Exam III Flashcards
Name 4 causes of DNA damage that would trigger repair pathways
Alkylation, reactive oxygen species, deamination, UV irradiation
What would remove a deaminated cytosine (uracil ) from a DNA strand?
uracil-n-glycosylase
What do DNA glycosylases do?
break glygosyl bond between damaged bases and sugar nucleotide
What is the relevance of methylated 5-methylcytosine?
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.
Why is vsp repair used for methylated cytosines?
This area is a hotspot for mutations bc it yields thymine instead of uracil.
What are ada and got?
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.
What are AlkB and AidB
alkylation repair enzymes
How does GO affect DNA?
Go is a reactive oxygen species that DNA Pol III will mispair it with A in aerobic organisms
What are MutM, MutY, and MutT and what do they do?
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
What happens if a cell is mutant for MutM ?
The cell will experience more oxidative stress
What happens if a cell is mutant for MutY?
Higher mutation rate as the wrong As will not be removed
What happens if a cell is mutant for MutT?
More GO in DNA
Describe alkylation in cells
Alkylating agents (EMS,Nitrosoguanidine) add alkyl groups to bases/phosphate groups
What 2 locations are hotspots for alkylation?
N7 of G and N3 of A
How does alkylation affect DNA?
distorts the helix and severely alters pairing.
How are alkylated bases removed?
Specific glycosylases. (AlkA in E.Coli) or methyltransferases
What do methyltransferases do?
Andwhat are the names of the two important ones?
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))
what is the adaptive response?
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.
What does UV irradiation do to a cell’s DNA?
Additional bonds between bases like thymine dimers or C/T bonds
What is the repair system for UV irradiation?
photoreactivation, which occurs when cell is exposed to visible light
What enzyme is responsible for uv irradiation damage repair?
photolyase (orange croissant)
What does photolyase do?
attach to dimer, cleave and leave
What are pyrimidine dimers?
abnormal links between bases caused by uv irradiation
How are alkylated bases solved?
specific n-glycosylases like alkA in e coli
or methyltransferases like ada(induced by adaptive response)/ogt
What is the mismatch repair system?
General system for repairing mismatched base pairs right after replication
What is the major flaw that makes mismatch repair not 100% at lowering spontaneous mutation rate?
It depends on whether the system recognizes and replaces the correct base pair on the correct strand or not
What does MutM, Y, and T do?
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
why is alkylation bad for DNA?
alters base pairing and distorts helix
who is in charge of mismatch editing?
dna pol
Describe the model for methyl directed mismatch repair (slight distortion) with mut S,H and L (and dam methylase)
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
Describe nucleotide excision repair
UvrABCD
Pol I and Ligase
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
