Chemical Components of the Cell

DNA replication and repair

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 Chemical Components of the Cell

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 Why do we start with chemistry?

 Water
 Carbon atoms –organic chemistry
 Chemical reactions

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 WATER

Hydrophilic
Hydrophobic

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 The outermost electrons determine how atoms interact!

Covalent

Single
Non-covalent

Double

Higher
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 Non-covalent Bonds
Strength (kcal/mole)
In vacuum In water
• Covalent bond 90 90

• Ionic bonds 80 3
• Hydrogen bonds 4 1

• van der Waals Attraction 0.1 0.1

• Hydrophobic forces

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Non-covalent bonds mediate formation of the functional
3D structure of macromolecules

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 Thermodynamics

Temperature
Collisions
Chemical rxns
Heat
Energy
Work
Brownian Motion

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Entropy

Measure of degree of disorder

or randomness
in a molecular system!

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 What we learned so far?
• Chemical Bonds : Covalent and Non-covalent
• Non-covalent bonds: Ionic, Hydrogen, Van der Waals and
Hydrophobic forces
• The strength of van der Waals interaction is independent of
environment – energy minimum
• Non-covalent bonds are important for the formation of 3D
structure of molecules
• Cell + Surrounding=Universe
• The relation between Brownian motion, collision, reaction,
heat, temperature, work and energy
• The entropy is a measure of disorder!

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 Chemical Components of the Cell

DNA replication and repair

Structure and Function of DNA

Chromosomal DNA and its packing
Replication and Repair

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Structure and Function of DNA

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 Major
groove

Minor
groove

What if it were parallel?

Nucleotide
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 Chromosomal DNA and its Packing

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 Levels of DNA packing

Chromatin

Nucleosome

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 Chromatin is
highly dynamic
in structure

Karyotype, 2X= 46
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 What we learned so far?
• DNA is a double helix which is made up of deoxyribose
nucleotides –A,T,G,C
• Nucleotides : Phosphate + 5 C sugar + Nitrogenous base
• The two helices run antiparallel to each other
• The phosphate and sugar constitutes the walls of the DNA
• DNA is not found naked but rather there is an
organizational level of packing.
• Nucleosome = DNA + histone; Nucleosome + nucleosome
= chromatin fiber ; condensed chromatin = chromosome.
• Typical chromosome is made up of a telomere, a
centromere and an origin of replication.

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 Replication and Repair

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• DNA replication proceeds with high fidelity but there might
occur some mutations!
• Mutations are difficult to investigate since the deleterious
ones are eliminated from the population by natural
selection!
• Some mutations may be silent : may not be deleterious or
may not affect the function of the protein!
• Mutation rates may be protein-specific!

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 Semi conservative
5’-3’ direction

DNA polymerase

It requires both a template and a primer

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 DNA polymerase serves for two purposes!

Proofreading Activities
• Before the nucleotide binds covalently – If it is not the correct
nucleotide then it easily detaches from the strand while the
enzyme moves along!
• After the nucleotide covalently attached – exonucleolytic activity!
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 5’-3’ direction is required both for elongation and
exonuclease activity of DNA polymerase

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 How is stable DNA double helix unwind ?

DNA helicase & single strand

DNA binding proteins,
Topoisomerase

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 The proteins at a Replication Fork Cooperate to
Form a Replication Machine

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 Differences between prokaryotic and eukaryotic replication fork

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 But what happens in chromosomes ?
In bacteria (single replication fork,
In eukaryotes
no nucleosomes & end problems)

Packing

End problem
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 End-replication problem at telomeres

Problem

Solution

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 DNA Repair:
Types of modifications

Oxidative damage, Hydrolytic attack, Uncontrolled methylation

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Thymine Dimer
 The deamination of DNA nucleotides

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 Chemical modifications of nucleotide if left unrepaired leads to mutation

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 What we learned so far?
• DNA replication is semi-conservative and proceeds in 5’-3’ direction
• DNA polymerase serves for two purposes: polymerization and editing of
DNA
• 5’-3’ direction is required for the exonuclease activity of DNA polymerase
• Leading and lagging strands – why are they called so?
• DNA helicase-topoisomerase-single strand binding proteins –primase
• Difference in replication between bacterial and eukaryotic chromosomes
• Problem with telomere
• DNA repair – Types of modifications
• Why does not DNA have uracil?

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