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Immunology > Bacterial Genetics > Flashcards

Bacterial Genetics Flashcards

1
Q

how can bacteria transfer info horizaontally

A

to another bactiera - end up with recombinant cell

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2
Q

bacteria can harbor genes on extra chromosomal elements called

A

plasmids

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3
Q

describe plasmids

A

much smaller than chromosome

encodes up to 100 genes

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4
Q

holoenzyme =

A

RNAP + Sigma factor

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5
Q

what does RNAP stand for

A

RNA polymerase

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6
Q

there are receptors that bind what during translation

A

N-formyl methionine (fMet)

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7
Q

operon concept

A

wasteful to produce enzymes if there is nothing for enzymes to work on. in operon they will be induced when needed or enzymes repressed when not needed

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8
Q

quorum sensing

A

Ability to establish cell-to-cell communication
Important for survival
e.g. biofilm production

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9
Q

draw organization of lac operon in e. coli

A

pg 7

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10
Q

gene that will encode repressor in lac operon

A

LacI

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11
Q

polycistornic mRNA

A

very long single RNA in lac operon

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12
Q

if lactose isn’t present, repressor protein does what

A

binds to operator site

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13
Q

if there is no lactose present was does RNA pol do

A

it can still bind to promoter but respresor is on operator so it doesn’t transcribe

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14
Q

when lactose is present

A

lactose binds to repressor so repressor can’t bind to operator site so RNA polymerase can ranscribe

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15
Q

quorum sensing

A

inductoin of gene expression in response to critical gene desnity

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16
Q

what is exxample of genes that are used with quorum sensing

A

biofilm

toxin genes

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17
Q

apathogenetic state regarding quarum sensing

A

QS regulated genes not on

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18
Q

as population of bacteria increases what stage

A

sufficient concentration of inducers and critical mass of baceria able to respond to inducers

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19
Q

what do inducers do

A

bind to receptor complex and turn on transcription of the regulated gene

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20
Q

what will the binding of inducer do

A

virulence gene - changes it from being harmless to being harmful

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21
Q

what is biofilm

A

mucopolysacharide layer that provide protection against
Phagocytosis
Dehydration
Antibiotic penetration

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22
Q

antigenic variation in regards to immunology

A

can give bacteria an advantage, can help them invade ongoing immune response
if bacteria can alter its structure the immunes systems antibiotic resistance may not longer be effective

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23
Q

genetic diversity allows bacteria to

A

have advantage if enviornment changes

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24
Q

name one way diversity helps bacteria

A

antibiotics - can aquire antibiotic resistance genes

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25
Q

four main mechanisms for gene transfer

A

Transposition, Transformation, Transduction, Conjugation

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26
Q

flagella are targets of what

why is this important

A

antibodies

salmonella (or other bacteria) can turn off gene that makes flagella to evade antibiotic response

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27
Q

how do flagella give bacteria advantage

A

allows them to invade

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28
Q

in some cases antibiotic resistance is due to mutation in

A

chromosome

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29
Q

what is another qy antibiotic resistance can happen

A

acquisition of mobile genetic elements:
plasmid
transpoon

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30
Q

plasmids usually encode

A

enzymes to degrade antibiotics

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31
Q

transposon

A

move pieces of DNA within the chrom. or from a plasmid

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32
Q

in many caese the DNA aquired by bacteria via horizontal gene transfer has to be

A

stabiized or else it will bedegraded

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33
Q

what are 2 mechanisms of recombination for bacteria to stabilize

A

homologous

non-homologous

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34
Q

homologous DNA recombination

A

Involves major bacterial DNA repair process (requires recombination enzymes (RecA))

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35
Q

dna recombined via homologous is usually

A

sort, linear pieces fo DNA

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36
Q

what does hologous DNA recombination require

A

substantial sequence homology between transferred DNA and target site

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37
Q

what will usually happen with homologous recombination

A

gene replacement

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38
Q

is all DNA uptaken in homologous recombination

A

no - the stuff taht isn’t is degraded

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39
Q

site specific recombination is also called

A

illegitimate or non-homologous recombination

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40
Q

what is requirement for site-specific recmobination

A

Requires only a small region of homology between transferred DNA and target site

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41
Q

foreign DNA in site-specific recombination is:

A

circular plasmid, phage, transposons

Requires restriction endonucleases (site-specific recombinases)

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42
Q

how are transposons integraded

A

site-specific recomination

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43
Q

what does site specific recombination result in

A

integraded DNA - all is taken up nothign is lost

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44
Q

is all DNA integrated in homologous recombination

A

no some is loss, what isn’t taken up is degraded

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45
Q

temperate phages integrate

A

dna into chromosome of cell that they infect

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46
Q

draw example of site-specific recombination and the steps

A

pg 19

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47
Q

what is result of site-specific recombination

A

gene insertion

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48
Q

what are four main mechanisms of gene transfer

A

transposition
transformation
conjugation
transduction

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49
Q

transposition is mediated by

A

transposons “jumping genes”

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50
Q

transposons

A

can jump to different genes and plasmids

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51
Q

transofmration

A

uptake of “naked” DNA

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52
Q

conjugation

A

one bacteria to another following cell-cell contact

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53
Q

two type of conjugation

A

transfer via what is on plasmid

transfer bacterial chromosomal change

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54
Q

transduction

A

mediated by bacterial phages

some of the phages make mistake and package wrong DNA

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55
Q

avirulent bacteria can be conferted to

A

virulent bacteria

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56
Q

what si the significance of gene transfer (one significance)

A

converstion to virulence

presentation of disease

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57
Q

what are common places converstion will take place that would cause virulence

A

pilli - promote adherance
toxins
enzymes that degrade basement membranes

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58
Q

transposons are flakned by

A

intdirect repeats

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59
Q

indirect repeats

A

sequence of nucleotides followed by that sequence in reverse

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60
Q

how can you get mutation due to transposon

A

b/c they insert themsef into genetic info, can cause mutation

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61
Q

PAI stand for

A

pathogenicity islands

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62
Q

PAi

A

find direct repeats, indicating there are transposons
they often contain virulence factors
they can be mobilized from one bacteria to another

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63
Q

examples of PAI

A

toxins
adhesins
antibiotic resistance genes

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64
Q

describe some properties of transposon

A
  1. Random movement: Transposable genetic elements can move from any DNA molecule to other DNA molecules. The movement is not totally random; there are preferred sites in a DNA molecule at which the transposable genetic element will insert.
  2. Not capable of self replication: The transposable genetic elements do not exist autonomously and thus, to be replicated they must be a part of some other replicon.
  3. Transposition mediated by site-specific recombination: Transposition requires little sequence homology. Transposition is mediated by an enzyme transposase that is encoded by the transposon.
  4. Transposition can be accompanied by duplication: For some transposons, transposition results in removal of the transposon from the original site and insertion at a new site. For other transposons, transposition is accompanied by the duplication of the transposon with one copy remaining at the original site and the other transposed to a new site.
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65
Q

what are the two methods of transposons

A

cut and paste

copy and paste

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66
Q

describe cut and paste and copy and paste of transposons

A

pg 26

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67
Q

transformation

A

Most important mechanism of
genetic exchange in gram
positive microorganisms
such as Streptococcus pneumoniae

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68
Q

to be able to take up DNA from enviornemtn bactiera has to be

A

competent

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69
Q

to become competent a bacteria has to be

A

stressed in some way

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70
Q

what is competence controlled by

A

competence factor (CF)

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71
Q

what does CF stand for

A

competence factor

72
Q

CF makes

A

gram positive bacteria capable of taking up DNA from enviornemnt

73
Q

what DNA is taken up by competenct bacteria

A

single strand

74
Q

dna plasmid can be taken up bia transofmration, does it require integration

A

no

75
Q

conjugation is most well studied in what kind of bacteria

A

most known in gram neg.

76
Q

conjugal plasmid encodes

A

fertility factor

77
Q

conjugal plasmid refered to

A

f factor

f factor plasmid

78
Q

to be donor bacterium have to have

A 
f pillus (sex pillus)
F posiive
79
Q

recepient has to have

A

NOT F pillus

is F negative

80
Q

there will only be conjugation b/w

A

f negative recipient

F positive donor

81
Q

conjugal plasmid has a number of important genes including

A

Tram operon
oriT
bacterial chromosome

82
Q

tra operon codes for

A

F pillus

83
Q

to be donor cell need what operon

A

tra

84
Q

where will be nicked for conjugation

A

Origin of transfer site

85
Q

what does Hfr stand for

A

high frequency recombinant

86
Q

f plasmid can also integrate by what

A

site specific recombination into bacterial chromosome

87
Q

when plasmid integrates via site specific recombination what is it called

A

Hfr cell

88
Q

Hfr will make (in conjugation)

A 
f pillus
(hfr is still donor cell)
89
Q

draw F factor plasmid and all components

A

pg 30

90
Q

what is considered male in bacteria

A

has f pilus

91
Q

draw out a F+ and F- cross

A

pg 31

92
Q

what kind of cleavage in conjugation

A

single strand

so both stands have conjugal plasmid and then both cells will be F+

93
Q

aquisition of conjugal plasmid is called

A

conjugation

94
Q

if there is no selective pressure for maintaining plasmid

A

they will get rid of the plasmid

95
Q

site specific recombination will be where

A

at insertion sequence

96
Q

where will single strand cleavage always be

A

oriT

97
Q

what is the last thing transferred

A

tra operon

98
Q

is the tra operon actually transferred

A

no it breaks down before that

99
Q

what will be transferred in integrated f plasmid single strand cleavage

A

the genes closest to OriT including bacterial chrom. genes

100
Q

draw out integrated conjugal plasmid and where it is cut

A

pg 34 & 35

101
Q

what is first step of Hfr conjugation

A

conjugal plasmid integrates into bacterial chromosome

102
Q

in Hfr conjugation where is it nicked

A

origin of transfer

103
Q

what has to happen to conjugation in order for their to be phenotypic change

A

it has to be incorporated/integrated into chrom. of recipient

104
Q

can transfer genes in Hfr conjugation that lie close to

A

oriT

105
Q

receipient in Hfr conjugation will always be

A

recipient

106
Q

how many genes are contained in bacterial chromosome

A

about 3000 genes

107
Q

different sigma factors allow expression of what

A

different sets of genes

108
Q

In order for RNA polymerase to bind to promoters, what is needed

A

sigma factor

109
Q

what does PAMP stand for

A

Pathogen-Associated Molecular Pattern

110
Q

N-formyl methionine is soluble

A

PAMP

111
Q

to evade the immune system, what can salmonella do

A

switch b/w two distinct flagellin proteins

cassette switching

112
Q

what happens in phase 2 of cassette switching

A

won’t have H1 being made b/c you’re making repressor that will block H1 bein gmade

113
Q

what happens in phase 1 of cassette switching

A

won’t make H2 or repressor of H1 but you will make H1

114
Q

draw out phase 2 of cassette switching

A

pg 13

115
Q

draw out phase 1 of cassette switching

A

pg 13

116
Q

what is another name for cassette switching

A

site-specific inversion

117
Q

where is tra operon on f factor plasmid

A

on opposite side of where cut is made (cut is made by oriT)

118
Q

what are the steps in conjugation

A

1- Donor cell produces pilus;
2- Pilus attaches to recipient cell, brings the two cells together;
3- The mobile plasmid is nicked and a single strand of DNA is then transferred to the recipient cell;
4- Both cells re circularize their plasmids, synthesize second strands, and reproduce pili. Both cells are now viable donors.

119
Q

as a F- cell obtains a copy of F factor, what does it become

A

F+

120
Q

what is the end result of a conjugation (one F+ cell giving copy of F factor to the F- cell)

A

both cells will be F+ males

121
Q

what does curing mean

A

F+ bacteria becomes F-

122
Q

conjugation vs. curing

A

conjucation: F- becomes F+

curing F+ becomes F-

123
Q

how can we promote curing

A

removing plasmids via chemical agents like acridine orange

124
Q

in quorum sensing what happens with a low density of inducers

A

they diffuse before they can act on QS receptor

125
Q

how can bacteria utilize antigenic variation

A

mutation
phase variation
uptake of new info (plasmid/antibiotic resistance)

126
Q

donor cells are (“sex”)

A

male

127
Q

recepient cells are (“sex”)

A

female

128
Q

why will the tra operon not be copied in an integrated conjugal plasmid

A

the conjugal core breaks down before it because of force

129
Q

Hfr cell will make contact with what cell

A

F- cell

130
Q

once contact from Hfr cell to F- cell is made, what happens

A

single strand cleavage at origin of transfer

131
Q

where is single strand cleavage always going to occur

A

origin of transfer (OriT)

132
Q

will the entire bacterial chromosome ever be transferred in conjugation

A

no

133
Q

what will receipient cell aquire in Hfr cross

A

chromosomal genes that lie closes to site of integration of F plasmid (opposite from F+ to F- cross)

134
Q

to be stabilized the donor DNA into recipient DNA has to be

A

stabilized

135
Q

pathogenicity islands are regions where there is concentration of

A

virulence factors

136
Q

when plasmids insert into the bacterial genome they have propencity for doing it at where

A

pathogenicity islands

137
Q

at the end of F+ to F- cross what happens

A

entire plasmid is transferred but NO chromosomal DNA and the receipient cell has become a F+ b/c of the plasmid it received

138
Q

at end of Hfr cross what happens

A

recipient still receipient b/c it doesn’t receive genes that encode for F pillus. the recipient can aquire chromosomal genes from donor.

139
Q

if the conjugation from Hfr is recombined vs. not recombined what happens

A

if recombined it will be incoroprated to genome if not recombined will be degraded

140
Q

what is transduction mediated by

A

viruses that infect bactera

141
Q

phages

A

viruses that infect bactera

142
Q

generalized transduction

A

mediated by lytic bacteria phages

: transfer of any bacterial gene from the disrupted cell

143
Q

specialized transduction

A

not a straight lytic cycle

bacterial phage integrates its genome into the bacterial chromosome

144
Q

specialized transduction mediated by

A

temperate phage or lysogenic phage (both bacterial phage)

145
Q

differnece b/w lysogenic and lytic phage

A

in lysogenic the phage is actually incorporated into the host chromosome. in lytic some DNA is incorporated into host chromosome but it doesn’t incorporate itself to replicate

146
Q

when lysogenic phage itegrates its bacteria into chromosome its called a

A

lysogen

147
Q

both form of transductio happen b/c during packing/assembly of bacteria phage, the bacteria phage makes a mistake

A

packages some bacteria chromosomal DNA instead of complete viral genome

148
Q

list steps of lytic infection (generalized transduction)

A

pg 41

149
Q

most of bacteria phages will encapsalate the

A

viral genome

150
Q

some bacteria phage (transducing phages) do what

A

make a mistake in packaging
package part of bacteria chromosomal DNA so when they infect another bacterial cell they inject some bacteria chromosomal DNA so it won’t go into lytic cycle

151
Q

if bacterial/chromosomal DNA (from bacteria lytic phage) is stabilized by recombination it can lead to

A

aquisition of genes by the receipient from the donor cell that was originally infected

152
Q

in specialized transduction the temperate/lysogenic phage initially

A

integrates self into chromosome of recipient cell

153
Q

what can reactivate bacteria phage from latent stage

A

stress

154
Q

when proviral DNA is excised from the chromosome it isn’t excised exactly he right way, so what comes out of chromosome (specialized transduction, lysogenic cycle)

A

part phage and part bacterial chromosomal DNA

155
Q

the part phage and part bacterial phage is packaged as what

A

transducing phage in some phage heads

156
Q

most important aspect of lysogenic cycle

A

during provirus phase itself

anythign encoding on proviral DNA (and many virulence factors are!) and can be expressed during latent stage

157
Q

compare generalized and specialized

A

pg 43

158
Q

generalized transduction goes straight into

A

straight into lytic cycle

159
Q

transducing phage

A

generated b/c during assembly we mispackage bacterial chromosomal DNA instead of phage DNA

160
Q

in specialized transduction what is first step

A

integration of phage DNA as provirus (or prophage) into chromosome of infected cell

161
Q

main diff. b/w lysogenic and lytic cycle

A

lytic phase in lysogenic cycle doens’t hapen immediatley, only after prophage is re-activated after latency

162
Q

lytic phage goes straight into

A

lytic cycle

163
Q

draw out lytic and lysogenic cycle

A

pg 44

164
Q

lysogenic

A

integration of phage dna as provirus

165
Q

really imporatnt feature of lysogenic/tempreate phages

A

lysogenic conversion

166
Q

when prophage Dna integrated dna is now called

A

lysogen

167
Q

lysogen harbors dna of

A

lysogenic phage

168
Q

anythign encoded on phage dna can

A

be expressed in lysogen

169
Q

what is example of what lysogen can express

A

toxin, etc

170
Q

Once integrated into the bacterial chromosome, these genes can cause the bacteria to produce the encoded

A

virulence factors (Lysogenic Conversion) resulting in disease.

171
Q

site where bacteria phages tend to integrate are

A

PAI (pathogenicity islands)

172
Q

pathogenicity islands are highly

A

mobilizable
transposons pop out
after death the islands can be taken up via transofmration
regions where phages insert by site specific recombination

173
Q

draw out gene transfer comparison b/w transformation conjugation & transduction

A

pg 48

174
Q

when phage has combination of host cell and its own DNA, what happens when it infects another cell

A

it won’t go into infectious cycle but the bacterial chromosomal genes can be stabilized by recombination into chromosome of receipient so receipient cell would aquire bacterial chromosomal DNA from donor cell originally infected

175
Q

to release transducing phase have to go into

A

lytic cycle

Immunology (12 decks)

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