DNA replication

Question 1

what are 3 basic differences between prokaryotic and eukaryotic DNA replication?

Answer 1

1- origins of replication- prokaryotes have one per chromosome, eukaryotes have many
2- eukaryotes have replication of telomeres
3- eukaryotes have nucleosome assembly

Question 2

what is the “mode” of DNA replication?

Answer 2

semi-conservative

Question 3

what experiment proved that DNA replication is semi-conservative?

Answer 3

Meselson-Stahl Experiment

used E coli grown in heavy nitrogen and compared densities of subsequent generations

Question 4

what property of DNA allows for each strand to serve as a template for the synthesis of the other?

Answer 4

complimentarity

Question 5

what model of replication is used by bacteria?

Answer 5

theta, circular template with circular product, no break in strand

Question 6

what model of replication is used by viruses, phages?

Answer 6

Rolling circle- a nuclease cleaves strand allowing for a linear product from a circular template

Question 7

what model of replication is used by eukaryotes?

Answer 7

linear

Question 8

in what direction is DNA replicated?

Answer 8

5’ to 3’

Question 9

how long are Okazaki fragments in prokaryotes vs. eukaryotes?

Answer 9

pro- 1000-2000 nt

euk- 100-200 nt

Question 10

at what sequence does DNA replication begin in prokaryotes?

Answer 10

OriC

Question 11

what is the function of DnaA?

Answer 11

protein that begins the initiation of replication by binding OriC (9 bp repeats) and opens sections of DNA by creating a bend to allow access for the replication proteins

Question 12

What is DnaB?

what is DnaC?

Answer 12

DnaB- also called DNA helicase opens DNA with energy from ATP
DnaC- loads DNA helicase

Question 13

where will DnaB open the DNA?

Answer 13

at AT rich region (easier to open here)

Question 14

what are SSBP?

Answer 14

single stranded binding proteins

stabilize single strands of DNA, help to prevent reannealing

Question 15

what positions DnaB?

Answer 15

DNA helicase loader (DnaC) places DNA helicase (DnaB) on the strands

Question 16

what synthesizes the RNA primer?

Answer 16

DNA primase

Question 17

what is the main prokaryote polymerase?

Answer 17

DNA polymerase III

Question 18

what holds pol III in place?

Answer 18

sliding clamp

Question 19

what positions the sliding clamp?

Answer 19

clamp loader

Question 20

what is the function of DNA gyrase?

Answer 20

also called topoisomerase II, creates negative supercoils to help keep DNA unwound

Question 21

what removes RNA primers and replaces them with DNA in prokaryotes?

Answer 21

RNase H- removes RNA

DNA pol I - replaces with DNA

Question 22

what fills in nicks in the DNA backbone?

Answer 22

DNA ligase

Question 23

what subunits compose the “core enzyme” in DNA pol III?

Answer 23

alpha, epsilon, theta

Question 24

what are the capabilities of the “core enzyme” in DNA pol III?

Answer 24

5’ to 3’ elongation

proofreading 3’ to 5’

Question 25

what subunit composes the "sliding clamp"?

Answer 25

beta

Question 26

what subunit composes the "clamp loader"?

Answer 26

gamma

Question 27

what is the function of the tau subunit?

Answer 27

dimerizes the pol IIIs of leading and lagging strands

Question 28

what is the function of DNA pol I in prokaryotic replication?

Answer 28

removes RNA primer, replaces with DNA via 5' to 3' exonuclease activity

Question 29

which enzymes involved in prokaryotic replication require energy from ATP?

Answer 29

DNA gyrase DNA ligase DNA helicase

Question 30

what is "Tus"?

Answer 30

termination utilization substance prevents the replication fork from advancing by blocking the movement of DNA helicase resulting in termination of replication

Question 31

what is the RNA primer needed?

Answer 31

because DNA polymerase needs at 3' OH to add to

Question 32

where does each new lagging strand fragment always start?

Answer 32

at the fork

Question 33

concentration of what controls DNA replication in prokaryotes?

Answer 33

DnaA

Question 34

function of acyclovir

Answer 34

antiviral used for HSV | stops RNA pol function

Question 35

function of AZT

Answer 35

HIV med | analog of thymine, terminates chain

Question 36

MOA of antimalarial drugs

Answer 36

target polymerase and topoisomerase II

Question 37

MOA of nalidixic acid and norfloxacin

Answer 37

used for UTI | target DNA gyrase to inhibit replication

Question 38

function of ORC in eukaryotes?

Answer 38

Origin recognition complex | binds to AT rich regions

Question 39

functions of cdc6 and cdt1

Answer 39

bind to ORC and recruit MCM complex

Question 40

function of MCM complex

Answer 40

helicase activity

Question 41

what are the components of the pre-replication complex?

Answer 41

ORC, cdt1, cdc6 and MCM complex

Question 42

what activates the pre-replication complex?

Answer 42

CDK and DDK kinases trigger S phase | remove cdc6 and cdt1

Question 43

recruitment of what proteins ill begin initiation?

Answer 43

CDC45 and GINs

Question 44

what is the CMG complex?

Answer 44

full 11 subunit replication complex

Question 45

what DNA pol is active on the leading strand in eukaryotes?

Answer 45

polymerase epsilon

Question 46

what is PCNA?

Answer 46

proliferating cell nuclear antigen | DNA clamp in eukaryotes

Question 47

what is the equivalent of clamp loader in eukaryotes?

Answer 47

replication factor C | RFC

Question 48

what places primers on the lagging strand in eukaryotes?

Answer 48

polymerase a (primase)

Question 49

what DNA pol is active on the lagging strand in eukaryotes?

Answer 49

polymerase delta

Question 50

what removes RNA primers in eukaryotes?

Answer 50

RNase H

Question 51

what reconnects the flaps left by RNase H?

Answer 51

FEN1 (short)- flap endonuclease 1 | DNA2 (long)

Question 52

what are telomeres?

Answer 52

unique sequences at the end of chromosomes, added by telomerase

Question 53

what is the "end replication problem"?

Answer 53

problem in linear chromosomes (eukaryotes), where there is no place to produce the RNA primer needed to start the last Okazaki fragment

Question 54

what forms telomerase?

Answer 54

protein and RNA

Question 55

what is the function of telomerase?

Answer 55

adds repeats (GC rich) that extends the DNA, filling in the gap due to the removal of RNA primer

Question 56

what is TERT?

Answer 56

telomerase reverse transcriptase

Question 57

what is TERC?

Answer 57

telomerase RNA component