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BIO107 - Cell and Molecular Biology > Replication - Part 1 > Flashcards

Replication - Part 1 Flashcards

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1
Q

Prokaryotic genome organization

A
  1. Lower DNA content
  2. Main genome: single major DNA molecule (cccDNA)
  3. Operons
  4. Few repetitive sequences: no introns
  5. Other genes: plasmid
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2
Q

Eukaryotic genome organization

A
  1. Higher DNA content
  2. Enclosed in a nuclear membrane
  3. Several linear DNA, chromosome
  4. Organization of coding sequences
  5. With telomere
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3
Q

DNA replication is __

A

Semi-conservative

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4
Q

What is maintained inthe DNA

A

Specific base pairing

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5
Q

Needed for initiation of replication

A

Primer

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6
Q

Direction of newly synthesized DNA strand

A

5’-3’ direction

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7
Q

Replication of DNA is __

A

Semi-discontinuous

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8
Q

Grows continuously

A

Leading strand

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9
Q

Grows in segments

A

Lagging strand

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10
Q

Connects the okazaki fragments

A

DNA ligase

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11
Q

How are nucleotides become linked

A

Condensation reaction to form phosphodiester linkage

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12
Q

Where replication begins and proceeds

A
  • begins at an origin
  • proceeds bidirectionally
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13
Q

What is involved in DNA replication

A

Several enzymes and proteins (replisomes)

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14
Q

How are bacterial genes usually written

A

3 lowercase italicized letters

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15
Q

Example of how the gene and gene products are written

A

dnaA (gene) -> Dna A (protein)

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16
Q

Replication proteins

A

Replisome

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17
Q

What are the replisomes

A
  1. Initiation protein
  2. DNA helicase/ DNA unwinding proteins
  3. Helix destabilizing proteins or single-strand binding proteins (SSBP)
  4. Primase
  5. DNA polymerases
  6. DNA ligase
  7. Topoisomerases
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18
Q

Initiation protein of E.coli

A

dnaA protein

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19
Q
  • recognizes the OriC
  • binds to it (~20-30 dnaA)
A

dnaA protein

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20
Q
  • local denaturation of DNA helix
  • Requires ATP
  • Binds ssDNA (not dsDNA)
A

DNA helicases/DNA unwinding proteins

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21
Q

2 helicases of E.coli

A
  1. Helicase II
  2. Rep protein
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22
Q
  • attaches to template for lagging strand
  • moves 5’–>3’
A

Helicase II

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23
Q
  • attached to template for leading strand
  • moves 3’–>5’
A

Rep protein

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24
Q

Bind to sites where template has been unwound but not yet duplicated

A

Helix Destabilizing Proteins or Single-strand Binding Proteins (SSBP)

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25
Q

Functions of Helix Destabilizing Proteins or Single-strand Binding Proteins (SSBP)

A
  1. prevent reannealing and tangling of ssDNA
  2. prevent formation of 2º structure
  3. protect ssDNA from nuclease degradation
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26
Q

Major SSB of eukaryotes

A

Replication protein A (RPA)

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27
Q

SSBPs are required to __ the unwound DNA

A

Iron out

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28
Q

Generate primers

A

Primases

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29
Q
  • short RNA chain (4-12 nts)
  • provides the 3’OH end needed by DNA polymerase during elongation
A

Primer

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30
Q
  • monomeric or heteromultimeric
  • 3 enzyme activities
A

DNA polymerase

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31
Q

3 enzymatic activities of DNA Polymerase

A
  1. 5’–>3’ polymerization activity
  2. 3’–>5’ exonuclease activity
  3. 5’–>3’ exonuclease activity
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32
Q

Add nucleotides onto the 3’OH end of a primer –> synthesize new DNA strands

A

5’–>3’ polymerization activity

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33
Q

property of DNA pol to remain attached to the template and incorporate nucleotides before detaching

A

Processivity

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34
Q

1 mistake per 10^9 or 10^10 nucs added

A

Fidelity

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35
Q

Proofreading

A

3’–>5’ exonuclease activity

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36
Q
  • removes RNA primers at the 5’ end
  • not present in eukaryotic DNA polymerase
A

5’–>3’ exonuclease activity

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37
Q

enzyme that perform 5’-3’ exonuclease activity in eukaryotes

A
  1. Rnase H
  2. Flap endonuclease 1 (FEN1)
  3. DNA pol delta
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38
Q
  • remove RNA primers
  • detects RNA-DNA hybrid in eukaryotes
A

Rnase H

39
Q

removes remaining bits or RNA primer in eukaryotes

A

Flap endonuclease 1 (FEN1)

40
Q

add/fill in the gaps from removal of primer in eukaryotes

A

DNA pol delta

41
Q

3 main DNA polymerases for replication

A
  1. DNA pol I
  2. DNA pol II
  3. DNA pol III
42
Q

Major repair enzyme

A

DNA pol I, II

43
Q

Elongating enzyme

A

DNA pol III

44
Q

Gene of DNA pol I

A

polA

45
Q

Gene of DNA pol II

A

polB

46
Q

Gene of DNA pol III

A

polC

47
Q

SOS repair

A

DNA pol IV, V

48
Q

Gene of DNA pol IV

A

dinB

49
Q

Gene of DNA pol V

A

umuD’2C

50
Q
  • Replicates both strands simultaneously
  • A dimer of 10 proteins
A

Bacterial DNA Polymerase III Holoenzyme

51
Q

Core enzyme of Bacterial DNA Polymerase III Holoenzyme

A
  • α – (5’->3’ polymerization)
    ε - (3’->5’ exonuclease/proofreading)
  • θ stimulates ε
52
Q

Sliding clamp of Bacterial DNA Polymerase III Holoenzyme

A

β2

53
Q

purpose of sliding clamp β2

A

helps the holoenzyme

54
Q

Clamp loader of Bacterial DNA Polymerase III Holoenzyme

A

(δδ’χΨ)2τ2γ2

55
Q

Keeps DNA polymerase attached to the template to allow duplication of long stretches of DNA

A

Sliding clamp

56
Q

Assembles the sliding clamp to the DNA

A

Clamp loader

57
Q

E. coli sliding clamp = __

A

eukaryotic PCNA

58
Q

Separates large fragment and 5’->3’ exonuclease

A

Subtilisin (proteolysis)

59
Q

Used in in vitro synthesis of dsDNA from ssDNA

A

Klenow fragment

60
Q

Eukaryotic DNA polymerases

A

α, β, γ, δ, ε, etc
(10 DNA polymerases)

61
Q

Location of DNA pol α

A

Nuclear

62
Q

Location of DNA pol β

A

Nuclear

63
Q

Location of DNA pol γ

A

Mitochondrial

64
Q

Location of DNA pol δ

A

Nuclear

65
Q

Location of DNA pol ε

A

Nuclear

66
Q

function of DNA pol α

A

priming and replication of lagging strand

67
Q

function of DNA pol β

A

repair

68
Q

function of DNA pol γ

A

mitochondrial

69
Q

function of DNA pol δ

A

replication of leading strand

70
Q

function of DNA pol ε

A

probably replication

71
Q

relative activity of α

A

~80%

72
Q

relative activity of DNA pol β

A

10-15%

73
Q

relative activity of DNA pol γ

A

2-15%

74
Q

MW of α

A

300,000

75
Q

MW of β

A

40,000

76
Q

MW of γ

A

180-300,000

77
Q

MW of δ

A

170-230,000

78
Q

MW of ε

A

255,000

79
Q

No. of subunits of α

A

4 (several)

80
Q

No. of subunits of β, γ, δ

A

1

81
Q

DNA polymerases with 3’-5’ exonuclease activity

A

γ, δ, ε

82
Q

seals nicks using ATP or NAD

A

DNA ligase

83
Q

what does the DNA ligase use to seal nicks

A

ATP or NAD

84
Q
  • relaxes DNA
  • removes negative supercoils
A

topoisomerases

85
Q

topoisomerase that relax only one strand

A

topoisomerase I

86
Q

topoisomerase that relax both strands

A

topoisomerase II

87
Q

in E.coli, topoisomerase or gyrase is involved in what?

A

deconcatenation

88
Q

process of releasing the final products of circular DNA replication

A

deconcatenation

89
Q

what stage of the cell cycle does DNA replication happen

A

S phase

90
Q

stages of replication

A
  1. initiation
  2. elongation
  3. termination
91
Q

recognition of positions on a DNA molecule where replication will begin

A

initiation

92
Q

copying of parent polynucleotide (template) at the replication fork

A

elongation

93
Q

completion

A

termination

BIO107 - Cell and Molecular Biology (18 decks)

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