Lecture 5 - DNA Repair

Question 1

what causes DNA damage?

Answer 1

chemical processes, carcinogens, and physical processes

Question 2

what does the body use to fix mutations?

Answer 2

using an undamaged strand and DNA repair

Question 3

what happens with an accumulation of mutations?

Answer 3

daughter DNA can carry mutations and can lead to cancer

Question 4

what is a lesion in this context?

Answer 4

DNA damage; unrepaired lesions become mutations

Question 5

What kind of mutations can occur?

Answer 5

substitutions - point mutations deletions - removing bases additions - adding bases

Question 6

what is a silent mutation?

Answer 6

change has no effect on gene function

Question 7

what is the ames test?

Answer 7

ames test uses salmonella strains that are unable to synthesize His. they are put on plate with mutagenic compound to see if they can grow as result of mutations. purpose is to determine the mutagenic potential of a compound. if growth is far away from compound then it is highly mutagenic

Question 8

what are mismatches?

Answer 8

mismatches are incorporations of incorrect nucleotides - mismatch repair

Question 9

what are abnormal bases?

Answer 9

abnormal bases occur from deamination, chemical alkylation or free radicals - base excision repair

Question 10

what are pyrimidine dimers?

Answer 10

pyrimidine dimers form when exposed to UV light; changes structure of DNA - nucleotide excision repair

Question 11

what are backbone lesions?

Answer 11

back bone lesions happen when exposed to free radicals or ionizing radiation - direct repair

Question 12

How does mismatch repair know which strand has the mismatch?

Answer 12

parent strand is methylated so any replication errors have to be in the unmethylated strand; this is why there is a delay in the methylation of the daughter strand by Dam methylase

Question 13

what did experiments show about mismatch repair and methylation?

Answer 13

if both strands are methylated then only a few errors are repaired, if both strands are unmethylated then neither strand is treated as correct

Question 14

what is the mechanism associated with mismatch repair?

Answer 14

1. MutS recognizes mismatch bp and forms a complex with MutL
2. using ATP it scans DNA to find a GATC methylated sequence
3. MutH binds to hemimethylated strands.
4. MutH, MutS, MutL forms a complex and starts endonuclease activity
5. MutH cleaves the non methylated DNA strand on the 5’ side of the G
6. DNA is unwound and DNA unmethylated strand is degraded 5’ to 3’ or 3’ to 5’ depending on the cut towards the mismatch
7. DNA Pol 3 and DNA ligase *helicase and SSB are still used

Question 15

what leads to cancer?

Answer 15

cancer is mostly caused by mutations in the regulation of cell division

Question 16

what can DNA glycosylases do?

Answer 16

DNA glycosylases can recognize lesions such as the deamination of cytosine and adenine (deamination of cytosine makes uracil) for base excision repair. the enzymes cleave the N-glycosyl bond between the base and the sugar

Question 17

what is an AP site?

Answer 17

an AP site or apurinic/apyrimidinic site created when DNA glycosylase cleaves the N-glycosyl bond b/w the base and pentose.

Question 18

what does uracil glycosylase do?

Answer 18

removes uracil because cytosine can deaminate spontaneously into uracil which doesn’t belong in DNA; cells lacking this enzyme have high GC to AT mutations

Question 19

What happens at AP sites in bacteria?

Answer 19

To repair the AP site, the whole nucleotide is removed not just the base, sometimes the region around the AP site is removed.

Question 20

What are the function of AP endonucleases?

Answer 20

AP endonucleases cut the DNA backbone around the AP site and removes the DNA entirely

Question 21

when is nucleotide excision repair needed?

Answer 21

when there are large distortions in the DNA. Lesions include pyrimidine dimers and 6-4 photoproducts from UV light

Question 22

How is nucleotide excision repair carried out?

Answer 22

in both eukary and prokary, a large chunk of DNA is taken out. in prokary, 12-13 nucleotides are removed using ABC excinuclease containing UvrA, UvrB, UvrC then DNA Pol 1 and ligase fix it up. in eukary, 27-29 get removed and DNA Pol epsilon and ligase fix it up

Question 23

what happens when there is no undamaged DNA to use as a template?

Answer 23

unrepaired lesion can cause replication fork to stall.

Question 24

How to repair without undamaged DNA as template?

Answer 24

use of another chromosome thru recombination to repair or through error prone translesion synthesis which can kill some cells and cause mutations in others, but some cells can live.

Question 25

what are TLS polymerases?

Answer 25

found in mammals and can recognize most forms of damage, but are limited to short sections of DNA to minimize mutagenic potential