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BIO107 - Cell and Molecular Biology > Replication - Part 2 > Flashcards

Replication - Part 2 Flashcards

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1
Q
  • always at the same position on a DNA molecule
  • “origin of replication”
A

initiation

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2
Q

origin of replication in prokaryotes, viruses

A

oriC

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3
Q

how many origin of replications are there in prokaryotes and viruses

A

single origin

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4
Q

how many origin of replications are there in eukaryotes

A

multiple

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5
Q

no. of replication origin in yeast

A

300 origins

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6
Q

no. of replication origin in humans

A

20,000 origins

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7
Q
  • segment of DNA that replicates from a single origin of replication
  • genome is divided into
A

replicons

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8
Q

origin of replication in E.coli

A

oriC

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9
Q

no. of base pairs in oriC

A

~245 bp

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10
Q

two parts of the oriC

A
  1. 13-nuc repeat motif
  2. 9-nuc repeat motif
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11
Q
  • repeated 3x
  • consensus seq: 5’GATCTNTTNTTTT3’
A

13-nuc repeat motif

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12
Q

how many times is the 13-nuc repeat motif repeated

A

3

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13
Q
  • repeated 5x
  • consensus seq: (di ma type kapoi)
A

9-nuc repeat motif

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14
Q

how many times is the 9-nuc repeat motif repeated

A

5

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15
Q

what is formed in the 13 nucleotide repeat motif once dnaA is present

A

melted region

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16
Q

binds to 9-nuc repeat of oriC

A

DnaA

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17
Q

what does the dnaA do

A

tortional stress on DNA

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18
Q

what happens at 13-nuc repeat of oriC

A

melting of helix

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19
Q

attaches to the melted region

A

dnaBC

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20
Q

later detaches

A

dnaC

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21
Q

what is formed after dnaC detaches

A

pre-priming complex

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22
Q

what does dnaB do

A

unwinds more DNA

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23
Q

releases tension during the unwinding of dnaB

A

DNA topoisomerase

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24
Q

attaches to ssDNA

A

SSB

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25
Q

primase that attaches to DNA

A

DnaG

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26
Q

initial assembly of the complex that initiates primer synthesis

A

primosome

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27
Q

dimer that binds after RNA primer is synthesized

A

DNA pol III

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28
Q

enhances binding of DNA pol III

A

sliding clamp

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29
Q

large protein complex that carries out DNA replication, starting at the replication origin

A

replisome

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30
Q

Detaches SSB once DNA pol III arrrives to copy template

A

replication mediator protein (RMP)

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31
Q

proofreads and replaces primers

A

DNA pol I

32
Q

seals nicks

A

DNA ligase

33
Q

what happens after DNA ligase seals nicks

A

termination of replication

34
Q

replication fork in 3D:
the DNA on the lagging strand is __

A

folded

35
Q

termination of replication

A

genetically determined

36
Q

hypotheses of termination of replication

A
  1. secondary structure hinders progress of replication fork
  2. terminus destablizes components of replication machinery
  3. protein binds terminus and modifies binding or action of replisome
37
Q

hinders progress of replication fork

A

secondary structure

38
Q

destablizies components at replication machinery

A

terminus

39
Q

binds terminus and modifies binding or action of replisome

A

protein

40
Q
  • defined termination sequence
  • 23bp consensus sequence
  • binding site of ter protein which has contra-helicase activity
A

ter element

41
Q

what binds to ter element

A

ter protein

42
Q

what does the ter protein have

A

contra-helicase activity

43
Q

replication models for circular DNA

A
  1. theta model
  2. rolling circle model
44
Q

DNA in theta model

A
  1. bacterial DNA
  2. λ DNA
45
Q

DNA in rolling circle model

A
  1. F factor
  2. ø X 174 DNA
  3. λ DNA
46
Q

products of theta replication

A

two circular DNA molecules

47
Q

where continuous DNA synthesis begin in rolling-circle model

A

3’ end of broken nucleotide strand

48
Q

how is replication initiated in rolling circle model

A

break in one of nucleotide strands

49
Q

what is released in rolling circle model

A
  1. ss linear DNA
  2. ds circular DNA
50
Q

creates a nick in rolling circular model

A

endonuclease

51
Q

origin of replication for yeast

A

ARS (autonomously replicating sequence)

52
Q

ARS subdomains

A
  1. A and B1 = ORS
  2. B2
  3. B3
53
Q

A and B1

A

ORS

54
Q

function of ORS

A

binding site of ORC

55
Q

ORC

A

origin replicating complex

56
Q

ORS

A

origin replication sequence

57
Q

function of B2

A

melting

58
Q

function of B3

A

binding site of ABF
- tortional stress on DNA

59
Q

ABF

A

ARS binding factor 1 protein

60
Q
  • tightly bound
  • cooperates in the synthesis of the first few nucleotides of the new polynucleotide
A

eukaryotic primase and DNA pol α

61
Q

synthesizes an RNA primer

A

primase

62
Q

no. of nucleotides of RNA in RNA primer

A

8-12

63
Q

extends the RNA primer by adding ~20 nucs of DNA

A

DNA pol α

64
Q

how many nucs does DNA pol α add to extend RNA primer

A

~20 nucs

65
Q

elongates RNA

A

DNA pol δ

66
Q

how many eukaryotic DNA polymerases are there

A

10

67
Q

for primer synthesis in eukaryotes

A

DNA pol α

68
Q

for mitochondrial DNA replication

A

DNA pol γ

69
Q

main elongating enzyme

A

DNA pol δ

70
Q

works with DNA pol δ by increasing its processivity

A

Proliferating cell nuclear antigen (PCNA)

71
Q

removes RNA primers in eukaryotes

A

RNase H, FEN1

72
Q

accuracy of DNA replication

A
  1. specificity of base pairing
  2. pre-synthetic error control
  3. proof-reading ability of DNA polymerase
73
Q

before the nucleotide is covalently added to the growing chain

A

pre-synthetic error control

74
Q

what does DNA pol undergo during pre-synthetic error contrl

A

conformational change

75
Q

what does the DNA pol do during pre-synthetic error control

A

double-checks exact base pair geometry

76
Q

DNA repair mechanisms to correct replication errors

A

proof-reading ability (3’-5’ exonuclease)

BIO107 - Cell and Molecular Biology (18 decks)

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