DNA Replication Flashcards
1
Q
list the 5 components required for DNA synthesis
A
- All 4 dNTPs
- A fragment of DNA to act as template
- DNA polymerase
- Mg2+ ions, which are required for DNA pol activity
- A primer providing a free 3’OH group
2
Q
explain how chain elongation is catalyzed by DNA pol
A
- DNA pol catalyzes the formation of a phosphodiester bond between the 3’OH group of the deoxyribose on the last nucleotide and the 5’ phosphate of the dNTP precursor
- The deoxynucleoside 5’ triphophsate provides the energy source for the reaction
- At each step in the lengthening the new DNA chain, DNA pol finds the correct precursor dNTP that can form a complementary base pair with the nucleotide on the template strand of the DNA
3
Q
explain the function of acycolvir
A
- Acyclovir gets converted to acyclovir triphosphate by the viral enzyme thymidine kinase, which can serve as a substrate for viral DNA pol
- Since it lacks a 3’OH group, it causes chain termination when it gets incorporated during viral DNA replication
4
Q
explain how arabinosides function
A
- The planar configuration of arabinosides induces DNA damage, and inhibits the activity of DNA polymerase. These are anti-cancer agents
5
Q
describe the process of wrong bases by DNA pol
A
- Rare tautomeric form of C (C*) happens to basepair with A and is thereby incorporated by DNA polymerase into the primer strand
- Rapid tautomeric shift of C* to normal cytosine (C) destroys its basepairing with A
- Unpaired 3’OH end of primer blocks further elongation of primer strand by DNA polymerase
- 3’ to 5’ exonuclease activity attached to DNA pol chews back to create a basepaired 3’OH end on the primer strand
- DNA pol continues the process of adding nucleotides ot the basepaired 3’OH end of the primer strand
6
Q
what’s the difference between prokaryote vs eukaryote replication
A
- Prokaryotes have circular genomes and therefore undergo Theta replication
- single origin of replication
- Eukaryotes have a linear genome and therefore undergo linear replication
- multiple origins of replication are required
7
Q
describe the function of initiator proteins (DNaA protein)
A
- binds to replication and breaks H-bonds between bases
8
Q
describe the function of DNA helicase (DNaB)
A
- DNA helicase opens the helix and binds primase to form primosome
9
Q
describe the function of helicase inhibitor (DNaC)
A
- Helicase inhibitor delivers helicase to DNA template
10
Q
describe the function of DNA primase
A
- DNA primase is an RNA polyererase that synthesizes an RNA primer on the lagging strand to enable DNA polymerase to synthesize DNA strand
11
Q
describe the function of DNA polyermase I
A
- DNA polymerase I removes the RNA primer and replaces it with DNA
- Synthesizes new DNA in the 5’ to 3’ direction, especially to extend Okizaki fragments
- 3’ to 5’ exonuclease activity to remove primers in lagging strand
- 3’ to 5’ proofreading activity
12
Q
describe the function of DNA polyermase III
A
- DNA polymerase III allows for the synthesis of leading and lagging strands
- Synthesizes new DNA in the 5’ to 3’ direction
- Exonuclease activity 3’ to 5’
13
Q
explain the function of single stranded binding protein (ssb)
A
- ssb binds to single stranded DNA in the replication bubble and prevents it from re-annealing or forming secondary structure
14
Q
describe the function of clamp protein
A
- Clamp protein tightly holds the DNA polymerase III onto the template for synthesis of long templates (increases expressivity) and releases DNA pol when it stalls at a region of ds DNA
15
Q
what problem does DNA polymerase encounter in eukaryotes?
A
- At the telomeres there are gaps at the 5’ end of the new DNA resulting from RNA primer removal
- DNA pol can only synthesize DNA in the 5’ to 3’ direction–therefore no new DNA synthesis can fill the gaps made by the missing primers
