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BCH Final > DNA replication > Flashcards

DNA replication Flashcards

1
Q

what does dna repliation require

A

activated substrated known as dNTPS (deoxyribonucleoside 5/-triphosphates) i.e. dCTP, dATP, dUTP, dGTP

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2
Q

double stranded DNA plus dNTPs reacted with polymerases makes

A

2 double stranded DNA

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3
Q

what are the generic four steps that in vivo occur simultaneously during DNA replication

A

initiation (starting the replication)
priming (primer=rna)
synthesis (replication happens)
termination

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4
Q

t/f

eukaryotes have circular chromosomes

A

false

prokaryotes have circular chromosomes

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5
Q

how many start sites for dna replication are there in prokaryotes & what are they called

A

one.

initiation site

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6
Q

t/f

DNA is replication is bidirectional

A

true

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7
Q

t/f

a second round of replication cannot begin until the first is completed

A

false

second round starts before first is done

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8
Q

where does initation of dna replication in prokaryotes start

A

OriC (origin of replication)

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9
Q

what are the OriC recognized by

A

the initatior protein known as DnaA

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10
Q

what type of repeats are adjacent to OriC

A

AT rich repeats

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11
Q

t/f

only in prokaryotes there are AT rich sequences near the replication initiation site

A

false

this is also true in eukaryotes

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12
Q

why are AT rich repeats important

A

they’re less stable that native DNA so can be used to form the replication bubble

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13
Q

what is the helicase in prokaryotes

A

DnaB

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14
Q

what is the role of SS binding proteins

A

they bind to SS regions of replication bubble and stop it from making secondary structures (bc secondary will hinder replication)

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15
Q

t/f

dna polymerase can initatiate new strand synthesis

A

f

no DNA poly can initiate, it needs to have a primer

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16
Q

what is needed to add dNTP DNA polymerases

A

need a 3’ hydroxyl group at the end of a base paired primer strand

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17
Q

in what direction is RNA primer created

A

5’ to 3’

all of dna synthesis happens in this direction

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18
Q

why is a primer needed in each fork i.e. 2

A

bc synthesis of dna is bidirectional

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19
Q

describe rna primer synthesis

A

primase DnaG is part of the primosome

primosome binds to both strands of the replication bubble –>makes short RNA primer

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20
Q

what is the role of DNA poly 1 in prokaryotes

A

remove the RNA primer (primer excision)

and DNA repair

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21
Q

role of dna poly 3 in prokary

A

replication –> chain elongation during DNA synthesis

and DNA repair

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22
Q

diff bn 3’ and 5’ exonucleases

A

3’ removes prna primers in 3’ to 5’ direction

5’ removes it 5’ to 3’ direction

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23
Q

why is dna replication the most accurate process

A

bc it has proof reading

3/ exonuclease checks it

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24
Q

3’ exonucleases are found in which dna polymerases

5’ found in which

A

poly 1 and 3 have 3’ exonucleases

only poly 1 has 5’ exonucleases

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25
Q

what is the processivity of dna poly 1 and 3

A

poly 1 = low to moderate

poly 3 = high processitivity

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26
Q

which polymerase removes rna primer

A

dna poly 1

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27
Q

which poly is involved in replicating dna

A

dna poly 3

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28
Q

what is processivity

A

measure of how many nucleotides can be added to dna strand as it’s growing before it disengages

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29
Q

what subunit serves as a sliding clamp that encircles DNA

A

beta

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30
Q

what is the role of the gamma complex

A

it is a clamp loader so helps get beta (sliding clamp) loaded onto dna

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31
Q

which subunit is a structural protein that holds things together

A

tau

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32
Q

what is contained within epsilon

A

3’ exonuclease used for proof reading

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33
Q

what is the role of theta

A

needed for 3’ exonuclease activity

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34
Q

t/f

each replication fork has one DNA poly 3 holoenzyme

A

true

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35
Q

what charge is the interior of the beta sliding clamp and why

A

neutral or negative bc for clamp to move on the dna needs to be repulsive
-dna is negative

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36
Q

t/f both strands of the replication fork are synthesized simultaneously

A

true

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37
Q

what is the difference bn how the leading and lagging strands are synthesized

A

the leading strand synthesized continuously

lagging synthesized discontinuously

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38
Q

in what direction in relation to the fork is dna synthesis occuring in the lagging strand

A

its being synthesized away from the fork

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39
Q

what is special of the backbone on the lagging strand

A

it has a nick on it

40
Q

okozaki fragments are made on which strand of the replication fork

A

lagging strand

41
Q

t/f

for the leading strand the fork has to open before new synthesis can be initiated

A

false

the LAGGING strand needs the fork to be open

42
Q

since both strands are made simultaneously how do both strands become in the same orientation

A

a loop is added on the lagging strand which puts the 2nd okozaki fragment in same orientation as the leading strand so the polymerase can move smoothly

43
Q

as the DS helix is being opened, helical tension is formed and ___ is needed to regulate it

A

topoisomerase

44
Q

dna poly 3 can recognize

A

mismatched base pairs (aka AG or CT)

45
Q

what is the role of epsilon subunit

A

removes mismatched pairs with it’s 3’ to 5’ exonuclease activity

46
Q

how is the chain extended after epsilon subunits remove mismatched base pairs

A

extended by dna poly 3

47
Q

where is the termination region in relation to OriC

A

180 degrees from it

48
Q

what are ter sites

A

termination sites in prokaryotes

has 6 sites oriented in opposite directions on either side of the 180 degree point

49
Q

why is the ter orientation in opp dir’s on either side of the 180 degrees

A

bc binds to the TUS protein

50
Q

in how many directions can the TUS protein go

A

one

the fork can pass right past it but can’t pass it in other direction

51
Q

what is the process of rna primers being removed by dna poly 1 called

A

nick translation

52
Q

how does nick translation work

A

dna poly 1 5’ exonuclease hydrolyses the RNA primers

simultaneously the 3’ end of the okazaki fragment (DNA) is extended by the incorporation of deoxyribonucleotides

53
Q

role of dna ligase

A

seals the nick

54
Q

what is the last step in termination of dna synthesis in prokaryotes

A

type 2 topoisomerase separated the 2 interlinking strands of the replicated circles and refolds the dna into supercoils

55
Q

what are the 4 similarities bn pro and euk dna replication

A
  1. semi conservative
  2. bidirectional
  3. short RNA primers req’d to initiate new strand synthesis
  4. leading strand made continuously
    lagging made discontinuously
56
Q

in eukaryotes

what is te role of dna poly gamma

A

replication of mitochondrial dna

57
Q

in euk

whats role of dna poly delta and epsilon

A

poly delta replicated the lagging strand

poly epsilon replicates the leading strand

58
Q

which strand does dna poly alpha replicate

A

both leading and lagging

59
Q

what is the inherent processivity of all 5 eukaryotic dna polymerases

A 
alpha-moderate
beta-low
gamma-high
delta-low
epsilon-high
60
Q

which eukaryotic dna poly has high processivity with PCNA

A

delta

61
Q

in the tertiary structure, where are nucleosome dissociated and where are they reassembled

A

dissociated ahead of the replication fork

reassembled on newly synthesized DNA

62
Q

what is the speed and size of the tertiary structure in replication

A

10 times slower

size of genome is massive

63
Q

what are present to accomodate the large size of the genome

A

multiple initation sites of replication known as ARS

64
Q

what are the highly repetitive sequences at the ends of linear chromosomes that protect the chromosome from being damaged

A

telomeres

65
Q

what is the origin of replication

in prok and euk

A

pro: OriC
Euk: ARS

66
Q

what is the bind origin of replication (i.e. what protein recognizes the origin of replication in each)
in prok and euk

A

pro: DnaA complex
euk: ORC

67
Q

what is the helicase

in prok and euk

A

pro: DnaB/C complex
euk: MCM

68
Q

what is used to stabilize SS DNA

in prok and euk

A

pro: SSBs
Euk: RPA

69
Q

what is used to increase processivity

in prok and euk

A

pro: Beta-subunit poly 3
euk: PCNA for DNA poly delta

70
Q

what is the clamp loader

in prok and euk

A

pro: gamma complexx
euk: RFC (replication factor C)

71
Q

what makes RNA primer

in prok and euk

A

Pro: DnaG
euk: DNA poly alpha

72
Q

what synthesizes DNA

in prok and euk

A

pro: DNA poly 3
Euk: DNA poly epsilon (leading strand)
DNA poly delta (lagging strand)
DNA poly gamma (mitochondria)

73
Q

what is used for the removal of RNA primers

in prok and euk

A

pro: DNA poly 1 (nick translation)
euk: RNAse H and Fen1 (flap endonuclease 1)

74
Q

what does RNAse H do

A

destroys DNA/RNA hybrids and removes the RNA from it

75
Q

diff bn exonuclease and endo

A

exo cuts from the ends

endo makes cut from within

76
Q

what genetic defect causes Aicardi-goutieres syndrome

A

RNAse H which acts on RNA/DNA hybrids and is involved in removal of RNA primers in eukaryotic replication

77
Q

during eukaryotic replication, a pre-replication complex (pre-RC) assembles on what

A

on the ARS which includes ORC(origin of replication), MCMs (inactive helicases) and other proteins

78
Q

how are helicases activated

A

by the addition of addtl proteins

-thats when it can start unwinding the DNA bc it;s active

79
Q

what is ARS rich in and what does that allow it to do

A

ARS is AT rich –> helps it open up inititial replication bubble

80
Q

t/f

more pre-RC are assembled (licensing) than used (firing)

A

true

81
Q

in order for replication in eukaryotes to start the helicase needs to be

A

activated so it can unwind the dna

82
Q

what keeps things regulated during eukaryotic replication

A

topoisomerase

-which work ahead of the replication fork to keep the DNA untangled

83
Q

what makes the leading and lagging strand into the same orientation

A

a loop

84
Q

what is RNaseH / FEN 1 doing during eukaryotic replication

A

taking out RNA primers

85
Q

what causes meier-gorlin syndrome (failure in growth)

A

mutations in genes that encode the proteins needed for the Pre-RC complex including: ORC
-bc of impaired replication licensing (aka assembly)

86
Q

what are the highly repetitive seq’s at the 3’ ends of linear chromosomes

A

telomeres

87
Q

what are telomeres added by

A

telomerase

88
Q

what is the protein compnent enzyme and the RNA component of telomerase

A

protein: hTERT = human telomerase reverse transcriptase
RNA: hTR = human telomerase RNA

89
Q

what does the telomerase use it’s rna component (hTR) for

A

to add repeats

-telomerase repositions itself to add each repeat

90
Q

how is the daughter strand synthesized

A

by unsing complementary base pairing by DNA poly alpha (puts RNA primer to synthesize the DNA)

91
Q

what is left when telomerase moves away

A

a single stranded 3’ overhang

92
Q

the telomere ends are protected by loops that are stabilized by binding of telomere-binding proteins called

A

TRF1 and TRF2

93
Q

telomere length is maintained by

A

telomerase

94
Q

what would happen in a dividing cell with little or no telomerase

A

not much short term
telomeres would shorten after rounds of replication
cells would die
cells would stop dividing

95
Q

telomeres shorten with each round of dna replication unless maintained by

A

telomerase

96
Q

what mutation causes Dyskeratosis congenita (which worsens with successive generations)

A

mutations in the catalytic domain (hTERT) or rna component of telomerase (hTR)

97
Q

diseases of telomere shortening show anticipation because

A

loss or partial loss of telomerase function leads to telomere shortening n the germ cells

BCH Final (5 decks)

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