Objectives:Objectives:

To know and identify the structure, To know and identify the structure, roles and classifications of roles and classifications of

basesbases sugarssugars nucleosidesnucleosides nucleotidesnucleotides DNAsDNAs RNAsRNAs

BasesBases

Nucleic Acids / Bases/Nucleic Acids / Bases/ DefinitionDefinitionNucleobases are:Nucleobases are:

Aromatic (planner)Aromatic (planner)

Heterocyclic, Nitrogen containing Heterocyclic, Nitrogen containing

Classified into:Classified into:

PurinePurine

PyrimidinePyrimidine(planner character facilitates their close (planner character facilitates their close

association or stacking which stabilizes association or stacking which stabilizes

double stranded DNA)double stranded DNA)

Hetero atoms are Hetero atoms are referred to referred to atoms other atoms other than C and H. than C and H. In biology they In biology they are N, O and Sare N, O and S

Nucleic Acids / Bases/StructureNucleic Acids / Bases/Structure

Pyrimidine

Imidazole

By the attachment of differentBy the attachment of different

groups to the rings, different typesgroups to the rings, different types

of Py and Pu are generated.of Py and Pu are generated.

NA / Bases/ ClassificationNA / Bases/ Classification

• Purine Bases (pu): Purine Bases (pu): • Major : (A)&(G)Major : (A)&(G)• Minor: Inosine(I) & Minor: Inosine(I) & methyl guanine(7mG) methyl guanine(7mG) • Unnatural : Unnatural :

MercaptopurineMercaptopurine,,

Allopurinol & Allopurinol &

8-Azaguanine 8-Azaguanine

• Pyrimidines (py): Pyrimidines (py):

• Major : (T), (C) & (U) Major : (T), (C) & (U)

•Minor: DHU , 5mC & 5hmCMinor: DHU , 5mC & 5hmC

•Unnatural: Fluorouracil (5FU) & Unnatural: Fluorouracil (5FU) & 6-aza cytosine( AZC) 6-aza cytosine( AZC)

Hot spot

NA / Bases/ Classification/ PyNA / Bases/ Classification/ Py

SugarsSugars

Nucleic Acids / SugarsNucleic Acids / Sugars

D-family

Aldo pentose

Furanose

β-Anomer

Ribose or deoxy Ribose

Numbered by Prime

Isomerism ( 2’ endo in DNA , 3’ endo in RNA)

NucleosidesNucleosides

Nucleic Acids / Nucleic Acids / NucleosidesNucleosidesStructure:Structure:

Isomerism:Isomerism:

Nomenclature:Nomenclature:

Roles: Roles:

Classification:Classification:

• β-N-glycosidic linkage of a base and a

pentose (1‘ to 9 in PU and 1‘ to

1 in PY).

• syn or anti conformation

• Name of the base + suffix sine for Pus(adenosine & guanosine)

• dine for PYs (uridine & thymidine)

• They are major part of nucleosides.

• Synthetic forms are used as drugs (Cytarabin)

Major:: Cytidine & deoxy cytidine.

• There are 8 major nucleosides.

Minor : ribothymidine (rT) & psudouracil (ΨU).

Unnatural : Cytarabin.

NucleotidesNucleotides

Building blockBuilding block

Coenzymes (NAD, FAD & Co-A)Coenzymes (NAD, FAD & Co-A)

Group transferGroup transfer

Energy carrierEnergy carrier ( ATP & GTP) ( ATP & GTP)

Regulatory roles:Regulatory roles: DrugsDrugs

• in lipid ( CDP-acylglycerol)in lipid ( CDP-acylglycerol)• in sugar( UDP-glucose)in sugar( UDP-glucose)• in protein (tRNA) synthesisin protein (tRNA) synthesis• methyl donor as methyl donor as SAM SAM

(S-adenosylmethionine)(S-adenosylmethionine)

•Second messenger for hormones(cAMP or GMP)•Allosteric regulator of many enzymes(ATP

& AMP in metabolic pathways)

• Synthetic pu & py analogs that contain

Halogens, thiols or additional nitrogen are employed

in:

Gout or Hyperuricemia(Allopurinol)

Chemotherapy of cancer ( cytarabine)

AIDS treatment ( azathioprine)

Immunosuppression responses during organ

transplantation ( azathioprine)

NA / Nucleosides Biomedical NA / Nucleosides Biomedical importanceimportance

Nucleic Acids / Nucleic Acids / NucleotidesNucleotides

Structure:Structure:

Isomerism:Isomerism:

Nomenclature:Nomenclature:

Roles:Roles:

Classification:Classification:

1-Nucleoside+ Phosphate group(s

=phospho ester of nucleosides

2-In most cases the phosphate

group is linked to the 5’ carbon.

3- They may have 1, 2,0r 3

phosphate groups.

They may have syn or anti conformation They may have syn or anti conformation

with with predominate anti conformerpredominate anti conformer..

1-Name of the nucleoside1-Name of the nucleoside

+ the number of phosphate group.+ the number of phosphate group.

2-Name of their corresponding acid2-Name of their corresponding acid

such as thymidylic or guanylic acidsuch as thymidylic or guanylic acid..

• Building block• Coenzymes (NAD, FAD & Co-A)• Group transfer• Energy carrier ( ATP & GTP)• Regulatory roles: • Drugs

MajorMajor:: CMP, dCMP, CDP, CTPCMP, dCMP, CDP, CTP

There are 24 major nucleotidesThere are 24 major nucleotides

MinorMinor : : cAMP, cGMPcAMP, cGMP

UnnaturalUnnatural : : Cytarabin Cytarabin

Nucleic Acid:Nucleic Acid:1-DNA1-DNA2-RNA2-RNA

Nucleic Acids /DNA/ Nucleic Acids /DNA/ StructureStructure Objectives Objectives

To know and identify different To know and identify different levels of levels of DNA organizationDNA organization

1- 1- PrimaryPrimary structure structure

2-2-SecondarySecondary structure structure

Different Different geometrygeometry of of

base pairsbase pairs & & base stepsbase steps

3-3-Higher orderHigher order of DNA structure of DNA structure

in in prokaryotesprokaryotes

in in EukaryotesEukaryotes

DNA / General factsDNA / General facts Its structure was discovered in 1953Its structure was discovered in 1953 It is a polyester compoundIt is a polyester compound Has acidic character Has acidic character

It is a polymer in which the monomers (nucleotides)are joined by PDE bonds between5’ and 3’ carbon atoms of two successive nucleotides.

Because of the phosphate

moiety, they have acidic

character (negatively charged).

Has polarityHas polarity It is double helixIt is double helix

DNA / General factsDNA / General facts

DNA has end-to-end

chemical Orientation

(3’ and 5’ ends) and

by convention it

is written in the

5’ ---- 3’ direction

• The two strand are:• 1- in opposite polarities• 2- stabled by different

bonds:

Hydrophobic bond

H bond

Different bonds and interactions inDifferent bonds and interactions in

Covalent:Covalent:

PDE bonds in the backbonePDE bonds in the backbone

Hydrogen: Hydrogen: between complementary basesbetween complementary bases Primary or Natural (Watson-Crick)Primary or Natural (Watson-Crick) Secondary Secondary or Hoogsteen pairingor Hoogsteen pairing ((non-Watson-Crick) non-Watson-Crick)

Hyrophobic Hyrophobic (van der Waals)(van der Waals)

between the stacked adjacent between the stacked adjacent base pairs.base pairs.

DNA / General factsDNA / General facts

Particular region Particular region bound to bound to protein clearly protein clearly depart from depart from the standard the standard conformationconformation

• Has specific groove (s)• It is flexible about its long axis It

• It may be linear or circular

• MOVIEMOVIE

DNA / Different ways to show DNA / Different ways to show primary structureprimary structure

5’ 3’

Primary structure is a huge linear polymer of dNTPs that are joined to each other by 5’-3’ PDE bonds.

Secondary structure of DNA / Secondary structure of DNA / Different ways to show itDifferent ways to show it

5’ 3’

3’ 5’

Secondary structure is formed by base pairing between two complementary strands. It may be B, A, Z or C-form.

What about DNA groovesWhat about DNA grooves

• They are generated because of the angle of base pairs

• They are important for the interaction with proteins

Why DNA is Helical?Why DNA is Helical? Mother Nature loves a helix! Mother Nature loves a helix!

DNA / Different secondary DNA / Different secondary structuresstructures

B (duplex)B (duplex) A (duplex)A (duplex) Z (duplex)Z (duplex)

2nd structure of DNA/ B- DNA2nd structure of DNA/ B- DNA Is the abundant formIs the abundant form Has 2 grooovesHas 2 groooves Has 10 (10.5)m bp/ turnHas 10 (10.5)m bp/ turn Is right handedIs right handed The stacked bases areThe stacked bases are perpendicular to the backboneperpendicular to the backbone Has a pitch per turn of helix 33.2 AHas a pitch per turn of helix 33.2 Aoo

Side and top view of B-DNA in ball-and-stick and space filling representation

The helix tilted 32˚ from the viewer to show minor (m) and major (M) grooves.

1. DNA molecule is 1. DNA molecule is very longvery long and has to be and has to be contained within cells that are so small. contained within cells that are so small.

2. In free form the 2. In free form the repulsionrepulsion of negatively of negatively charged DNA is responsible for the large charged DNA is responsible for the large volume occupied by DNA.volume occupied by DNA.

3. 3. ChromosomesChromosomes are are compacted DNAscompacted DNAs.. 4. Double helices can be compacted and form 4. Double helices can be compacted and form

higher order structures that are referred to higher order structures that are referred to super helicessuper helices which are shorter and thicker. which are shorter and thicker.

5. In cells there are some 5. In cells there are some positively chargedpositively charged proteinsproteins that responsible for the compaction ( that responsible for the compaction ( supercoilingsupercoiling) of DNA.) of DNA.

6. 6. Histons Histons in eukaryotes and in eukaryotes and histonhiston like like proteins in prokaryotes .proteins in prokaryotes .

Supercoiling/ general factsSupercoiling/ general facts

Higher order of DNA structure Higher order of DNA structure Supercoiling/ TopoisomerismSupercoiling/ Topoisomerism

Definition:Definition: Where it can be find:Where it can be find: When it can be formed:When it can be formed: Different names: Different names: Different types:Different types: The special type of isomerism

that is find in supercoiled DNA

Where the two ends of a DNA molecule are fixed , the molecule exhibit a superstructure under

certain conditions. When the base pairing is interrupted and a local region unwind such as during replication, transcription and binding of many binding protein to DNA.

superhelix supertwist supercoil.

Relax: There is no superhelix turn

Positive: The handness of double and

super helix are the same

Negative: The handness of double and

super helix are opposite

TopoisomersesTopoisomersesMechanism of their function:Mechanism of their function:

Class 1 class 2

..

Supercoiling In EukaryotesSupercoiling In Eukaryotes

Human beings have roughly 3 billion base pairs of DNA in 23 chromosomes (haploid).

Yeast has 13 million base pairs in 17 chromosomes

Distance between bases is 3.4 Angstrom

For human this would be 3.4×3×109 Angstroms. This equals 1.02 meters per haploid genome, 2.04 meters per cell

The size of the nucleus is roughly 10 micrometers in diameter

DNA Compaction( higher order of DNA Compaction( higher order of DNA structure)DNA structure)

Double helixDouble helix (Nucleosomes) 10 (Nucleosomes) 10 nm fibrilnm fibril 30 nm fiber30 nm fiber loops on scaffoldloops on scaffold

heterochromatinheterochromatin

chromosomechromosome

Different level of Eukaryotic DNA Different level of Eukaryotic DNA compaction (Chromosome Structure)compaction (Chromosome Structure)

Nucleosome formation.Nucleosome formation. 10 nm fibril 10 nm fibril 30 nm fiber30 nm fiber 300 nm loops (Rosette)300 nm loops (Rosette) 700 nm helix700 nm helix

Chromatin

Euchromatin

Heterochromatin

[Transcriptionally active]

[Transcriptionally inactive]

Operational ClassificationOperational Classification

Structural genes, rRNA genes, regulatory regions, etc.

Centromeric chromatin Attachment sites to nuclear matrix

Histones/Histones/ Classification & Classification & structurestructure

Classification:Classification: H1H1 H2aH2a H2bH2b H3 H3 H4H4& & Numbers of their variantsNumbers of their variants

Histone Structure and Histone Structure and nucleosome assemblynucleosome assembly

Nucleosome with & without H1

+ +

++

++

- -------

- - - - - --

Nucleosome/ top & side Nucleosome/ top & side viewview

centromere

telomere

Objectives: After studying this session you have to know :

Primary structure, secondary and Tertiary structure of RNA.

Structure and function of tRNA. Structure and function of rRNA. Structure and function of mRNA.

RNA StructureRNA Structure

RNA StructureRNA Structure It has It has riboseribose instead of deoxyribose so, it instead of deoxyribose so, it

is more is more labilelabile and more reactive than and more reactive than DNA.DNA.

As a result of more liability, RNA is As a result of more liability, RNA is cleaved into mononucleotides by cleaved into mononucleotides by alkaline solutionalkaline solution..

It has thymine instead of It has thymine instead of uraciluracil.. Like DNA it can be Like DNA it can be double/singledouble/single

stranded, stranded, linearlinear / / circularcircular.. Unlike DNA, RNA may have Unlike DNA, RNA may have different different

tridimentionaltridimentional structure. structure.

Different level of RNA StructureDifferent level of RNA Structure Its Its primary structureprimary structure is a is a

relatively short linear polymer relatively short linear polymer of ribonucleotides. Such as of ribonucleotides. Such as linear form of tRNA.linear form of tRNA.

Secondary structureSecondary structure may may be stem-loop, hairpin or other be stem-loop, hairpin or other types. Such as clover leaf types. Such as clover leaf form of tRNA.form of tRNA.

RNA-RNARNA-RNA and and RNA-DNA RNA-DNA helices exist in helices exist in A-formA-form..

Tertiary structureTertiary structure is formed is formed between the flexible loops, between the flexible loops, such as pesudoknot. Such as such as pesudoknot. Such as L-shaped tRNA.L-shaped tRNA.

Secondary structure of RNAs

The importance of The importance of tridimentional structure of tridimentional structure of RNAsRNAs

Phe tRNA (yeast)A hammerhead ribozyme

A typical right-handed single-stranded RNA

RNA functionsRNA functions

Structural functionStructural function such as ribosomesuch as ribosome

Catalytic function Catalytic function (ribozyme)(ribozyme) for for example in splicing and self-splicing, example in splicing and self-splicing, rRNA play a catalytic role in peptide rRNA play a catalytic role in peptide bond formation.bond formation.

Regulatory functionRegulatory function such as 5’ an 3’ such as 5’ an 3’ UTRs of mRNA in the rate of protein UTRs of mRNA in the rate of protein synthesis.synthesis.