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CSF Block 5 > DNA replication > Flashcards

DNA replication Flashcards

1
Q

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

A

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

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2
Q

what is the “mode” of DNA replication?

A

semi-conservative

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3
Q

what experiment proved that DNA replication is semi-conservative?

A

Meselson-Stahl Experiment

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

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4
Q

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

A

complimentarity

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5
Q

what model of replication is used by bacteria?

A

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

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6
Q

what model of replication is used by viruses, phages?

A

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

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7
Q

what model of replication is used by eukaryotes?

A

linear

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8
Q

in what direction is DNA replicated?

A

5’ to 3’

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9
Q

how long are Okazaki fragments in prokaryotes vs. eukaryotes?

A

pro- 1000-2000 nt

euk- 100-200 nt

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10
Q

at what sequence does DNA replication begin in prokaryotes?

A

OriC

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11
Q

what is the function of DnaA?

A

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

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12
Q

What is DnaB?

what is DnaC?

A

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

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13
Q

where will DnaB open the DNA?

A

at AT rich region (easier to open here)

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14
Q

what are SSBP?

A

single stranded binding proteins

stabilize single strands of DNA, help to prevent reannealing

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15
Q

what positions DnaB?

A

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

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16
Q

what synthesizes the RNA primer?

A

DNA primase

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17
Q

what is the main prokaryote polymerase?

A

DNA polymerase III

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18
Q

what holds pol III in place?

A

sliding clamp

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19
Q

what positions the sliding clamp?

A

clamp loader

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20
Q

what is the function of DNA gyrase?

A

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

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21
Q

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

A

RNase H- removes RNA

DNA pol I - replaces with DNA

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22
Q

what fills in nicks in the DNA backbone?

A

DNA ligase

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23
Q

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

A

alpha, epsilon, theta

24
Q

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

A

5’ to 3’ elongation

proofreading 3’ to 5’

25
Q

what subunit composes the “sliding clamp”?

A

beta

26
Q

what subunit composes the “clamp loader”?

A

gamma

27
Q

what is the function of the tau subunit?

A

dimerizes the pol IIIs of leading and lagging strands

28
Q

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

A

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

29
Q

which enzymes involved in prokaryotic replication require energy from ATP?

A

DNA gyrase
DNA ligase
DNA helicase

30
Q

what is “Tus”?

A

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

31
Q

what is the RNA primer needed?

A

because DNA polymerase needs at 3’ OH to add to

32
Q

where does each new lagging strand fragment always start?

A

at the fork

33
Q

concentration of what controls DNA replication in prokaryotes?

A

DnaA

34
Q

function of acyclovir

A

antiviral used for HSV

stops RNA pol function

35
Q

function of AZT

A

HIV med

analog of thymine, terminates chain

36
Q

MOA of antimalarial drugs

A

target polymerase and topoisomerase II

37
Q

MOA of nalidixic acid and norfloxacin

A

used for UTI

target DNA gyrase to inhibit replication

38
Q

function of ORC in eukaryotes?

A

Origin recognition complex

binds to AT rich regions

39
Q

functions of cdc6 and cdt1

A

bind to ORC and recruit MCM complex

40
Q

function of MCM complex

A

helicase activity

41
Q

what are the components of the pre-replication complex?

A

ORC, cdt1, cdc6 and MCM complex

42
Q

what activates the pre-replication complex?

A

CDK and DDK kinases trigger S phase

remove cdc6 and cdt1

43
Q

recruitment of what proteins ill begin initiation?

A

CDC45 and GINs

44
Q

what is the CMG complex?

A

full 11 subunit replication complex

45
Q

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

A

polymerase epsilon

46
Q

what is PCNA?

A

proliferating cell nuclear antigen

DNA clamp in eukaryotes

47
Q

what is the equivalent of clamp loader in eukaryotes?

A

replication factor C

RFC

48
Q

what places primers on the lagging strand in eukaryotes?

A

polymerase a (primase)

49
Q

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

A

polymerase delta

50
Q

what removes RNA primers in eukaryotes?

A

RNase H

51
Q

what reconnects the flaps left by RNase H?

A

FEN1 (short)- flap endonuclease 1

DNA2 (long)

52
Q

what are telomeres?

A

unique sequences at the end of chromosomes, added by telomerase

53
Q

what is the “end replication problem”?

A

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

54
Q

what forms telomerase?

A

protein and RNA

55
Q

what is the function of telomerase?

A

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

56
Q

what is TERT?

A

telomerase reverse transcriptase

57
Q

what is TERC?

A

telomerase RNA component

CSF Block 5 (18 decks)

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