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POD Exam 1 > Mutation and Recombination > Flashcards

Mutation and Recombination Flashcards

1
Q

Bacterial evolution follows what rule

A

Darwin’s natural selection theory

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2
Q

mutation of the resistance occurs in the bacteria independently of what

A

antibiotics

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3
Q

what role does antibiotics play in bacterial reistance

A

environmental factor that selects the mutation

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4
Q

name 2 ways large amounts of antibiotics are released to the envirnment

A
  1. animal feeding

2. inappropriate medical use

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5
Q

When animal was sick, why would the farmer give antibiotic

A

prevent spread of animal’s infection

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6
Q

Why do farmer’s today use antibiotics on all their animals

A

accelerate their growth

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7
Q

name 4 molecular changes of bacteria

A
  1. mutation
  2. recombination
  3. bacteriaphage
  4. genetic exchange
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8
Q

how can mutations be classified

A

nucleotide replacement
mutation
insertions and deletions

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9
Q

what are types of nucleotide replacement mutations

A

silent
missense
nonsense mutation

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10
Q

silent mutation

A

does not have any phenotypic consequence

doesn’t change amino acid sequence of protein

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11
Q

missense mutation

A

change amino acid that changes sequence to make a different amino acid

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12
Q

nonsense mutation

A

generates a premature stop codon

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13
Q

in-frame insertion mutation

A

insertion of extra amino acid sequence to protein

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14
Q

in-frame deletion mutation

A

deletion of segment of amino acid sequence in a protein

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15
Q

out-of-frame insertion or deletion

A

frame-shift mutation

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16
Q

how can DNA replication mutate DNA

A

spontaneous mutation

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17
Q

name 2 ways DNA itself can be damaged or mutated

A

exposure to radiation (UV and X-ray)

chemical mutagenesis

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18
Q

name 2 direct effects of UV light

A
  1. induce 2 kinds of pyrimidine dimmers

2. cross-linking of any sugar and base that are close to each other

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19
Q

when UV induces 2 kinds of pyrimidine dimers, which ones

A

5,6 cyclobutane pyrimidine dimmers

6-4 photoproduct

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20
Q

how does UV indirectly mutate DNA

A

induce reactive oxygen, which is highly mutagenic

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21
Q

what can X-ray cause

A

break backbone of phosphodiester bond of DNA, causes deletions

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22
Q

what are 3 types of chemical mutagenesis

A

base analogs
base modifiers
intercalators

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23
Q

mutagenic base analog: 2-aminopurine or 2AP is the analog to what amino acid?

A

adenine

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24
Q

mutagenic base analog: 2-aminopurine or 2AP pairs with what nucleotide in DNA base pairing. what should it be paring with

A

cystosine

thymidine

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25
Q

What is the difference between 2-aminopurine or 2AP and adenine

A

2AP: amino group at 2
adenine: carbon at 2

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26
Q

mutagenic base analog: 5-bromouracil is the analog to

A

thymidine

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27
Q

Diference between 5-bromouracil and thymidine

A

5-bromouracil: bromine at 5

thymidine: methyl at 5

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28
Q

what does the bromo group do to 5-bromouracil

A
  • keto group on carbon 4 switches between enol and keto state
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29
Q

what does 5’-bromouracil pair with in keto state and enol state

A

keto: adenine (correct)
enol: guanine

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30
Q

the common mutagen for deamination is

A

nitrous acid

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31
Q

deamination of adenine

A

produces hypoxanthine

pairs cystine instead of thymidine

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32
Q

deamination of cytosine

A

produces uracil

pairs with adenine instead of guanine

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33
Q

deamination of guanine

A

produces xanthine

benign modification because it pairs with cytosine

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34
Q

in DNA methylation what is the target nucleotide base

A

cytosine

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35
Q

why do bacterial cells have DNA methylation

A

helps host distinguish own DNA from foreign DNA

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36
Q

why do eukorytoic cells have DNA methylation

A

key role in gene silencing

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37
Q

due to DNA methylation, deamination of 5-methylcytosine produces what? what is significant about this

A

normal base thymidine

little change to DNA, hard to detect

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38
Q

base modification: Name 2 alkylation agents

A

ethyl methanesulfonate

nitrosoguandine (NTG)

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39
Q

what products does nitrosoguanidine (NTG) make? and what nucleotide bases do they pair with

A

O6-methyl-Guanine - pairs with T

O4-methyl thymidine - pairs with G

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40
Q

why is nitrosoguanidine (NTG) very mutagenic

A

hard to detect since there are subtle DNA distortion

41
Q

what can induce reactive oxygen

A

UV
X-ray
paraquat (herbicide)

42
Q

what is the most mutagenic lesion caused by reactive oxygen? what does it pair with

A

8-oxo guanine

pairs with A instead of C

43
Q

What do intercalators do? what do they cause?

A

slide between base pairs of DNA helix

cause insertion or deletion mutations

44
Q

give 3 examples of intercalators

A

ethidium bromide
acridine orange dyes
notorious aflatoxins

45
Q

what is ethidium bromide used for in microbiology labds

A

detecting DNA

46
Q

how are aflatoxins produced

A

mold on peanuts, tree nuts, corns

47
Q

what can modify aflatoxins to make a reactive epoxide moiety

A

cytochrome p450

48
Q

epoxide moiety from the aflatoxins form with what to cause what

A

N-7 of guanosine

G:C –> T:A

49
Q

a very important mutation caused by deamination is the what mutation

A

C –>T

50
Q

photoreactivation repairs what

A

cyclobutane pyrimidine dimmers caused by UV radiation

51
Q

what enzyme is responsible for photoreactivation

A

photopyase

52
Q

what organisms have photoreactivation

A

all

53
Q

After photolyase binds to pyrimidine dimers what happens next

A

FADH absorbs energy from live

energy activates photolyase - cuts and fuses DNA

54
Q

what does nucleotide excision or UvrABC endonuclease pathway do

A

cuts damaged nucleotides off the DNA

55
Q

How does nucleotide excision or UvrABC endonuclease work

A
  • 2 UvrA and 1 UvrB - looks for damages on DNA
  • finds damage, UvrA leaves
  • UvrC binds UvrB
  • UvrC endonuclease cuts upstream
  • UvrB endonuclease cuts downstream
  • UvrD separates damaged DNA
  • DNA polymerase I - resynthesize gap
  • DNA ligase - reconnects
56
Q

UvrD is what type of molecue

A

DNA helicase

57
Q

for cells not receiving UV irradation, the expression of UmuC and UmuD are inhibited by what? where does it attach

A

LexA protein dimer

operator upstream of the UmuC and UmuD genes

58
Q

What domains does LexA have

A

one for dimmerization

one for DNA binding

59
Q

when can LexA protein dimer bind DNA

A

only when LexA is dimmerized

60
Q

what genes are used in the SOS inducible repair system

A

UmuC

UmuD

61
Q

what happens when ssDNA get UV radaition

A

ssDNA binds to RecA
RecA bind LexA
LexA autocleaved
- lifts suppression off of UmuC and UmuD

62
Q

UmuC and UmuD bind to what and allows for what

A

DNA polymerase II

allows DNA polymerase III to bypass damaged nucleotides to replicate DNA

63
Q

What is the downfall of SOS inducible repair system

A

many mistakes in daughter DNA

64
Q

Another name for SOS inducible repair system

A

error prone repair

mutagenic repair

65
Q

homologous recombination

A

exchanging DNA sequences between 2 homologous DNA molecules

66
Q

Most bacteria genome is what

A

haploid

67
Q

the partial diploid in bacteria is called

A

merodiploid

68
Q

how does bacteria have merodiploids

A

bacteria accepts DNA from other bacteria cells

69
Q

what are 3 types of genetic exchange in bacteria

A

transduction
conjugation
transformation

70
Q

what are the 3 steps in homologous recombination

A
  1. generation of single-stranded free 3’ end
  2. invade homologous DNA duplex (holiday junction)
  3. resolve holiday junction
71
Q

what is the outcome of homologous recombination

A

recombinant genotypes

gene conversion

72
Q

nonhomologous recombination: transposons

A

DNA elements that hop from one location in DNA to another

73
Q

homing DNA

A

encode some RNA introns or protein intron

-not transposons

74
Q

Retrotransposons

A

have RNA intermediate

-not transposons

75
Q

what are 3 types of transposons

A

insertion sequence elements (IS element)
complex composite transposons
T2A family

76
Q

IS element contains what

A

gene for transposition

77
Q

The IS element have what type of repeats

A

inverted

78
Q

Outside the IS element has what kind of repeats

A

direct repeat sequence of host DNA

79
Q

Complex transposons, what is in central region

A

gene for antibiotic resistance

80
Q

what is the central region surrounded by in complex transposons? direction

A

insertion sequence elements

-can be in same or opposite direction

81
Q

T2A family of transposons (Tn3): what type of repeats are at the end

A

inverted

82
Q

T2A family of transposons (Tn3): contains what gene

A

for transposase
resolution site
gene for antibiotic resistance

83
Q

what do resolution site and resolvase mediate

A

site specific recombination during the transposition of transposons

84
Q

TnA family transposons are transposed by

A

replicative transposition

85
Q

How does IS and composite transposons move and integrate to a different site

A

nonreplicative

cut-and-paste mechanism for transpositition

86
Q

explain replicative transposition

A
  1. cut transposon out of donor
  2. reconnect transposon at target
  3. replicate transposon
  4. both copies line up @ resolution site
  5. resolvase - site specific recombination between res sites
  6. release 1 copy back to donw
87
Q

consequences of transposition

A
  1. inactivate gene
  2. activate quiescent gene
  3. insert SI element next to drug resistance gnen
  4. portable regions for homologous recombination
88
Q

site-specific recombination

A

non-homolgous recombination between 2 specific sites in DNA

89
Q

site-specific recombination: recombination between 2 direct repeats does what to DNA

A

delete DNA sequence between them

90
Q

site-specific recombination: recombination between 2 inverted repeats does what to DNA

A

invert DNA sequence between them

91
Q

site of specific recombination is mediated by what

A

site-specific recombinases

92
Q

site-specific recombinases recognizes what 3 sites

A

resolves
integrase
invertase

93
Q

integrase

A

integration of phage DNA into bacterial host DNA

94
Q

in salmonella what is phase variation

A

bacteria expresses Flagellin H1 protein then switch to Flagellin H2

95
Q

how does salmonella do phase variation

A

H2 promoter next to H2 gene

-acitvates H2/represses H1

96
Q

what is the target site for Hin invertase? what is the repeat like

A

Hin experssion casette
H2 promotor
inverted repeats

97
Q

what does Hin invertase do?

A

mediates site specific recombinant between the inverted repeats

  • H2 promoter separated from H2 protein
  • H1 expressed
98
Q

during salmonella, does the Hin promoter get moved away from Hin gene

A

no

99
Q

phase variation of fimbria synthesis/tail fiber protein synthesis

A

allows bacteria/bacteriophages to attach to different types of eukarytoic cell

POD Exam 1 (17 decks)

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