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Genetics 380 > DNA Mutation and Repair > Flashcards

DNA Mutation and Repair Flashcards

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1
Q

wild type sequence

A

most common (normal) seq; all changes in DNA base seq are referred to as mutations

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2
Q

mutations

A

helpful/neutral/detrimental, necessary for evolution, one mechanism whereby organisms acquire new characteristics

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3
Q

reverse mutation (reversion)

A

replaces original (forward) mutation & restores the wild type genotype and phenotype

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4
Q

suppressor muation

A

at another site but it compensates for the mutation & restore the wild type phenotype; can hide or suppress the effects of other mutations; ind is double mutant w normal phenotype

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5
Q

intragenic

A

w/i the same gene’s coding seq

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6
Q

intergenic

A

in second gene’s coding seq

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7
Q

germline mutations

A

present in either (or both) the sperm or the egg that made the ind therefore present in every cell the ind has

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8
Q

somatic mutations

A

arise after fertilization during cell replication/division/differentiation/migration therefore only present in a subset of the inds cells; arise in S phase gets passed down to 1/4th of the descendants of the original cell; occurred after fertilization and only existed in subset of parent’s cells

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9
Q

conditional mutation

A

only cause consequences under certain conditions

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10
Q

deletions & duplications

A

rand from single nucleotides to pieces of chromosome that are large enough to include many genes in them

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11
Q

inversion & translocations

A

rearrange large pieces of chromosomes

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12
Q

numerical abnormalities

A

entire chromosomes can be added or deleted

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13
Q

point mutation

A

substitution, deletion, or addition of single nucleotide

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14
Q

transition

A

purine-purine substitution or pyrimidine-pyrimidine substitution

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15
Q

transversion

A

purine-pyrimidine substitution or vise versa

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16
Q

missense mutation

A

single nucleotide substitution causes one amino acid to replace another

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17
Q

nonsense mutation

A

single nucleotide substitution creates STOP codon at site of mutation and truncates protein

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18
Q

silent muations

A

do not change organism’s phenotype

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19
Q

synonymous mutation

A

doesn’t change AA content of protein; may change splicing of mRNA

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20
Q

neutral mutation

A

changes AA content of protein but has no functional consequences

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21
Q

genetic code is degenerate

A

partially redundant

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22
Q

in-frame deletion or insertion

A

insertion/deletion involving multiple of 3 so it doesn’t shift the reading frame - AA seq will be normal before and after mutation

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23
Q

frame shift muation

A

insertion/deletion doesn’t involve multiple of 3 bases - reading frame of ribosome gets shifted; all AA after are abnormal

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24
Q

coding sequence mutation

A

change activity of each molecule of the protein

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25
Q

mutation in promoter & other regulatory seqs

A

affect rate at which gene makes its protein i.e. # of protein molecules in the body

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26
Q

trinucleotide repeats

A

3 bases get repeated w diff people having diff # of repeated units in string; found in coding regions & regulatory sequences; can expand during meiosis; larger repeated string gets = more it disrupts gene function; expansions are most common but sometimes repeat can contract; expand vs contract depends on parent of origin - more likely to contract during spermatogenesis than oogenesis; can cause strand slippage

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27
Q

fragile X syndrome

A

due to expanding CGG repeat in X chromosome (Xq28) of FMR1 gene which gets methylated - silencing the gene; FraX trinucleotide repeat can also contract during meiosis - more likely during spermatogenesis, asymptomatic males carrier pass repeat to daughters who may not be affected but will pass down to children which may be big enough to affect them

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28
Q

common fragile sites

A

all over the genome in everyone’s chromosomes - not associated w disease

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29
Q

rare fragile sites

A

associated w diseases ex: Fragile X syndrome - fragile site depicted here

30
Q

genetic anticipation

A

when repeat expands through meiosis subsequent generations are affected earlier and more severely than previous generation

31
Q

transposable elements (aka transposons)

A

move from one place to another w/i same cell’s DNA; “cut and paste” and leave or make copy of themselves and “copy and paste” themselves into another location; 45% of human genome comes from transposons; generate direct flanking repeats when they insert; can disrupt genes if inserted in gene’s regulatory seq but can jump back out & restore gene function

32
Q

inverted repeats

A

help transposable elements break out of their places

33
Q

transposase

A

enzyme that makes staggered cut in DNA; creates short single stranded overhangs that are complementary to each other; transposon inserts between ends of the cut; enables transpositions

34
Q

inverted terminal repeat

A

part of transposon

35
Q

direct flanking repeat

A

not part of the transposon - it is created as result of transposition process

36
Q

retrotransposons

A

use reverse transcription

37
Q

transposable element as activator

A

if it has seq capable of acting as promoter

38
Q

transposable element & chromosome rearrangements

A

can disrupt activity of genes

39
Q

cell methylation

A

methylates DNA in region of transposon which inhibits production of transposase

40
Q

interfering RNAs

A

used by cell to interrupt transposase production

41
Q

spontaneous mutations

A

errors during DNA replication; hydrolytic & other reactions can cause base change sin DNA after replicaiton

42
Q

induced mutations

A

environmental agents such as UV light or radon; chem exposures; metabolic by products such as superoxide ion O2-

43
Q

mutagens

A

agents that induce mutations

44
Q

wobble/non Watson-Crick basepairing

A

ability to pair w atypical base bc of shifts in arrangement of hydrogen bonds; leads to replication errors

45
Q

depurination

A

hydrolysis removes purine ring from adenine and guanines = results in mutation if not corrected quickly

46
Q

deamination

A

converts between pyrimidines by hydrolysis of NH2 group

47
Q

chemical mutagens

A

change # of H bonds the base makes

48
Q

5-Bromouracil

A

replaces A thymine but bonds w A guanine

49
Q

reactive oxygen species

A

oxidize guanine to 8-oxoguanine which pairs w/ A rather than C as G should; created by normal metabolism

50
Q

intercalating agents

A

insert themselves btwn nucleotides; inc distance btwn neighboring basepairs confusing DNA polymerase & causing insertion & deletions in DNA (ex: acridine orange, ethidium bromide)

51
Q

UV and ionizing radiation

A

break DNA strands; cause cells to form highly reactive free radicals = cause breaks in DNA = attempt to fix may result in mutations

52
Q

pyrimidine dimers

A

caused by sun’s UV rays; bonds form between neighboring Cs or Ts in same DNA strand preventing DNA rep; eukaryotes have special DNA polymerase eta that puts AA across pyrimidine dimer and restores DNA

53
Q

mismatch repair mechanism

A

repairs: replication errors, including mispaired bases and strand slippage

54
Q

direct repair mechanism

A

repairs: pyrimidine dimers, other specific types of alterations

55
Q

base excision repair mechanism

A

repairs: abnormal bases modified bases and pyrimidine dimers

56
Q

nucleotide excision repair mechanism

A

repairs: DNA damage that distorts that double helix, including abnormal bases, modified bases, and pyrimidine dimers

57
Q

direct repair

A

repaired directly by chemical reactions that restore the original base w/o removing anything ex: pyrimidine dimers

58
Q

photolyase

A

uses light E to break bonds in pyrimidine dimers which enables bases to make their proper bonds w their complementary bases again; direct repair

59
Q

06-methylguanine DNA methyltransferase

A

removes the methyl group if guanine gets methylated; direct repair

60
Q

base mismatches

A

repairs by base excision; mismatched bases forms bubbles in DNA double helix which are recognized by repair systems

61
Q

singe nucleotide damage (ex: deaminations)

A

repaired by base excision

62
Q

DNA polymerase beta

A

fills gap from base excision in eukaryotes; has no proofreading ability; 10 new mutations uncorrected per day: sometimes error leaves DNA ligase unable to seal gap; AP endonuclease comes in

63
Q

AP endonuclease

A

returns and excises nucleotide allowing DNA polymerase beta another chance to put the right nucleotide in

64
Q

nucleotide excision repair

A
  1. recognize problem 2. remove bad nucleotide(s) 3. replace w proper nucleotide(s) 4. seal w DNA ligase
65
Q

methylation

A

differentiates old DNA strand from new one

66
Q

DNA damage bypass

A

DNA polymerase fills in 2nd gap created by excision; newly synthesized strand is available as template

67
Q

non homologous end joining

A

repair double stranded breaks; ends join back together results in deletion in the chromosome

68
Q

homology-direct repair (HDR)

A

repairs double stranded breaks; two types; homologous chromosome used as template to fill gap on one of the broken strands

69
Q

non crossover synthesis dependent strand annealing (SDSA)

A

repairs double stranded breaks; gap in other strand is filled using newly repairs strand as template

70
Q

double strand break repair (DSBR)

A

gap in other strand is filled using other strand of homologous chromosome as template

Genetics 380 (11 decks)

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