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BIOC3021 > DNA Repair and Replication > Flashcards

DNA Repair and Replication Flashcards

1
Q

what are the 3 fundamental condition of DNA replication?

A

semiconservative, bidirectional, semi discontinuous

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2
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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3
Q

what is the name of the site of origin in unidirectional replication?

A

Ori-C

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4
Q

okazaki fragments are liked via ____ bonds

A

covalent

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5
Q

in what direction is the leading strand synthesized?

A

5’ to 3’

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6
Q

what enzyme synthesizes DNA?

A

DNA polymerase

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7
Q

____ ____ is the enzyme that links together okazaki fragments

A

DNA ligase

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8
Q

what are the 3 phases of DNA replication?

A

initiation, elongation, termination

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9
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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10
Q

what is the role of DnaA protein?

A

bind to oriC to separate the strands of the double helix

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11
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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12
Q

what is the role of DnaB protein?

A

bind to the separated strands to unwind the double helix

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13
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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14
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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15
Q

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

A

DNA gyrase (DNA topoisomerase 2)

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16
Q

____ copies of the DnaA protein bind to oriC

A

multiple

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17
Q

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

A

DnaC and DnaT

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18
Q

DnaB subunits come in the form of a ____

A

hexomere

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19
Q

DnaB subunits come in the form of a ____

A

hexamer

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20
Q

SSB subunits come in the form of _____

A

tetromers

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21
Q

SSB subunits come in the form of _____

A

tetramers

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22
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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23
Q

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

A

primase

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24
Q

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

A

DNA polymerase 3 holoenzyme

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25
Q

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

A

beta

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26
Q

what second enzyme is associated with DNA polymerase 1?

A

DNA ligase

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27
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

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28
Q

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

A

10

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29
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

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30
Q

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

A

episilon

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31
Q

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

A

theta (O)

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32
Q

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

A

2

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33
Q

what is the middle core of DNA polymerase 3 holoenzyme?

A

gamma

34
Q

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

A

gamma complex

35
Q

what are the components of the gamma complex?

A

gamma, delta, delta prime, chi, si

36
Q

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

A

1 tau, 2 beta

37
Q

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

A

to bring about proper assembly

38
Q

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

A

ter

39
Q

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

A

tus

40
Q

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

A

histones, nucleosomes, chromatin fibers

41
Q

are histones positively or negatively charged?

A

positively charged to bind to the negatively charged DNA

42
Q

what occurs to disrupt the positive charges on the histones so they fall off?

A

acetylation (binding of acetyl group to neutralize)

43
Q

how many DNA polymerases are needed in eukaryotic DNA replication?

A

5

44
Q

what eukaryotic DNA polymerase functions in the initiation of nuclear DNA replication by initiating the addition of DNA nucleotides to the end of the primer?

A

alpha

45
Q

what eukaryotic DNA polymerase is the principle DNA polymerase in replication, and grows the okazaki fragments?

A

delta

46
Q

what eukaryotic DNA polymerase cooperates with delta to produce the leading strand?

A

epsilon

47
Q

what eukaryotic DNA polymerase functions in DNA repair?

A

beta

48
Q

what eukaryotic DNA polymerase is the DNA replicating enzyme of the mitochondria

A

gamma

49
Q

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

A

alpha

50
Q

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

A

alpha

51
Q

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

A

delta

52
Q

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

A

epsilon

53
Q

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

A

gamma

54
Q

what eukaryotic DNA polymerase has low fidelity?

A

beta

55
Q

what eukaryotic DNA polymerases have low processivity?

A

alpha, beta

56
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

57
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)

58
Q

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

A

Cdc6 (no active role)

59
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)

60
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

61
Q

ORC is duplicated during the ___ phase

A

S

62
Q

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

A

5’

63
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

64
Q

telomerase adds sequences of ______ bases

A

TTAGGG

65
Q

____ ____ occur when pyrimidine bases such as T are covalently linked by UV light

A

pyrimidine dimers

66
Q

___ ___ ____ is when DNA corrects errors introduced when DNA is replicated

A

mismatch repair system

67
Q

___ ___ _____ acts on single bases damaged by oxidation or other chemical modifications

A

base excision repair

68
Q

_____ ____ ____ repairs large regions of damaged DNA

A

nucleotide excision repair

69
Q

______ ___-_______ is correcting DNA double strand breaks caused by radiation or when free radicals are repaired

A

nonhomologous end-joining

70
Q

___ _____ uses homologous recombination to repair double strand breaks that occur ding cell division cycle

A

recombination repair

71
Q

__ ____ ___ _____ are when chemically modified bases are directly repaired

A

direct reversal repair systems

72
Q

photolyase, an enzyme that repairs thymine dimers, is an example of what repair mechanism?

A

direct reversal repair systems

73
Q

to ID the strand with the incorrect base in mismatch repairs, ____ groups are detected as only being on the old strand

A

methyl

74
Q

the strand ____ the methyl groups in mismatch repair is the new strand

A

without

75
Q

what 3 enzymes are needed during mismatch repair to remove the incorrect nucleotide and replace it?

A

endonuclease, exonuclease, DNA polymerase 3, DNA ligase

76
Q

in base excision repair, ___ ____ removes the damaged based by cleaving the glycosidic bone between the base and deoxyribose

A

DNA glycosylase

77
Q

in base excision repair, an _____ cleaves the backbone to remove the deoxyribose and phosphate group

A

endonuclease

78
Q

in base excision repair, an _______ removes a number of additional nucleotide residues that are not damaged to create space for DNA polymerase 1 to come in and add a patch of DNA

A

exonuclease

79
Q

an ____ site is created in base excision repair after cleavage

A

AP (apurinic, apyrimidinic)

80
Q

in base excision repair, ___ _____ ____ fills in the made gap with a patch of DNA

A

DNA polymerase 1

BIOC3021 (25 decks)

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