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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
What is the difference between 2-aminopurine or 2AP and adenine
2AP: amino group at 2 adenine: carbon at 2
26
mutagenic base analog: 5-bromouracil is the analog to
thymidine
27
Diference between 5-bromouracil and thymidine
5-bromouracil: bromine at 5 | thymidine: methyl at 5
28
what does the bromo group do to 5-bromouracil
- keto group on carbon 4 switches between enol and keto state
29
what does 5'-bromouracil pair with in keto state and enol state
keto: adenine (correct) enol: guanine
30
the common mutagen for deamination is
nitrous acid
31
deamination of adenine
produces hypoxanthine | pairs cystine instead of thymidine
32
deamination of cytosine
produces uracil | pairs with adenine instead of guanine
33
deamination of guanine
produces xanthine | benign modification because it pairs with cytosine
34
in DNA methylation what is the target nucleotide base
cytosine
35
why do bacterial cells have DNA methylation
helps host distinguish own DNA from foreign DNA
36
why do eukorytoic cells have DNA methylation
key role in gene silencing
37
due to DNA methylation, deamination of 5-methylcytosine produces what? what is significant about this
normal base thymidine | little change to DNA, hard to detect
38
base modification: Name 2 alkylation agents
ethyl methanesulfonate | nitrosoguandine (NTG)
39
what products does nitrosoguanidine (NTG) make? and what nucleotide bases do they pair with
O6-methyl-Guanine - pairs with T | O4-methyl thymidine - pairs with G
40
why is nitrosoguanidine (NTG) very mutagenic
hard to detect since there are subtle DNA distortion
41
what can induce reactive oxygen
UV X-ray paraquat (herbicide)
42
what is the most mutagenic lesion caused by reactive oxygen? what does it pair with
8-oxo guanine | pairs with A instead of C
43
What do intercalators do? what do they cause?
slide between base pairs of DNA helix | cause insertion or deletion mutations
44
give 3 examples of intercalators
ethidium bromide acridine orange dyes notorious aflatoxins
45
what is ethidium bromide used for in microbiology labds
detecting DNA
46
how are aflatoxins produced
mold on peanuts, tree nuts, corns
47
what can modify aflatoxins to make a reactive epoxide moiety
cytochrome p450
48
epoxide moiety from the aflatoxins form with what to cause what
N-7 of guanosine | G:C --> T:A
49
a very important mutation caused by deamination is the what mutation
C -->T
50
photoreactivation repairs what
cyclobutane pyrimidine dimmers caused by UV radiation
51
what enzyme is responsible for photoreactivation
photopyase
52
what organisms have photoreactivation
all
53
After photolyase binds to pyrimidine dimers what happens next
FADH absorbs energy from live | energy activates photolyase - cuts and fuses DNA
54
what does nucleotide excision or UvrABC endonuclease pathway do
cuts damaged nucleotides off the DNA
55
How does nucleotide excision or UvrABC endonuclease work
- 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
UvrD is what type of molecue
DNA helicase
57
for cells not receiving UV irradation, the expression of UmuC and UmuD are inhibited by what? where does it attach
LexA protein dimer | operator upstream of the UmuC and UmuD genes
58
What domains does LexA have
one for dimmerization | one for DNA binding
59
when can LexA protein dimer bind DNA
only when LexA is dimmerized
60
what genes are used in the SOS inducible repair system
UmuC | UmuD
61
what happens when ssDNA get UV radaition
ssDNA binds to RecA RecA bind LexA LexA autocleaved - lifts suppression off of UmuC and UmuD
62
UmuC and UmuD bind to what and allows for what
DNA polymerase II | allows DNA polymerase III to bypass damaged nucleotides to replicate DNA
63
What is the downfall of SOS inducible repair system
many mistakes in daughter DNA
64
Another name for SOS inducible repair system
error prone repair | mutagenic repair
65
homologous recombination
exchanging DNA sequences between 2 homologous DNA molecules
66
Most bacteria genome is what
haploid
67
the partial diploid in bacteria is called
merodiploid
68
how does bacteria have merodiploids
bacteria accepts DNA from other bacteria cells
69
what are 3 types of genetic exchange in bacteria
transduction conjugation transformation
70
what are the 3 steps in homologous recombination
1. generation of single-stranded free 3' end 2. invade homologous DNA duplex (holiday junction) 3. resolve holiday junction
71
what is the outcome of homologous recombination
recombinant genotypes | gene conversion
72
nonhomologous recombination: transposons
DNA elements that hop from one location in DNA to another
73
homing DNA
encode some RNA introns or protein intron | -not transposons
74
Retrotransposons
have RNA intermediate | -not transposons
75
what are 3 types of transposons
insertion sequence elements (IS element) complex composite transposons T2A family
76
IS element contains what
gene for transposition
77
The IS element have what type of repeats
inverted
78
Outside the IS element has what kind of repeats
direct repeat sequence of host DNA
79
Complex transposons, what is in central region
gene for antibiotic resistance
80
what is the central region surrounded by in complex transposons? direction
insertion sequence elements | -can be in same or opposite direction
81
T2A family of transposons (Tn3): what type of repeats are at the end
inverted
82
T2A family of transposons (Tn3): contains what gene
for transposase resolution site gene for antibiotic resistance
83
what do resolution site and resolvase mediate
site specific recombination during the transposition of transposons
84
TnA family transposons are transposed by
replicative transposition
85
How does IS and composite transposons move and integrate to a different site
nonreplicative | cut-and-paste mechanism for transpositition
86
explain replicative transposition
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
consequences of transposition
1. inactivate gene 2. activate quiescent gene 3. insert SI element next to drug resistance gnen 4. portable regions for homologous recombination
88
site-specific recombination
non-homolgous recombination between 2 specific sites in DNA
89
site-specific recombination: recombination between 2 direct repeats does what to DNA
delete DNA sequence between them
90
site-specific recombination: recombination between 2 inverted repeats does what to DNA
invert DNA sequence between them
91
site of specific recombination is mediated by what
site-specific recombinases
92
site-specific recombinases recognizes what 3 sites
resolves integrase invertase
93
integrase
integration of phage DNA into bacterial host DNA
94
in salmonella what is phase variation
bacteria expresses Flagellin H1 protein then switch to Flagellin H2
95
how does salmonella do phase variation
H2 promoter next to H2 gene | -acitvates H2/represses H1
96
what is the target site for Hin invertase? what is the repeat like
Hin experssion casette H2 promotor inverted repeats
97
what does Hin invertase do?
mediates site specific recombinant between the inverted repeats - H2 promoter separated from H2 protein - H1 expressed
98
during salmonella, does the Hin promoter get moved away from Hin gene
no
99
phase variation of fimbria synthesis/tail fiber protein synthesis
allows bacteria/bacteriophages to attach to different types of eukarytoic cell

POD Exam 1 (17 decks)

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