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[OS 201] 3rd Exam > Lippincott - DNA Structure, Replication, Repair > Flashcards

Lippincott - DNA Structure, Replication, Repair Flashcards

1
Q

DNA

A

polymer of deoxyribonucleoside monophosphates covalently linked by 3’–>5’ phosphodiester bonds

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2
Q

main bond in DNA

A

phosphodiester bond

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3
Q

phosphodiester bond connects:

A

3’-hydroxyl group of one nucleotide to 5’ hydroxyl group of adjacent nucleotide

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4
Q

3’ end

A

end with the free hydroxyl

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5
Q

5’ end

A

end with the free phosphate

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6
Q

what enzyme family cleaves DNA

A

deoxyribonucleases

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7
Q

what enzyme family cleaves RNA

A

ribonucleases

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8
Q

orientation of single stranded DNA in double helix

A

antiparallel

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9
Q

type of bond that mediates base pairing

A

hydrogen bond

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10
Q

DNA - adenine pairs with:

A

thymine

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11
Q

DNA - guanine pairs with:

A

cytosine

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12
Q

DNA - thymine pairs with:

A

adenine

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13
Q

DNA - cytosine pairs with:

A

guanine

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14
Q

methods of DNA denaturation

A

altering pH (ionization), melting DNA

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15
Q

number of H bonds between guanine and cytosine

A

3

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16
Q

number of H bonds between adenine and thymine

A

2

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17
Q

which bases are purines

A

adenine, guanine

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18
Q

which bases are pyrimidines

A

thymine, cytosine

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19
Q

number of rings in purines

A

2

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20
Q

number of rings in pyrimidines

A

1

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21
Q

what base pairing denatures at higher temperatures? why?

A

GC, because of greater number of H bonds

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22
Q

process of reforming the double helix from single strands of DNA

A

renaturation or reannealing

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23
Q

process of separating the double helix of DNA

A

denaturation

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24
Q

major stuctural forms of the double helix

A

B form, A form, Z form

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25
Q

B form

A

right handed helix with 10 residues per turn, main form of chromosomal DNA

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26
Q

A form

A

right handed helix with 11 residues per turn, produced by dehydrating the B form

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27
Q

Z form

A

left handed helix with 12 residues per turn, occur naturally in regions with alternating purines and pyrimidines (ex. poly GC)

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28
Q

region where active DNA synthesis occurs

A

replication fork

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29
Q

DnaA protein

A

binds to specific nucleotide sequences at origin, causing AT rich regions in the origin to melt

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30
Q

DNA helicase

A

actively unwinds the double helix

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31
Q

SSB

A

single strand binding proteins; keep the ssDNA separated and protect it from nucleases

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32
Q

type of enzyme that counteracts supercoiling

A

DNA topoisomerases

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33
Q

DNA topoisomerase I

A

relax both negative and positive supercoils, does not use up ATP

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34
Q

DNA topoisomease II

A

relaxes both negative and positive supercoils, requires ATP

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35
Q

DNA gyrase

A

creates negative supercoils in order to counteract positive supercoils

36
Q

enzyme that copies the DNA templates

A

DNA polymerase

37
Q

DNA polymerase - direction of reading

A

3’–>5’

38
Q

leading strand

A

3’–>5’ strand of template; needs only one promoter, synthesized continuously

39
Q

lagging strand

A

5’–>3’ strand of template; needs multiple promoters; synthesized discontinuously

40
Q

stretches of discontinuous DNA in lagging strand

A

okazaki fragments

41
Q

RNA primer

A

short stretch of RNA required by DNA polymerase to begin replication

42
Q

responsible for RNA primer synthesis

A

primase

43
Q

responsible for catalysis of DNA chain elongation

A

DNA polymerase III

44
Q

DNA polymerase - direction of synthesis

A

5’–>3’

45
Q

substrates of DNA polymerase III

A

5’ deoxyribonucleoside triphosphates

46
Q

when each new deoxynucleoside monophosphate is attached to the growing chain by DNA polymerase III, what is released?

A

pyrophosphate

47
Q

for DNA synthesis to occur, what 4 substrates must be present?

A

dATP, dTTP, dCTP, dGTP

48
Q

2 main activities of DNA polymerase III

A

5’–>3’ polymerase; 3’–>5’ exonuclease

49
Q

5’–>3’ polymerase activity of DNA polymerase III

A

for synthesis of new DNA strand

50
Q

3’–>5’ exonuclease activity of DNA polymerase III

A

for proofreading

51
Q

responsible for excision of RNA primer

A

DNA polymerase I

52
Q

activities of DNA polymerase I that allows it to complete its function

A

[1] 5’–>3’ exonuclease activity to remove the primer
[2] 5’–>3’ polymerase activity to fill in the gap with deoxyribonucleotides
[3] 3’–>5’ exonuclease acitivity to proofread

53
Q

difference between 5’–>3’ exonucleases and 3’–>5’ exonucleases

A

5’–>3’ exonucleases can remove groups of altered nucleotides (up to 10) in the 5’–>3’ direction

54
Q

exonucleases used by DNA polymerase III

A

3’–>5’ exonuclease

55
Q

exonucleases used by DNA polymerase II

A

3’–>5’ exonuclease

56
Q

exonucleases used by DNA polymerase I

A

3’–>5’ exonuclease, 5’–>3’ exonuclease

57
Q

responsible for sealing nicks between okazaki fragments after excision and replacement of RNA primers

A

DNA ligase

58
Q

DNA polymerases in prokaryote replication

A

DNA polymerases I, II, III

59
Q

DNA polymerases in eukaryote replication

A

DNA polymerases alpha, epsilon, delta, beta, gamma

60
Q

DNA polymerase alpha

A

has primase activity

61
Q

DNA polymerase beta

A

for gap filling in DNA repair

62
Q

DNA polymerase gamma

A

replicates mitochondrial DNA

63
Q

DNA polymerase delta

A

elongates okazaki fragments in lagging strand

64
Q

DNA polymerase epsilon

A

elongates leading strand

65
Q

telomeres - structure

A

complexes of noncoding DNA + proteins at ends of chromsoomes

66
Q

telomeres - function

A

mediate structural integrity, protect from nuclease attack, allow repair systems to distinguish ends of DNA

67
Q

responsible for maintaining telomeric length

A

telomerase

68
Q

reverse transcriptase

A

synthesize DNA from RNA template

69
Q

classes of histones

A

H1, H2A, H2B, H3, H4

70
Q

charge of histones at physiologic pH

A

+

71
Q

make up core of histone beads

A

H2A, H2B, H3, H4

72
Q

location and function of H1

A

bind to linker DNA between beads, facilitates packing of histones into more complex structures

73
Q

effect of UV radiation on DNA

A

fusing together of pyrimidine to form pyrimidine dimers (ex. thymine dimers)

74
Q

effect of high energy ionizing radiation on DNA

A

double strand breaks

75
Q

principle of methyl-directed mismatch repair

A

recognition of the parent strand as the methylated strand –> repairs are then based on the parent strand

76
Q

responsible for recognizing mismatch in methyl directed mismatch repair

A

Mut

77
Q

enzyme involved in repair of damage from UV radiation

A

UV specific endonuclease

78
Q

xeroderma pigmentosum

A

inability to repair UV damage, extensive mutation due to exposure to sunlight

79
Q

involved in removal of abnormal bases

A

specific glycosylases

80
Q

involved in recognition and repair of AP site

A

AP endonucleases (recognition of missing base), deoxyribose phosphate lyase (removal of base-free sugar phosphate), DNA polymerase, DNA ligase

81
Q

deoxyribose phosphate lyase

A

removes the base-free sugar phosphate residue in repair of AP sites

82
Q

methods of repair of double strand breaks

A

[1] nonhomologous end-joining repair

[2] homologous recombination repair

83
Q

nonhomologous end-joining repair

A

crude ligation of DNA on either end of double strand break; prone to mutation (some DNA is lost)

84
Q

homologous recombination repair

A

use of homologous DNA as a template to restore lost DNA from double strand breaks

85
Q

enzymes in homologous recombination repair

A

enzymes that perform genetic recombination between homologous chromosomes during meiosis

[OS 201] 3rd Exam (10 decks)

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