DNA Mutation and Repair Flashcards
1
Q
Any hereditary change in the DNA sequence
A
mutation
2
Q
different from the “wild type”
A
mutant
3
Q
agents that cause mutation
A
mutagen
4
Q
Types of mutation based on the number of bases changed
A
- base substitution (point mutation and frameshift mutation)
- multiple/chromosomal mutation
- numerical chromosomal aberrations
5
Q
change from purine to purine or pyrimidine to pyrimidine
A
transition point mutation
6
Q
change from purine to pyrimidine or pyrimidine to purine
A
transversion point mutation
7
Q
insertion of a base causes the RF to shift to the?
A
left
8
Q
deletion of a base causes the RF to shift to the?
A
right
9
Q
types of chromosomal mutation
A
- insertion
- duplication
- deletion
- inversion
- translocation
10
Q
addition or loss of 1 or a few chromosomes
A
aneuploidy
11
Q
duplication or addition of genomes
A
euploidy
12
Q
change in base results to no change in the AA sequence
A
silent mutation or neutral mutation
13
Q
change in base in the intronic regions
A
silent mutation or neutral mutation
14
Q
change in base leads to a different AA
A
missense mutation
15
Q
change in base leads to translation termination
A
nonsense mutation
16
Q
types of mutagenesis
A
- spontaneous
- induced
17
Q
Types of spontaneous mutations
A
- uncorrected mismatches
- tautomerization
- replication slippage
- spontaneous depurination
- spontaneous deamination
18
Q
amine form of A pairs with
A
T
19
Q
imine form of A pairs with
A
C
20
Q
keto form of T pairs with
A
A
21
Q
enol form of T pairs with
A
G
22
Q
keto form of G pairs with
A
C
23
Q
enol form of G pairs with
A
T
24
Q
amino form of C pairs with
A
G
25
imine form of C pairs with
A
26
what can happen when the template DNA loops out during replication
base may fail to be complemented
27
what can happen when the new DNA loops out during replication?
base may be complemented twice
28
What happens during spontaneous depurination
the N-glycosidic bond between a purine base and the deoxyribose sugar is broken
29
what happens to C during spontaneous deamination
converts to U
30
T occurred after spontaneous deamination, what was the original form?
5mC (5-methylcytosine)
31
What are the six types of induced mutation?
chemical mutagens
1. base analogs
2. base-modifying agents
3. intercalating agents
physical mutagens
4. UV radiation at 260 nm
5. ionizing radiation
6. heat
32
Base analog of T
5-bromouracil
33
keto form of 5-bromouracil pairs with?
A
34
enol form of 5-bromouracil pairs with?
G
35
illustrate the effect of the introduction of a 5-bromouracil
see illustration
1. keto B pairs with A
2. shift of keto B to enol B
3. enol B pairs with G
4. shift of enol B to keto B
5. keto B pairs with A
and G is paired with C
36
base analog of A
2-aminopurine
37
3 modifying agents
1. deaminating agent
2. hydroxylating agent
3. alkylating agent
38
nitrous acid
deaminating agent
39
sulfur dioxide
deaminating agent
40
sodium bisulfite
deaminating agent
41
hydroxylamine
hydroxylating agent
42
what happens to G in the presence of nitrous acid?
G converts to X which pairs with C (no change in base pairs)
43
what happens to C in the presence of nitrous acid?
C converts to U which pairs with A (C=G pairing --> T=A)
44
what happens to A in the presence of nitrous acid
A converts to H which pairs with C (A=T pairing --> G=C)
45
what happens to C in the presence of sodium dioxide
converted to U
46
what happens to C in the presence of hydroxylamine
C converts to HAC which pairs with A (C=G pairing --> T=A)
47
epoxides
alkylating agent
48
tetraethyl lead
alkylating agent
49
nitroso-derivatives
alkylating agent
50
MMS/EMS
methyl-/ethylmethane sulfate - alkylating agent
51
what happens to G in the presence of MMS
converts to O6mG which pairs with T (G=C --> A=T)
52
ethidium bromide
intercalating agent
53
acridine orange
intercalating agent
54
2 mechanisms of intercalating agents
1. intercalation can result in insertion in the DNA
2. loss of intercalating agent can result in deletion
55
4 possible effects of inducing UV radiation of 260 nm
1. dimerization of pyrimidine bases
2. formation of (6-4) lesions and (6-4) photoproducts
3. shifting of C to imine tautomer
4. interchain dimerization
56
4 possible effects of inducing ionizing radiation
1. formation of rare enol tautomers
2. removal of C from the DNA
3. shifting of C to imine tautomer
4. production of ss/ds breaks
57
induced mutation by heat?
water-induced cleavage of the ß-N-glycosidic bonds can cause removal of bases or can result in AP sites
58
3 biological agents that can induce mutations
1. transposable elements
2. viruses
3. bacteria
59
suppression mutation within the same gene
intragenic suppression
60
suppression mutation involving different genes
intergenic suppression
61
what is suppressor mutation
an initial mutation is masked or compensated by a second mutation from a different site/location (can be either intragenic or intergenic)
62
Importance of mutation in the germ cell.
Mutations in the germ cells are heritable, which means they can be transmitted to the next generations.
63
Why do mutations occur in low frequency?
Mutations are rarely observed because the cell has effective repair systems against unwanted changes in the DNA. It may also be due to mutations happening in the somatic cells (not the germ cells) so the mutations are only observed in tissues or a group of cells, and are not inherited.
64
Kinds of DNA repair mechanisms
1. direct repair
2. base excision repair (BER)
3. nucleotide excision repair (NER)
4. mismatch repair
5. double strand base repair
6. SOS response
65
3 types of damages that are repaired directly
1. nicks
2. alkylation damage
3. cyclobutyl damage
66
enzyme: repairs nicks
DNA ligase
67
adenosine deaminase (ADA) repairs?
alkylation damage in E. coli
68
human MGMT repairs?
alkylation damage in humans
69
enzyme: repairs cyclobutyl damage
photolyase (via photoreactivation)
70
2 main enzymes involved in BER
1. DNA glycosylase
2. AP endonuclease
71
function of DNA glycosylase in BER
removes damaged base
72
function of AP endonuclease in BER
cuts DNA in the damaged region (incision)
73
mechanism of BER
1. recognition of damage
2. excision
- damage is removed by DNA glycosylase, forming a baseless site, and is excised by AP endonuclease
3. resynthesis by DNA polymerase ß and DNA ligase
74
NER enzymes in bacteria
uvrA
uvrB
uvrC
75
mechanism of NER
recognition
- uvrA and uvrB trimer attaches
- uvr A is detaches
- uvrC attaches
excision
- uvrB and uvrC cuts the segment
- helicase II removes the single strand
- uvrB bridges the gap
resynthesis
- replacement and resynthesis of bases by DNA Pol I and DNA ligase
76
2 major types of MMR
1. long patch
2. short patch
77
3 major enzymes of MMR in prokaryotes
Mut S
Mut H
Mut L
78
counterpart of Mut S in eukaryotes
hMSH2/hMSH6
79
counterpart of Mut H in eukaryotes
none/unknown
80
counterpart of Mut L in eukaryotes
hMLH1
81
5 steps in the MMR system
1. recognition of the mismatch by Mut S
2. production of nicks where Mut H determines which strand contains the mismatch
3. Mut L recruits Mut S and Mut H to form the key intermediate complex
4. Mismatch is excised by exonuclease and DNA helicase
5. resynthesis by DNA Pol I and DNA ligase
82
2 types of DSBR
1. homologous recombination
2. non-homologous end-joining
83
steps of NHEJ
1. recognition and binding of Ku and DNA-PKcs proteins
2. DNA-PKc activates XRCC4
3. XRCC4 activates ligase IV
4. DNA ligase IV seals breaks
84
function of Ku in NHEJ
recognition of break and binding of DNA-PKcs
85
function of DNA-PKcs in NHEJ
activates XRCC4
86
function of XRCC4 in NHEJ
activates DNA ligase IV
87
function of DNA ligase IV in NHEJ
seals breaks
88
mutasome in SOS response
DNA Pol V (2 UmuD and 1 UmuC proteins)
89
2 major proteins in SOS response
1. RecA
2. LexA
90
function of RecA in SOS response
acts as co-protease (with ATPase and ssDNA binding)
91
function of LexA in SOS response
repressor; autoregulatory protein
92
mechanism of SOS response
1. DNA damage produces ss gap
2. RecA proteins bind to the ssDNA
3. LexA is inactivated (via activated proteolysis)
4. error-prone resynthesis/replication
