4 forces that stabilizes DNA
- Van der Waals interaction
- Hydrophobic effects
- Electrostatic interactions of phosphate
- Watson Crick base pairs
How does VDW stabilize force work?
Driving force is base stacking,
How does hydrophobic effects force work?
Hydrophobic bases buried in the interior of the helix, has zipzper like effect
What are the two most important stabilizing forces?
VDW and hydrophobic effects
How does electrostatic interaction work?
offset by divalent cations Mg @+ and cationic proteins
How does Watson Crick base pairs force work?
H bonds provide specificity, G-C 3 H bonds, AT 2 H bond
What is a DNA intercalating agents?
Intercalating agents are aromatic ring, planar and fits between two moleculrs. In DNA, it’s between stacked bases. Causes structural distortion in DNA.
An agent is ethidium bromide.
What does semi conservative mean in DNA replication?
The DNA stays intact but there is two daughter strands as replication occurs.
How does conservative replication work?
- Template: DNA directs DNA polymerase
- DNA polymerase requires selectivity from H bond - Watson - Crick base pairs
- Nucleophilic attack (3’ -OH)
- Hydrolysis, PPi
Steps are the same in prokaryotes and eukaryotes
Describe the direction of replications.
They’re bidirectional 5 to 3
What are okzaki fragments?
The partial complementary DNA bands on the lagging strand
how do you fix the gaps in lagging strands?
Need RNA primers, DNA ligase
What is a processive enzyme?
efficient enzymes that binds on to its template and stays on under catalysis. There’s different rates for different processive enzymes. But they are much faster than enzymes that latches on and lets go
Describe DNA Pol 1
Processive Enzyme
Adds correct nucleotide
3 —> 5 exonuclease activity (high proof reading leads to high fidelity of Pol 1)
5—->3 exonuclease activity to edit RNA primers, add DNA. Essential function is to remove lagging strands (nick translation)
How does Nick translation occur?
- Pol 1: 5—>3 exo activity
- Cleaves nicked DNA
- removes RNA
- Polymerase catalytic activity (adds to 3”OH is fragment 2)
- DNA ligase
- lagging strand and DNA repair have similar catalytic mechanism
Catalytic steps is the same in repair of normal function
Wht are the 3 separate catalytic sites for Pol 1?
Polymerase function, 3 to 5 primer, 5 to 3 exonuclease activity
Klenow fragment charcteristics
cleaved domain with polymerase and 3—>5 exonuclease activity (editing complex); separate catalytic sites (25 A) - DNA conformational shift
what would happen if POL 1 was gone?
It would be lethal, since it’s important to get rid of gaps in the lagging strand and have semiconservative regulation.
What does SSB, single stranded binding protein do?
Prevents ssDNA from forming secondary strcuture, protection from nucleases.
What happens to the lagging strand in Pol 1 nick translation for E. Coli.
lagging strand loops around
Pol 1 only occurs in
prokaryotes
How are mutations removed? Four ways.
- Levels of dNTPs changes through out the cycle.
- Polymerases have two stage rxn: protein conformational change. Doesn’t do catalysis till it sense the right H bond, then the “finger collapses.”
- 3 —> 5 exo functions of pol I and pol III, fixes mistakes while synthesizing
- Enzymes systems to repair DNA from enzymatic or environmental insults
Where do the majority of errors occurs in dividing cells?
over 3 quarters are done by polymerase errors
What are some types of environmental consequences that causes DNA damage
UV light, ionizing radiation, chemical agents (alkylating agents)
