Lecture 5: Regulation of Gene Expression Flashcards
(214 cards)
1
Q
_____: All DNA in a
given cell
A
genome
2
Q
what is the study of the genome?
A
genomics- study whole genome
3
Q
______: All RNAs at a given
moment
A
transcriptome
4
Q
what is the study of the transciptome?
A
transcriptomics! Study transcription
activity at a given time
5
Q
______: All proteins in a
given cell
A
proteome
6
Q
what is the study of the proteome?
A
proteomics- study entire complement of proteins
7
Q
T/F: Cells with identical genomes can have different transcriptomes and proteomes
A
true!!!! dependent on external conditions- epigenetics!
8
Q
Proteome is the basis for ______
A
phenotype- observable traits!
9
Q
Microbes regulate protein function in two distinct ways by using
mechanisms to…
A
- Control the amount of an enzyme or other protein
* Vary the amount of mRNA made (transcriptional control)
* Vary the amount of protein made (translational control) - Control the activity of an enzyme or other protein
* Post-translational regulatory processes
10
Q
why is controlling the amount of mRNA produced on the gene economical to the cell?
A
Expressed only when the products are needed and in the amount needed
Conserves energy
Prevents interference between expressed products
11
Q
______: Process by which the output of genes is changed depending on the state of
the cell, i.e. the physiological conditions
A
regulation of gene expression
12
Q
regulation of gene expression is modulated by what…
A
DNA-binding proteins
13
Q
Interactions between ______ and ______ are central to replication,
transcription, and translation, and also to the regulation of these processes
A
proteins and nucleic acids
14
Q
Protein-nucleic acid interactions may be _____ or ______, depending on
whether the protein attaches anywhere along the nucleic acid or binds to a specific
site
A
specific or non-specific
15
Q
Most DNA-binding proteins interact with DNA in a _______
A
sequence-specific manner
16
Q
Most DNA-binding proteins interact with DNA in a sequence-specific manner, where is this specificity provided?
A
by interactions between specific amino acid side chains
of the proteins and specific chemical groups on the nitrogenous bases and the
sugar-phosphate backbone of the DNA
17
Q
The ______ of DNA is the main site of protein binding due to the size of
the protein
A
major groove
18
Q
_____ are often homodimeric proteins
A
DNA binding proteins
19
Q
_______: Composed of two identical
polypeptide subunits, and each
subunit is subdivided into
domains (regions with a specific
structure and function)
* Domain interacts specifically with
a region of DNA in the major
groove
A
DNA binding proteins
20
Q
Most common domain for DNA binding proteins is the ________ structure
A
helix-
turn-helix (HTH)
21
Q
______: The turn linking the helices
contain 3 amino acids (typically
first of is glycine)
* 1st helix interacts specifically
with DNA
* 2nd helix stabilizes the 1st helix
via hydrophobic interactions
A
helix-turn-helix (HTH structure)
22
Q
what are the two proteins involved with gene expression?
A
sigma factors
transcription factors
23
Q
_______ has six factors: σS for proteins need under starvation conditions, σN involved
in nitrogen metabolism, σH and σE for heat shock, σF for chemotaxis and σD (σ70)
for most constitutive and exponential phase genes
A
E. coli
24
Q
________ = control the rate of gene transcription by binding to
specific DNA sequences
A
Transcription factors
25
_______ of gene expression → positive regulation
Activator
26
an _____- of gene expression Binds to DNA and helps recruits sigma factor/RNA polymerase
activator
27
______ of gene expression → negative regulation
Repressor
28
a ______ of gene expression Binds to DNA blocking access of sigma factor/RNA polymerase
repressor
29
Transcription factors are encoded by ________
regulatory genes
30
_______: Affect expression of one or few genes
* Affect expression of many genes → regulon (i.e. group of genes/operons
controlled by one regulator)
* Regulate its own expression → autoregulation
regulatory genes
31
if aTF regulates its own expression its called...
autoregulation
32
if a TF affects expression of many genes its a....
regulon
33
_____: group of genes/operons
controlled by one regulator
regulon
34
_______:
Group of genes that function in related processes
* One transcriptional unit controlled by a single promoter and other cis-acting
sequences required for expression and regulation
* Regulatory gene not considered to be part of operon unless co-transcribed under
autoregulation
operon
35
E. coli chromosome encodes ~ 4000 genes, how many are present during ideal conditions?
~800 mRNA
36
why do we regulate gene expression?
Allows the cell to conserve energy and materials
37
cellular proteins can be... (2)
constitutive
inducible or repressible
38
______:
* Gene is always expressed, thus protein is always present
* Ex. central pathway components → encoded by “housekeeping genes”
Constitutive
39
_________:
* Gene expression is regulated in response to change in environmental signals and
stresses, growth phase changes, nutrient and physiological status, etc.
Inducible or repressible
40
_______: Enzymes that catalyze the synthesis of a specific
product are not made if the product is already
present in the medium in sufficient amounts
enzyme repression
41
enzyme repression usually affects ______ pathways
biosynthetic (anabolic) enzymes
ex: arginine
42
T/F: Generally, the final product of a particular
biosynthetic pathway represses the enzymes of
the pathway
true!! Ensures that the organism does not waste
energy and nutrients synthesizing unneeded
enzymes
43
________: The opposite of enzyme repression. An
enzyme is made only when its substrate
is present
enzyme induction
44
enzyme induction usually affects _____ pathways
degradative (catabolic)
enzymes
ex: lactose
45
______: Typically are cell metabolites, such as substrates or end products of the pathways
they regulate indirectly by affecting activity of transcription factors associated
with the pathways
effectors
46
what are the two kinds of effectors?
inducers and corepressors
47
______:
* Substance that induces enzyme synthesis
Inducers
48
_______:
* Substance that represses enzyme synthesis
Corepressors
49
_______: Binding of inducer activates DNA
binding function of activator protein
inducible expression
49
______: Binding of corepressor activates DNA
binding function of repressor protein
repressible expression
49
_________:
* Binding of effector to a domain (i.e. enzyme, DNA binding protein) can change
conformation of target to active or inactive form; different from DNA binding
domain
Allosteric regulation
50
all regulatory systems employing repressors have the same underlying mechanism: what is it?
Prevention of mRNA synthesis by the activity of specific repressor proteins that
are themselves under the control of specific small effector molecules
51
T/F: The role of the repressor is to stop transcription
true
52
Generally, repressors interact with the ______ located downstream of the
promoter region
operator
53
Regulation by repressors is called ________
negative control
54
T/F: expression of genes are turned off and on like light switches
false!!!
DNA-binding proteins vary in concentration and affinity so control is quantitative
thus basal (i.e. low level) transcription
55
All regulatory systems employing activators have the same underlying mechanism: what is it?
Activation of mRNA synthesis by the activity of specific activator proteins of which
a subset are under the control of specific small effector molecules
56
The role of the activator is to start _________ by recruitment of the RNA
polymerase + sigma factor to the promoter region
transcription
57
Generally, activators interact with the _______ located upstream of
the promoter region
activator binding site
58
Regulation by activators is called ______
positive control
59
T/F: Activator binding site can be located proximally to the promoter region
true! Makes contact with recruited RNA polymerase holoenzyme
60
If binding site is further upstream by several hundred basepairs, then the activator
bound-DNA must be _____ to be make contact with the RNA polymerase to
activate transcription
looped
61
_______: Two or more genes of which the
expression is controlled by one
promoter and one terminator
* Single polycistronic message ensures
that the encoded products are
translated at the same time
operon (one location of binding)
62
______: A specific DNA-binding protein
binds only at those genes or
operons that it controls
regardless of whether it is
functioning as an activator or
repressor
regulon (multiple locations of binding, series of operons controlled as a unit)
63
what is the main difference in regulation of a operon and regulon?
operon: Controlled by a single promoter/operator
regulon: Controlled by a shared regulatory protein but with independent promoters
64
T/F: regulon genes are found together on the genome
false!! CAN be spread across genome (also can be found as multiple operons), each gene/operon has its own mRNA transcribed
65
_______: Contains genes (lacZ,Y,A) necessary to catabolize lactose
* Polycistronic message
lac operon
66
In absence of lactose, LacI ______ binds operator region
repressor
67
in the lac operon, _____ is... Constitutively expressed, functional
* Prevents RNA polymerase holoenzyme from binding the promoter
* No transcription
LacI
68
what are the enzymes encoded by the lac operon?
LacY, LacZ, LacA
69
_____ → Lac permease: transports lactose into the cell
LacY
70
_____ → β-galactosidase: cleaves lactose into glucose and galactose
LacZ
71
______ → transacetylase: modifies lactose and lactose analogs; may prevent toxic
buildup in the bacterial cytoplasm
LacA
72
Catabolic enzymes of lac operon only required when ______ is in growth medium
lactose
73
when lactose is present in growth medium, ______ binds to LacI repressor changing its conformation into an inactive
form and falls off operator sequence
Allolactose
74
what happens to the lac operon when lactose is present?
Lactose is transported into the cytoplasm (LacY permease)
* Lactose is converted (minor reaction) to allolactose by β-galactosidase (LacZ)
* Allolactose binds to LacI repressor changing its conformation into an inactive
form and falls off operator sequence
* RNA polymerase holoenzyme can now transcribe the lac operon
75
what is the major reaction of the lac operon?
Lactose is cleaved (major reaction) into glucose and galactose by β-galactosidase (LacZ)
76
what is the minor reaction of the lac operon?
Thus, allolactose (minor reaction) serves as the inducer to turn on lac operon (i.e. inducible
operon)
77
T/F: lac operon is still an example of negative control because of LacI repressor
true!!
78
Even when “transcription is turned off” for the lac operon – there is still a very low base rate of
transcription (i.e. ________)
basal transcription
79
T/F: Even when lactose is absent there will be low rate of transcription
true!! Enough to induce gene expression, should lactose appear in the medium
80
______: Mechanism of global control that controls the use of carbon sources if more than
one is present
Catabolite Repression (i.e. The Glucose Effect)
81
what type of sugar does the cell always prefer?
glucose- best carbon and energy source DUH (glycolysis)
82
T/F: synthesis of specific catabolic enzymes for other carbon sugars is
inhibited by glucose
true!!
83
_______:
* Two log phases separated by a short lag phase
Diauxic growth
84
when diauxic growth is occuring, what happens in the 1st log phase, lag phase, and 2nd log phase?
1st log phase → lac operon is repressed
* Lag phase → expression of lac operon
begins
* 2nd log phase → catabolism of lactose
85
what are the three components invloved in the catabolic repression of the lac operon?
1. Activator binding site for CAP (CAP site)
2. Catabolite Activator Protein (CAP) (a.k.a.
CRP – cyclic AMP receptor protein)
3. Cyclic AMP (cAMP)
* Derived from a nucleic acid precursor
(regulatory nucleotide)
86
________:
* Responsible for transporting sugars into the cell including glucose
* Richness of carbon source influences PEP:pyruvate ratio
PTS [Phosphoenolpyruvate (PEP) phosphotransferase system]
87
catabolic repression:
When _______ is present:
* Low PEP:pyruvate ratio
* PTS is busy moving glucose into the
cell
* LacY inhibited by IIAGlc
high glucose
88
catabolic repression:
When there is _______:
* High PEP:pyruvate ratio
* P-IIAGlc activates the enzyme adenylate
cyclase
* Produces cAMP
* LacY uninhibited
low glucose
89
cAMP is an _____, turns on expression of the lac operon
inducer (positive control mechanism)
90
When glucose is absent but
lactose is present, level of cAMP
is ______:
* cAMP binds to CAP
* CAP-cAMP binds to activator
binding (CAP) site
* Allows binding of RNA
polymerase
* Transcription can proceed
high
91
When glucose and lactose are
present, level of cAMP is ______:
* cAMP does not bind to CAP
* CAP is inactive thus cannot
bind activator binding site
* RNA polymerase is not recruited
to promoter
* Transcription is very low or turned
off
low
92
dual control of the lac operon involves both _____ and ______ control mechanisms
positive AND negative
93
what is the positive control mechanism of the lac operon?
Positive → cAMP binds CAP; CAP-cAMP
binds CAP site; glucose must be absent
94
what is the negative control mechanism of the lac operon?
Negative → LacI must be absent from
operator thus need allolactose; lactose must
be present
95
T/F: for optimal transcription of the lac operon, only the positive control mechanism should be present
false!!! both conditions (pos/neg control) must be present- dual control!
96
______: Contains genes (trpE – trpA) needed for synthesis of the amino acid tryptophan →
Polycistronic mRNA
trp operon
97
trpR gene encoding regulatory TrpR located (separately) ______ of trp operon
upstream
98
the _______ of the trp operon is...
Constitutively expressed but inactive (i.e. aporepressor)
* Functions as a repressor when activated
trpR gene
99
When levels of tryptophan in cytoplasm are ______, then trp operon should be
transcribed
low
100
TrpR is constitutively expressed but inactive so cannot bind operator....
* So________ can transcribe trp operon because there is nothing to stop
the transcription process
* mRNA is produced and translated to make enzymes → tryptophan is made
RNA polymerase
101
When levels of tryptophan in cytoplasm are _____, then trp operon should be shut
down
high
102
Free tryptophan in cytoplasm binds to aporepressor ____ triggering conformation
into an active repressor
TrpR (tryptophan is a co-repressor!!)
103
Active TrpR binds operator blocking access of promoter to _______
* No transcription of trp operon
RNA polymerase
104
The trp operon is a _______; negative transcriptional control
repressible operon
105
______: Form of transcriptional control exerted after transcription initiation, but before
completion of transcription
attenuation
106
(attenuation) The leader sequence folds into ____________: the first allows continued synthesis of mRNA while the second causes premature
termination
two alternative secondary structures
107
T/F: Folding of the mRNA (into the two alternative secondary structures of attenuation) depends either on events at the ribosome or on the
activity of regulatory proteins, depending on the organism
true!!! transcription/translation processes is coupled
108
why is attenuation control absent in eukaryotes?
the processes of transcription and
translation are spatially separated
109
______ = level of enzymes higher in absence of tryptophan
trpR null mutant, cell is continuously transcribing trp operon... wasting cell resources!
110
what are the possible hairpin structures of attenuation regulation in the trp operon?
Possible hairpin structures → 1:2, 2:3 or 3:4
* Level of tryptophanyl-tRNA (tRNATrp) determines which of alternative hairpin
structures will form
111
____ hairpin structure pauses RNA polymerase to allow time for ribosome to load to trp operon
1:2
112
Cells regulate cell metabolism in response to many different environmental
fluctuations, like....?
Changes in temperature, pH, oxygen, nutrient availability
and changes in other cells
113
______: Changes in number of other cells present
quorum sensing
114
Cells receive signals from environment and transmit them to the specific target to
be regulated, what are some of these signals?
effector molecules, usually by cell surface transduction
115
______: Majority of signals are detected by a cell surface sensing system that transmits the
signal to the rest of the regulatory machinery
signal transduction
116
______: consists of a specific sensor kinase usually located in the cytoplasmic
membrane and a response regulator protein in the cytoplasm
two-component regulatory systems
117
step 1: 2-component regulatory system
When detecting a signal, kinase phosphorylate themselves
(________) at a specific histidine residue (_________)
autophosphorylation
histidine kinase
118
step 2: 2-component regulatory system
______ is then transferred from the kinase to the _______ thereby activating its
function as a DNA-binding protein that regulates transcription in a positive or negative manner
Phosphate
response regulator
119
step 3: 2-component regulatory system
Response regulator is then
dephosphorylated by a
_______ to complete the
regulatory circuit and terminate
the response
phosphatase
120
why is a feedback loop necessary for 2-component regulatory systems
Feedback loop necessary to
ensure a functional balanced
regulatory system
121
_____ are protein channels that allow metabolites to cross outer membrane
Porins
122
______ (dissolved solute concentration) controls relative levels of OmpF and
OmpC porins in outer membrane
Osmolarity
123
_____ osmotic pressure in cell → synthesis of larger-sized OmpF increases
Low
124
_____ osmotic pressure in cell→ synthesis of smaller-sized OmpC increases
High
125
Changes in osmotic pressure are detected by _____
EnvZ histidine kinase
126
When shift in osmotic pressure occurs, EnvZ is autophosphorylated and transfer phosphate group to
response regulator _____
OmpR
127
Low osmotic pressure → OmpR-P _____ transcription of ompF
activates
128
High osmotic pressure → OmpR-P represses transcription ompF, and activates
transcription of _____
ompC
129
Expression of ompF and ompC is
dependent on concentration of ____
OmpR-P
130
Intracellular level of OmpR-P is finely
tuned by dual EnvZ functions (kinase
and phosphatase) of which ratios are
modulated in response to ______
of the growth medium
osmolarity
131
In E. coli, there are almost 50 two-component systems- which ones did we discuss in class?
nitrogen utilization
pho regulation
porin regulation
132
In the Ntr regulatory system:
Response regulator is nitrogen regulator I (NRI) and sensor kinase is ________
nitrogen
regulator II (NRII)
133
_____- regulates ammonia levels in the cell; switches between kinase activity to
phosphatase activity (i.e. dual function) depending on the nitrogen status of the cell
NRII
134
Activity of NRII is controlled by the state of signal-transducing protein ____
PII
135
_________:
Plays an important role in nitrogen metabolism by regulating diverse range of
transcription factors, enzymes and membrane transport proteins
* Activity of PII proteins on their regulatory cascade depends on whether they have
been covalently modified (post-translational regulation)
* Uridylylation (addition of UMP group)
* Adenylylation (addition of AMP group)
PII protein
136
Necessity of ammonia assimilation is
through glutamine sensing by ____
GlnD
137
If glutamine concentration is _____, then
GlnD transduces this signal through
binding of glutamine of which levels are
insufficient to do so
low
138
GlnD adds on _____ group to PII
UMP
139
PII-UMP then activates glutamine
synthetase by inducing removal of _____
AMP
group
140
PII-UMP activates kinase activity of NRII (autophosphorylation) thereby
phosphorylating response regulator NRI (NRI-P) which activates _____
nitrogen assimilation
genes
141
________ is key energy-
requiring enzyme in ammonia
assimilation and must be tightly
regulated to conserve energy if cellular
levels of nitrogen are high as sensed by
glutamine pool
Glutamine synthetase
142
Once glutamine levels are sufficient,
then glutamine binds to GlnD
activating its function to...
remove
UMP from PII
143
Unmodified PII stimulates phosphatase activity of kinase NRII thereby no NRI-P,
and thus no _______
transcription
144
_______ is essential
* for nucleic acids DNA and RNA
* For membrane synthesis along with energy generation and cell signaling
* As a phosphate biological buffer to contribute to pH homeostasis
Phosphorus
145
____ is often a limiting nutrient
phosphorus
146
_____ – dimeric histidine kinase and phosphatase
PhoR
147
____ – response regulator that, when in phosphorylated form, binds to Pho boxes
within promoter regions upstream of genes
PhoB
148
________:
* Form a high-affinity Pi transporter [Member of the ATP-binding cassette (ABC) superfamily]
PstSCAB proteins
149
_______: 1. PstS protein is a periplasmic phosphate-binding protein → binds and presents Pi to
transmembrane components PstC and PstA
2. ATP, binding across the PstB dimer interface, undergoes hydrolysis triggering
conformational change of “the gate” from outward-facing to inward facing allowing Pi
access to cytoplasm
3. Cycle continues with release of ADP and rebinding of ATP to PstB
PstSCAB proteins
150
______:
* Peripheral membrane protein that modulates Pi transport through PstSCAB complex
* Acts like a brake to prevent too much Pi import
PhoU
151
_____ activity is controlled by PstSCAB transporter and PhoU
PhoR
152
High environmental and cytoplasmic Pi levels → favours _____ in its phosphatase
conformation
PhoR
153
Low environmental Pi levels → favours _____ in its autokinase conformation
PhoR
154
______: Genus of gram-positive Bacteria that contains many species that produce antibiotics which
is an energy-intensive process limited by high phosphate conditions
streptomyces
155
_____: In natural habitat, produces antibiotics to kill competing cells of other bacterial species for
phosphate resources
streptomyces
156
When Pi levels in
excess, PhoP is
______
dephosphorylated
157
______: Regulatory mechanism that assesses population density
quorum sensing
158
______: Widespread among gram-negative Bacteria; found in many gram-positive species
and in some Archaea
quorum sensing
159
_____: approach is used to ensure that sufficient cell numbers of their own species are
present before initiating activities that require a certain cell density to work
effectively
quorum sensing
160
Quantified by concentration of specific signal molecules produced by bacterial cells
of the same species → ______
autoinducer
161
autoinducers typically....
Typically diffuses freely across the cell envelope in either direction
* High concentrations achieved inside the cell only if many cells are nearby
162
Several different classes of autoinducers exist: what are the three?
1. Specific to bacterial species → first identified
were the acyl homoserine lactones (AHLs)
* Acyl groups are functional groups containing
carbonyl and alkyl groups
* AHLs of different species of gram-negative
bacteria feature acyl groups of different lengths
2. 3. Interspecies communication → e.g. cyclic furan
derivative AI-2
* Common among gram-negative Bacteria
Gram-positive Bacteria and some Archaea
generally use small peptides
163
Auto-inducers function to trigger ______
gene transcription, directly binding a transcriptional regulator or activating a two-component system
164
______: Behavior of cells moving towards attractants and away from toxins
chemotaxis
165
T/F: Sense change in concentration of a chemical over time rather than the absolute
concentration of the chemical stimulus
true!!
166
Sensed information regulates direction of ________-
flagellar rotation
167
Mechanism of chemotaxis depends upon a
______ of multiple proteins
signal cascade
168
Sensory proteins sense attractants/repellants
and interact with cytoplasmic sensor kinases
→ ________
Methyl-accepting chemotaxis proteins
(MCPs)
169
Thousands of MCPs cluster to form large hexagonal
arrays known as ______ which
are located in the cytoplasmic membrane
and/or cytoplasm
chemoreceptors
170
E. coli possesses ___ transmembrane chemoreceptors
* Each composed of 5 different MCPs that are specific for certain compounds
4
171
T/F: In general, MCPs bind attractants/repellents directly
true!!
172
MCP binding of an attractant/repellent triggers interactions with the cytoplasmic proteins
______
CheA and CheW
173
T/F: CheA (sensor kinase) and CheW (response regulator) for chemotaxis
false!! CheA and CheY
174
explain the two steps of regulation of chemotaxis
1) When MCPs bind to an attractant or release a repellant, coupling protein CheW is inactive
and autophosphorylation of CheA is inhibited
2) When MCP binds a repellent or releases an attractant, conformational change is
induced and CheA is autophosphorylated (CheA-P)
* CheA-P phosphorylates CheY (CheY-P) which leads to clockwise flagellar rotation →
tumbling cells (move randomly)
* CheZ dephosphorylates CheY returning cells to “runs”
175
Increase in repellent concentration promotes ______ (↑CheY-P)
tumbling
176
Increase in attractant concentration promotes runs as tumbles are ______ (↓CheY-P)
suppressed
177
Once stimulus has been responded to, sensory system needs to reset to await further signals
→ _____
adaptation
178
_____ MCPs no longer respond to attractants but sensitive to repellents
______ MCPs respond strongly to attractants but insensitive to repellents
Fully methylated
Unmethylated
179
Control of methylation: chemotaxis protein ____ methylates MCPs; _____ demethylates
MCPs
CheR
CheB-P
180
_____ of attractants
* Rate of autophosphorylated CheA is low, which leads to unphosphorylated CheY and CheB →
cell swims smoothly in a run
High level
Methylation of the MCPs increases during this period because CheB-P is not present to
demethylate (because there is no CheA-P)
181
______ of repellents
* Rate of autophosphorylated CheA is high, which leads to CheY-P (tumbling cells) and CheB-P
(demethylation)
High level
182
Fully methylated MCPs respond best to an _______ and send a signal
for cell tumbling to move off in a random direction while MCPS are slowly demethylated
increasing gradient of repellents
183
Chemotaxis achieves the ability to monitor small changes in concentrations (______) of both
attractants and repellents over time
gradients
184
what are the two non-coding RNAs?
tRNA and rRNA
185
sRNAs exert their effects by base-pairing directly to other RNA molecules (i.e. mRNAs)
which have regions of complementary sequence
* Modulates the _______ of the target mRNA
translation rate
186
sRNAs alter the translation of their mRNA target by four different mechanisms. For _____ of the
mechanisms, sRNAs basepair to their target mRNA to affect changes to protein expression
two
187
The other two mechanisms affect ______; binding of the sRNA to its target either
increases or decreases degradation of the transcript by ribonucleases, thus modulating
protein expression
mRNA stability
188
_______ (multicopy inhibitor of OmpF)
* One of the first sRNAs discovered
* Part of MicF is complementary to 5’ end of ompF gene including translation
initiation region (TIR)
* Expression of micF under control of four transcriptional activators including OmpR
sRNA MicF
189
_______: RNA molecules that specifically recognize and bind other molecules, including low-
molecular-weight metabolites
riboswitches
190
Binding does not require complementary basepairing, but does require folding
of RNA into a specific 3D structure that recognizes the target molecule... this would be called...?
tertiary structure
191
______: Specifically affect gene expression levels through transcriptional or translational
control depending on the type of switch
riboswitches
192
T/F: Microorganisms must often survive nutrient-limited conditions and exposure to
environmental stressors such as extreme pH, oxidative stress, and antibiotic exposure
true
193
________:
* Widely distributed regulatory mechanism used by bacteria to survive nutrient
deprivation and environmental stresses
* Balances the metabolic state of the cell
* Activation results in shutdown of macromolecule synthesis and the activation of
survival pathways
* Responsive to decreased availability of amino acids
Stringent response mechanism
194
When growth of the cell is
limited by a shortage of amino
acids, the pool of uncharged
tRNAs increases relative to
______
charged tRNAs
195
Eventually uncharged tRNA is
inserted into the ribosome
resulting in ribosome stalling, and
leading to ______- by
RelA
(p)ppGpp synthesis
196
stringent stress responses are Triggered by accumulation of unusual nucleotide guanosine tetraphosphate (ppGpp)
termed _______
alarmones
197
ppGpp is first made as guanosine pentaphosphate (pppGpp) by transferring two
phosphates from ATP to the 3’ OH of GTP, but then it is quickly converted to ppGpp
by phosphatase Gpp → collectively referred to as _______
(p)ppGpp
198
Synthesis of (p)ppGpp is done by ____ using ATP as a phosphate donor
RelA
199
RelA is associated with the ____ ribosomal subunit, and
activated by a signal from the ribosome during amino acid
limitation
50S
200
Intracellular levels of ppGpp is during
amino acid starvation are also regulated
by _____
SpoT
201
T/F: SpoT is bifunctional; it has pppGpp
synthesis activity as well as hydrolase
activity that degrades ppGpp
true!! can make AND degrade
202
SpoT does not associate with ribosomes
but instead monitors changes in carbon
metabolism through direct interaction
with ______
acyl carrier protein (ACP)
203
_____ plays a crucial role in fatty acid biosynthesis
by binding to short-chain fatty acids and
accepting additional fatty acid substrates to build
longer fatty acid chains
* ____ bound by long-chain fatty acids have low
affinity to binding SpoT
ACP
204
Synthesis of rRNA and tRNA ceases almost immediately
* Protein and DNA synthesis curtailed, but biosynthesis of new amino acids is
activated (synthesized by proteins made anew by existing ribosomes)
* Eventually, synthesis of rRNAs and in turn ribosomes, resumes but at a ___
reflective of the cell’s reduced growth rate
new rate
205
T/F: Bacterial cells often respond to nutrient limitation and stressors by entering into stationary
phase of growth
true!!
206
Switch is controlled by activating a regulon recognized by the alternative sigma factor ______
(a.k.a. σS or σ38), also called stationary sigma factor
RpoS
207
The RpoS regulon comprises over _____ genes including those associated with nutrient
limitation, resistance to DNA damage, biofilm formation, and responses to osmotic,
oxidative and acid stresses
400
208
what are the three levels of control of RpoS
Transcriptional, translation and post-translational regulatory mechanisms
rpoS transcription increases in response to ppGpp
* Translation of rpoS transcripts is positively regulated by sRNAs expressed during stress
conditions
* RpoS is susceptible to degradation during non-stressful conditions
209
______ proteins help counteract
protein damage and assist the cell in
recovering from stress
Heat shock
210
Genes encoding heat shock proteins
grouped into a regulon controlled by
alternative sigma factor _____
RpoH
211
Under normal conditions, RpoH is
degraded by ____
DnaK
212
If under heat shock conditions, then
_____ is busy with folding denatured
proteins leaving ______ alone to
complex with RNA polymerase for
transcription initiation of heat shock
genes
DnaK
RpoH
