DNA repair

Question 1

what are the major methylated bases in prokaryotes

Answer 1

adenine and cytosine

Question 2

why do prokaryotes methylate their own DNA

Answer 2

to protect against invading bacteria and viruses

Question 3

draw the N6-methyladenine and N4-methyl cytosine structures

Answer 3

look at slide 3 on repair ppt for confirmation

-methyl added to the NH2s they had sticking out

Question 4

what does methylation in prokaryotes do to the bacterias dna

Answer 4

protects the bacteria dna from cleavage by restriction endonucleases

Question 5

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

Answer 5

mismatch error correction

Question 6

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

Answer 6

yes

Question 7

what base(s) is/are methylated in eukaryotes

Answer 7

cytosine into 5-methylcytosine

Question 8

draw the methyl cytosine structure

Answer 8

compare to slide 5

-CH3 added to carbon 5

Question 9

t/f

all Cytosines are methylated in eukaryotes

Answer 9

false

they get clustered into islands but not all are methylated

Question 10

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

Answer 10

5’ to G

Question 11

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

Answer 11

it is also methylated

Question 12

t/f

methylation in eukaryotes is heritable

Answer 12

true

Question 13

t/f

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

Answer 13

false

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

Question 14

what enzyme is methylation carried out by after replication

Answer 14

maintenance methylase

Question 15

when are sites of methylation selected

Answer 15

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

Question 16

what does methylation control

Answer 16

gene expression such as globin genes

Question 17

what does promoter methylation regulate

Answer 17

gene expression

Question 18

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

Answer 18

inactive

-when promoter unmethylated, the globin is active

Question 19

how can the inactivity of methylated genes be reversed

Answer 19

by treatment of 5-azacytidine

Question 20

what can 5-azacytidine be metabolized into

Answer 20

dCTP and incorporated into DNA

Question 21

draw the 5’ azacytidine

Answer 21

check slide 10 for verification

-there’s a third N

Question 22

what can be used as a potential treatment for Beta thalassemia

Answer 22

5-azacytidine

Question 23

replication in 5-azacytidine does what to the methylation

Answer 23

leads to loss of methylation

Question 24

loss of methylation from 5-azacytidine results in

Answer 24

increased gene expression

Question 25

t/f | DNA mutation can occur in one way

Answer 25

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

Question 26

what does deamination of 5-methylcytosine do to the base

Answer 26

becomes thymine

Question 27

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

Answer 27

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

Question 28

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

Answer 28

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

Question 29

transition point mutation is a change in what

Answer 29

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

Question 30

list examples of transition mutation

Answer 30

GC to AT or | AT to GC

Question 31

transversion point mutation is a damage in which

Answer 31

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

Question 32

list an example of transversion mutation

Answer 32

AT to TA transversion

Question 33

what is deletion or insertion mutations

Answer 33

addition or removal of one or more base pairs

Question 34

what does deletion or insertion mutations lead to

Answer 34

frame shifts

Question 35

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

Answer 35

for one AA

Question 36

what does insertion mutation do

Answer 36

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

Question 37

what does deletion mutation do

Answer 37

deletion of 1 nucleotide in a gene shifts the reading frame

Question 38

what can photodimerization result in

Answer 38

in the intra strand dimerization of adjacent thymines

Question 39

reactive oxygen species can cause

Answer 39

a range of types of dna damage

Question 40

what is an example of direct repair of a damaged base

Answer 40

repair of O6-alkylguanine

Question 41

bases can be damaged by a number of mechanisms including

Answer 41

exposure to a methylating or ethylating agent | ex. chemo

Question 42

direct repair of a damaged base cause base modification in mostly

Answer 42

purines

Question 43

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

Answer 43

thymine

Question 44

if O6-alkylguanine is not repaired what can it cause

Answer 44

a GC to AT transition

Question 45

what does O6-methylguanine DNA methyltransferase (MGMT) do

Answer 45

transfers the methyl group from O6-methylguanine to itself | -it self alkylates and restores the guanine

Question 46

what happens in excision repair

Answer 46

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

Question 47

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

Answer 47

nucleotide excision repair

Question 48

photodimerization of pyrimidines examples

Answer 48

TT,CC,CT

Question 49

photodimerization of pyrimidines can result in what

Answer 49

intra strand cross links

Question 50

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

Answer 50

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

Question 51

what are the two mechanisms of nucleotide excision repair in eukaryotes

Answer 51

global genome NER Transcription-coupled NER for description look at slide 34

Question 52

what is the XP variant in translesional DNA synthesis

Answer 52

DNA polymerase N(squiggly N)

Question 53

what are NER proteins named after

Answer 53

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

Question 54

what does DNA-N-glycosylases do

Answer 54

removes incorrect bases in DNA during base excision repair

Question 55

what is an example of base excision repair

Answer 55

deamination of cytosine into uracil

Question 56

what does deamination of cytosine cause if not repaired

Answer 56

a GC to AT transition mutation

Question 57

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

Answer 57

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

Question 58

during replication DNA is proofread for mistakes by

Answer 58

DNA poly 3 epsilon subunit

Question 59

mismatch repair does what

Answer 59

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

Question 60

what is the prokaryotic mechanism for mismatch repair

Answer 60

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

Question 61

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

Answer 61

pro: MutS euk: MSH

Question 62

what is constitutional mismatch repair deficiency caused by

Answer 62

homozygous mutations in mismatch repair genes | -genes affected are MSH (mismatch repair in humans)