Mutation and Recombination Flashcards
Bacterial evolution follows what rule
Darwin’s natural selection theory
mutation of the resistance occurs in the bacteria independently of what
antibiotics
what role does antibiotics play in bacterial reistance
environmental factor that selects the mutation
name 2 ways large amounts of antibiotics are released to the envirnment
- animal feeding
2. inappropriate medical use
When animal was sick, why would the farmer give antibiotic
prevent spread of animal’s infection
Why do farmer’s today use antibiotics on all their animals
accelerate their growth
name 4 molecular changes of bacteria
- mutation
- recombination
- bacteriaphage
- genetic exchange
how can mutations be classified
nucleotide replacement
mutation
insertions and deletions
what are types of nucleotide replacement mutations
silent
missense
nonsense mutation
silent mutation
does not have any phenotypic consequence
doesn’t change amino acid sequence of protein
missense mutation
change amino acid that changes sequence to make a different amino acid
nonsense mutation
generates a premature stop codon
in-frame insertion mutation
insertion of extra amino acid sequence to protein
in-frame deletion mutation
deletion of segment of amino acid sequence in a protein
out-of-frame insertion or deletion
frame-shift mutation
how can DNA replication mutate DNA
spontaneous mutation
name 2 ways DNA itself can be damaged or mutated
exposure to radiation (UV and X-ray)
chemical mutagenesis
name 2 direct effects of UV light
- induce 2 kinds of pyrimidine dimmers
2. cross-linking of any sugar and base that are close to each other
when UV induces 2 kinds of pyrimidine dimers, which ones
5,6 cyclobutane pyrimidine dimmers
6-4 photoproduct
how does UV indirectly mutate DNA
induce reactive oxygen, which is highly mutagenic
what can X-ray cause
break backbone of phosphodiester bond of DNA, causes deletions
what are 3 types of chemical mutagenesis
base analogs
base modifiers
intercalators
mutagenic base analog: 2-aminopurine or 2AP is the analog to what amino acid?
adenine
mutagenic base analog: 2-aminopurine or 2AP pairs with what nucleotide in DNA base pairing. what should it be paring with
cystosine
thymidine
What is the difference between 2-aminopurine or 2AP and adenine
2AP: amino group at 2
adenine: carbon at 2
mutagenic base analog: 5-bromouracil is the analog to
thymidine
Diference between 5-bromouracil and thymidine
5-bromouracil: bromine at 5
thymidine: methyl at 5
what does the bromo group do to 5-bromouracil
- keto group on carbon 4 switches between enol and keto state
what does 5’-bromouracil pair with in keto state and enol state
keto: adenine (correct)
enol: guanine
the common mutagen for deamination is
nitrous acid
deamination of adenine
produces hypoxanthine
pairs cystine instead of thymidine
deamination of cytosine
produces uracil
pairs with adenine instead of guanine
deamination of guanine
produces xanthine
benign modification because it pairs with cytosine
in DNA methylation what is the target nucleotide base
cytosine
why do bacterial cells have DNA methylation
helps host distinguish own DNA from foreign DNA
why do eukorytoic cells have DNA methylation
key role in gene silencing
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
base modification: Name 2 alkylation agents
ethyl methanesulfonate
nitrosoguandine (NTG)
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
why is nitrosoguanidine (NTG) very mutagenic
hard to detect since there are subtle DNA distortion
what can induce reactive oxygen
UV
X-ray
paraquat (herbicide)
what is the most mutagenic lesion caused by reactive oxygen? what does it pair with
8-oxo guanine
pairs with A instead of C
What do intercalators do? what do they cause?
slide between base pairs of DNA helix
cause insertion or deletion mutations
give 3 examples of intercalators
ethidium bromide
acridine orange dyes
notorious aflatoxins
what is ethidium bromide used for in microbiology labds
detecting DNA
how are aflatoxins produced
mold on peanuts, tree nuts, corns
what can modify aflatoxins to make a reactive epoxide moiety
cytochrome p450
epoxide moiety from the aflatoxins form with what to cause what
N-7 of guanosine
G:C –> T:A
a very important mutation caused by deamination is the what mutation
C –>T
photoreactivation repairs what
cyclobutane pyrimidine dimmers caused by UV radiation
what enzyme is responsible for photoreactivation
photopyase
what organisms have photoreactivation
all
After photolyase binds to pyrimidine dimers what happens next
FADH absorbs energy from live
energy activates photolyase - cuts and fuses DNA
what does nucleotide excision or UvrABC endonuclease pathway do
cuts damaged nucleotides off the DNA
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
UvrD is what type of molecue
DNA helicase
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
What domains does LexA have
one for dimmerization
one for DNA binding
when can LexA protein dimer bind DNA
only when LexA is dimmerized
what genes are used in the SOS inducible repair system
UmuC
UmuD
what happens when ssDNA get UV radaition
ssDNA binds to RecA
RecA bind LexA
LexA autocleaved
- lifts suppression off of UmuC and UmuD
UmuC and UmuD bind to what and allows for what
DNA polymerase II
allows DNA polymerase III to bypass damaged nucleotides to replicate DNA
What is the downfall of SOS inducible repair system
many mistakes in daughter DNA
Another name for SOS inducible repair system
error prone repair
mutagenic repair
homologous recombination
exchanging DNA sequences between 2 homologous DNA molecules
Most bacteria genome is what
haploid
the partial diploid in bacteria is called
merodiploid
how does bacteria have merodiploids
bacteria accepts DNA from other bacteria cells
what are 3 types of genetic exchange in bacteria
transduction
conjugation
transformation
what are the 3 steps in homologous recombination
- generation of single-stranded free 3’ end
- invade homologous DNA duplex (holiday junction)
- resolve holiday junction
what is the outcome of homologous recombination
recombinant genotypes
gene conversion
nonhomologous recombination: transposons
DNA elements that hop from one location in DNA to another
homing DNA
encode some RNA introns or protein intron
-not transposons
Retrotransposons
have RNA intermediate
-not transposons
what are 3 types of transposons
insertion sequence elements (IS element)
complex composite transposons
T2A family
IS element contains what
gene for transposition
The IS element have what type of repeats
inverted
Outside the IS element has what kind of repeats
direct repeat sequence of host DNA
Complex transposons, what is in central region
gene for antibiotic resistance
what is the central region surrounded by in complex transposons? direction
insertion sequence elements
-can be in same or opposite direction
T2A family of transposons (Tn3): what type of repeats are at the end
inverted
T2A family of transposons (Tn3): contains what gene
for transposase
resolution site
gene for antibiotic resistance
what do resolution site and resolvase mediate
site specific recombination during the transposition of transposons
TnA family transposons are transposed by
replicative transposition
How does IS and composite transposons move and integrate to a different site
nonreplicative
cut-and-paste mechanism for transpositition
explain replicative transposition
- cut transposon out of donor
- reconnect transposon at target
- replicate transposon
- both copies line up @ resolution site
- resolvase - site specific recombination between res sites
- release 1 copy back to donw
consequences of transposition
- inactivate gene
- activate quiescent gene
- insert SI element next to drug resistance gnen
- portable regions for homologous recombination
site-specific recombination
non-homolgous recombination between 2 specific sites in DNA
site-specific recombination: recombination between 2 direct repeats does what to DNA
delete DNA sequence between them
site-specific recombination: recombination between 2 inverted repeats does what to DNA
invert DNA sequence between them
site of specific recombination is mediated by what
site-specific recombinases
site-specific recombinases recognizes what 3 sites
resolves
integrase
invertase
integrase
integration of phage DNA into bacterial host DNA
in salmonella what is phase variation
bacteria expresses Flagellin H1 protein then switch to Flagellin H2
how does salmonella do phase variation
H2 promoter next to H2 gene
-acitvates H2/represses H1
what is the target site for Hin invertase? what is the repeat like
Hin experssion casette
H2 promotor
inverted repeats
what does Hin invertase do?
mediates site specific recombinant between the inverted repeats
- H2 promoter separated from H2 protein
- H1 expressed
during salmonella, does the Hin promoter get moved away from Hin gene
no
phase variation of fimbria synthesis/tail fiber protein synthesis
allows bacteria/bacteriophages to attach to different types of eukarytoic cell
