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1

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

origin of replication

2

most prokaryotes have -- per circular genome

one replicon

3

agrobacteria have linear chromosomes and --

multiple replicons

4

E. coli -- has 245 bp

OriC

5

OriC has a -- followed by --

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

6

origin of replication of yeast

ARS1

7

core sequence of ARS1

A/TTTTAA/GTTTA/T

8

ori-binding proteins of E. coli

DnaA

9

ori-binding proteins in yeast

ORC

10

methylate all E. coli GATC sequence

Dam methylase

11

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

refractory period

12

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

30,000-50,000

13

Different cell types use -- sets of origin of replications

different

14

a eukaryotic genome have many origins of replication per --

chromosome

15

timing of origin activation is related to the --

packing of the local chromatin

16

dsDNA contains two -- but DNA synthesis can only be 5' to 3'

antiparallel ssDNA

17

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

1 origin and 2 forks (bidirectional)

18

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

constant

19

one replication bubble has two forks growing in --

the opposite direction

20

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

5' to 3' direction

21

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

1-2 kb

22

strand that is synthesized continuously

leading strand

23

strand that is synthesized discontinuously

lagging strand

24

-- are needed for DNA replication

RNA primers

25

DNA polymerase can only synthesize DNA if there is --

an existing polynucleotide primer...short RNA sequences

26

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

true

27

-- is the RNA polymerase that synthesizes the short RNA primer

primase

28

DNA replication is a -- process

DNA template-dependent polymerization

29

replication of sDNA proceeds in -- directions

opposite (bidirectional)

30

DNA replication starts from replication origins that possess --

specific DNA sequences

31

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

true

32

required substrates for DNA synthesis

dNTP and primer

33

DNA is synthesized by extending the -- of the primer

3' end

34

The DNA catalyzes the -- of a deoxyribonucleotide to the 3' OH end of a polynucleotide chain

stepwise addition

35

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

pyrophosphate

36

DNA polymerase has -- ability

proofreading

37

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

exonuclease

38

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

"spontaneous" mutations

39

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

10^4

40

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

10^10

41

A -- suggests why DNA is always synthesized from 5' to 3'

need for proofreading

42

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

replication origins

43

topoisomerase release supercoil that results from --

DNA unwinding

44

-- stabilize ssDNA before replication

SSB proteins/RPA

45

primase is a --

DNA dependent RNA polymerase

46

primase uses -- to make short RNA primers

DNA as a template

47

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

DNA pol alpha

48

eukaryotic primers has -- nucleotides

10

49

one RNA primer is made every -- nucleotides on lagging strand

200

50

DNA ligase connects

backbone of DNA

51

DNA ligase uses -- to activate the 5' end at the neck before forming the new bond

a molecule of ATP

52

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

coupled

53

holds DNA polymerase on the DNA

regulated sliding clamp

54

ATP binding to clamp loader -->

opens sliding clamp

55

ATP hydrolysis locks sliding clamp around DNA and -- clamp loader

releases

56

sliding clamps -- the DNA polymerase processivity

increase

57

main synthesizing enzymes in prokaryotes

DNA pol III

58

main synthesizing enzymes in eukaryotes (lagging)

DNA pol delta

59

main synthesizing enzymes in eukaryotes (leading)

DNA pol epsilon

60

prokaryotic clamp and loader

B clamp and gamma clamp loader

61

eukaryotic clamp and loader

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

62

remove RNA primers in prokaryotes

DNA pol I

63

remove RNA primers in eukaryotes

RNase H and FEN1

64

fill in gaps from removed RNA primer in prokaryotes

DNA pol I

65

fill in gaps from removed RNA primer in eukaryotes

DNA pol delta

66

connects the Okazaki fragments

DNA ligase

67

if DNA cannot rapidly rotate -->

torsional stress will build up

68

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

supercoiling

69

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

more

70

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

true

71

topoisomerase I has -- at the active site

tyrosine

72

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

covalently

73

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

phosphotyrosine linkage

74

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

spontaneous reformation

75

topoisomerase II is used to separate --

2 double helices that are interlocked

76

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 --

protein gate

77

prokaryotic DNA replication begins at the

OriC

78

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

13-mer region

79

denatured 13-mer region recruits

DnaB (helicase) and DnaC (helicase loader) complex

80

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

ssDNA

81

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

replicative DNA helices

82

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

helicase loaders

83

helicase and primase form

primosome

84

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

periodic binding

85

-- is kicked out before DNA pol comes in

SSB proteins

86

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

a single complex

87

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

loops back

88

prokaryotic helicase

DnaB

89

eukaryotic helicase

Mcm

90

prokaryotic helicase loaders

DnaC

91

eukaryotic helicase loaders

Cdc6 and Cdt1

92

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

ORC

93

Mcm helicase + ORC -->

prereplicative complex

94

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

prereplicative complex

95

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

activate Mcm
inactivate ORC

96

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 --

dephosphorylated

97

Mcm helicase moves along the --

leading strand template

98

bacterial helicase moves along the --

lagging strand template

99

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

primase-DNA pol alpha complex

100

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

Pol epsilon PCNA-Rfc complex

101

-- synthesize the Okazaki fragment

pol delta PCNA-Rfc complex

102

RNA-DNA primers are removed by

RNaseH and FEN1

103

in eukaryotes -- fill in gaps with dNTPS

DNA pol delta

104

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

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

105

histones are mainly synthesized in

S phase

106

physical ends of linear chromosoe

telomeres

107

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

12-16 nucleotides

108

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

attack by exonuclease

109

last regions of DNA to be replicated

telomere

110

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

daughter DNA strand

111

adds telomeric sequences to the ends of each linear chromosome

telomerase

112

telomerase is a large --

protein-RNA complex

113

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

reverse transcriptase

114

stem cells divide slowly but don't

shorten telomere

115

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

shelterin

116

T/F: most adult somatic cells lack telomerase

true

117

what has telomerase activity?

stem cells, germ line cells, tumor cells

118

somatic cells with short telomeres cease dividing

replicative cell senescence