Exam III

Question 1

Name 4 causes of DNA damage that would trigger repair pathways

Answer 1

Alkylation, reactive oxygen species, deamination, UV irradiation

Question 2

What would remove a deaminated cytosine (uracil ) from a DNA strand?

Answer 2

uracil-n-glycosylase

Question 3

What do DNA glycosylases do?

Answer 3

break glygosyl bond between damaged bases and sugar nucleotide

Question 4

What is the relevance of methylated 5-methylcytosine?

Answer 4

Very short patch (vsp) repair is used. Where vsr endonuclease binds to TG mismatch and makes a break next to the T , T gets removed and DNA pol I inserts the C.

Question 5

Why is vsp repair used for methylated cytosines?

Answer 5

This area is a hotspot for mutations bc it yields thymine instead of uracil.

Question 6

What are ada and got?

Answer 6

Alkylation repair mechanism methyltransferase proteins (not enzymes as they are not catalysts) that repair alkylated bases by removing the alkyl group and putting it on themselves instead.

Question 7

What are AlkB and AidB

Answer 7

alkylation repair enzymes

Question 8

How does GO affect DNA?

Answer 8

Go is a reactive oxygen species that DNA Pol III will mispair it with A in aerobic organisms

Question 9

What are MutM, MutY, and MutT and what do they do?

Answer 9

Genes that prevent and repair DNA damage from GO.
M: Glycosylase that removes the 8-oxo base. MutM is induced by oxidative stress where GO is present in cells.
Y: Glycosylase that removes the adenine that paired with GO
T: Prevent GO from entering the DNA by degrading oxoGTP to oxoGMP

Question 10

What happens if a cell is mutant for MutM ?

Answer 10

The cell will experience more oxidative stress

Question 11

What happens if a cell is mutant for MutY?

Answer 11

Higher mutation rate as the wrong As will not be removed

Question 12

What happens if a cell is mutant for MutT?

Answer 12

More GO in DNA

Question 13

Describe alkylation in cells

Answer 13

Alkylating agents (EMS,Nitrosoguanidine) add alkyl groups to bases/phosphate groups

Question 14

What 2 locations are hotspots for alkylation?

Answer 14

N7 of G and N3 of A

Question 15

How does alkylation affect DNA?

Answer 15

distorts the helix and severely alters pairing.

Question 16

How are alkylated bases removed?

Answer 16

Specific glycosylases. (AlkA in E.Coli) or methyltransferases

Question 17

What do methyltransferases do?
Andwhat are the names of the two important ones?

Answer 17

They remove methyl group from base and place it on themselves, and eventually become deactivated and degraded. Therefore they are not enzymes. (Ada (stationary cells)and Ogt (actively growing cells))

Question 18

what is the adaptive response?

Answer 18

The adaptive response repairs alkylation damage. While a few alkylation repair proteins exist in the cell normally, when exposed to an alkylating agent, repair mechanisms get triggered. Think of this like a bacterial vaccine. If E. coli is exposed to a small amount of alkylating agent, it will produce even stronger response if it comes across alkylating agents in the future.

Question 19

What does UV irradiation do to a cell’s DNA?

Answer 19

Additional bonds between bases like thymine dimers or C/T bonds

Question 20

What is the repair system for UV irradiation?

Answer 20

photoreactivation, which occurs when cell is exposed to visible light

Question 21

What enzyme is responsible for uv irradiation damage repair?

Answer 21

photolyase (orange croissant)

Question 22

What does photolyase do?

Answer 22

attach to dimer, cleave and leave

Question 24

What are pyrimidine dimers?

Answer 24

abnormal links between bases caused by uv irradiation

Question 25

How are alkylated bases solved?

Answer 25

specific n-glycosylases like alkA in e coli
or methyltransferases like ada(induced by adaptive response)/ogt

Question 26

What is the mismatch repair system?

Answer 26

General system for repairing mismatched base pairs right after replication

Question 27

What is the major flaw that makes mismatch repair not 100% at lowering spontaneous mutation rate?

Answer 27

It depends on whether the system recognizes and replaces the correct base pair on the correct strand or not

Question 28

What does MutM, Y, and T do?

Answer 28

Oxidative damage in DNA (GO).
M makes the Go leave
Y “y are you here?” removes incorrect adenine
T “NO TRESPASSING” does not allow Go to enter DNA

Question 29

why is alkylation bad for DNA?

Answer 29

alters base pairing and distorts helix

Question 30

who is in charge of mismatch editing?

Answer 30

dna pol

Question 31

Describe the model for methyl directed mismatch repair (slight distortion) with mut S,H and L (and dam methylase)

Answer 31

S binds to miSmatch. Complex forms with H and L proteins. H makes an incision. Nick extended to a gap by nucleases. UvrD helicase. Need Dna pol III and Ligase to resynthesize and seal. Dam methylase is used on the new and correct Adenine

Question 32

Describe nucleotide excision repair
UvrABCD
Pol I and Ligase

Answer 32

Very important general repair mechanism for DNA damage such as uv irradiation. Damaged nucleotides are cut out and replaced. Very nonspecific repair though, and it only recognizes general MAJOR distortions of the helix, not lesions like base mispairing.
UvrA/B/C.
A: binds to dna nonspecifically
B: forms complex w A and nicks it
C: forms complex and nicks in other direction
D: helicase activity
Pol I and Ligase used