dr. parvin pasalar tehran university of medical sciences دانشگاه علوم پزشكي...
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Dr. Parvin Pasalar
Tehran University of Medical Sciences
دانشگاه علوم پزشكي وخدمات بهداشتي درماني تهران
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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
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BasesBases
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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
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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.
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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
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• 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
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SugarsSugars
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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)
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NucleosidesNucleosides
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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.
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NucleotidesNucleotides
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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
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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
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Nucleic Acid:Nucleic Acid:1-DNA1-DNA2-RNA2-RNA
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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
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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).
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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
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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.
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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
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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.
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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.
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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
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Why DNA is Helical?Why DNA is Helical? Mother Nature loves a helix! Mother Nature loves a helix!
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DNA / Different secondary DNA / Different secondary structuresstructures
B (duplex)B (duplex) A (duplex)A (duplex) Z (duplex)Z (duplex)
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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.
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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
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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
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TopoisomersesTopoisomersesMechanism of their function:Mechanism of their function:
Class 1 class 2
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..
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Supercoiling In EukaryotesSupercoiling In Eukaryotes
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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)
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Double helixDouble helix (Nucleosomes) 10 (Nucleosomes) 10 nm fibrilnm fibril 30 nm fiber30 nm fiber loops on scaffoldloops on scaffold
heterochromatinheterochromatin
chromosomechromosome
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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
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Chromatin
Euchromatin
Heterochromatin
[Transcriptionally active]
[Transcriptionally inactive]
Operational ClassificationOperational Classification
Structural genes, rRNA genes, regulatory regions, etc.
Centromeric chromatin Attachment sites to nuclear matrix
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Histones/Histones/ Classification & Classification & structurestructure
Classification:Classification: H1H1 H2aH2a H2bH2b H3 H3 H4H4& & Numbers of their variantsNumbers of their variants
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Histone Structure and Histone Structure and nucleosome assemblynucleosome assembly
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Nucleosome with & without H1
+ +
++
++
- -------
- - - - - --
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Nucleosome/ top & side Nucleosome/ top & side viewview
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centromere
telomere
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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
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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.
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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.
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Secondary structure of RNAs
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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
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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.