Nucleic Acids

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• Nucleic Acid Structure

Dr. Parvin Pasalar Tehran University of Medical
Sciences
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• Objectives
• To know and identify the structure, roles and
  classifications of
• bases
• sugars
• nucleosides
• nucleotides
• DNAs
• RNAs

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Bases
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Nucleic Acids / Bases/ Definition

• Nucleobases are
• Aromatic (planner)
• Heterocyclic, Nitrogen containing
• Classified into
• Purine
• Pyrimidine

Hetero atoms are referred to atoms other than C
and H. In biology they are N, O and S
(planner character facilitates their close
association or stacking which stabilizes double
stranded DNA)
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Nucleic Acids / Bases/Structure
Imidazole
Pyrimidine

• By the attachment of different
• groups to the rings, different types
• of Py and Pu are generated.

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NA / Bases/ Classification

• Purine Bases (pu)
• Major (A)(G)
• Minor Inosine(I) methyl guanine(7mG)
• Unnatural
• Mercaptopurine,
• Allopurinol
• 8-Azaguanine

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NA / Bases/ Classification/ Py
Hot spot

• Pyrimidines (py)
• Major (T), (C) (U)
• Minor DHU , 5mC 5hmC
• Unnatural Fluorouracil (5FU) 6-aza cytosine(
  AZC)

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Sugars
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Nucleic Acids / Sugars
D-family Aldo pentose Furanose ß-Anomer Ribose or
deoxy Ribose Numbered by Prime Isomerism ( 2
endo in DNA , 3 endo in RNA)
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Nucleosides
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Nucleic Acids / Nucleosides

• ß-N-glycosidic linkage of a base and a pentose
  (1 to 9 in PU and 1 to 1 in PY).

• Major Cytidine deoxy cytidine.
• There are 8 major nucleosides.
• Minor ribothymidine (rT) psudouracil (?U).
• Unnatural Cytarabin.

• Structure
• Isomerism
• Nomenclature
• Roles
• Classification

• They are major part of nucleosides.
• Synthetic forms are used as drugs (Cytarabin)

• Name of the base suffix sine for Pus(adenosine
  guanosine)
• dine for PYs (uridine thymidine)

• syn or anti conformation

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Nucleotides
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NA / Nucleosides Biomedical importance

• 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)

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

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

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

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Nucleic Acids / Nucleotides

• 1-Name of the nucleoside
• the number of phosphate group.
• 2-Name of their corresponding acid
• such as thymidylic or guanylic acid.

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.

• Structure
• Isomerism
• Nomenclature
• Roles
• Classification

They may have syn or anti conformation with
predominate anti conformer.

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

• Major CMP, dCMP, CDP, CTP
• There are 24 major nucleotides
• Minor cAMP, cGMP
• Unnatural Cytarabin

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Nucleic Acid1-DNA2-RNA
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Nucleic Acids /DNA/ Structure

• Objectives
• To know and identify different levels of DNA
  organization
• 1- Primary structure
• 2-Secondary structure
• Different geometry of
• base pairs base steps
• 3-Higher order of DNA structure
• in prokaryotes
• in Eukaryotes

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DNA / General facts

• Its structure was discovered in 1953
• It is a polyester compound
• Has acidic character

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

Because of the phosphate moiety, they have
acidic character (negatively charged).
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DNA / General facts

• Has polarity
• It is double helix

• The two strand are
• 1- in opposite polarities
• 2- stabled by different bonds
• Hydrophobic bond
• H bond

DNA has end-to-end chemical Orientation (3
and 5 ends) and by convention it is written in
the 5 ---- 3 direction
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Different bonds and interactions in

• Covalent
• PDE bonds in the backbone
• Hydrogen
• between complementary bases
• Primary or Natural (Watson-Crick)
• Secondary or Hoogsteen pairing
• (non-Watson-Crick)
• Hyrophobic (van der Waals)
• between the stacked adjacent
• base pairs.

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DNA / General facts

• Has specific groove (s)
• It is flexible about its long axis It
• It may be linear or circular

• Particular region bound to protein clearly depart
  from the standard conformation

• MOVIE

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DNA / Different ways to show primary structure

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

5 3
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Secondary structure of DNA / Different ways to
show it
Secondary structure is formed by base pairing
between two complementary strands. It may be B,
A, Z or C-form.
5
3
3
5
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What 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? Mother Nature loves a helix!
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DNA / Different secondary structures

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

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2nd structure of DNA/ B- DNA

• Is the abundant form
• Has 2 groooves
• Has 10 (10.5)m bp/ turn
• Is right handed
• The stacked bases are
• perpendicular to the backbone
• Has a pitch per turn of helix 33.2 Ao

The helix tilted 32 from the viewer to show
minor (m) and major (M) grooves.
Side and top view of B-DNA in ball-and-stick and
space filling representation
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• Supercoiling
• Topoisomerism

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Supercoiling/ general facts

• 1. DNA molecule is very long and has to be
  contained within cells that are so small.
• 2. In free form the repulsion of negatively
  charged DNA is responsible for the large volume
  occupied by DNA.
• 3. Chromosomes are compacted DNAs.
• 4. Double helices can be compacted and form
  higher order structures that are referred to
  super helices which are shorter and thicker.
• 5. In cells there are some positively charged
  proteins that responsible for the compaction (
  supercoiling) of DNA.
• 6. Histons in eukaryotes and histon like
  proteins in prokaryotes .

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Higher order of DNA structure Supercoiling/
Topoisomerism

• Definition
• Where it can be find
• When it can be formed
• Different names
• Different types

• 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.

• The special type of isomerism
• that is find in supercoiled DNA

• 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

• superhelix
• supertwist
• supercoil.

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Topoisomerses

• Mechanism of their function

Class 1
class 2
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.
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Supercoiling In Eukaryotes
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DNA Compaction( higher order of DNA structure)
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 3.43109 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
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Double helix? (Nucleosomes) 10 nm fibril ? 30
nm fiber ? loops on scaffold ?
heterochromatin ? chromosome

• Hierarchy

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(No Transcript)
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Different level of Eukaryotic DNA compaction
(Chromosome Structure)

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

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Operational Classification
Euchromatin
Transcriptionally active
Structural genes, rRNA genes, regulatory regions,
etc.
Chromatin
Heterochromatin
Transcriptionally inactive
Centromeric chromatin Attachment sites to nuclear
matrix
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Histones/ Classification structure

• Classification
• H1
• H2a
• H2b
• H3
• H4
• Numbers of their variants

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Histone Structure and nucleosome assembly
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Nucleosome with without H1
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Nucleosome/ top side view
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centromere
telomere
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RNA Structure

• 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.

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RNA Structure

• It has ribose instead of deoxyribose so, it is
  more labile and more reactive than DNA.
• As a result of more liability, RNA is cleaved
  into mononucleotides by alkaline solution.
• It has thymine instead of uracil.
• Like DNA it can be double/single stranded, linear
  / circular.
• Unlike DNA, RNA may have different tridimentional
  structure.

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Different level of RNA Structure

• Its primary structure is a relatively short
  linear polymer of ribonucleotides. Such as linear
  form of tRNA.
• Secondary structure may be stem-loop, hairpin or
  other types. Such as clover leaf form of tRNA.
• RNA-RNA and RNA-DNA helices exist in A-form.
• Tertiary structure is formed between the flexible
  loops, such as pesudoknot. Such as L-shaped tRNA.

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Secondary structure of RNAs
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The importance of tridimentional structure of RNAs
A typical right -handed single -stranded RNA
A hammerhead ribozyme
Phe tRNA (yeast)
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RNA functions

• Structural function such as ribosome
• Catalytic function (ribozyme) for example in
  splicing and self-splicing, rRNA play a catalytic
  role in peptide bond formation.
• Regulatory function such as 5 an 3 UTRs of mRNA
  in the rate of protein synthesis.