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BIOL 3421 - molecular biochem > repair and recombination > Flashcards

repair and recombination Flashcards

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1
Q

define mutation

A

permanent change in DNA sequence

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2
Q

T or F: most mutations are neutral or harmful

A

true

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3
Q

T or F: many mutations are advantageous

A

false; they’re rarely advantageous

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4
Q

list 2 ways in which mutations can be caused by

A

spontaneous mistakes in DNA replication or by environmental mutagens

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5
Q

what is a silent mutation

A

a mutation within non-coding DNA or a mutation that doesn’t affect the resulting protein product

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6
Q

what is the purpose of the ames test

A

to identify chemicals that promote mutations

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7
Q

define carcinogen

A

a chemical that promotes mutations

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8
Q

describe how the ames test works

A

use a bacteria that has been mutated to not produce His. Grow on a His free medium + put the mutagen in the middle. if the mutagen enhances mutations, the bacteria will be mutated to produce His, and we will see growth

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9
Q

T or F: different bacterial strains can be sensitive to different types of mutations

A

true

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10
Q

describe how rat liver extract can be used to predict if the mutagen would harm mammalian DNA as well as bacterial DNA

A

isolate extract that is His-. Plate on medium lacking His and incubate. Pos result = high number of His- to His+ suggests presence of a strong mutagen

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11
Q

what is mismatch repair

A

corrects non-complimentary mismatches made by DNA pol III that were missed by pol III proofreading

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12
Q

what is base-excision repair

A

removes bases with structural abnormalities

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13
Q

what is nucleotide-excision repair

A

removes the entire nucleotide when there is an abnormal base that causes distortions in the overall helical structure

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14
Q

what is direct repair

A

fixes damage or abnormal bases without removing the nucleotide first

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15
Q

dam methylation is used in which type of repair

A

mismatched repair

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16
Q

describe the activities of dam methylation

A

it permits discrimination of the template strand. It methylates both strands, but the template is methylated first so there is a short period in which it’s the only one that’s methylated. This is how we know which base pair in the mismatch was the correct one

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17
Q

during mismatch repair, what happens if both strands had become methylated

A

no repair occurs

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18
Q

during mismatch repair, what happens if neither strand had become methylated

A

repair occurs indiscriminately on broth strands

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19
Q

mismatch repair: which protein complex bind mismatched base pairs

A

MutL-MutS

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20
Q

structure of MutL-MutS?

A

clamp-like

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21
Q

T or F: MutL-MutS binds to mismatched base pairs in an ATP-dependent process

A

true

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22
Q

describe the mechanism of MutL-MutS

A

they bind to the mismatch and then slide along the strand until they reach a hemimethylated site

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23
Q

how far away does the mismatch need to be from the hemimethylated site

A

1000bp

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24
Q

which sequence is methylated by dam methylase

A

5’-GATC-3’

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25
in the 5'-GATC-3' sequences, which base is methylated + where on that base
adenine is methylated on the N6 position
26
what happens when MutL-MutS reaches the hemimethylated site
they encounter MutH
27
what does MutH do once MutL-MutS arrives at the hemimethylated site
MutH has endonuclease activity and will cleave the unmethylated strand on the 5' side of the G in the GATC sequence
28
mismatch repair: describe what happens when the mismatch is on the 5' side of the cleavage site
unmethylated strand in unwound and degraded 3'-5' from nick to mismatch
29
mismatch repair: describe what happens when the mismatch is on the 3' side of the cleavage site
unmethylated strand in unwound and degraded 5'-3' from nick to mismatch
30
for mismatch repair, list 5 enzymes/proteins that are required
helicase, exonuclease, pol III, SSBs, and ligase
31
T or F: mismatch repair is very costly
true
32
why is mismatch repair costly
up to 1000 additional dNTPs are required to fix just one mismatched pair
33
in base-excision repair, what type of reaction causes the mistake
deamination
34
what is a common deamination
C to U
35
T or F: deamination is spontaneous + non-enzymatic
true
36
base-excision repair: which enzyme family recognizes base lesions
DNA glycosylases
37
what do DNA glycosylases do
they recognize base lesions and remove the offending base
38
how do DNA glycosylases remove the offending base in base-excision repair
they cleave the N-glycosyl bond
39
cleavage of the N-glycosyl bond leads to which type of nucleotide
abasic (lacking a base)
40
list the two types of abasic nucleotides
apurinic or apyrimidinic
41
in base-excision repair, how is it fixed if there is no glycosylase
the N-b-glycosyl bond between the pentose and the base can hydrolyze
42
base-excision repair: once an abasic nucleotide is present, what happens
AP (abasic) endonuclease nicks the DNA backbone either directly 5' or directly 3' to the missing base
43
base-excision repair: once an AP endonuclease nicks the DNA backbone beside the missing base, what happens
pol I uses its 5'-3' exonuclease activity to remove a few bases starting from the nick + it replaces them. ligase then seals the nick
44
nucleotide-excision repair: what can cause large distortions in helical structure
UV light
45
nucleotide-excision repair: give an example of a large distortion to helical structure that can be caused by UV light
thymine dimerization
46
nucleotide-excision repair: describe how much DNA must be removed to make the repair
larger chunks need to be removed
47
nucleotide-excision repair: which enzyme is used to make the large repair
excinuclease
48
nucleotide-excision repair: describe the actions of excinuclease
hydrolyzes two phosphodiester bonds. One nick is created on either side of the lesion
49
nucleotide-excision repair: how many phosphodiester bonds does excinuclease hydrolyze
2
50
nucleotide-excision repair: once two nicks are made by excinuclease activity, what happens
helicase removes the offending DNA fragment, then pol I replaces them, and ligase seals the nick
51
which disease is caused by defects in nucleotide-excision repair machinery
Xeroderma Pigmentosum
52
describe the symptoms of Xerodoma Pigmentosum
extreme sunlight sensitivity, freckling, increased risk of skin cancers, irritated eyes/impaired vision, increased risk of eye cancers
53
name the enzyme that is very good at repairing thymine dimers
photolyase
54
which organisms have photolyase
bacteria and plants
55
T or F: humans synthesize photolyase
false! only plants and bacteria do
56
when is direct repair used (ie what was the damaged caused by)
direct repair is used to repair damage caused by alkylation
57
direct repair: give an example of alkylation that occurs
guanine --> O6-methylguanune
58
direct repair: what does O6-methylguanine base pair with
pairs with T instead of C
59
direct repair: describe the mechanism
methyltransferase can transfer the methyl of O6-methylguanine to one of it's cysteines. This inactivates the protein permanently but regenerates the guanine
60
when do double stranded breaks and ssDNA occur
occur when a replication fork runs into already damaged DNA
61
what happens when the replication fork runs into already damaged DNA
the replisome usually falls off
62
how do double stranded breaks get repaired
by a mechanism involving homologous recombination
63
describe how homologous recombination is involved with fixing DNA with no template
the accurate nucleotides are determined from the homologous chromosome
64
DNA damage with no template: which enzyme is used to replicate DNA with lesions
DNA pol V
65
describe the error rate of DNA pol V
it can replicate over lesions that would normally stall other polymerases, but with a much higher error rate
66
what is homologous recombination
rearrangement of genetic info between chromosomes that share extended regions of (almost) identical sequences
67
homologous recombination: describe the events that occur after a replication fork collapses upon encountering a DNA nick and the 5' end of the dsDNA is degraded
the exposed 3' end is bound to recombinase, which facilitates another 3'-5' strand to invade and undergo complimentary base pairing with the now exposed 3' end. The structure can migrate along the strand and create an X-like crossover known as a Holliday intermediate. Nucleases cleave the Holliday, and the strands are re-ligated, and the replication fork is re-established
68
homologous recombination: what protein is responsible for the initial 5' degradation
RecBCD
69
homologous recombination: which types of activity does RecBCD have
both helicase and exonuclease
70
homologous recombination: which is the recombinase that promotes strand invasion
RecA
71
homologous recombination: what does RecA do
it forms a long filament on ssDNA with up to several thousand subunits
72
homologous recombination: what does RecBCD do
assists in removing the SSBs from ssDNA and then allowing RecA to bind
73
list the 3 purposed of homologous recombination
helps repair DNA damage, helps to physically link chromatids for proper division during meiosis I, enhances genetic diversity
74
what does meiosis I separate
homologous chromosomes
75
T or F: cohesins keep homologues together
false! there are no cohesins. only sister chromatids have cohesins
76
what is aneuploidy
incorrect number of chromosomes in a daughter cell
77
in humans, when does egg production begin
week 12 of gestation (before female is even born)
78
describe meiosis from gestation to ovulation
meiosis is initiated in the fetal germ line cells. Cells proceed through most of meiosis I, where chromosomes line up and generate cross overs. The process then stops with the crossovers in place, until just before ovulation
79
T or F: the longer the arrested stage of meiosis, the higher risk of aneuploidy when the homologues finally separate
true

BIOL 3421 - molecular biochem (20 decks)

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