BSCI330 DNA replication and repair

Question 1

what are the 6 problems that DNA replication has to solve

Answer 1

◦ strand polarity
	◦ unzip DNA
	◦ processivity
	◦ untangling DNA as it gets unwound
	◦ only making a single copy
	◦ making an accurate copy

Question 2

why do eukaryotes have more complications than prokaryotes

Answer 2

due to a linear genome and the presence of histones

Question 3

what is semi-conservative

Answer 3

replication is semi-conservative - each daughter strand of DNA has one strand from parental, one is new

Question 4

solutions to strand polarity problem

Answer 4

all synthesis is 5’ -> 3’. Okazaki fragments are synthesized on the lagging strand. DNA ligase seals gap between successive fragments.

the leading strand is synthesized continuously. Lagging strand synthesizes short stretch, jumps back, repeat (Okazaki fragments)

Question 5

solutions to unzip DNA problem

Answer 5

DNA helicase unzips the DNA it uses ATP and acts as a rotary engine, separating hydrogen bonds to deparate DNA double helix. Unzipped DNA is stabilized by single-stranded DNA binding proteins

Question 6

what is processivity

Answer 6

enzyme continues to synthesize a polymer as a long continuous stretch without falling off

Question 7

solutions to processivity problem

Answer 7

sliding clamp holds the DNA polymerase in place. the clamp is loaded on DNA by a clamp loader that uses ATP hydrolysis to lock the clamp in place.

Question 8

what does the helicase do

Answer 8

unwinds DNA to allow the replication fork to move

Question 9

why can a DNA molecule not rotate freely

Answer 9

torsional stress will build up

Question 10

what relieves torsional stress

Answer 10

topoisomerases

Question 11

what are the two types of topoisomerases

**KNOW FOR FINAL

Answer 11

‣ topoisomerase I: nick and swivel mechanism and topoisomerase II: gating mechanism

Question 12

what does topoisomerase I do

**KNOW FOR FINAL

Answer 12

it performs a nucleophilic attack and makes a nick in one strand of the DNA. once broken, the strands can unwind.

No ATP required

Question 13

how does topoisomerase I reseal the nick

**KNOW FOR FINAL

Answer 13

the hydroxyl on the broken strand does a nucleophilic attack on the tyrosine phosphate linkage and reforms the bond

Question 14

what does topoisomerase II do

**KNOW FOR FINAL

Answer 14

allows two double helices to pass by each other to relieve stress

topoisomerase II binds to one helix and makes a double-stranded break in the DNA. a gate allows second double helix to pass through broken one. the enzyme brings the two ends together and reseals the break.

Question 15

how does topoisomerase II reseal

**KNOW FOR FINAL

Answer 15

ATP hydrolyzed to reseal

enzyme attaches covalently to both strands of one DNA helix

Question 16

what are the differences/similarities between topoisomerase I and topoisomerase II

**KNOW FOR FINAL

Answer 16

both mechanisms have nuclease activity

(II) gating makes a double-strand break, (I) nick method makes a single-strand break

(II) gating requires ATP hydrolysis

Question 17

where does DNA replication occur

Answer 17

origin of replication

Question 18

why is AT easy to break

Answer 18

only has 2 hydrogen bonds, whereas GC has 3 hydrogen bonds, so origin has higher AT content

Question 19

what direction does leading strand go in

Answer 19

heilcase direction

Question 20

what direction does lagging strand go in

Answer 20

going away from replication fork

Question 21

when will the origin not fire

Answer 21

if it’s not methylated

Question 22

solution to only making a single copy of DNA

Answer 22

prokaryotic origins have a refractory period