1.
-41: Class II CAP promoters (galP1)
CAP dimer centered at ___
upstream CAP subunit via AR1
downstream CAP subunit via AR2 and AR3
2.
61.5: Class I CAP promoters (Plac)
CAP dimer centered at -___
downstream CAP subunit binds via its AR1
3.
70: ppGpp reprograms RNAP
1) Change promoter specificity of RNAPsigma70
2) Increased ability of other sigma factors to compete for RNAP
sigma factors compete for limiting amounts of core RNAP
- increasing one sigma factor decreases transcription of genes dependent on other sigma factors
- ppGpp increases sigma^s production
-> increases transcription from sigma^s dependent promoters
-> decreases transcription from sigma^__dependent promoters
RNAPsigma^s requires ppGpp for initiation in vivo -> ppGpp regulates sigma^s production and activity
4.
90: CAP and crp modulon
Tight nucleoprotein complexes at promoters
DNA wraps around proteins
CAP induces __ degree bend in DNA
5.
A: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) RelA - ribosome-associated ppGpp synthetase
2) SpoT - bifunctional
a) catalyzes hydrolysis of ppGpp
ppGpp -> ppG + ppi
b) alternate SpoT, forms ppGpp using ATP
ppG + _TP -> ppGpp + _MP
6.
A: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in _ site
Signal - ppGpp
Regulator - RNAP
Response - 1) Decrease translation machinery synthesis; 2) Increase aa biosynthetic enzymes
Return - SpoT hydrolysis of ppGpp
7.
aa: Stringent response: overall mechanism
1) Drop in [__] leads to drop in [__-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
8.
aa: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of __
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ppGpp
Regulator - RNAP
Response - 1) Decrease translation machinery synthesis; 2) Increase aa biosynthetic enzymes
Return - SpoT hydrolysis of ppGpp
9.
aa biosynthetic: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ppGpp
Regulator - RNAP
Response - 1) Decrease translation machinery synthesis; 2) Increase __ ________ enzymes
Return - SpoT hydrolysis of ppGpp
10.
aa tRNA: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [__-_____]
2) Lack of _-____ causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
11.
activation: global regulation: regulatory networks
crp modulon - part of a regulatory network
-principles of hierarchial organization
1) Dominant over operon/regulon control
2) _________ by CAP:cAMP depends on binding affinity
12.
activator: CAP:cAMP binds to crp modulon promoters
CAP:cAMP acts in a variety of modes
1) Class I _____
2) Class II ______
3) Repressor
13.
active: ppGpp reprograms RNAP
binds close to the _____ site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
14.
adaptation: crp modulon
involved in catabolite repression
include genes that handle _____ to particular (usually poor) growth conditions
include catabolic / non-catabolic genes
15.
affinity: CAP
- dimer
- CTD contains DNA-binding HTH motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change -> increase _____ for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
16.
allosteric: Global regulation: coordination devices
1) _______ regulator
- repressor or activator recognizes particular NT sequence common to controlling region of member operons (e.g. CAP)
2) Alternate sigma factor
3) ______ regulator + sigma factor
4) Metabolites
17.
alone: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
cAMP:CAP ____ required to activate promoter
promoters can be class I (e.g. Plac)or class II
specificity through promoter-specific repressors (e.g. lac) or transcription of another regulator (e.g. cAMP: CAP induces melR -> MelR activates melAB
2) Co-activation
3) Repression
4) Co-repression
18.
alphaCTD: CAP Co-activation
e.g. Pbad
arabinose induces conformational change in AraC
-> alter half-site preference of AraC
-> CAP-binding site occurs between I1 and O1
-> CAP binding helps break I1-O2 repression loop (i.e. helps AraC-arabinose bind to I2)
CAP also makes specific contacts with RNAP _______
19.
AR1: Class I CAP promoters (Plac)
CAP dimer centered at -61.5
downstream CAP subunit binds via its __
20.
AR1 AR2 AR 3: Class II CAP promoters (galP1)
CAP dimer centered at -41
upstream CAP subunit via ___
downstream CAP subunit via ___ and ___
21.
arabinose: CAP Co-activation
organization and position of CAp binding sites vary tremendously
Underlying reasons
1) Activator 1 repositions Activator 2
2) Both activators contact RNAP
e.g. Pbad
______ induces conformational change in AraC
-> alter half-site preference of AraC
22.
ATP: ppGpp is synthesized by two enzymes
both synthetic reactions require ___
1) RelA - ribosome-associated ppGpp synthetase
Activated RelA catalyzes two rxns:
ATP + GTP -> pppGpp + AMP
ATP + GDP -> ppGPP + AMP
2) SpoT
23.
autoregulation: stringent response
_________ - r-proteins bind to rRNA in ribosome;
have similar binding site on own mRNA - if r-proteins accumulate, they bind their own mRNA, preventing translation.
24.
bend: CAP
- dimer
- CTD contains DNA-binding HTH motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change
-> reorients two DNA-binding domains of dimer
-> increase affinity for DNA
CAP: cAMP complex induces ~90 degree ____ in DNA
25.
beta: ppGpp reprograms RNAP
binds close to the active site (interact with ____ and ___' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
26.
bifunctional enzymes: Control theory
- revealed two mechanisms that biological systems utilize to ensure robustness
1) Integral feedback
2) ______ __________
27.
binding affinity: hierarchy of transcriptional activation within modulon
- based on variation in ______ _______ of sites
- sites within high affinity filled first (i.e. as cAMP levels begin to rise)
28.
binding affinity: global regulation: regulatory networks
crp modulon - part of a regulatory network
-principles of hierarchial organization
1) Dominant over operon/regulon control
2) Activation by CAP:cAMP depends on _____ ______
29.
binding affinity: global regulation: regulatory networks
crp modulon - part of a regulatory network
-principles of hierarchial organization
1) Dominant over operon/regulon control
2) ______ ______ dictates activation by CAP:cAMP
30.
biosynthesis proteolysis: Stringent response
-aims to conserve and redirect energy
characterized by two simultaneous physiological responses:
1) Shutdown of ribosome synthesis
2) Up-regulation of aa ________ and _______
+ temporary cessation of new rounds of DNA replication
+ Decrease in synthesis rates of phospholipids, carbohydrates and murein
31.
C: crp modulon
promoters integrate information derived from 2 distinct signals
1) Overall nutritional status (via CAP and cAMP)
2) Availability of _ sources (through regulators and effectors)
32.
cAMP: CAP
- dimer
- CTD contains DNA-binding HTH motif
- NTD contains ____ binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change
-> reorients two DNA-binding domains of dimer
-> increase affinity for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
33.
cAMP: crp modulon
global regulator - CAP, DNA binding protein
effector molecule - ____, an 'alarmone'
34.
cAMP: [____]i (cAMP in the cell) signals nutritional status of cell
35.
cAMP: crp modulon
global regulator - CAP, DNA binding protein
effector molecule - cAMP, an 'alarmone'
CAP is activated by binding of ____
36.
CAP: crp modulon
global regulator - ___, DNA binding protein
effector molecule - cAMP, an 'alarmone'
37.
CAP: CAP Co-activation
e.g. Pbad
arabinose induces conformational change in AraC
-> alter half-site preference of AraC
-> ___-binding site occurs between I1 and O1
-> ___ binding helps break I1-O2 repression loop (i.e. helps AraC-arabinose bind to I2)
CAP also makes specific contacts with RNAP alpha CTD
38.
CAP cAMP: crp modulon
promoters integrate information derived from 2 distinct signals
1) Overall nutritional status (via ___ and ____)
2) Availability of C sources (through regulators and effectors)
39.
change: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) ______ promoter specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
40.
CheB: Control theory
Chemotaxis
Input - chemoattractant (binding)
Output - direction of flagella rotation
Info processed by CheA and CheY
Integral feedback occurs via ____ - phosphorylation state of ____ affects methylation of MCP, and therefore CheA activity
actually a closed loop - info from output feeds back into control circuit
41.
chemoattractant: Control theory
Chemotaxis
Input - __________ (binding)
Output - direction of flagella rotation
Info processed by CheA and CheY
Integral feedback occurs via CheB - phosphorylation state of CheB affects methylation of MCP, and therefore CheA activity
actually a closed loop - info from output feeds back into control circuit
42.
circuits: Control theory
- using engineering principles to analyze _____ that process inputs and carry out specific responses
- involves in silico modeling
43.
class I class II: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
cAMP:CAP alone required to activate promoter
promoters can be ____ _ (e.g. Plac)or ____ __
specificity through promoter-specific repressors (e.g. lac) or transcription of another regulator (e.g. cAMP: CAP induces melR -> MelR activates melAB
2) Co-activation
3) Repression
4) Co-repression
44.
co-activation: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) __-________
3) Repression
4) Co-repression
45.
co-repression: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
3) Repression
4) __-_________
46.
common: hierarchial organization of genes
stimulon
large group of operons that respond together to an environmental stimulus
not necessarily controlled through a _____ regulatory system
-> i.e. identifying a set of genes as stimulon provides no info on organization/mechanism of regulation
47.
competitive: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) Increase ________ factor of other sigma factors for RNAP
48.
complex: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
- ______ promoter
- cAMP:CAP act synergestically within operon specific activator
- organization and position of CAP binding sites vary tremendously
3) Repression
4) Co-repression
49.
consensus: CAP
recognizes a 22 bp palindromic sequence
-aaaTGTGAtntanaTCACAttt
- like sigma factor recognition sequences, CAP-binding sequences sometimes diverge from ________
-> highly divergent sequences bind CAP more weakly
-> _________ sequence does not occur naturally (rare) -> bind cAMP: CAP too strongly.
50.
conserve redirect: Stringent response
-aims to _____ and ______ energy
characterized by two simultaneous physiological responses:
1) Shutdown of ribosome synthesis
2) Up-regulation of aa biosynthesis and proteolysis
+ temporary cessation of new rounds of DNA replication
+ Decrease in synthesis rates of phospholipids, carbohydrates and murein
51.
conserved: stringent response
-scarce aa ______ for making new enzymes that allow cell to adapt to new condition and resume growth
52.
contiguously: hierarchial organization of genes
operon
- a group of genes of related function that occur _________ in the genome
- transcribed from a single promoter as a polycistronic mRNA
53.
contiguously: hierarchial organization of genes
regulon
- a group of genes of related function
- not all occur ________ in the genome
- transcription is regulated by a single regulatory protein
(e.g. ara genes, involved in uptake/catabolism of arabinose, are arranged in 4 transcriptional units, under control of a common regulatory protein AraC. subset of tehse genes occur in operons)
54.
coordinated: Single stimulus can trigger response in multiple modulons (through different mechanisms) e.g. glucose addition affects catabolite repression members and stringent response global regulatory networks
_______ activity of multiple genes - essential to cellular functions
55.
covalent: Regulator activity
-mediated by synthesis, degradation, ligand binding, ______ modification (regulatory enzyme)
56.
crp: hierarchial organization of genes
modulon
best example is the ___ modulon
57.
crp modulon: ___ _____
involved in catabolite repression
include genes that handle adaptation to particular (usually poor) growht conditions
include catabolic / non-catabolic genes
58.
crp modulon: CAP:cAMP binds to ___ ______ promoters
CAP:cAMP acts in a variety of modes
1) Class I Activator
2) Class II Activator
3) Repressor
59.
crystallographic: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / ________ evidence
1) Change promoter specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
60.
decreased: Stringent response
-global network responding to any type of nutritional stress (shift to poorer C, energy or N source) that results in _______ growth rate
61.
degradation: Regulator activity
-mediated by synthesis, _______, ligand binding, covalent modification (regulatory enzyme)
62.
different: Transducer - device that receives signal from one device and passes it to another usually in _______ form
63.
dimer: CAP
- ____
- CTD contains DNA-binding HTH motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change
-> reorients two DNA-binding domains of dimer
-> increase affinity for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
64.
direction: Control theory
Chemotaxis
Input - chemoattractant (binding)
Output - ______ of flagella rotation
Info processed by CheA and CheY
Integral feedback occurs via CheB - phosphorylation state of CheB affects methylation of MCP, and therefore CheA activity
actually a closed loop - info from output feeds back into control circuit
65.
divergent: CAP
recognizes a 22 bp palindromic sequence
-aaaTGTGAtntanaTCACAttt
- like sigma factor recognition sequences, CAP-binding sequences sometimes diverge from consensus
-> highly ______ sequences bind CAP more weakly
-> consensus sequence does not occur naturally (rare) -> bind cAMP: CAP too strongly.
66.
DNA: Stringent response
-aims to conserve and redirect energy
characterized by two simultaneous physiological responses:
1) Shutdown of ribosome synthesis
2) Up-regulation of aa biosynthesis and proteolysis
+ temporary cessation of new rounds of ___ replication
+ Decrease in synthesis rates of phospholipids, carbohydrates and murein
67.
DNA: crp modulon
global regulator - CAP, ___ binding protein
effector molecule - cAMP, an 'alarmone'
68.
DNA binding domains: CAP
- dimer
- CTD contains DNA-binding HTH motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change
-> reorients two ___-______ ______ of dimer -> increase affinity for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
69.
dominant: global regulation: regulatory networks
crp modulon - part of a regulatory network
-principles of hierarchial organization
1) ________ over operon/regulon control
2) Activation by CAP:cAMP depends on binding affinity
70.
dominant: hierarchial organization of genes
modulon
global regulator is epistatic
-> regulation is superimposed (______) over individual regulators
71.
effector: crp modulon
global regulator - CAP, DNA binding protein
______ molecule - cAMP, an 'alarmone'
72.
eliminated: glucose-limiting conditions
[cAMP]i is high
[cAMP:CAP] is high
catabolite repression is _______ (maximal / eliminated)
capacity to synthesize all modulon enzymes is maximal
73.
elongation: stringent response
ppGpp production lowers [GTP]
GTP is required for polypeptide ________on ribosome
-> reduces rate of protein synthesis
74.
environmental: hierarchial organization of genes
stimulon
large group of operons that respond together to an ________ stimulus
not necessarily controlled through a common regulatory system
-> i.e. identifying a set of genes as stimulon provides no info on organization/mechanism of regulation
75.
enzymes: stringent response
-scarce aa conserved for making new ______ that allow cell to adapt to new condition and resume growth
76.
epistatic: hierarchial organization of genes
modulon
global regulator is _______
-> regulation is superimposed (domiannt) over individual regulators
77.
exponentially growing: ppGpp reprograms RNAP
1) Change promoter specificity of RNAPsigma70
-sigma70 is the major sigma factor in _______ ______ cells
- ppGpp destabilizes open complex of RNAPsigma70 at growth-associated promoters (e.g. Prrn)
- positively regulates sigma-70 dependent genes associated with maintenance and stress defence (frequency of initiation by RNApsigma70 increased)
2) Increase competitive factor of other sigma factors for RNAP
78.
feedback: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (sensor)
3) Sensor generates Signal
4) Signal affects activity of a Regulator
- directly
- indirectly (mediated by Transducer)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-______ control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
79.
G: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) RelA - ribosome-associated ppGpp synthetase
Activated RelA catalyzes two rxns:
ATP + _TP -> pppGpp + AMP
ATP + _DP -> ppGPP + AMP
2) SpoT
80.
genes: hierarchial organization of genes
operon
- a group of ____ of related function that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
81.
global: how is coordination achieved?
1) Independently adjustable controls of specific pathways
2) ______ systems of regulation
3) Hierarchial regulatory organizations
82.
global: crp modulon
______ regulator - CAP, DNA binding protein
effector molecule - cAMP, an 'alarmone'
83.
global: crp modulon promoters (lac operon promoter, ara regulon promoter...etc) are often regulated by several transcription factors
-> operon/regulon specific activators/regulators + _____ regulator (cAMP:CAP)
84.
global regulator: hierarchial organization of genes
modulon
- group of operons/regulons, under the control of a common ____ ______in addition to individual operon/regulon specific regulatory proteins
85.
global regulator: ppGpp is a _____ ______
86.
global regulatory system: Stringent response
-a ________ ________ ______ responding to any type of nutritional stress (shift to poorer C, energy or N source) that results in decreased growth rate
87.
global signal: crp modulon
[cAMP] reflects metabolic flux
-> represents a ______ ________
88.
growth: Stringent response
-global network responding to any type of nutritional stress (shift to poorer C, energy of N source) that results in decreased _____ rate
89.
growth: stringent response
- as aa supply is increased, temporary restrictions lifted one by one, and cell can resume ____ at slower rate (return to prestimulus state)
90.
growth survival: Product of member genes (i.e. whose transcription is affected by regulator) - perform some cellular function to promote cell ______ or _____
91.
GTP: stringent response
ppGpp production lowers [___]
____ is required for polypeptide elongation on ribosome
-> reduces rate of protein synthesis
92.
hierarchial: how is coordination achieved?
1) Independently adjustable controls of specific pathways
2) Global systems of regulation
3) _______ regulatory organizations
93.
hierarchial: Systems biology - provides unparalleled insights into global networks, proteomics, transcriptomics, protein-protein interaction networks, gene disruptions
1) provide data on several levels: transcription, translation, enzyme activity. does not invariably change in parallel.
2) Provide data on
a) interconectivity of networks
b) ________ organization
c) robustness (control theory)
94.
high: glucose-limiting conditions
[cAMP]i is ___
[cAMP:CAP] is ___
catabolite repression is eliminated
capacity to synthesize all modulon enzymes is maximal
95.
high affinity: hierarchy of transcriptional activation within modulon
- based on variation in binding affinity of sites
- sites within ____ ______ filled first (i.e. as cAMP levels begin to rise)
96.
HTH: CAP
- dimer
- CTD contains DNA-binding ___ motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to RNAP
- binding of cAMP induces conformational change
-> reorients two DNA-binding domains of dimer
-> increase affinity for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
97.
I: Class _ CAP promoters (Plac)
CAP dimer centered at -61.5
downstream CAP subunit binds via its AR1
98.
II: Class __ CAP promoters (galP1)
CAP dimer centered at -41
upstream CAP subunit via AR1
downstream CAP subunit via AR2 and AR3
99.
increase: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) ______ competitive factor of other sigma factors for RNAP
100.
independently adjustable: how is coordination achieved?
1) ________ _______ controls of specific pathways
2) Global systems of regulation
3) Hierarchial regulatory organizations
101.
individual: hierarchial organization of genes
modulon
global regulator is epistatic
-> regulation is superimposed (domiannt) over _______ regulators
102.
inducer: cAMP-CAP "cocks" crp regulon promoters, but individual promoters won't fire unless inducing metabolite is also present.
-> induction of particular operons/regulosn requires presence of particular ______
103.
insensitive: A robust control circuit should relatively be ______ to "noise" or perturbations
104.
insufficient: stringent control network critical for stasis survival
E. coli enters stasis when insufficient ________ for growth (stationary phase)
stringent resposne induces stationary phase genes, including many survival-related genes
stationary phase genes under control of sigma^s
- not induced in mutants defective in stringent control
-> such mutants die prematurely in stasis
105.
integral feedback: Control theory
- revealed two mechanisms that biological systems utilize to ensure robustness
1) ______ _______
2) Bifunctional enzymes
106.
interconnectivity: Systems biology - provides unparalleled insights into global networks, proteomics, transcriptomics, protein-protein interaction networks, gene disruptions
1) provide data on several levels: transcription, translation, enzyme activity. does not invariably change in parallel.
2) Provide data on
a) _________ of networks
b) hierarchial organization
c) robustness (control theory)
107.
levels: Systems biology - provides unparalleled insights into global networks, proteomics, transcriptomics, protein-protein interaction networks, gene disruptions
1) provide data on several ______: transcription, translation, enzyme activity. does not invariably change in parallel.
2) Provide data on
a) interconectivity of networks
b) hierarchial organization
c) robustness (control theory)
108.
ligand: Regulator activity
-mediated by synthesis, degradation, _____ binding, covalent modification (regulatory enzyme)
109.
low: rich media (LB, glucose-saturating)
[cAMP]i is ___
no cAMP:CAP complexes
crp modulon gene repressed by CAP-dependent global control system
lac operon or ara regulon not induced, even if specific inducer is present
110.
maintenance: ppGpp affects a broad range of physiological processes
1) Negatively regulate cell proliferation and growth genes (e.g. rrn genes)
2) Positively regulate _________ genes (e.g. (sigmaS) and his (histidine biosynth.) genes)
111.
maintenance stress: ppGpp reprograms RNAP
1) Change promoter specificity of RNAPsigma70
-sigma70 is the major sigma factor in exponentially growing cells
- ppGpp destabilizes open complex of RNAPsigma70 at growth-associated promoters (e.g. Prrn)
- positively regulates sigma-70 dependent genes associated with ______ and ____ defence (frequency of initiation by RNApsigma70 increased)
2) Increase competitive factor of other sigma factors for RNAP
112.
maximal: glucose-limiting conditions
[cAMP]i is high
[cAMP:CAP] is high
catabolite repression is eliminated
capacity to synthesize all modulon enzymes is _______ (maximal / eliminated)
113.
metabolic flux: crp modulon
[cAMP] reflects ______ ______
-> represents a global signal
114.
metabolite: cAMP-CAP "cocks" crp regulon promoters, but individual promoters won't fire unless inducing _______ is also present.
-> induction of particular operons/regulosn requires presence of particular inducer
115.
metabolites: Global regulation: coordination devices
1) Allosteric regulator
2) Alternate sigma factor
3) Allosteric regulator + sigma factor
4) _______
- (alarmones; low MW) - can activate regulators or act in other ways. (e.g. cAMP, ppGpp)
116.
mRNA: stringent response
autoregulation - r-proteins bind to rRNA in ribosome;
have similar binding site on own ____ - if r-proteins accumulate, they bind their own _____, preventing translation.
117.
multifactorial: adaptation to an environmental stimulus is a coordinated series of linked events
- not simply a group of independent responses by individual enzymes, genes, operons
they are coordinated with each other, and to the bigger picture of the cell's physiology.
most environmental shifts are _________ (i.e. >1 parameter changes)
118.
mutational: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> ________ / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
119.
necessarily: hierarchial organization of genes
stimulon
large group of operons that respond together to an environmental stimulus
not _________ controlled through a common regulatory system
-> i.e. identifying a set of genes as stimulon provides no info on organization/mechanism of regulation
120.
networks: Interconnectivity
Regulatory networks overlap
Many genes belong to several _____
Within _____, genes arranged in hierarchies
Understanding interrelatedness and connectivity of network -> critical to understanding how bacteria respond to environmental changes
121.
no: rich media (LB, glucose-saturating)
[cAMP]i is low
__ (no / lots of) cAMP:CAP complexes
crp modulon gene repressed by CAP-dependent global control system
lac operon or ara regulon not induced, even if specific inducer is present
122.
not induced: rich media (LB, glucose-saturating)
[cAMP]i is low
no cAMP:CAP complexes
crp modulon gene repressed by CAP-dependent global control system
lac operon or ara regulon ______ (induced / not induced), even if specific inducer is present
123.
nutrient: E. coli contains >200 reguilatory networks, classified into
1) ______ limitation (C, energy, N, P sources)
2) Oxidation/reduction
3) Stress and damage
4) Physiology and morphology
124.
nutrient: Stimulus-response pathway
Stimulus - change in _____ availability, temperature, or toxicitiy
Sensor/ Transducer / Regulator - proteins
125.
nutrient building block: hierarchial organization of genes
operon
- a group of genes of related function that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
what does "related function" mean?
genes that function in the same physiological process
pathway that catabolizes a particular _____ or biosynthesizes a particular _____ _______
126.
nutritional: [cAMP]i (cAMP in the cell) signals ______ status of cell
127.
nutritional status: crp modulon
promoters integrate information derived from 2 distinct signals
1) Overall ______ _______ (via CAP and cAMP)
2) Availability of C sources (through regulators and effectors)
128.
nutritional stress: Stringent response
-global network responding to any type of _______ _____ (shift to poorer C, energy or N source) that results in decreased growth rate
129.
operon: hierarchial organization of genes
_____
- a group of genes of related function that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
130.
operon regulon: crp modulon promoters (lac operon promoter, ara regulon promoter...etc) are often regulated by several transcription factors
-> _____/______ specific regulators + global regulator (cAMP:CAP)
131.
operons: hierarchial organization of genes
stimulon
large group of ________ that respond together to an environmental stimulus
not necessarily controlled through a common regulatory system
-> i.e. identifying a set of genes as stimulon provides no info on organization/mechanism of regulation
132.
operons regulons: hierarchial organization of genes
modulon
- group of _____/______, under the control of a common global regulator in addition to individual ______/_____ specific regulatory proteins
133.
opposing: Robustness - two mechanisms that biological systems utilize to ensure robustness:
1) Integral feedback
2) Bifunctional enzymes
-catalyze rxns that modify target in "_______" manners
a) SpoT - hydrolysis/synthesis of ppGpp
b) Sensor kinases - catalyze phosphorylation/dephosphorylation of target regulators
Rxns are not truly reversible - respective enzymes catalyze rxns that have opposite effects on target molecules
134.
opposite: Robustness - two mechanisms that biological systems utilize to ensure robustness:
1) Integral feedback
2) Bifunctional enzymes
-catalyze rxns that modify target in "opposing" manners
a) SpoT - hydrolysis/synthesis of ppGpp
b) Sensor kinases - catalyze phosphorylation/dephosphorylation of target regulators
Rxns are not truly reversible - respective enzymes catalyze rxns that have ______effects on target molecules
135.
organize: Stimulus-response pathway - ways to _____ mass of info related to network
136.
overlap: Interconnectivity
Regulatory networks _____
Many genes belong to several networks
Within networks, genes arranged in hierarchies
Understanding interrelatedness and connectivity of network -> critical to understanding how bacteria respond to environmental changes
137.
oxidation reduction: E. coli contains >200 reguilatory networks, classified into
1) Nutrient limitation
2) _______/______ (electron transport, different TEA)
3) Stress and damage
4) Physiology and morphology
138.
palindromic: CAP
recognizes a 22 bp ________ sequence
-aaaTGTGAtntanaTCACAttt
- like sigma factor recognition sequences, CAP-binding sequences sometimes diverge from consensus
-> highly divergent sequences bind CAP more weakly
-> consensus sequence does not occur naturally (rare) -> bind cAMP: CAP too strongly.
139.
phospholipids carbohydrates murein: Stringent response
-aims to conserve and redirect energy
characterized by two simultaneous physiological responses:
1) Shutdown of ribosome synthesis
2) Up-regulation of aa biosynthesis and proteolysis
+ temporary cessation of new rounds of DNA replication
+ Decrease in synthesis rates of _______, _______ and ____
140.
phosphorylation: Transduction - ____________ - common mechanism of signal transduction
141.
physiological: hierarchial organization of genes
operon
- a group of genes of related function that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
what does "related function" mean?
genes that function in the same _________ process
pathway that catabolizes a particular nutrient or biosynthesizes a particular building block
142.
physiology morphology: E. coli contains >200 reguilatory networks, classified into
1) Nutrient limitation
2) Oxidation/reduction
3) Stress and damage
4) _______ and ________ (stationary phase, sporulation, virulence)
143.
pleiotropic: hierarchial organization of genes
modulon
mutation global regulator causes _______ phenotypes -> affect expression of all modulon members
144.
polycistronic: hierarchial organization of genes
operon
- a group of genes of related function that occur contiguously in the genome
- transcribed from a single promoter as a ________ mRNA
145.
polyphosphate: stringent resposne
__________:ppGpp increases regulated proteolysis
-> increases intracellular concentration of __________
146.
positively: ppGpp affects a broad range of physiological processes
1) Negatively regulate cell proliferation and growth genes (e.g. rrn genes)
2) _______ regulate maintenance genes (e.g. rpoS (sigmaS) and his (histidine biosynth.) genes)
147.
ppG: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) RelA - ribosome-associated ppGpp synthetase
2) SpoT - bifunctional
a) catalyzes hydrolysis of ppGpp
ppGpp -> ppG + ppi
b) alternate SpoT, forms ppGpp using ATP
___ + ATP -> ppGpp + AMP
148.
ppGpp: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) _____ accumulates
7) _____ binds to RNAP
8) Binding of _____ reprograms RNAP causing a series of physiological responses
149.
ppGpp: RNAPsigma^s requires ____ for initiation in vivo -> _____ regulates sigma^s production and activity
150.
ppGpp: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ______
Regulator - RNAP
Response - 1) Decrease translation machinery synthesis; 2) Increase aa biosynthetic enzymes
Return - SpoT hydrolysis of ppGpp
151.
ppGpp: relA mutants , during aa starvation
1) Do not shut off tRNA / rRNA synthesis
-> accumualte rRNA
2) Do not accumulate _____
152.
ppGpp: Stringent response
- mediated by an alarmone - _____ (guanosine tetraphosphate)
153.
ppi: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) RelA - ribosome-associated ppGpp synthetase
2) SpoT - bifunctional
a) catalyzes hydrolysis of ppGpp
ppGpp -> ppG + __
b) alternate SpoT, forms ppGpp using ATP
ppG + ATP -> ppGpp + AMP
154.
precise robust: Integral feedback - standard engineering method for achieving ______, _____ control of circuit outputs
155.
precision reproducibility: Robustness - _______ and _________ of an output to a given input
156.
prestimulus: stringent response
- as aa supply is increased, temporary restrictions lifted one by one, and cell can resume growth at slower rate (return to _________ state)
157.
prestimulus equilibrium: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (sensor)
3) Sensor generates Signal
4) Signal affects activity of a Regulator
- directly
- indirectly (mediated by Transducer)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to ________ conditon or to new ________ consonant with changed environment
158.
proliferation growth: ppGpp affects a broad range of physiological processes
1) Negatively regulate cell _______ and ____ genes (e.g. rrn genes)
2) Positively regulate maintenance genes (e.g. rpoS (sigmaS) and his (histidine biosynth.) genes)
159.
promoter: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
3) Repression
CAP-binding site overlaps ______ elements (e.g. cyaP2)
4) Co-repression
160.
promoter: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change ______ specificity of RNAPsigma70
2) Increase competitive factor of other sigma factors for RNAP
161.
promoters: ppGpp reprograms RNAP
1) Change promoter specificity of RNAPsigma70
-sigma70 is the major sigma factor in exponentially growing cells
- ppGpp destabilizes open complex of RNAPsigma70 at growth-associated _______ (e.g. Prrn)
- positively regulates sigma-70 dependent genes associated with maintenance and stress defence (frequency of initiation by RNApsigma70 increased)
2) Increase competitive factor of other sigma factors for RNAP
162.
promoters: CAP:cAMP binds to crp modulon ______
CAP:cAMP acts in a variety of modes
1) Class I Activator
2) Class II Activator
3) Repressor
163.
protein: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
3) Repression
4) Co-repression
repression requires a second ____ in addition to CAP:cAMP
164.
proteins: stringent response
blocking transcription of tRNA and rRNA genes
-> lower levels of r-________
165.
proteomics microarray: ppGpp is a global regulator
how would you study the physiological effects of a global regulator?
1) _______ and _______
2) Proteomes of WT and ppGpp^0 cells compared as they enter C starvation
166.
regulation: hierarchial organization of genes
stimulon
large group of operons that respond together to an environmental stimulus
not necessarily controlled through a common regulatory system
-> i.e. identifying a set of genes as stimulon provides no info on organization/mechanism of _________
167.
regulator: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (sensor)
3) Sensor generates Signal
4) Signal affects activity of a ______
- directly
- indirectly (mediated by Transducer)
5) ______ controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
168.
regulators effectors: crp modulon
promoters integrate information derived from 2 distinct signals
1) Overall nutritional status (via CAP and cAMP)
2) Availability of C sources (through _______ and ______)
169.
regulatory: hierarchial organization of genes
operon
- a group of genes of related function that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
- transcription is controlled as a unit by a _______ protein (e.g. lac operon (3 genes, Lac I repressor), araBAD operon (3genes, AraC)
170.
regulatory: hierarchial organization of genes
regulon
- a group of genes of related function
- not all occur contiguously in the genome
- transcription is regulated by a single ________ protein
(e.g. ara genes, involved in uptake/catabolism of arabinose, are arranged in 4 transcriptional units, under control of a common regulatory protein AraC. subset of tehse genes occur in operons)
171.
regulatory: hierarchial organization of genes
moderon
- group of operons/regulons, under the control of a common global regulator in addition to individual operon/regulon specific ________proteins
172.
RelA: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates _____
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
173.
RelA: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) ___ - ribosome-associated ppGpp synthetase
Activated ___ catalyzes two rxns:
ATP + GTP -> pppGpp + AMP
ATP + GDP -> ppGPP + AMP
2) SpoT
174.
RelA SpoT: basal levels of ppGpp maintained by balance of synthetic activity of ____and hydrolytic activity of ____
175.
relA spoT: How would you construct a ppGpp^0 strain?
disrupt ____ and ____
176.
related function: hierarchial organization of genes
operon
- a group of genes of _____ ______ that occur contiguously in the genome
- transcribed from a single promoter as a polycistronic mRNA
177.
related function: hierarchial organization of genes
regulon
- a group of genes of ______ ______
- not all occur contiguously in the genome
- transcription is regulated by a single regulatory protein
(e.g. ara genes, involved in uptake/catabolism of arabinose, are arranged in 4 transcriptional units, under control of a common regulatory protein AraC. subset of tehse genes occur in operons)
178.
relaxed: relA mutants , during aa starvation
1) Do not shut off tRNA / rRNA synthesis
-> accumualte rRNA
2) Do not accumulate ppGpp
known as '________' strains
179.
repositions: CAP Co-activation
organization and position of CAp binding sites vary tremendously
Underlying reasons
1) Activator 1 ______ Activator 2
2) Both activators contact RNAP
e.g. Pbad
arabinose induces conformational change in AraC
-> alter half-site preference of AraC
180.
repressed: rich media (LB, glucose-saturating)
[cAMP]i is low
no cAMP:CAP complexes
crp modulon gene _______ (repressed/activated) by CAP-dependent global control system
lac operon or ara regulon not induced, even if specific inducer is present
181.
repression: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
3) _________
4) Co-repression
182.
repression: crp modulon
involved in catabolite ______
include genes that handle adaptation to particular (usually poor) growth conditions
include catabolic / non-catabolic genes
183.
repression loop: CAP Co-activation
e.g. Pbad
arabinose induces conformational change in AraC
-> alter half-site preference of AraC
-> CAP-binding site occurs between I1 and O1
-> CAP binding helps break I1-O2 ______ ______ (i.e. helps AraC-arabinose bind to I2)
CAP also makes specific contacts with RNAP alpha CTD
184.
repressor: CAP:cAMP binds to crp modulon promoters (lac operon promoter, ara regulon promoter...etc)
CAP:cAMP acts in a variety of modes
1) Class I Activator
2) Class II Activator
3) _______
185.
respond: Interconnectivity
Regulatory networks overlap
Many genes belong to several networks
Within networks, genes arranged in hierarchies
Understanding interrelatedness and connectivity of network -> critical to understanding how bacteria ______ to environmental changes
186.
reversible: Robustness - two mechanisms that biological systems utilize to ensure robustness:
1) Integral feedback
2) Bifunctional enzymes
-catalyze rxns that modify target in "opposing" manners
a) SpoT - hydrolysis/synthesis of ppGpp
b) Sensor kinases - catalyze phosphorylation/dephosphorylation of target regulators
Rxns are not truly ______ - respective enzymes catalyze rxns that have opposite effects on target molecules
187.
ribosomal: stringent response
-shutting down transcription of rrn genes
-shutting down translation of _______ protein / elongation factor genes
-> conserve 50% of aa and energy resources
188.
ribosome: Stringent response
-aims to conserve and redirect energy
characterized by two simultaneous physiological responses:
1) Shutdown of ______ synthesis
2) Up-regulation of aa biosynthesis and proteolysis
+ temporary cessation of new rounds of DNA replication
+ Decrease in synthesis rates of phospholipids, carbohydrates and murein
189.
ribosomes: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes _______ to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
190.
RNAP: CAP Co-activation
organization and position of CAP binding sites vary tremendously
Underlying reasons
1) Activator 1 repositions Activator 2
2) Both activators contact ____
e.g. Pbad
arabinose induces conformational change in AraC
-> alter half-site preference of AraC
191.
RNAP: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to ____
8) Binding of ppGpp reprograms ____ causing a series of physiological responses
192.
RNAP: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ppGpp
Regulator - ____
Response - 1) Decrease translation machinery synthesis; 2) Increase aa biosynthetic enzymes
Return - SpoT hydrolysis of ppGpp
193.
RNAP: CAP
- dimer
- CTD contains DNA-binding HTH motif
- NTD contains cAMP binding pocket
- Other parts responsibel for specific contacts to ____
- binding of cAMP induces conformational change
-> reorients two DNA-binding domains of dimer
-> increase affinity for DNA
CAP: cAMP complex induces ~90 degree bend in DNA
194.
RNAPsigma: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of ________70
2) Increase competitive factor of other sigma factors for RNAP
195.
robustness: Systems biology - provides unparalleled insights into global networks, proteomics, transcriptomics, protein-protein interaction networks, gene disruptions
1) provide data on several levels: transcription, translation, enzyme activity. does not invariably change in parallel.
2) Provide data on
a) interconectivity of networks
b) hierarchial organization
c) ______ (control theory)
196.
rrn: stringent response
-shutting down transcription of ___ genes
-shutting down translation of ribosomal protein / elongation factor genes
-> conserve 50% of aa and energy resources
197.
rRNA: relA mutants , during aa starvation
1) Do not shut off tRNA / ____ synthesis
-> accumualte ____
2) Do not accumulate ppGpp
198.
s: ppGpp reprograms RNAP
1) Change promoter specificity of RNAPsigma70
2) Increased ability of other sigma factors to compete for RNAP
sigma factors compete for limiting amounts of core RNAP
- increasing one sigma factor decreases transcription of genes dependent on other sigma factors
- ppGpp increases sigma^_ production
-> increases transcription from sigma^_ dependent promoters
-> decreases transcription from sigma^70-dependent promoters
RNAPsigma^_ requires ppGpp for initiation in vivo -> ppGpp regulates sigma^s_production and activity
199.
selective advantage: relA/spoT have conserved function in all bacteria
-> stringent response is a fundamental cellular process that provides _____ ______ to prokaryotes during nutritional, and perhaps other stresses
some bacteria have single bifunctional protein (fusion of RelA/SpoT)
200.
sensor: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (_____)
3) _____ generates Signal
4) Signal affects activity of a Regulator
- directly
- indirectly (mediated by Transducer)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
201.
sensor kinases: Robustness - two mechanisms that biological systems utilize to ensure robustness:
1) Integral feedback
2) Bifunctional enzymes
-catalyze rxns that modify target in "opposing" manners
a) SpoT - hydrolysis/synthesis of ppGpp
b) _____ ______ - catalyze phosphorylation/dephosphorylation of target regulators
Rxns are not truly reversible - respective enzymes catalyze rxns that have opposite effects on target molecules
202.
sigma: Global regulation: coordination devices
1) Allosteric regulator
2) Alternate _____ factor
- programs RNAP to recognize promoters of member operons
3) Allosteric regulator + _____ factor
4) Metabolites
203.
sigma: stringent control network critical for stasis survival
E. coli enters stasis when insufficient nutrients for growth (stationary phase)
stringent resposne induces stationary phase genes, including many survival-related genes
stationary phase genes under control of _____^s
- not induced in mutants defective in stringent control
-> such mutants die prematurely in stasis
204.
sigma: ppGpp reprograms RNAP
binds close to the active site (interact with beta and beta' subunits) -> mutational / crystallographic evidence
1) Change promoter specificity of RNAPsigma70
2) Increase competitive factor of other _____ factors for RNAP
205.
signal: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (sensor)
3) Sensor generates _____
4) _____ affects activity of a Regulator
- directly
- indirectly (mediated by Transducer)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
206.
signal: Transducer - device that receives _____from one device and passes it to another usually in different form
207.
Simple activation: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) _____ ______
2) Co-activation
3) Repression
4) Co-repression
208.
SpoT: ppGpp is synthesized by two enzymes
both synthetic reactions require ATP
1) RelA - ribosome-associated ppGpp synthetase
2) ____ - bifunctional
a) catalyzes hydrolysis of ppGpp
ppGpp -> ppG + ppi
b) alternate ____, forms ppGpp using ATP
ppG + ATP -> ppGpp + AMP
209.
SpoT: Robustness - two mechanisms that biological systems utilize to ensure robustness:
1) Integral feedback
2) Bifunctional enzymes
-catalyze rxns that modify target in "opposing" manners
a) ____ - hydrolysis/synthesis of ppGpp
b) Sensor kinases - catalyze phosphorylation/dephosphorylation of target regulators
Rxns are not truly reversible - respective enzymes catalyze rxns that have opposite effects on target molecules
210.
SpoT: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits ____
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
211.
SpoT ppGpp: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ppGpp
Regulator - RNAP
Response - 1) Decrease translation machinery synthesis; 2) Increase aa biosynthetic enzymes
Return - ____ hydrolysis of _____
212.
stall: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to ____ at codon requiring limiting aa-tRNA
3) Uncharged tRNA eventually enters A site of stalled ribosome
4) Uncharged tRNA binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
213.
stasis: stringent control network critical for ____ survival
E. coli enters ____ when insufficient nutrients for growth (stationary phase)
stringent response induces stationary phase genes, including many survival-related genes
stationary phase genes under control of sigma^s
- not induced in mutants defective in stringent control
-> such mutants die prematurely in stasis
214.
stimulus: Stimulus response pathway
1) Environmental _____
2) Affects some cellular target (sensor)
3) Sensor generates Signal
4) Signal affects activity of a Regulator
- directly
- indirectly (mediated by Transducer)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
215.
stimulus: Single _____ can trigger response in multiple modulons (through different mechanisms) e.g. glucose addition affects catabolite repression members and stringent response global regulatory networks
Coordinated activity of multiple genes - essential to cellular functions
216.
stimulus response: Stringent response is a form of ____-______ pathway
217.
stimulus response: _____-_____ pathway - ways to organize mass of info related to network
218.
stress and damage: E. coli contains >200 reguilatory networks, classified into
1) Nutrient limitation
2) Oxidation/reduction
3) _____ and ____ (oxidative, radiation, high and low T)
4) Physiology and morphology
219.
stringent response: relA/spoT have conserved function in all bacteria
-> ______ ______ is a fundamental cellular process that provides selective advantage to prokaryotes during nutritional, and perhaps other stresses
some bacteria have single bifunctional protein (fusion of RelA/SpoT)
220.
survival: stringent control network critical for stasis survival
E. coli enters stasis when insufficient nutrients for growth (stationary phase)
stringent resposne induces stationary phase genes, including many _____-related genes
stationary phase genes under control of sigma^s
- not induced in mutants defective in stringent control
-> such mutants die prematurely in stasis
221.
synergestically: CAP and crp modulon
single regulator (CAP:cAMP) can act in different ways
1) Simple Activation
2) Co-activation
- complex promoter
- cAMP:CAP act ___________ within operon specific activator
- organization and position of CAP binding sites vary tremendously
3) Repression
4) Co-repression
222.
synthesis: Regulator activity
-mediated by _______, degradation, ligand binding, covalent modification (regulatory enzyme)
223.
temperature: Stimulus-response pathway
Stimulus - change in nutrient availability, _______, or toxicitiy
Sensor/ Transducer / Regulator - proteins
224.
toxicitiy: Stimulus-response pathway
Stimulus - change in nutrient availability, temperature, or ______
Sensor/ Transducer / Regulator - proteins
225.
transducer: Stimulus response pathway
1) Environmental stimulus
2) Affects some cellular target (sensor)
3) Sensor generates Signal
4) Signal affects activity of a Regulator
- directly
- indirectly (mediated by _______)
5) Regulator controls output
- usually adaptive response to environment
e.g. expression of a catabolic pathway in presence of some C source
-Feedback control mechanism often present
-> permits return to prestimulus conditon or to new equilibrium consonant with changed environment
226.
translation machinery: Interpretation of stringent response as stimulus-response pathway
Stimulus - Decrease of supply of aa
Sensor - RelA-ribosome; detects uncharged tRNA in A site
Signal - ppGpp
Regulator - RNAP
Response - 1) Decrease _______ ______ synthesis; 2) Increase aa biosynthetic enzymes
Return - SpoT hydrolysis of ppGpp
227.
uncharged tRNA: Stringent response: overall mechanism
1) Drop in [aa] leads to drop in [aa-tRNA]
2) Lack of aa-tRNA causes ribosomes to stall at codon requiring limiting aa-tRNA
3) ______ ____ eventually enters A site of stalled ribosome
4) _________ ____ binding activates RelA
5) aa starvation concomitantly inhibits SpoT
6) ppGpp accumulates
7) ppGpp binds to RNAP
8) Binding of ppGpp reprograms RNAP causing a series of physiological responses
