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Biochemistry > origins of mutations and DNA repair > Flashcards

origins of mutations and DNA repair Flashcards

1
Q

somatic vs germline mutation

A

germline is passed on, inherited

somatic can cause cancer

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2
Q

gene mutations vs chromosome and genome

A

gene mutations affect only one gene, only one base
chromosomal mutations affect many genes
genome mutations affect entire chromosomes

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3
Q

point mutation types, causes, effects

A

silent: no change in codon, no effect on protein
missense: change in codon, decrease in function
nonsense: codon changed to stop, truncation
RNA processing: affects splice site, addition or deletion

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4
Q

small insertions and deletions

A

type of gene mutation

include strand slippage/triplet repeat expansion and frameshift mutation

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5
Q

strand slippage/triplet repeat expansion

A

CAG/CTG repeats can result in single strand loops during replication because strand can be displaced or slipped
new DNA will carry extra triplets

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6
Q

frameshift mutation

A

caused by intercalating agents (acridine dyes, ethidium bromide, doxorubicin)
insertion or deletion of one or more nucleotides
results in “frameshift” where codons downstream of mutation are altered
nonfunctional protein or shortened

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7
Q

incorrect recombination

A

incorrect alignment during recombination may cause unequal crossover
nonhomologous regions are exchanged, leading to gain/loss of gene

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8
Q

clinical correlation of unequal crossover

A

alpha thalassemia

cri-du-chat

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9
Q

miss-segregation/nondisjunction

A

incomplete separation of chromosomes during anaphase I or II
germ cells end up with more or fewer chromosomes than normal
frequency of nondisjunction increases with maternal age
trisomy, monosomy, triploidy, or tetraploidy

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10
Q

depurination

A

purine (A or G) can be cleaved off, forming an abasic site where deoxyribose lacks a base
can cause mutations

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11
Q

deamination

A

cytosine can be converted to uracil via spontaneous deamination
U pairs with A in next replication, producing GC to AT transition mutation
repaired via base excision repair

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12
Q

DNA polymerase

A

elongates DNA during replication

also aids in repair, has proofreading activity

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13
Q

DNA helicase

A

unwinds DNA double helix for replication

uses ATP

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14
Q

DNA ligase

A

connects Okazaki fragments at end of replication

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15
Q

exonuclease

A

a

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16
Q

primase

A

synthesizes RNA primer necessary for replication of lagging strand

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17
Q

strand-directed mismatch repair

A

corrects replication errors during G2 phase
MSH2 recognizes mismatch near single-strand nick, signals need for repair
MLH1 coordinates excision of incorrect BP
gap is filled by DNA polymerase
backup plan to polymerase delta

18
Q

clinical correlation of strand-directed mismatch repair

A

hereditary nonpolyposis colorectal carcinoma (HNPCC)

19
Q

base excision repair

A

repairs damage due to deamination
C that has been converted to U is recognized and removed by uracil DNA glycosylase
glycosylase hydrolyzes U, leaves bond intact
AP endonuclease recognizes missing base, cuts strand on one side of missing base
DNA phosphodiesterase removes deoxyribose phosphate
DNA polymerase and ligase fill and seal gap

20
Q

nucleotide excision repair

A

repairs thymine dimers that form as a result of UV light
distortion in helix identified, then helicase separates strands
excision endonuclease cuts at either side of lesion
polymerase and ligase re-synthesize damaged strand

21
Q

clinical correlation of nucleotide excision repair

A

xeroderma pigmentosum

extreme sensitivity to light, excessive freckling, carcinoma/melanoma

22
Q

nonhomologous end joining

A

fixes DS breaks
repair proteins bring together ends of broken strands, but nucleotides are lost at breakpoint
usually used to repair noncoding DNA regions, therefore does not result in nonfunctional proteins

23
Q

homologous end joining

A

uses recombination to fix broken DNA
undamaged homologous chromosome is used as template for repair of damaged chromosome
allows repair of DS breaks WITHOUT LOSS of information

24
Q

proofreading activity of polymerase

A

polymerase delta has 3’-5’ exonuclease activity
edits 3’ end of growing strand during S phase
rereads strand and if base pairing is wrong, hydrolyzes phosphodiester bond and starts over until correct

25
Q

cytarabine

A

analogue of cytidine
competes with dNTPs for binding of DNA polymerase, blocking DNA replication
S phase inhibitor
used in AML and non-Hodgkin’s

26
Q

cyclophosphamide

A 
forms DNA crosslinks, blocking DNA uncoiling
blocks replication
triggers apoptosis
bi-functional alkylating agent
used in Hodgkin's, breast, lung, etc.
27
Q

doxorubicin

A

targets topo II, topo poisoning by trapping at replication sites
can cause frameshift mutation by intercalating during replication

28
Q

radiation

A

causes cross-linking of pyrimidines, usually thymine, producing dimers
thymine dimers can block replication in next round

29
Q

oxidative damage

A

commonly occurs at guanine residues due to high oxidation potential
ROS oxidizes guanine to 8-hydroxyguanine
8H can pair with adenine, resulting in GC to AT transition mutation

30
Q

clinical correlation of triplet repeat expansion

A

Huntington disease

fragile X and myotonic dystrophy

31
Q

gene polymorphism

A

genes may have more than two sequence variants that are slightly different from one another
equally acceptable variants, called polymorphic sequence variants

32
Q

Huntington disease

A

triplet expansion in coding region

abnormal protein contains > 30 adjacent glutamines

33
Q

fragile X and myotonic dystrophy

A

tandem repeats of nucleotides in untranslated region of FMR1 or DMPK

34
Q

trisomy 13

A

Patau syndrome

35
Q

trisomy 18

A

Edward syndrome

36
Q

trisomy 21

A

Down syndrome

37
Q

monosomy

A

missing copy of chromosome dur to nondisjunction

always lethal in autosomes

38
Q

mosaicism

A

embryonic cell loses third chromosome in setting of trisomy, forming a normal cell
other embryonic cells still trisomic –> mosaic nature of phenotype

39
Q

chromatin mutations

A

type of genome mutation

caused by changes in DNA methylation or histone protein modification

40
Q

DNA repair mechanisms

A 
base excision repair
nucleotide excision repair
non-homologous end joining
homologous end joining
strand-directed mismatch repair
proofreading by DNA polymerase

Biochemistry (7 decks)

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