Finals - DNA Repair Mechanisms Flashcards
(90 cards)
1
Q
Different DNA repair mechanisms
A
- direct repair
- excision repair
- mismatch repair
- double-stranded break repair
- SOS response
2
Q
- involves chemical reversal of the damage without breaking the phosphodiester backbone of the DNA
- not dependent on a template since the damage does not alter the sequence within which it occurs.
A
Direct repair
3
Q
where direct repair happens
A
- nicks
- alkylation damage
- cyclobutyl dimers
4
Q
sinlge-strand breaks in DNA where a phosphodiester bond is missing
A
nicks
5
Q
repairs nicks
A
DNA ligase
6
Q
what does DNA ligase do
A
glues phosphodiester bonds
7
Q
- repaired through enzymatic transfer of alkyl group from nucleotide to their own polypeptide chains
- removed by ADA
A
alkylation damage
8
Q
ADA
A
Adenosine deaminase
9
Q
Ex of alkylation damage repair
A
- ADA enzyme of E. coli
- Human MGMT
10
Q
MGMT
A
methyl guanine – DNA methyl transferase
11
Q
what does ADA do
A
- removes methyl and puts it on its cystein residue
- alkylated base is free from alkyl
12
Q
what does human MGMT do
A
interacts with alkylating agents during chemotherapy
13
Q
- repaired by DNA photolyase
- need presence of light
A
cyclobutyl dimers
14
Q
what repairs cyclobutyl dimers
A
DNA photolyase
15
Q
- perhaps the best known DNA lesion affecting a single DNA strand
- it is an intrastrand cross-link in which two adjaent pyrimidines are connected by a cyclobutane ring
A
pyrimidine dimer (PD)
16
Q
where pyrimidine dimer most frequently form
A
two thymines (thymine dimer)
17
Q
Steps in direct repair of cyclobutyl dimers
A
- Photolyase needs to be activated by UV. Chromophore abosorbs UV light and energy is transfered to FADH (noncovalent bonding).
- FADH’s electron is transferred to pyrimidine dimer causing it to split
- Restores and hydrogen bonds are formed (renaturation)
18
Q
UV wavelength in activation of photolyase
A
320-370nm
19
Q
wavelength chromophore absorbs
A
300-500nm
20
Q
involves excision of a single damaged base, followed by resynthesis
A
base excision repair
21
Q
Enzymes in base excision repair
A
- DNA glycosylase
- AP endonuclease
- DNA polymerase β
- DNA ligase
22
Q
- involved in the removal of damaged base
- creates AP site
A
DNA glycosylase
23
Q
what does DNA glycosylase create
A
apurinic/apyrimidinic site (AP site)
24
Q
incise posphodiester backbone adjacent to AP site
A
AP endonuclease
25
- fill the gap created during base excision repair
- incorporate nucleotide
DNA polymerase β
26
seals the backbone during base excision repair
DNA ligase
27
Summary of Base Excision Repair
1. DNA glycosylase removes damaged base and creates apurinic/apyrimidinic site (AP site)
2. AP endonuclease incise phophodiester backbone adjacent to AP site
3. DNA pol β fill the gap by incorporating nucleotide
4. DNA ligase seals nick
28
- repairs damage affecting longer strands, 2-30 bases
- used by the ell for bulky DNA damage
Nucleotide excision repair
29
length of damage during nucleotide excision repair
2-30 bases
30
nucleotide excision repair is used by the cell for what?
bulky DNA damage
31
mediated by gene products of uvrA, uvrB, or uvrC
NER in bacteria
32
- involves XPA, XPB, XPC, XP6 proteins
- CSA and CSB proteins
- ERCC7, RPA, and RAD 23 proteins
NER in eukaryotes
33
inherited condition characterized by an extreme sensitivity to ultraviolet radiation (UVR), which is present in sunlight and may also be found in some types of artificial lighting
Xeroderma pigmentosum
34
what is absent in people with Xeroderma pigmentosum
Nucleotide excision repair (NER)
35
Summary of Nucleotide Excision Repair
1. uvrB with uvrA scans damaged DNA
2. uvrA helps uvrB recognize damaged part
3. uvrA released, uvrC attaches, helicase II unwinds
4. uvrC with uvrB excise the damaged part and some nucleotides near are also cut
5. uvrB bridges the gap
6. DNA pol I incorporate complemetary nucleotides
7. DNA ligase seal nicks
36
Nucleotide excision repair (NER):
scans damaged DNA
uvrB with uvrA
37
Nucleotide excision repair (NER):
helps uvrB recognize damaged part
uvrA
38
Nucleotide excision repair (NER):
what happens after recognition of damaged part
- uvrA released, uvrC attaches
- helicase II unwinds
39
Nucleotide excision repair (NER):
- excise or cut the damaged part
- some nucleotides near the damaged are also excised
uvrC with uvrB
40
Nucleotide excision repair (NER):
bridges the gap
uvrB
41
Nucleotide excision repair (NER):
incorporate complementary nucleotides
DNA pol I
42
Nucleotide excision repair (NER):
ligate nicks
DNA ligase
43
- happens in new strand DNA
- corrects mismatched nucleotide
- strand specific
- repairs new strand DNA -? methylation pattern
Mismatch Repair
44
serves as guide to find damage during mismatch repair
methylation pattern
45
Essential MMR proteins in prokaryotes
1. Mut S
2. Mut H
3. Mut L
46
MisMatch repair prokaryotes:
recognizes mismatched bp
Mut S
47
- MisMatch repair prokaryotes:
very weak endonuclease, activated when bound to Mut L
- distinguish the strand containing mismatch
Mut H
48
forms complex with Mut S and Mut H
Mul L
49
Essential MMR proteins in eukaryotes
1. Msh 2/ Msh 6
2. Msh 2 / Msh 3
50
MisMatch repair:
detects mismatch
mut S
51
MisMatch repair prokaryotes:
serve as a guide for Mut H
methyl group (already programmed)
52
MisMatch repair prokaryotes:
needed for mut L to work
MutH and MutS
53
MisMatch repair prokaryotes:
site where there is a methyl group (complementary)
mut H
54
MisMatch repair prokaryotes:
unwinds
DNA helicase II
55
MisMatch repair prokaryotes:
cuts
exonuclease (Mut H)
56
MisMatch repair in humans
1. short mismatch
2. long mismatch
57
short mismatch
MSH2 & MSH6
58
long manuscript
MSH2 & MSH3
59
Mismatch repair in humans steps
1. mismatch
2. recognition
3. sliding clamp
4. exonuclease
5. resynthesis
60
- creates complex to lock mismatch
- ATP is used
MSH2 & MSH6
61
Mismatch Repair:
pushes DNA pol
sliding clamp
62
Mismatch Repair:
- cuts from mismatch towards 3'
- removes mismatch DNA
exonuclease I
63
Mismatch Repair:
fills in gap
DNA pol delta
64
recombination is a form of ds break repair
double-stranded break repair
65
Two types of double-stranded break repair
1. homologous recombination
2. non-homologous end-joining
66
Homologous recombination:
break are equal
blunt-end break
67
Homologous recombination:
- cut the blunt-end further
- creates overhangs or sticky ends that are easier to complement
5'-3' exonuclease
68
Homologous recombination:
forms displacement loop
strand invasion
69
Homologous recombination:
promotes formation of displacement loop
Rad 51
70
Homologous recombination steps
1. ds-break
2. 5'-3' exonuclease
3. strand invasion
4. DNA synthesis
5. ligation
6. branch migration
71
- growing list of enzymes are involved
- time requiring
- some nucleotide will be lost, degraded
- introduce deletions
non-homologous end-joining in humans
72
enzyme in non-homologous end joining
DNA end-processing enzymes
73
Non-homologous end-joining:
binds to the break
Ku70/80
74
Non-homologous end-joining:
activates XRCC4 protein
DNA-PKcs
75
Non-homologous end-joining:
- DNA-end processing enzyme
- trim/fill the gaps to make the ends compatible for ligation
artemis
76
Non-homologous end-joining:
needed to activate ligase
XRCC4-Ligase IV complex
77
Non-homologous end-joining:
- interact to XRCC4-ligase IV complex
- stimulate ligase activity of LIgase IV
cernunnos-XLF
78
Non-homologous end-joining:
aligned and ligated
DNA
79
- in bacteria
- inducible
- allows DNA replication to proceed through a highly damaged region
- by-passes DNA damage* error-prone
SOS response
80
initiation of the SOS response
1. activation of RecA
2. degradation and inactivation of LexA
3. expression of DNA polymerase V
81
- acts as protease when bound to ds DNA
- binds ssDNA
activation of RecA
82
- lexA is the repressor of RecA gene when RecA protein is not needed.
- when there is extensive damage, RecA is producd
Degradation and inactivation of LexA
83
umuD and umuC proteins
expression of DNA pol V
84
complex of proteins that answers mutation problems
mutasome
85
SOS response:
produced when there is extensive damage
recA
86
how is SOS response inactivated with Lex A
LexA represses all genes that are involved in SOS response.
87
SOS response:
degrades lexA to activate the genes. This will be translated into SOS proteins
initiation of the SOS response
88
SOS response:
- main SOS protein
- no sense of proof-reading
DNA pol V
89
gene for DNA pol V
umuC,D
90
what happens when there are mutations
1. accumulate mutation
2. no efficient repair
3. advantage/deleterious
