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Life Science 3 > Lecture 10 > Flashcards

Lecture 10 Flashcards

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1
Q

specific sequence in the genome in which dsDNA is first opened up for replication

A

origin of replication

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2
Q

most prokaryotes have – per circular genome

A

one replicon

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3
Q

agrobacteria have linear chromosomes and –

A

multiple replicons

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4
Q

E. coli – has 245 bp

A

OriC

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5
Q

OriC has a – followed by –

A

tandem array of three A-T rich 13-mer regions followed by five 9-mer DnaA binding sites

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6
Q

origin of replication of yeast

A

ARS1

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7
Q

core sequence of ARS1

A

A/TTTTAA/GTTTA/T

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8
Q

ori-binding proteins of E. coli

A

DnaA

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9
Q

ori-binding proteins in yeast

A

ORC

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10
Q

methylate all E. coli GATC sequence

A

Dam methylase

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11
Q

methylation of E. coli replication origin creates a – for DNA synthesis initiation

A

refractory period

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12
Q

approximately – origins of replication are used each time a human cell divides

A

30,000-50,000

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13
Q

Different cell types use – sets of origin of replications

A

different

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14
Q

a eukaryotic genome have many origins of replication per –

A

chromosome

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15
Q

timing of origin activation is related to the –

A

packing of the local chromatin

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16
Q

dsDNA contains two – but DNA synthesis can only be 5’ to 3’

A

antiparallel ssDNA

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17
Q

Which of the following is correct for the replication direction?

  • 2 origins and 2 growing ends
  • 1 origin and 1 fork
  • 1 origin and 2 forks
A

1 origin and 2 forks (bidirectional)

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18
Q

replication bubble gets increasingly longer from both directions but the center is –

A

constant

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19
Q

one replication bubble has two forks growing in –

A

the opposite direction

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20
Q

At each replication fork, two ssDNA are replicated in the –

A

5’ to 3’ direction

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21
Q

labeled replicating DNA show many – fragments being formed (termed Okazaki fragments)

A

1-2 kb

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22
Q

strand that is synthesized continuously

A

leading strand

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23
Q

strand that is synthesized discontinuously

A

lagging strand

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24
Q

– are needed for DNA replication

A

RNA primers

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25
Q

DNA polymerase can only synthesize DNA if there is –

A

an existing polynucleotide primer…short RNA sequences

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26
Q

T/F: RNA primers are needed in both prokaryotes and eukaryotes

A

true

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27
Q

– is the RNA polymerase that synthesizes the short RNA primer

A

primase

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28
Q

DNA replication is a – process

A

DNA template-dependent polymerization

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29
Q

replication of sDNA proceeds in – directions

A

opposite (bidirectional)

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30
Q

DNA replication starts from replication origins that possess –

A

specific DNA sequences

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31
Q

T/F: each strand of DNA is synthesized continuously and discontinuously

A

true

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32
Q

required substrates for DNA synthesis

A

dNTP and primer

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33
Q

DNA is synthesized by extending the – of the primer

A

3’ end

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34
Q

The DNA catalyzes the – of a deoxyribonucleotide to the 3’ OH end of a polynucleotide chain

A

stepwise addition

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35
Q

the DNA pol synthesizing reaction is driven by a large, favorable free-energy change cause by the release of – and its subsequent hydrolysis to 2 molecules of inorganic phosphate

A

pyrophosphate

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36
Q

DNA polymerase has – ability

A

proofreading

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37
Q

can remove wrong nucleotide one at a time from the ends of polynucleotides

A

exonuclease

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38
Q

pretty good but not perfect DNA pol proofreading ability is one of the reasons for – in the genome

A

“spontaneous” mutations

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39
Q

there is about 1 error for every – polymerization event during RNA or protein synthesis

A

10^4

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40
Q

there is about 1 error for every –polymerization event during DNA replication

A

10^10

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41
Q

A – suggests why DNA is always synthesized from 5’ to 3’

A

need for proofreading

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42
Q

helicase binds to – to unwind dsDNA to create ssDNA at the replication fork

A

replication origins

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43
Q

topoisomerase release supercoil that results from –

A

DNA unwinding

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44
Q

– stabilize ssDNA before replication

A

SSB proteins/RPA

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45
Q

primase is a –

A

DNA dependent RNA polymerase

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46
Q

primase uses – to make short RNA primers

A

DNA as a template

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47
Q

in eukaryotes, – synthesizes short DNA from the RNA primer, resulting in an RNA-DNA hybrid

A

DNA pol alpha

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48
Q

eukaryotic primers has – nucleotides

A

10

49
Q

one RNA primer is made every – nucleotides on lagging strand

A

200

50
Q

DNA ligase connects

A

backbone of DNA

51
Q

DNA ligase uses – to activate the 5’ end at the neck before forming the new bond

A

a molecule of ATP

52
Q

The energetically unfavorable nick-sealing reaction is driven by being – to the energetically favorable process of ATP hydrolysis

A

coupled

53
Q

holds DNA polymerase on the DNA

A

regulated sliding clamp

54
Q

ATP binding to clamp loader –>

A

opens sliding clamp

55
Q

ATP hydrolysis locks sliding clamp around DNA and – clamp loader

A

releases

56
Q

sliding clamps – the DNA polymerase processivity

A

increase

57
Q

main synthesizing enzymes in prokaryotes

A

DNA pol III

58
Q

main synthesizing enzymes in eukaryotes (lagging)

A

DNA pol delta

59
Q

main synthesizing enzymes in eukaryotes (leading)

A

DNA pol epsilon

60
Q

prokaryotic clamp and loader

A

B clamp and gamma clamp loader

61
Q

eukaryotic clamp and loader

A

PCNA (proliferating cell nuclear antigen) and RFC (replication factor C)

62
Q

remove RNA primers in prokaryotes

A

DNA pol I

63
Q

remove RNA primers in eukaryotes

A

RNase H and FEN1

64
Q

fill in gaps from removed RNA primer in prokaryotes

A

DNA pol I

65
Q

fill in gaps from removed RNA primer in eukaryotes

A

DNA pol delta

66
Q

connects the Okazaki fragments

A

DNA ligase

67
Q

if DNA cannot rapidly rotate –>

A

torsional stress will build up

68
Q

some of the tension can be taken up by – whereby the DNA double helix twists around itself

A

supercoiling

69
Q

If the tension continues to build up, the replication fork will eventually stop because further unwinding require – energy than the helicase can provide

A

more

70
Q

T/F: Topoisomerase I cleave one strand of DNA and ligates the two ends of the broken strand

A

true

71
Q

topoisomerase I has – at the active site

A

tyrosine

72
Q

DNA topoisomerase – attaches to a DNA phosphate thereby breaking a phosphodiester bond linkage in one strand

A

covalently

73
Q

original phosphodiester bond energy is stored in the – making the reaction reversible

A

phosphotyrosine linkage

74
Q

– of the phosphodiester bond regenerates both the DNA helix and the DNA topoisomerase

A

spontaneous reformation

75
Q

topoisomerase II is used to separate –

A

2 double helices that are interlocked

76
Q

topoisomerase II make as reversible covalent attachment to the two strands of one of the double helices creating a double-strand break and forming a –

A

protein gate

77
Q

prokaryotic DNA replication begins at the

A

OriC

78
Q

around 10 DnaA moleucules bind to the DnaA binding sites which wrap around the DnaA proteins causing the DNA at the – to unpair

A

13-mer region

79
Q

denatured 13-mer region recruits

A

DnaB (helicase) and DnaC (helicase loader) complex

80
Q

DnaC helps DnaB bind to the – at the 13-mer regino

A

ssDNA

81
Q

helicase loading proteins prevent the – from inappropriately entering other single-stranded binding proteins

A

replicative DNA helices

82
Q

– inhibit the helices until they are properly loaded at the replication origin

A

helicase loaders

83
Q

helicase and primase form

A

primosome

84
Q

– of the primase produces the short RNA primers that generate the Okazaki fragment

A

periodic binding

85
Q

– is kicked out before DNA pol comes in

A

SSB proteins

86
Q

DNA polymerase machinery on each strand work together as part of –

A

a single complex

87
Q

the template with the lagging strand – in order for the DNA pol complex to travel in the same direction…towards the replication fork

A

loops back

88
Q

prokaryotic helicase

A

DnaB

89
Q

eukaryotic helicase

A

Mcm

90
Q

prokaryotic helicase loaders

A

DnaC

91
Q

eukaryotic helicase loaders

A

Cdc6 and Cdt1

92
Q

– stay behind after helices moves on to prevent another round of replication before mitosis is finished

A

ORC

93
Q

Mcm helicase + ORC –>

A

prereplicative complex

94
Q

an origin of replication can only be used if a – forms in G1 phase

A

prereplicative complex

95
Q

At the beginning of S phase, kinases phosphorylate Mcm and ORC, – the former and – the latter

A

activate Mcm

inactivate ORC

96
Q

A new pre replicative complex cannot form at the origin until the cell progresses to the next G1 phase, when the bound ORC has been –

A

dephosphorylated

97
Q

Mcm helicase moves along the –

A

leading strand template

98
Q

bacterial helicase moves along the –

A

lagging strand template

99
Q

– synthesizes short RNA-DNA primers on each strand, which mark the starting points to be replicated

A

primase-DNA pol alpha complex

100
Q

– replaces the primase-DNA pol alpha complex generating the leading strand

A

Pol epsilon PCNA-Rfc complex

101
Q

– synthesize the Okazaki fragment

A

pol delta PCNA-Rfc complex

102
Q

RNA-DNA primers are removed by

A

RNaseH and FEN1

103
Q

in eukaryotes – fill in gaps with dNTPS

A

DNA pol delta

104
Q

the two DNA pol complexes on both strand work together and move –

A

in the same direction (lagging stand loops back to accommodate)

105
Q

histones are mainly synthesized in

A

S phase

106
Q

physical ends of linear chromosoe

A

telomeres

107
Q

3’ end of G rich strand extends – beyond the 5’ end of the complementary C-rich strand

A

12-16 nucleotides

108
Q

3’ overhand region is bound by specific proteins that serve to protect the ends of linear chromosomes from

A

attack by exonuclease

109
Q

last regions of DNA to be replicated

A

telomere

110
Q

– resulting from lagging strand synthesis would become shorter at each cell division

A

daughter DNA strand

111
Q

adds telomeric sequences to the ends of each linear chromosome

A

telomerase

112
Q

telomerase is a large –

A

protein-RNA complex

113
Q

telomerase has – activity that can synthesize DNA from its RNA template

A

reverse transcriptase

114
Q

stem cells divide slowly but don’t

A

shorten telomere

115
Q

single stranded 3’ end will fold into a T loop with specialized telomere binding proteins – to protect the end of the DNA molecule

A

shelterin

116
Q

T/F: most adult somatic cells lack telomerase

A

true

117
Q

what has telomerase activity?

A

stem cells, germ line cells, tumor cells

118
Q

somatic cells with short telomeres cease dividing

A

replicative cell senescence

Life Science 3 (20 decks)

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