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BCH Final > DNA repair > Flashcards

DNA repair Flashcards

1
Q

what are the major methylated bases in prokaryotes

A

adenine and cytosine

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2
Q

why do prokaryotes methylate their own DNA

A

to protect against invading bacteria and viruses

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3
Q

draw the N6-methyladenine and N4-methyl cytosine structures

A

look at slide 3 on repair ppt for confirmation

-methyl added to the NH2s they had sticking out

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4
Q

what does methylation in prokaryotes do to the bacterias dna

A

protects the bacteria dna from cleavage by restriction endonucleases

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5
Q

in prokaryotes, methylation of adenine residues in the GATC sequence in involved in what correction

A

mismatch error correction

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6
Q

is prok, when the A is methylated in the parent strand is the A in the daughter strand also methylated?

A

yes

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7
Q

what base(s) is/are methylated in eukaryotes

A

cytosine into 5-methylcytosine

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8
Q

draw the methyl cytosine structure

A

compare to slide 5

-CH3 added to carbon 5

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9
Q

t/f

all Cytosines are methylated in eukaryotes

A

false

they get clustered into islands but not all are methylated

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10
Q

is 5-methylcytosine usually found in C resides that are 3’ to G or 5’ to G

**we know this is euk bc 5-methylcytosine is methylation only in euk

A

5’ to G

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11
Q

in euk’s when a C in one strand is methylated, what happens to the C in the complementary strand

A

it is also methylated

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12
Q

t/f

methylation in eukaryotes is heritable

A

true

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13
Q

t/f

after the parent strands with methylated cytosines are replicated, the daughter strands are immediately methylated

A

false

there’s a period immediately after replication where the daughter strand is unmethylated

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14
Q

what enzyme is methylation carried out by after replication

A

maintenance methylase

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15
Q

when are sites of methylation selected

A

during gametogenesis and embryogenesis during periods of demethylation and de novo methylation

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16
Q

what does methylation control

A

gene expression such as globin genes

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17
Q

what does promoter methylation regulate

A

gene expression

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18
Q

when the promoter is methylated, is the globin gene active or inactive

A

inactive

-when promoter unmethylated, the globin is active

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19
Q

how can the inactivity of methylated genes be reversed

A

by treatment of 5-azacytidine

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20
Q

what can 5-azacytidine be metabolized into

A

dCTP and incorporated into DNA

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21
Q

draw the 5’ azacytidine

A

check slide 10 for verification

-there’s a third N

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22
Q

what can be used as a potential treatment for Beta thalassemia

A

5-azacytidine

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23
Q

replication in 5-azacytidine does what to the methylation

A

leads to loss of methylation

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24
Q

loss of methylation from 5-azacytidine results in

A

increased gene expression

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25
Q

t/f

DNA mutation can occur in one way

A

f
can be in a number of ways (radiation, ROS, chemical, mistakes during replication, deamination of a cytosine or 5methylcytosine)

26
Q

what does deamination of 5-methylcytosine do to the base

A

becomes thymine

27
Q

deamination of 5-methylcytosine converting into thymine is an example of what mutation

A

point mutation change in a single base pair from GC to AT

28
Q

why would deamination of a 5-methcytosine be dangerous if it was not repaired

A

because thymine isn’t seen as an abnormal base by repair enzymes

29
Q

transition point mutation is a change in what

A

purine-pyrimidine base pair changed into a DIFFERENT purine-pyrimidine base pair

30
Q

list examples of transition mutation

A

GC to AT or

AT to GC

31
Q

transversion point mutation is a damage in which

A

purine-pyrimidine base pair is changed into a pyrimidine-purine base pair

32
Q

list an example of transversion mutation

A

AT to TA transversion

33
Q

what is deletion or insertion mutations

A

addition or removal of one or more base pairs

34
Q

what does deletion or insertion mutations lead to

A

frame shifts

35
Q

dna is a 3 base code in which 3 bases codes for what

A

for one AA

36
Q

what does insertion mutation do

A

insertion of 1 nucleotide into a gene which causes a frame shift

37
Q

what does deletion mutation do

A

deletion of 1 nucleotide in a gene shifts the reading frame

38
Q

what can photodimerization result in

A

in the intra strand dimerization of adjacent thymines

39
Q

reactive oxygen species can cause

A

a range of types of dna damage

40
Q

what is an example of direct repair of a damaged base

A

repair of O6-alkylguanine

41
Q

bases can be damaged by a number of mechanisms including

A

exposure to a methylating or ethylating agent

ex. chemo

42
Q

direct repair of a damaged base cause base modification in mostly

A

purines

43
Q

O6-alkylguanine has a high probability of being base paired with what during replication

A

thymine

44
Q

if O6-alkylguanine is not repaired what can it cause

A

a GC to AT transition

45
Q

what does O6-methylguanine DNA methyltransferase (MGMT) do

A

transfers the methyl group from O6-methylguanine to itself

-it self alkylates and restores the guanine

46
Q

what happens in excision repair

A

damaged DNA is recognized, removed, and then replaced by DNA polymerase

47
Q

intra strand thymine dimers caused by UV irradiation is an example of what

A

nucleotide excision repair

48
Q

photodimerization of pyrimidines examples

A

TT,CC,CT

49
Q

photodimerization of pyrimidines can result in what

A

intra strand cross links

50
Q

what are the steps in mucleotide excision repair of intra strand thymine dimers in prokaryotes

A
  1. recognition of damage
  2. repair proteins stall at damage
  3. bend DNA
  4. UvrA displaced and UvrC joins complex
  5. endonuclease cuts 3’ then 5’ to the damage and a helicase removes damaged pieces
  6. dna poly 1 replaces the excised dna
  7. nick in backbone sealed by dna ligase
51
Q

what are the two mechanisms of nucleotide excision repair in eukaryotes

A

global genome NER
Transcription-coupled NER

for description look at slide 34

52
Q

what is the XP variant in translesional DNA synthesis

A

DNA polymerase N(squiggly N)

53
Q

what are NER proteins named after

A

those damaged in Xeroderma pigmentosum patients (i.e. XP)

54
Q

what does DNA-N-glycosylases do

A

removes incorrect bases in DNA during base excision repair

55
Q

what is an example of base excision repair

A

deamination of cytosine into uracil

56
Q

what does deamination of cytosine cause if not repaired

A

a GC to AT transition mutation

57
Q

what is the mechanism of base excision repair of mismatched uracil by uracil dna N-glycosylase

A
  1. recognition of damage
  2. base removed from backbone
  3. endonuclease cuts backbone 5’ to the damage
  4. nick translation by dna poly 1
  5. nick in backbone sealed by dna ligase
58
Q

during replication DNA is proofread for mistakes by

A

DNA poly 3 epsilon subunit

59
Q

mismatch repair does what

A

scans nacent dna for errors like mismatched bases, single base insertions or deletions
if error found, it’s corrrected by mismatch pair

60
Q

what is the prokaryotic mechanism for mismatch repair

A
  1. recognize damge
  2. mutHLS xomplex searches for GATC seq closest to damage
  3. mutH (endonuclease) cuts the backbone 5’ to the G in GATC seq
  4. helicase unwinds DNA past damage
  5. exonuclease removes dna past damage
  6. dna poly 3 fills the gap
  7. nick in backbone sealed by DNA ligase
61
Q

what genes are used for DNa mismatch/damage recognition in prok and eu

A

pro: MutS
euk: MSH

62
Q

what is constitutional mismatch repair deficiency caused by

A

homozygous mutations in mismatch repair genes

-genes affected are MSH (mismatch repair in humans)

BCH Final (5 decks)

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