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DNA Repair Flashcards

1
Q

factors that lead to DNA damage

A

UV light, chemicals, radiation, pH, smoking, basic chemistry of nucleic acids

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2
Q

short term consequences of DNA damage

A

reduced proliferation, altered gene expression, apoptosis

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3
Q

long term consequences of DNA damage

A

aging, diseases like cancer

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4
Q

difference between DNA damage and DNA mutation

A

DNA damage becomes DNA mutation if the DNA replicates before there is a chance of repairing the damage

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5
Q

two types of mutation

A

spontaneous or induced

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6
Q

induced mutation is due to

A

exposure

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7
Q

two classes of spontaneous mutations

A

errors during replication (only happens in S phase of cell division)

spontaneous lesions (chemical changes that happen spontaneously when cell is resting)

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8
Q

ability of certain chemicals to exist as a mixture of two interconvertible isomers

A

tautomerism

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9
Q

thymine spends more time in which one of its isomeric phase

A

spends more time in its keto from than its enol form

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10
Q

what happens if replication occurs while thymine is in its enol form

A

its enol form pairs with G instead of pairing with A hence leading to a spontaneous mutation

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11
Q

difference in values of DNA polymerase error rate vs. actual error rate

A

DNA pol rate = 1/100,000 bp

actual rate = 1/10,000,000bp

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12
Q

characteristics of DNA pol that helps correct bp mistakes

A

DNA pol has a 3’ - 5’ exonuclease activity where it backs up and corrects mistakes

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13
Q

defect in BLM gene and DNA helicase

A

Bloom Syndrome

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14
Q

BLM gene is needed for what

A

replication repair and recombination

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15
Q

characteristics of bloom syndrome

A
  • smaller than average
  • narrow chin, prominent nose and ears
  • facial rash (pigment and dilated blood vessels) upon exposure to sun
  • often get diabetes and have neurological, lung and immune system deficiencies
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16
Q

what is going on with the chromosomes of those with Bloom Syndrome

A

chromosomal instabilities - lots of chromosomal breaks and sister chromatid exchanges
(higher chance of getting cancer)

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17
Q

rare autosomal recessive disorder that has increased spontaneous chromosome breakage which is made worse by exposure to DNA cross linking agents

A

Fanconi anemia (associated with DNA repair)

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18
Q

people with Fanconi anemia have an increased risk of what

A

neoplasia

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19
Q

Fanconi anemia is associated with how many genes

A

8 different genes - locus heterogenity

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20
Q

distinguishing characteristic of Fanconi anemia

A

dislocated thumb

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21
Q

common places for frameshift mutations

A

where there are base repeats

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22
Q

causes of frameshift mutation

A
  • slipping of DNA pol during replication of base repeats

- DNA loops and kinks at these points and one or more bases are not copied or copied twice

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23
Q

changes that occur in resting cell due to chemical nature of the DNA

A

spontaneous lesions

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24
Q

types of spontaneous lesions

A

deamination, depurination, oxidative damage

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25
most common type of spontaneous lesion
depurination
26
mechanism of depurination
breaking of glycosidic bond between purine base and sugar and purine is lost but the backbone stays intact - if it persists --> mutation
27
mechanism of deamination
amine group lost from cytosine and it forms uracil
28
why is deamination easy to fix
easy to fix because DNA does not have uracil
29
what is the issue when deamination occurs in CpG islands
the cytosine are methylated there so 5 methyl cytosine would deaminate to thymidine --> now have T-G pair --> both of which are normal bases ---> so would be repaired to TA or CG ---> mutational hotspot made
30
mutational hotspots include what
CpG islands where 5 methyl cytosine are present and places with repeated bases
31
oxidative damage is a result of
production of reactive oxidative compounds due to oxidative metabolism
32
how to prevent oxidative damage
you cannot ...unless you stop breathing ha!
33
problem with oxidative damage
it places oxygen on nucleotide bases making it able to pair with the wrong bases ---> mispairing with A leading to possible transversion
34
increase frequency of normal mutations
mutagens
35
serious mutagens in our evironment
* UV (from sun or tanning beds) * ionizing radiation (from space or the ground) • aflatoxin (from moldy grain) * benzene * formaldehyde * mustard gases
36
not so serious mutagens in our environment
* alcohol (acetaldehyde breakdown product) • barbequed hamburgers * cigarettes * anything fun
37
gamma rays, x-rays, and radioactive particles are all
ionizing radiation
38
where do we get most radiations from
the ground - terrestrial radiation
39
ionizing mutation can cause extensive damage of DNA which includes
heritable mutations - pass it on to next generation (offspring)
40
what happens to adjacent thymine residues in presence of UV light
form deleterious photoproducts such as thymine dimers/pyrimidine dimers --> 6-4 photoproduct (6-4PP) and cyclobutane pyrimidine dimers (CPD)
41
what do thymine dimers/pyrimidine dimers do
interfere with normal pairing and block replication
42
ways to fix DNA damage
nucleotide excision, base excision, mismatch repair
43
which one of the mechanisms of fixing DNA damage is post replication repair
mismatch repair
44
how are thymine/pyrimidine dimers repaired
nucleotide excision - removing a few base pairs (up to 30) around damaged site
45
how are DNA damage by methylation or oxidation repaired
base excision - repairs a single or just a few of the damaged bases by removing it
46
mechanism of excision repair
recognition of damage and removal of damaged base or bases around the damage using specific repair proteins replacement of excised region using shared repair proteins
47
what protein removes sugar phosphate from damaged DNA
endonucleases
48
mutation in 9 different NER genes
Xeroderma Pigmentosum (AR)
49
incidence of xeroderma pigmentosa is higher in what population
Japan
50
characteristic of Xeroderma Pigmentosa
extreme sun sensitivity, freckled with hyperpigmented skin lesions, ocular tumors, conjunctivitis, DNA damage cumulative and irreversible
51
protein that recognizes specific damaged bases in DNA
DNA glycosylases
52
removes small repeats that tend to expand (triplet repeat disorders)
mismatch repair
53
which one of the repair mechanisms show strand discrimination and how?
mismatch repair due to methylation in prokaryotes due to methylation and replication machinery in eukaryotes
54
mismatch missed by proofreading is recognized by
MMR protein
55
repair occurs in what phases in mismatch repair
S phase if missed by proofreading | or G2 when genome is scanned for errors
56
result of mutations in genes encoding mismatch repair proteins (MSH2 or MLH1 and more)
hereditary nonpolyposis colon cancer
57
hereditary nonpolyposis colon cancer results in
microsatellite instability - simple repetitive DNA sequences show size variability due to inaccurate replication
58
A 25-year old male spends a lot time basking in the sun, and also in tanning beds. Which type of DNA damage occurs with this behavior?
pyrimidine/thymine dimer
59
A 12 year old pediatric cancer patient is found to have a germline mutation in a gene encoding a DNA helicase. He is relatively small for his age, and he develops a rash when exposed to sunlight. Which of the following is contraindicated for the treatment of his cancer?
CT scan, x-rays, UV tanning bed, DNA damaging agents
60
with this type of break, there is a high probability of loss of genetic material
double strand breaks
61
two mechanisms for repairing double stranded break
non-homologous end joining (more common) and recombination repair (uses homologous chromosome hence less error than NHEJ)
62
BRCA1 and BRCA2 are involved in what processes when DNA can't be repaired
DNA repair and apoptosis
63
higher risk of developing ovarian cancer with mutation in which protein
BRCA1 (55%)
64
good outcome of errors in DNA/DNA damage
they allow for evolution
65
which errors can result in cancer and aging
somatic errors
66
which errors can result in genetic diseases visited on your descendants
germline errors
67
DNA repair genes are susceptible to mutation which can result in
increased error rate and genome instability (bloom syndrome)
68
defect in ATM - a serine threonine kinase that detects DNA damage and activates cell cycle arrest and DNA repair protein
ataxia telangiectasia
69
ataxia telangiectasia affects
cerebellum (=ataxia), immune system, ocular telangiectasia
70
ATM/ATR - mediated signaling pathway
genotoxic stress --> sensor proteins --> apical kinases --> signal relay proteins --> effector proteins --> responses

Genetics (19 decks)

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