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Molecular Biology > Molecular Basis of Mutation > Flashcards

Molecular Basis of Mutation Flashcards

1
Q

what is a mutation?

A

an alteration in the nucleotide sequence of a DNA molecule

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2
Q

what are the 2 ways mutation can occur?

A
  • errors in DNA replication (spontaneous mutations)

- caused by mutagens

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3
Q

why don’t mutations caused by errors in DNA replication happen often?

A

DNA polymerases proofreading properties

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4
Q

can mutations be caused by mistakes made by DNA polymerase?

A

yes

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5
Q

what’s base tauterism?

A

mutations caused by isomers of bases with slightly different chemical structures

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6
Q

how does base tauterism affect DNA?

A

affect the hydrogen bonds between base pairs, leading to incorrect bonding e.g. A-C

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7
Q

do amino- bases show normal base pairing?

A

yes

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8
Q

do keto- bases show normal base pairing?

A

yes

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9
Q

do imino- bases show normal base pairing?

A

no

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10
Q

do enol- bases show normal base pairing

A

no

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11
Q

what are mutagens?

A

chemical or environmental agents that cause changes in DNA molecules

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12
Q

what are the 2 important ways in which mutagens can cause mutations?

A
  • base analogs

- direct structural change

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13
Q

what’s a base analog?

A

a chemical that can substitute for a normal nucleobase in nucleic acids

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14
Q

what adds base analogs?

A

polymerase

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15
Q

what are direct structural changes?

A

when a physical component is added which changes the DNA

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16
Q

which is an important base analog?

A

5-bromouracil (5bU)

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17
Q

what is 5bU an analog of?

A

Thymine

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18
Q

what does keto-5bU pair with?

A

adenine

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19
Q

what’s the problem with 5bU?

A

the enol tautomer is very common and it pairs with G instead of T

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20
Q

what do deaminating agents do?

A

change the structures of some nucleotides by removing an Amine group

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21
Q

give 2 examples of deaminating agents

A
  • nitrous acid

- sodium bisulphite

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22
Q

what does deamination of adenine give?

A

hypoxanthine

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23
Q

what does hypoxanthine base pair with?

A

C (not T)

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24
Q

what does the deamination of cytosine give?

A

uracil

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25
Q

what does uracil base pair with? instead of?

A

A instead of G

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26
Q

what does the deamination of Guanine give?

A

xanthine

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27
Q

what does xanthine do?

A

blocks DNA replication

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28
Q

what are 2 other examples of agents causing structural changes to nucleotides?

A
  • alkylating agents (add alkyl groups)

- intercalating agents (insert between pase pairs)

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29
Q

give an example of an aklylating agent

A

ethylmethane sulphonate

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30
Q

give an example of an intercalating agent

A

ethidium bromide

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31
Q

what does ethidium bromide do?

A

causes errors during DNA replication e.g. polymerase adding in an additional base

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32
Q

what can Ultraviolet radiation do?

A

cause base dimerization

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33
Q

what is base dimerization?

A

where bases on the same strand join together

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34
Q

which dimers are particularly bad?

A

Thymine dimers

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35
Q

what can heat do?(2)

A

cause detachment of bases

can give rise to AP site

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36
Q

what’s an AP site?

A

apurine/apyrimidinic - leads to missing BP through the hydrolysis of B-N- glycosidic bond

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37
Q

what are the 4 types of mutation repair?

A
  • direct
  • excision
  • mismatch
  • nonhomologous end joining
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38
Q

what’s direct repair?

A

damaged nucleotide–> enzyme comes in –> changes it –> returns to correct nucleotide (rare)

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39
Q

what’s excision repair?

A

region around the damaged nucleotide is removed and then the region is resynthesized, damage on one but but template on other used for resynthesis

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40
Q

what’s mismatch repair?

A

the same as excision, except the damage is mismatched nucleotides base pairing

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41
Q

what’s nonhomologous and joining repair?

A

when a clear cut/clean break is in DNA e.g. by radiation or chemical. they are brought back together to give a correct sequence/ intact DNA

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42
Q

what sort of nucleotide alteration does direct repair correct?

A

alternation caused by mutagen

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43
Q

how common is direct repair?

A

quite uncommon

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44
Q

for each change in a nucleotide, what is needed in direct repair?

A

a specific enzyme

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45
Q

how many enzymes do humans have involved in direct repair?

A

12

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46
Q

what are the 2 types of excision repair?

A

base

nucleotide

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47
Q

what happens in base excision repair?

A

only the single, mutated base is removed and replaced

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48
Q

what happens in nucleotide excision repair?

A

a longer piece of DNA containing the altered bases is removed

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49
Q

what’s the mechanism of base- excision repair in E.coli?

A
  • begins with the removal of the damaged base by a DNA- glycosylase enzyme (breaks glycosidic bond)
  • resulting AP site is then filled in (enzymes remove sugar and replice the entire nucleotide- not just the base), gap filled in and phosphodiester bond is formed
50
Q

is nucleotide excision repair common?

A

yes

51
Q

what carries out nucleotide excision repair?

A

UvrABC endonuclease

52
Q

what’s the mechanism of nucleotide excision repair?

A
  • the damaged nucleotide causes helix distortion
  • this is detected by the endonuclease (A detects distortion, B binds to the damaged area), the endonuclease is now active
  • B subunit cuts downstream of damage and C subunit cuts upstream of damage
  • Helicase II removes this section
  • B subunit remains in the gap, protecting exposed DNA
  • new strand is synthesised and is ligated together
53
Q

what sort of errors does mismatch repair correct?

A

errors in replication

54
Q

how is the parent or daughter strand of DNA distinguished to find which contains the error?

A

the parent strand is methylated - in e.coli

55
Q

what recognises mismatch?

A

MutH and MutS enzymes

56
Q

what’s the mechanism of mismatch repair?

A 
MutS recognises the mismatched base and MutH binds upstream of the damage
MutH cleaves this section 
DNA helicase II removes this strands
strand now exposed 
strand repaired
57
Q

what’s the difference between endonucleases and exonucleases?

A

endonucleases go from the end

exonucleases go from the middle

58
Q

what does Nonhomologous end joining correct?

A

DNA breaks (complete cuts of both strands)

59
Q

in nonhomologous end joining what distinction is important?

A

the real breaks in DNA from the ends of chromosomes

60
Q

what distinguishes the real breaks from the ends of chromosomes?

A

telomeres mark the natural ends of chromosomes

61
Q

what’s the mechanism of nonhomologous end joining in humans?

A
  • double strand break
  • Ku proteins attach to both sides of break
  • they’re attracted to both ends of broken DNA and eachother
  • pull DNA back together
62
Q

what’s a point mutation?

A

when one base pair is replaced with another

63
Q

what’s a transition point mutation?

A

purine to purine/ pyrimidine to pyrimidine (same)

64
Q

what’s a transversion point mutation?

A

purine pyrimidine (different)

65
Q

what’s an insertion mutation?

A

where one or more base pairs are inserted

66
Q

what’s a deletion mutation?

A

one or more base pairs are deleted

67
Q

what’s an inversion mutation?

A

2+ base pairs are excised and reinserted in the opposite direction

68
Q

what’s a synonymous mutation?

A

where the point mutation has no effect on the amino acid sequence

69
Q

what’s a synonymous mutation AKA?

A

silent mutation

70
Q

what’s a non-synonymous mutation?

A

where a point mutation changes the AA sequence

71
Q

what’s a non-synonymous mutation AKA?

A

missense mutation

72
Q

what’s a nonsense mutation?

A

where a point mutation changes the AA into a stop codon

73
Q

what does the effect on a nonsense mutation depend on?

A

how far into the gene coding for a protein the stop codon occurs (worse if it’s found nearer the beginning)

74
Q

what’s a readthrough mutation?

A

where a point mutation changes a stop codon into an AA (causes longer proteins)

75
Q

what’s a frameshift mutation?

A

a change in the reading frame, all codons downstream of the mutation are changed

76
Q

how could an insertion/deletion not change the reading frame?

A

if a whole codon (3 bases) are inserted/deleted

77
Q

what’s the CFTR protein?

A

a chloride channel on the cell surface and is responsible for proper balance of salt and water within a cell

78
Q

what does a mutation in CFTR cause?

A

dysfunction in the salt and water balance leading to thick mucous and excessive loss of salt in sweat

79
Q

what’s the most common CFTR mutation in the UK?

A

F508 mutation

80
Q

what occurs in the F508 mutation?

A

deleltion of 3 nucleotides, removes a codon for phenylalanine
CFTR protein still made but doesn’t reach cell surface

81
Q

what’s the second most common CFTR mutation?

A

G542X mutation

82
Q

what occurs in the G542X mutation?

A

nonsense mutation changes glycine to stop codon

CFTR protein isn’t made

83
Q

what’s the 3rd most common CFTR mutation?

A

G551D

84
Q

what occurs in the G551D mutation?

A

a non- synonymous mutation changes a glycine (G) to an aspartic acid (D)
CFTR protein is made and reaches cell surface, however works at 4% the normal rate

85
Q

what’s a second site reversion?

A

another mutation restores the correct AA sequence

86
Q

what’s a supression?

A

a mutation in the tRNA genes supresses nonsense mutations in protein coding genes

87
Q

what is a phenotype?

A

biological characteristics

88
Q

what are most organisms, in terms of gene number?

A

diploid

89
Q

if there’s a mutation in one gene, does it always affect the genotype?

A

no- it could be recessive

90
Q

what’s haplosufficiency?

A

when a mutation in only one gene is all that’s required to cause disease

91
Q

give an example of haplosufficiency

A

Alagille syndrome

92
Q

what’s trisomy?

A

3 copies of a chromosome

93
Q

what causes down syndrome?

A

trisomy of chromosome 21

94
Q

what is monosomy also known as?

A

aneuploidy

95
Q

what does monosomy 7 lead to?

A

bone marrow failure –> high risk of leukemia

96
Q

what is chromosome translocation?

A

when part of one chromosome becomes attached to another chromosome

97
Q

what’s the Philadelphia chromosome a common cause of?

A

leukemia

98
Q

what happens in a philadelphia chromosome?

A

the control region of the gene for cell division is lost, therefore the gene is switched on all the time and cell division is uncontrolled

99
Q

what is molecular cloning?

A

cutting, joining and propagating recombinant DNA

100
Q

very generally, how does molecular cloning occur?

A
  • isolate DNA
  • cut DNA
  • insert into vector (recombinant)
  • introduce recombinant vector into bacteria
  • amplify recombinant growth
101
Q

what cuts/splices DNA?

A

restriction endonucleases

102
Q

what sort of sequence do restriction endonucleases cut?

A

palindromic sequences

103
Q

what do different restriction endonucleases have?

A

different sequence specificities

104
Q

what’s a palindromic sequence?

A

one where the complementary sequence is the same

105
Q

How is the DNA cut?

A

by restriction endonucleases
cut is staggered- cut at the same nucleotides on both sides but not parallel
this means that there’s an overhang- sticky end

106
Q

what 2 enzymes allow the cut DNA to join with bacterial vector?

A

ligase

photophatase

107
Q

what does phosphatase do?

A

allows a stable ligated molecule of recombinant plasmid

108
Q

what are DNA libraries?

A

isolation and separation of individual sequences within a cell

109
Q

what genes are found in a genomic library?

A

all (genome)

110
Q

what genes are found in the transcriptome/ DNA library?

A

only expressed genes

111
Q

what’s cDNA (complementary DNA)?

A
  • makes up the transcriptome
  • libraries from different tissues make up different sequences
  • no unsubscribed sequences
112
Q

what’s genomic DNA?

A
  • all sequences in genome
  • same sequences in all tissues
  • introns and exons
113
Q

what is the process of mRNA–> cDNA?

A

reverse transcription

114
Q

how is a cDNA library made?

A
  • isolate mRNA
  • convert to cDNA (reverse transcriptase)
  • insert into a vector and transform (into bacteria)
  • colonies of bacteria grow- 1 sequence per colony
115
Q

how is a Genome DNA library made?

A

isolate DNA
cut it up- restriction endonucleases
insert into vector
grow colonies- each colony has a different fragment of DNA to represent your genome

116
Q

is enhancer found in cDNA or genomic?

A

genomic

117
Q

is promoter found in cDNA or genomic?

A

genomic

118
Q

is 5’UTR found in cDNA or genomic?

A

both

119
Q

are exons found in cDNA or genomic?

A

both

120
Q

is 3’UTR found in cDNA or genomic?

A

both

121
Q

is intergenic DNA found in cDNA or genomic?

A

genomic

122
Q

are introns found in cDNA or genomic?

A

genomic

Molecular Biology (4 decks)

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