1C: DNA replication and repair

Question 1

what is the semiconservative model of DNA replication?

Answer 1

each daughter strand remains paired with its complementary parental strand (so each parent DNA transforms into two daughter DNA where one strand is new but one comes from the parental strand)

Question 2

what is the conservative model of DNA replication?

Answer 2

both daughter strands pair up and both parent strands pair up.

Question 3

what is the dispersive model of DNA replication?

Answer 3

daughter strands have a mixture of parental and newly synthesized DNA

Question 4

what were the steps of Meselson and Stahl’s experiment?

Answer 4

1) bacteria grown in 15N (heavy nitrogen) medium. the isotope was incorporated into the nitrogenous bases of their DNA.
2) bacteria transferred to 14N (light nitrogen) medium, resulting in all newly formed nitrogenous bases being light.
3) DNA extracted from bacteria after each generation in new media. centrifuged in special solution to separate DNA of different densities

Question 5

what were the results of the Meselson and Stahl’s experiment? how did this compare to the potential predicted results?

Answer 5

after one generation, all DNA was mid weight. after two generations, some DNA was mid weight and some was light.
this is aligns with the predicted weights for the semiconservative model of replication.

Question 6

what were the predicted banding patterns for the 3 replication models?

Answer 6

➞ semiconservative: after gen 1 is all mid weight, after gen 2 is some mid weight some light weight.

➞ conservative: after gen 1 and after gen 2 both have some heavy and some light.

➞ dispersed: after gen 1 is mid weight, after gen 2 is mid but slightly lighter

Question 7

to which end can nucleotides be added?

Answer 7

only the 3’-OH end

Question 8

in what direction does DNA synthesis occur?

Answer 8

5’ to 3’

Question 9

what provides energy for formation of new phosphodiester bond?

Answer 9

hydrolysis of pyrophosphate

Question 10

what are 2 properties of polymerases?

Answer 10

1) cannot synthesize new strands from scratch (must build off a primer)
2) has a single active side that can catalyze 4 different reactions (incorporation of the 4 DNA bases)

Question 11

what is a replisome?

Answer 11

molecular machine made up of all the enzymes that replicate DNA

Question 12

what does helicase do?

Answer 12

unwinds the double helix by breaking hydrogen bonds

Question 13

what does primase do?

Answer 13

synthesizes RNA primers for DNA polymerase

Question 14

what does single-strand binding protein do?

Answer 14

stabalizes ssDNA (single-stranded) before replication by preventing reannealing so the strands can serve as templates

Question 15

what does topoisomerase do? (what is an alternate name for it?)

Answer 15

removes twistiness of DNA ahead of the replication fork by cleaving the DNA, turning it, and reattaching
(alt name: gyrase)

Question 16

what does polymerase III do?

Answer 16

synthesizes DNA by adding nucleotides to primer

Question 17

what does polymerase I do?

Answer 17

removes the RNA primer and fills the gaps left by the primer with DNA

Question 18

what does the sliding clamp do?

Answer 18

attaches polymerase III to the DNA template. makes replication more efficient (smoother, faster)

Question 19

what does ligase do?

Answer 19

joins the ends of the DNA segments by forming phosphodiester bonds

Question 20

what are the two new strands of DNA formed by the replication fork called?

Answer 20

➞ leading strand

➞ lagging strand

Question 21

what is the leading strand?

Answer 21

the strand that is synthesized continuously (synthesized in the same direction as the movement of the replication fork)

Question 22

what is the lagging strand?

Answer 22

the strand that is discontinuously synthesized (synthesis is in the direction opposite to the movement of the replication fork)

Question 23

what are Okazaki fragments?

Answer 23

small DNA fragments formed during synthesis of the lagging strand

Question 24

in what direction is the template strand read in DNA replication? why?

Answer 24

3’ to 5’ because it must be build 5’ to 3’ and the strands must be antiparallel

Question 25

what is initiation? (DNA replication of bacterial chromosomes)

Answer 25

unwinding and separation of the two template DNA strands at the origin of the replication site (ori)

Question 26

what is elongation? (DNA replication of bacterial chromosomes)

Answer 26

simultaneous synthesis of the two DNA strands from the template strands by DNA polymerase

Question 27

what is termination? (DNA replication of bacterial chromosomes)

Answer 27

DNA replication stops upon reaching termination site or the end of the chromosome

Question 28

what is the end replication problem?

Answer 28

since RNA primers are required for polymerases to build off of, the RNA that connects to the very beginning of the strand has no way of being replaced by DNA, which would result in the DNA strand being shortened with every replication.

Question 29

what is the solution to the end replication problem?

Answer 29

the telomere (which is grown in gametes and stem cells)

Question 30

what is telomerase?

Answer 30

enzyme that restores shortened telomeres.

Question 31

how does telomerase work?

Answer 31

it connects to the 3’ end of the DNA with some RNA on the bottom (as a template). it builds more DNA onto the 3’ end of the template DNA using the telomerase RNA as a template. then telomerase disconnects and some primer puts down RNA and starts the normal DNA replication cycle over again

Question 32

where is telomerase present?

Answer 32

gametes and stem cells (this is why newborns have longer telomeres than their parents).
NOT present in most eukaryotic cells, so telomeres shorten as an individual ages

Question 33

how can cancers use telomerase?

Answer 33

many cancers acquire mutations that activate telomerase to negate the limitation of rapid cell division, resulting in formation of tumours that don’t stop growing on their own like normal cells.

Question 34

what is a telomere?

Answer 34

a buffer of highly repetitive noncoding DNA that protects actual genes from the shortening that occurs with every cell division

Question 35

what are the 3 types of damage repair mechanism that correct DNA damage?

Answer 35

➞ proofreading
➞ mismatch repair
➞ excision repair

Question 36

what is the process of proofreading?

Answer 36

1) polymerase III is synthesizing the new strand
2) polymerase (rarely, 1/10 000 times) adds incorrect base
3) polymerase recognizes the mistake, reverses, and uses exonuclease (which moves 3’ to 5’) to remove the nucleotide from the strand
4) polymerase resumes polymerization

Question 37

what is the chance of mismatches caused by polymerase (including proofreading)?

Answer 37

1/10 000 000

Question 38

what is the process of mismatch repair (MMR)?

Answer 38

1) binding protein MutS and MutL recognize mismatch damage.
2) MutH endonuclease nicks daughter strand sever nucleotides away from the mismatch
3) exonuclease Exo1 excises region of daughter strand surrounding the mismatch in the 5’-3’ direction
4) polymerase III fills gap and repairs mismatch
5) nick left after gap sealed by ligase

Question 39

which errors does MMR deal with?

Answer 39

replication errors not corrected by proofreading