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microbio > week 6/7 ish > Flashcards

week 6/7 ish Flashcards

1
Q

what does it mean that microbial chromosomes are streamlined

A

less intergenic space, smaller regulatory regions than larger eukaryotic counterparts

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2
Q

operons

A

clusters of genes that share the same promoter and are transcribed as a single large mRNA

bacterial transcriptional unit

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3
Q

true or false: introns are very rare in yeast and prokaryotes

A

true

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4
Q

intergenic sequences

A

promoters, enhancers, repressors, spacers

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5
Q

true or false: intergenic sequences are bigger in prokaryotes

A

false, smaller

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6
Q

microbes are extremely “gene……” compared to multicellular eukaryotes

A

dense

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7
Q

true or false: the majority of eukaryotic DNA is the essential, backbone genetic information

A

false; non-coding dna accounts for a greater percentage

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8
Q

operons consist of 4 main parts:

A

upstream activator site
promoter
operator
structural genes

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9
Q

polycistronic

A

contain multiple ORF that encode amino acids

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10
Q

upstream activator site

A

DNA sequence upstream of a promoter that increases transcription via binding of activator proteins

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11
Q

promoter

A

region on DNA to which RNA polymerase binds to initiate transcription

specific to sigma factors

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12
Q

sigma factors

A

interchangeable subunits of the RNA polymerase

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13
Q

operator

A

DNA sequence which decreases transcription via binding of repressor proteins

usually overlaps promoter

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14
Q

structural genes

A

genes encoded by the operon

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15
Q

why would genes be found on the same operon

A

belong to the same pathway

account for different subunits of a particular protein

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16
Q

gene expression is highest for genes at the……end of the transcript

A

5’

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17
Q

polar effects

A

disrupt translation of downstream genes

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18
Q

4 examples of operons hosting genes with related functions

A

arg
lac
trp
fim

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19
Q

gene expression is highly…….

A

coordinated
(regulons)

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20
Q

ribosomal release factors and signaling sequences are needed to ensure proper…..

A

translation

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21
Q

unlike eukaryotes, bacteria do not have a membrane-bound…….so mRNAs are not……..or……or……before translation

A

nucleus

capped, tailed, targeted

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22
Q

in prokaryotes, translation can begin before

A

transcription is completed

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23
Q

beads on a string

A

multiple ribosomes can load onto the nascent transcript

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24
Q

poly-A tails are signals of……in prokaryotes

A

decay

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25
Q

transcription in bacteria begins with:

A

RNA polymerase fusing with the sigma factor

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26
Q

Sigma Factor

A

promoter-recognizing subunit

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27
Q

the Sigma Factor recognizes the…… that is located…..

A

Pribnow box
upstream from the mRNA start site
(-10 and -35 regions)

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28
Q

sigma factors allow for a coordinated……response

A

transcriptional

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29
Q

o70 RpoD
E. coli sigma factor sequence and function

A

TTGACA
normal growth

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30
Q

o38 RpoS

A

CCGGCG
general stress response

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31
Q

regulon

A

sigma factors
or
activators/repressors
facilitate coordinated expression of genes and rapid response to environmental stimuli

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32
Q

once transcription begins, the sigma factor…..

A

releases

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33
Q

transcription then continues until……

A

the termination site is reached

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34
Q

transcription termination in bacteria:

A

one goal, two possibilities

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35
Q

possibility 1 termination:

A

factor independent termination: stem-loop followed by a U poly-track

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36
Q

possibility 2 termination:

A

factor dependent termination: rut site + Rho factor

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37
Q

when transcription is terminated by Rho, the DNA will….

A

encode a rut site and a Rho-sensitive binding site downstream of the coding region

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38
Q

once transcribed, Rho can bind to the rut site on the nascent mRNA transcript and move up the mRNA until it comes in contact with…….

A

the paused RNA polymerase

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39
Q

when Rho catches up to the RNA polymerase, it will perform a……..to release the RNA-DNA hybrid. this causes the RNA polymerase to…..

A

helicase activity
dissociate and terminate transcription

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40
Q

translation in bacteria uses the….. ribosome

A

80S

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41
Q

translation initiation is a…..step process

A

2

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42
Q

step 1 of translation initiation

A

30S subunit lines up with the ribosomal binding site, initiator tRNA binds

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43
Q

how is the start codon ensured to be aligned in the P-site

A

16S ribosomal RNA aligns with the Shine-Dalgarno Sequence

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44
Q

step 2 of translation initiation:

A

50S is added and elongation can begin

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45
Q

why/how beads on a string ?

A

translation can re-initiate as soon as the first ribosome clears the beginning of the transcript

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46
Q

translational coupling

A

closer together cistrons
@ stop codon, 50S disassociates
30S keeps going, hits next SD and then 50S reassociates and translation restarts

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47
Q

de novo internal translation initiation

A

further apart cistrons
@ stop codon, entire ribosome disassociates
at next SD, 30S reassociates, 50S binds, translation re-initiates

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48
Q

constitutively expressed

A

“always on”

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49
Q

inducible

A

these genes can be “turned on” and “turned off”

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50
Q

what kinds of genes are constitutively expressed

A

essential genes/ central processes
ex) replication, transcription, translation, main metabolism, etc.

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51
Q

what kinds of genes are inducible

A

non-essential genes/ auxiliary processes
ex) amino acid, nucleic acid biosynthesis, transporters, etc.

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52
Q

arg operon

A

encodes proteins involved with the biosynthesis of arginine

“on” by default and can be turned off by repression

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53
Q

when the cell has enough free arginine, then there will be free arginine that can be…..

this causes a conformational change, allowing the ArgR repressor to……

A

bound by the ArgR repressor

bind the arg operator and stop transcription

54
Q

arg operon regulation is what type of regulation? and what does this mean

A

pre-transcriptional

gene product expression is controlled before transcript is made

55
Q

change in transcription factor’s ability to bind is a form of…….

A

allosterism

56
Q

lac operon

A

encodes proteins involved with lactose metabolism

“off” by default, can be turned on by induction

57
Q

when the cell encounters and uptakes allolactose, it is bound by the…..

this causes a conformational change, releasing the LacI repressor and inducing……

A

LacI repressor

transcription

58
Q

polar effects

A

operon is not repressed but an early gene gets a nonsense mutation

*genes downstream of the polar mutation have reduced or no expression

59
Q

fim operon: OFF phase

A

FimB and FimE are expressed
fim promoter faces the inverse direction

60
Q

phase variation

A

a reversible switch between on/off expressing phase

61
Q

fim operon: ON phase

A

only FimB is expressed
fim promoter faces the forward direction

62
Q

post-transcriptional regulation: Attenuation and the trp operon

A

trp operon has a leader peptide which encodes 2 complimentary stem loops: regular + termination signal with U poly-track

63
Q

when cell has enough tryptophan, there will be lots of……

ribosome will translate……..and a ……..loop will form

A

trp-tRNA’s

leader peptide

termination stem

64
Q

when cell is low on tryptophan, there will be a lack of……

ribosome will stall on…… and an……..loop will form between regions…..and……

A

trp-tRNA’s

leader peptide

anti-terminator stem

2 and 3

65
Q

what are mutations

A

any heritable change in the DNA sequence of a cell

66
Q

where do mutations come from

A

mistakes during cell division
exposure to DNA-damaging agents in environment

67
Q

5 major outcomes of mutations

A

increase
decrease
change
eliminate
no effect

68
Q

3 major classes of mutations

A

base substitutions
indels
structural variants

69
Q

base substitutions + 3 types

A

most common mutation
silent–> same amino acids produced
missense–> different amino acid produced
nonsense–> early stop codon

70
Q

outcome of base substitution is increased function only if……..

A

the cell needs higher expression of the gene/operon

71
Q

indels are common but generally restricted to…….regions

A

repetitive

72
Q

indel mutations

A

insertion/ deletion
frameshift - extensive missense

73
Q

effect of +/- 3 indel

A

gain or lose amino acid

74
Q

structural variants are more rare, but effects are…….

A

larger

75
Q

structural variants

A

large deletions/ insertions

gain/loss of gene or operon

76
Q

6 types of structural variants

A

deletion insertion
tandem duplication
interspersed duplication
inversion
translocation

77
Q

2 theories ab mutations/evolution

A

selection
neutral

78
Q

selection theory

A

mutations = deleterious or advantageous
natural selection can act on them all

79
Q

neutral theory

A

mutations = rarely advantageous; mostly deleterious or neutral
natural selection cannot act on neutral (no phenotype)

80
Q

whether a mutation is good/bad/neutral depends on…….

A

its environment

81
Q

microbes have the lowest………..but they have huge population sizes which = quick……..

A

mutation rates
evolution

82
Q

1.0x 10^6 mutations/mL/generation
1 % mutations are beneficial
= ?

A

10,000 beneficial mutations per generation

83
Q

stress-induced mutagenesis

A

stressful conditions temporarily increase replicative mutation rate

84
Q

WT mutation rate

A

higher/steeper curve
blue

85
Q

hypermutator mutation rate

A

variability around mode genotype
wider/lower
red

86
Q

population without mutator cells:
before, during, long term effect

A

before stress: low genetic variability
during stress: massive cell death
long term: extinction

87
Q

population of constitutive mutators:
before, during, long term effect

A

before stress: high genetic variability
during stress: survival of cells carrying mutations
long term: expansion of adaptive mutants

88
Q

spontaneously/ subpopulations of transiently mutator cells:
before, during, long term effect

A

before: low overall population mutation rates

during: survival of cells w/adaptive mutations generated in transient mutator subpopulation

long term: expansion of adaptive mutants/ low overall population mutation rates

89
Q

Ames test

A

determines of a compound is a mutagen by looking for revertants

  1. grow His auxotroph in histidine media
  2. take fraction of culture + expose to possible mutagen
  3. plate treated+nontreated samples on no-His media
  4. count colonies after overnight incubation

if possible mutagen contains more colonies than control = mutagen is confirmed

90
Q

vertical gene transfer

A

transfer of variation from parent to offspring

91
Q

horizontal gene transfer

A

direct transfer of variation between unrelated cells

92
Q

3 methods for horizontal gene transfer

A

conjugation, transformation, transduction

93
Q

conjugation

A

= discussion of transfer of plasmids

one bacterium transfers genetic material to another through direct contact

94
Q

transformation

A

exogenous genetic material is directly taken up and incorporated by a cell through its cell membrane

95
Q

transduction

A

DNA is transferred from one bacterium to another by a virus

96
Q

plasmids are……. acquired and…….. transmitted

A

horizontally
vertically

97
Q

low copy number

A

less than 5 copies
can be larger bc few

98
Q

medium copy number

A

5-50 copies

99
Q

high copy number

A

50-hundreds copies

100
Q

can’t maintain large plasmids @ high copy number bc……

A

it’s energetically draining

101
Q

replication regulation is related to the plasmid’s……

A

oriP
1 oriP detected, plasmid can replicate

102
Q

low copy double plasmids w/ similar trip cannot replicate bc……

A

2 oriP’s would be detected, can’t replicate; one oriP would be lost in next generation

103
Q

replication of high copy number plasmids is……..

A

unregulated

104
Q

high copy plasmids are partitioned into offspring cells……

A

randomly

105
Q

conjugation requires a……….

A

sex pilus

106
Q

this sex plus is……..encoded

A

plasmid

107
Q

donor cell

A

contains plasmid encoding pilus

108
Q

recipient cell:

A

does not contain plasmid

109
Q

5 functional types of plasmids

A

fertility F
resistance R
Col
Degrative
Virulence

110
Q

F plasmid function

A
  1. donor cell attaches w/pilus, draws cells together
  2. cells contact one another
  3. one strand of plasmid DNA transfers
  4. recipient synthesizes a complimentary strand to become an F+ cell; donor synthesizes a complementary strand, restoring its complete plasmid
111
Q

why is conjugation is risky?

A

expression of the pills results in susceptibility to bacteriophage

112
Q

R plasmids

A

for resistance to antimicrobials, heavy metals, acid, stresses

113
Q

Col

A

encode proteins that kill surrounding bacteria, colicines

114
Q

degrative plasmids

A

for genes that allow bacteria to break down a new substance

115
Q

virulence

A

encode genes that make the bacterium a better pathogen

116
Q

naive cells can acquire new functions from…..of plasmids

A

HGT

117
Q

plasmids are expensive to maintain and can be lost if they aren’t………..

A

actively needed

118
Q

recombination ensures that function is…….

A

retained long term

119
Q

phage (bacteriophage)

A

viruses that specifically infect bacterial cells

120
Q

phage receptors

A

cell surface proteins that are often targeted by phages for cell access

121
Q

common phage receptors

A

flagella, pili, iron transporters, LPS

122
Q

only……..phage can form a prophage and intergrate into the genome

A

temperate

123
Q

cryptic prophages

A

prophages acquire mutations that trap them on the bacterial chromosome

124
Q

deletion of different prophages from E Coli results in………

A

reduced stress tolerance (reduced growth)

125
Q

transformation

A

free DNA from the environment is incorporated into a recipient cell and brings about a genetic change

126
Q

competent

A

able to take up DNA and be transformed

127
Q

genetically determined

A

requires the use of genetically encoded DNA uptake machinery

128
Q

chemically induced

A

E. coli must be

requires cells to be treated with chemicals that permeabilize their membranes, allowing DNA to enter the cell

129
Q

genetically determines competence process

A
  1. bacterium lyses and releases its cell contents and DNA
  2. cell surface proteins on competent recipient cell binds a DNA fragment
  3. recipient cell uptakes a single strand of the free DNA fragment
  4. RecA recombination protein facilitates the integration of DNA fragment into the bacterial genome
  5. competent cell permanently retains new function encoded by the once exogenous DNA
130
Q

how is E. coli made chemically competent

A

CaCl2 and heat shock = make membrane permeable

microbio (5 decks)

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