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BIOCHEM > DNA replication > Flashcards

DNA replication Flashcards

1
Q

what are the 3 fundamental condition of DNA replication?

A

semiconservative
bidirectional
semi discontinuous

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2
Q

What does it mean when DNA replication is semiconserative?

A

The two DNA stands separate and each is copied so the new DNA double helices contain one original strand and one newly synthesized strand

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3
Q

What does it mean when DNA replication is bidirectional?

A

Replication proceeds in both directions from an origin of replication

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4
Q

What does it mean when DNA replication is semidiscontinuous?

A

One of the two strands is copied discontinuously as a set of fragments called Okazaki fragments which are then joined to form an intact strand

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5
Q

How many nucleotides long are Okazaki fragments in Ecoli?

A

1000-2000 nucleotides long

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6
Q

How many nucleotides long are Okazaki fragments in eukaryotes?

A

100,000 nucleotides

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7
Q

How many replication origins are there?

A

30,000

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8
Q

in the semi conservative method, one strand of the newly synthesized strand is ____ to the original

A

complementary (A-T, C-G)

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9
Q

okazaki fragments are liked via ____ bonds

A

covalent

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10
Q

in what direction is the leading strand synthesized?

A

5’ to 3’

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11
Q

what enzyme synthesizes DNA?

A

DNA polymerase

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12
Q

What two things cause semi-discontinuous DNA replication?

A
  1. DNA polymerases only synthesize DNA 5’ to 3’
  2. The two DNA strands of the double helix must be in opposite directions
    (one 5’ to 3’, one 3’ to 5’)
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13
Q

what are the 3 phases of DNA replication?

A

initiation, elongation, termination

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14
Q

what is the initiation factor that binds to OriC to separate the strands of the double helix?

A

DnaA protein

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15
Q

DnaB protein is a ____, or DNA-unwinding protein

A

helicase

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16
Q

what is the role of DnaA protein?

A

bind to oriC to separate the strands of the double helix

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17
Q

what helicase binds to the separated strands and moves alone the DNA to unwind the DNA double helix?

A

DnaB protein

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18
Q

what is the role of DnaB protein?

A

bind to the separated strands to unwind the double helix

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19
Q

what is the protein that prevents the two unwound DNA strands from coming back together?

A

SSB (single-stranded DNA binding protein)

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20
Q

what is the role of SSB (single-strand DNA binding protein)?

A

prevent the separated strands from coming back togehter

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21
Q

what protein relieves stress in the helical DNA caused by the unwinding?

A

DNA gyrase (DNA topoisomerase 2)

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22
Q

DnaA protein binds to the ___ __ ____

A

origin of replication (oriC)

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23
Q

The binding of DnaA protein ____ ____ at the origin of replication

A

separates the strands

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24
Q

DnaB protein is delivered to the replication forks by ___ and ___ proteins

A

DnaC and DnaT

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25
Q

DnaB protein moves along the DNA, unwinding the __ __

A

double helix

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26
Q

what two proteins are responsible for bringing in the DnaB protein?

A

DnaC and DnaT

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27
Q

DnaB subunits come in the form of a ____

A

hexomere

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28
Q

DnaB subunits come in the form of a ____

A

hexamer

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29
Q

SSB subunits come in the form of _____

A

tetromers

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30
Q

SSB subunits come in the form of _____

A

tetramers

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31
Q

what are the two enzymes responsible for DNA unwinding during the elongation phase?

A

DNA helicase (DnaB), gyrase (topoisomerase 2)

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32
Q

what enzyme is responsible for synthesizing an RNA primer that is needed for DNA replication in the elongation phase?

A

primase enzyme

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33
Q

what enzyme is used in the elongation phase to synthesize the new DNA strands?

A

DNA polymerase 3 holoenzyme

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34
Q

What seven proteins replicate the DNA double helix?

A
  1. DNA polymerase lll holoenzyme
  2. DNA helicase
  3. DNA gyrase
  4. primase
  5. single stranded DNA binding protein
  6. DNA polymerase l
  7. DNA ligase
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35
Q

what subunit of DNA polymerase 3 acts as a “sliding clamp” that hold the DNA polymerase onto the DNA strand?

A

beta

36
Q

what second enzyme is associated with DNA polymerase 1?

A

DNA ligase

37
Q

what enzyme during elongation is responsible for binding to the region of the primers that will begin the Okazaki fragment to cut it out and replace it with a patch of DNA?

A

DNA polymerase 1

38
Q

how many subunits are a part of DNA polymerase 3 holoenzyme?

A

10

39
Q

what part of DNA polymerase 3 holoenzyme is involved in polymerase activity of linking new nucleotides to the end of the growing chain via covalent linkages?

A

alpha

40
Q

what part of DNA polymerase 3 holoenzyme has 3’ to 5’ proofreading activity?

A

episilon

41
Q

What is the main subunit of DNA polymerase lll?

A

alpha

42
Q

what part of DNA polymerase 3 holoenzyme stimulates the proofreading activity?

A

theta

43
Q

How many subunits does the “core” DNA polymerase lll have?

A

3 subunits (alpha, episilon, theta)

44
Q

In DNA polymerase 3 holoenzyme, how many core units of A,E,T are present?

A

2

45
Q

what is the middle core of DNA polymerase 3 holoenzyme?

A

gamma

46
Q

what complex keeps together the 2 A,E,T cores?

A

gamma complex

47
Q

what are the components of the gamma complex?

A

gamma, delta, delta prime, chi, si

48
Q

how many tau and beta are present at each A,E,T core?

A

1 tau, 2 beta

49
Q

what is the role of tau in DNA polymerase 3 holoenzyme?

A

to bring about proper assembly

50
Q

at termination, what is the name of the termination region?

A

ter

51
Q

what is the termination protein that is bound to the termination region (ter) to help bring about termination?

A

tus

52
Q

In termination, the two bidorectional replication forks continue to move around the circular E.coli chromosome until they meet at a ____ ____ and replication is terminated

A

termination region (Ter region)

53
Q

DNA in higher cells interact with ____ proteins to form ______ and ______ ______

A

histones, nucleosomes, chromatin fibers

54
Q

The beads on a string nucleosome fiber is ___ nm

A

10

55
Q

The beads on a string nucleosome fiber with DNA is wrapped around ___ _____

A

histone proteins

56
Q

A chromatin fiber is __ nm

A

30

57
Q

A chromatin fiber is produced by helical coiling of the ___ ____

A

nucleosome fiber

58
Q

are histones positively or negatively charged?

A

positively charged to bind to the negatively charged DNA

59
Q

What Eukaryotic DNA polymerase is the principal DNA polymerase in eukaryotic DNA replication?

A

Polymerase delta

60
Q

What Eukaryotic DNA polymerase functions in the initiation of nuclear DNA replication?

A

Polymerase alpha

61
Q

What Eukaryotic DNA polymerase cooperates with DNA polymerase delta?

A

Polymerase epsilon

62
Q

What Eukaryotic DNA polymerase functions in DNA repair?

A

Polymerase beta

63
Q

What Eukaryotic DNA polymerase DNA replicating enzyme of mitochondria?

A

Polymerase gamma

64
Q

How many DNA polymerases are needed in eukaryotic DNA replication?

A

5

65
Q

What two eukaryotic DNA polymerases work together to synthesize most of DNA?

A

Polymerase delta and epsilon

66
Q

What eukaryotic DNA polymerase forms primers and begins to add DNA nucleotides?

A

Polymerase alpha

67
Q

What eukaryotic DNA polymerase synthesizes short patches of DNA?

A

Polymerase beta

68
Q

polymerase ___ has 4 subunits with 2 involved in DNA replication and 2 involved in primase (RNA) synthesis

A

alpha

69
Q

what eukaryotic DNA polymerase has the 4 subunits of PolA1, PolA2, Prim1, and Prim2?

A

alpha

70
Q

what eukaryotic DNA polymerase has the 5 subunits of PolyD1, PolyD2, PolyD3, PolyD4, and PCNA (clamp)?

A

delta

71
Q

what eukaryotic DNA polymerase has the 3 subunits of Pole, Pole2, and Pole3?

A

epsilon

72
Q

what eukaryotic DNA polymerase has the 2 subunits of PolG and PolG2?

A

gamma

73
Q

what eukaryotic DNA polymerase has low fidelity?

A

beta

74
Q

what eukaryotic DNA polymerases have low processivity?

A

alpha, beta

75
Q

what is the eukaryotic protein that bind to to the replication origins and is important to bringing about the assembly of the pre-replicative complex?

A

ORC

76
Q

what is the eukaryotic protein that acts as a helicase to unwind the double helix at replication origins and separate DNA strands?

A

MCM (replaces DnaA and DnaB)

77
Q

what is the eukaryotic protein that brings about the binding of the MCM proteins to the replication origins?

A

Cdc6 (no active role)

78
Q

what is the eukaryotic protein that is a kinase complex that initiates DNA replication by adding phosphate groups to ORC, MCM, and Cdc6 proteins?

A

cyclin CDK (negative charged phosphate changes protein folding and activates them)

79
Q

in eukaryotes, a pre-replication complex is formed by the binding of ____ and ____ proteins to the replication origin where ____ protein is bound

A

Cdc6, MCM, ORC

80
Q

ORC is duplicated during the ___ phase

A

S phase

81
Q

a gap is produced at the ___ end by the removal of the RNA primer

A

5’

82
Q

_____ is the enzyme responsible for extending the 3’ end in eukaryotes by adding TTAGGG repeats so that DNA polymerase can extend the 5’ end

A

telomerase

83
Q

Cyclin-CDK initiates DNA replication by adding ___ ___ to ORC, MCM, and Cdc6 proteins

A

phosphate groups

84
Q

telomerase adds sequences of ______ bases

A

TTAGGG

85
Q

A gap is produced at the 5’ end by removal of the ____ ____

A

RNA primer

86
Q

Telomerase extends the 3’ end by adding ______ repeats

A

TTAGGG

87
Q

DNA polymerase can then extend the __ end

A

5’

BIOCHEM (16 decks)

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