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QUIZ 3 > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

four basic rules of DNA replication

A

semi conservative, 5’ to 3’ direction, semi-discontinuous, defined origin and proceeds bidirectionally

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2
Q

DNA synthesis proceeds in _ direction

A

5’ to 3’

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3
Q

DNA can only add free nucleotides to _

A

3’ -OH

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4
Q

leading strand

A

continuous synthesis

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5
Q

lagging strand

A

discontinuous synthesis

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6
Q

all DNA polymerases require _

A

a primer (usually RNA) that provides a free 3’ OH group

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7
Q

properties of DNA polymerases

A

template-directed, dNTPs, free 3’-OH group, 5’ to 3’ direction, possess 3’ to 5’ exonuclease activity

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8
Q

e. coli origin of replication

A

only one site in bacteria –> OriC

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9
Q

oriC

A

AT-rich region with protein-bound region

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10
Q

helicase

A

breaks hydrogen bonds between two strands of DNA to unwind at OriC

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11
Q

primase

A

lays down RNA primer and recruits DNA polymerase

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12
Q

SSB

A

single stranded binding protein –> binds to prevent reannealing

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13
Q

gyrase

A

relieves tension

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14
Q

ATP

A

provides energy for helicase and gyrase

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15
Q

polymerase mechanism

A

positions dNTP so there can be nucleophilic attack by 3’ OH –> pyrophosphate is released

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16
Q

DNA pol III

A

synthesizes both leading and lagging strands; has 3’ to 5’ exonuclease activity

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17
Q

ligase

A

seals nick between Okazaki fragments

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18
Q

DNA polymerase I

A

removes primers from fragments (on 3’) and replaces gap with correct nucleotide –> 5’ to 3’ exonuclease

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19
Q

DNA polymerase I has both _

A

5’ to 3’ and 3’ to 5’ exonuclease activity

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20
Q

How does DNA III polymerase ensure proccessivity?

A

has 2 beta subunit encircle the DNA to prevent it from disassociating (pol I will randomly fall off)

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21
Q

DNA polymerase II

A

DNA repair in 3’ to 5’ direction

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22
Q

quinolones

A

ciproflaxin

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23
Q

quinolone action

A

disrupts type II topoisomerase, inhibiting gyrase from preventing super coiling

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24
Q

anthrax treatment

A

quinolones

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25
RNA dependent DNA polymerase
reverse transcriptase
26
retroviral infection
RNA genome that reverse transcribes to DNA --> integrates into host genome
27
reverse transcriptase does not have _
proofreading capability, so if an analog is incorporated, synthesis can be blocked by this "chain terminator"
28
drugs for treating AIDS
AZT (zidovudine)
29
AZT (zidovudine)
analog of thymine --> HIV reverse transcriptase will bind --> AZT has no 3' -OH so nothing can be added --> chain terminator
30
Why does AZT get taken up by reverse transcriptase?
it is converted to triphosphate form once in the cells, causing reverse transcriptase to bind with higher affinity than to dTTP
31
differences in eukaryotic and prokaryotic DNA
eukaryotic genomes are bigger, replication occurs during a small portion of the cell cycle, DNA is bound by histones, chromosomes are linear
32
DNA polymerase alpha
replication initiation; only one with primase
33
DNA polymerase delta
synthesize lagging strand
34
DNA polymerase beta
DNA repair
35
DNA polymerase gamma
mitochondrial replication
36
DNA polymerase epsilon
leading strand replication
37
G1 phase
RNA and protein synthesis only
38
S phase
DNA synthesis doubles amount of DNA in the cell
39
G2 phase
no DNA synthesis
40
M phase
mitosis
41
G0 phase
withdrawal from cell cycle
42
ARS
autonomous replication sequence containing a conserved 11bp sequence for binding sites of several proteins
43
What happens if ARS is removed/inserted into another DNA?
confers DNA replication in a cellular extract
44
proteins that bind ARS
ORC and ABF
45
ORC
origin recognition complex
46
ABF
ARS binding factor
47
What happens during G1 stage?
ABF and ORC bind, recruiting other proteins needed --> DNA replication is not activated until these proteins are phosphorylated (by cdk's)
48
What happens after phosphorylation of ARS proteins?
helicase binds to separate strands and begin replication, phosphorylated proteins leave
49
as soon as ARS is replicated _
ABF and ORC rebind
50
polymerase alpha is replaced with _
pol epsilon on leading strand and pol delta on lagging strand
51
both pol epsilon and pol delta have _
3' to 5' nuclease activity
52
RNase H
digests the RNA primers
53
How are RNaseH gaps filled?
DNA polymerase delta
54
RPA
helix-destabilizing proteins (same as single stranded binding protein) --> prevents re-annealing to allow polymerases to bind
55
polymerase complex
polymerase epsilon, PCNA (clamp), and RFC (clamp loader)
56
PCNA & RFC have same role as _
beta subunits on DNA pol III in prokaryotes
57
difference in lagging strand synthesis between prokaryotes and eukaryotes
in prokaryotes, DNA pol III does both leading and lagging; in eukaryotes, there are two separate polymerases
58
lagging strand polymerase complex
pol delta, RFC, and PCNA
59
telomeres
regions of repetitive noncoding DNA plus proteins located at end of linear chromosomes --> prevent DNA from being deleted since chromosomes are shortened each round of replication
60
telomere repeat sequence
TTAGGG
61
telomerase
extends telomeres
62
telomerase 2 components
RNA-directed DNA polymerase, RNA template
63
Which cells have telomerase?
germ cells and stem cells and blood cells; usually not somatic
64
somatic cells have a _
limited replication potential, so do not need telomerase --> once telomere is gone, cell stops dividing
65
cancer cells
express telomerase to provide unlimited dividing potential
66
telomeres too long
will live too long, allowing for mutation
67
telomeres too short
increases senescence
68
mtDNA replication
pre-formed RNA transcripts hybridize to lagging strand as DNA leading strand proceeds --> after leading strand is replicated, polymerase will come back, remove RNA, and start synthesizing lagging strand DNA
69
mechanism of quinolone antibiotics
inhibit topoisomerase II (gyrase) --> prevents topoisomerase from removing supercoils, stopping DNA replication
70
influenza
replicates with an RNA-dependent RNA-polymerase; RNA virus
71
ribavirin
nucleoside analog; anti-viral drug which is active against a number of DNA and RNA viruses --> stops viral RNA synthesis
72
nucleoside analogs
arabinosylcytosine, fludarbine, remdesivir
73
fludarabine
purine analog that inhibits DNA polymerase; used for chemotherapy
74
arabinosylcytosine
cytidine analog, chemotherapy drug
75
remdesivir
adenosine analog; interferes with viral RNA-dependent RNA polymerase; used for COVID-19, and ebola

QUIZ 3 (12 decks)

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