Module 6 - Regulation of Gene Expression Flashcards
1
Q
What is gene expression?
A
A process where information from a gene is used in the synthesis of a functional gene product (often a protein)
2
Q
How do cells conserve energy?
A
Not all the genes are expressed all the time
3
Q
What are constitutive genes?
A
Genes that are constantly on
4
Q
What are some examples of constitutive genes?
A
Genes involved in glycolysis, transcription, and translation
5
Q
What are inducible genes?
A
Genes that are needed when a substrate is present
6
Q
What are the three levels of gene expression?
A
Transcriptional, translational, and post-translational
7
Q
What is transcriptional control of gene expression?
A
Binding of RNA polymerase to the promoter and initiating transcription
8
Q
What is translational control of gene expression?
A
Binding of the ribosome to mRNA for continued translation
9
Q
What is post-translational control of gene expression?
A
Modification of the protein to activate, inhibit, or degrade it
10
Q
What are enzymes?
A
Biological catalysts
11
Q
How can the activity of an enzyme be altered?
A
By changing its confirmation due to modifications, or by using inhibitors
12
Q
What modifications can be done to an enzyme to alter its function?
A
Phosphorylation, acetylation, methylation, and glycosylation
13
Q
What is a competitive inhibitor?
A
An inhibitor that competes directly with the substrate for the active site of the enzyme
14
Q
What is a non-competitive inhibitor?
A
An inhibitor that binds to an allosteric site
15
Q
What is an allosteric site?
A
A site other than the active site on the enzyme
16
Q
What is another name for allosteric inhibition?
A
Feedback inhibition
17
Q
What happens when the enzyme activity is modified?
A
The biochemistry of the cell is changed
18
Q
True or false: modifying an enzyme is a conservative process
A
False: it does not save much energy
19
Q
How come modifying an enzyme is not a conservative process?
A
It still takes a lot of energy to create the enzyme in the first place
20
Q
What is a better way for the cell to save energy?
A
By only producing the enzyme when it is needed
21
Q
How do most of the control mechanisms in bacteria work?
A
By preventing transcription (and thus translation) of genes when not required
22
Q
What does the operon mechanism suggest?
A
A method where regulatory genes can direct cell metabolism by altering rates of transcription of functional genes
23
Q
What is an operon?
A
A transcriptional unit with a series of structural genes and their transcriptional regulatory elements
24
Q
If a cell requires three proteins for a single process, how should they be regulated?
A
They should either all be produced or not produced at the same time
25
When was the first eukaryotic operon found?
In the 1990s
26
True or false: operons are only found in prokaryotes
False: while this was originally thought to be true, eukaryotic operons have been discovered
27
What does expression of prokaryotic operons lead to?
Polycistronic mRNA
28
What is polycistronic mRNA?
mRNA that encodes for 2 or more proteins
29
What is the majority of mRNA in eukaryotic cells?
Monocistronic mRNA
30
What is monocistronic mRNA?
mRNA that encodes for one protein
31
What are the structural genes of the lac operon?
lacZ, lacY, and lacA
32
What is another name for LacY?
Permease
33
What does LacY do?
Facilitates the uptake of lactose
34
What is another name for LacZ?
Beta-galactosidase
35
What does LacZ do?
Breaks down lactose enzymatically
36
What is another name for LacA?
Beta-galactosidase transacetylase
37
What does LacA do?
It is not well understood currently
38
Where does RNA polymerase bind to?
The promoter
39
Where do regulatory proteins bind to?
The operator
40
What do regulatory proteins do?
Modulate the ability of RNA polymerase to bind to the promoter
41
What does LacI do?
Inhibits the lac operon
42
What is negative control?
When regulatory proteins inhibit operon transcription
43
What is positive control?
When regulatory proteins facilitate operon transcription
44
What happens when lactose enters the cell?
It gets metabolized to glucose and galactose by beta-galactosidase
45
What two simple sugars make up lactose?
Glucose and galactose
46
What is allolactose?
An isomer of lactose
47
What reaction produced allolactose?
Beta-galactosidase converts lactose into allolactose
48
What does allolactose do?
It acts as an inducer of the lac operon (it turns it on)
49
What is a promoter?
The site on the DNA bound by RNA polymerase
50
What is an activator?
A protein that binds to a site on the DNA
51
What does a promoter do?
It directs initiation of transcription
52
What does an activator do?
It assists binding of RNA polymerase to the promoter
53
What is an activator binding site?
A site on the DNA bound by an activator
54
What is a repressor?
A protein that binds to the operator site to inhibit transcription
55
What is an operator?
A site on the DNA bound by a repressor
56
What is an effector?
A small molecule that binds to an activator or a repressor
57
What does an effector do?
Modifies gene regulation activity by being an inducer or corepressor
58
What is an inducer?
An effector than increases transcription
59
How does an inducer work?
It either enables an activator or disables a repressor
60
What is a corepressor?
An effector that decreases transcription
61
How does a corepressor work?
By enabling a repressor
62
What is LacI?
A repressor molecule
63
What does LacI do?
Binds to the operator as a dimer to interfere with the binding of RNA polymerase
64
What is the effector of the lac operon?
Allolactose
65
What type of proteins are usually effectors?
Intermediates of the related metabolic pathway
66
What happens to the lac operon in the absence of lactose?
Transcription is off due to LacI binding to the operator
67
What happens to the lac operon in the presence of lactose?
Allolactose acts as an inducer by inhibiting LacI, thus promoting transcription
68
What type of effector is allolactose?
An inducer (it inhibits LacI)
69
How does allolactose work?
It inactivates LacI by changing its shape so it can't bind to the operator
70
What types of reactions are usually done by negative control?
Catabolic pathways in the absence of substrates
71
How many structural genes are in the trp operon?
6
72
What happens to the trp operon in the absence of tryptophan?
The repressor cannot bind to the operator, and the structural genes are transcribed
73
What happens to the trp operon in the presence of tryptophan?
Tryptophan acts a corepressor to allow the repressor to bind to the operator region
74
What is the effector molecule in the trp operon?
Tryptophan
75
What type of effector is tryptophan?
A corepressor
76
What type of control is the lac operon (considering lactose)?
Negative control
77
What type of control is the lac operon (considering glucose)?
Positive control
78
What type of control is the trp operon?
Negative control
79
True or false: the activator protein always binds directly to the activator site
False: there could be another protein involved
80
What is the activator protein in the lac operon?
CRP
81
What does CRP stand for?
cAMP receptor protein
82
What is the co-activator of CRP?
cAMP
83
How does CRP work?
When bound to cAMP, it binds to the activator site to promote binding of RNA polymerase to the promoter
84
What do E. coli cells grow best in?
Glucose (as opposed to lactose)
85
How come E. coli cells grow better in glucose than lactose?
Glucose can enter glycolysis directly, while lactose must first be converted into glucose and galactose
86
What is needed for the lac operon to be transcriped?
The repressor (LacI) must be unbound, and the activator (CRP) must be bound
87
When there is glucose present, what are the cAMP levels?
Low
88
Where glucose is absent, what are the cAMP levels?
High
89
What is catabolite repression?
When a catabolite is preferred over another, so there is repression of the catabolism of the nonpreferred catabolite
90
What happens when glucose is absent and lactose is present in a cell?
The operon has the activator, and there is transcription
91
What happens when glucose and lactose is absent in a cell?
The operon has the activator and the repressor, so there is low transcription
92
What happens when glucose is present and lactose is absent in a cell?
The operon has the repressor, so there is no transcription
93
What happens when glucose and lactose is present in a cell (in terms of the operon)?
The operon has no repressor or activator, so there is low transcription
94
What happens when glucose and lactose are available (in terms of sugar availability)?
Glucose is used first, and then lactose is used
95
What is a diauxic growth curve?
A growth curve caused by the use of two metabolites
96
When does a diauxic growth curve occur?
When a cell has both glucose and lactose available
97
What is the shape of a diauxic growth curve?
Logistic (steep at the ends, flat in the middle)
98
What happens when glucose becomes depleted in diauxic growth?
Beta-galactosidase and permease must be produced before the cells can use lactose
99
What does the flat region on the diauxic growth represent?
The cells not growing because they have to produce the enzymes of the lac operon
100
What happens during the lag phase of diauxic growth?
The cells are not growing because they are producing LacZ and LacY
101
What did scientists use to understand the role of LacI?
Mutants that constitutively expressed beta-galactosidase (even in absence of lactose)
102
What does I- refer to?
Inducer negative mutants (mutants that constitutively expressed beta-galactosidase)
103
What happened when a wild type copy of the lac region was inserted as a plasmid in I- mutants?
They could now be induced for expression of beta-galactosidase
104
What was the conclusion of putting a wild type copy of the lac region in I- mutants?
LacI was diffusable
105
How was it discovered that LacI was diffusable?
It was able to complement a lac mutant, even on a separate piece of DNA (plasmid)
106
What does O- refer to?
Mutants that had a mutation at the operator site
107
What happened when a wild type copy of the lac region was inserted as a plasmid in O- mutants?
There was still constitutive expression of beta-galactosidase
108
What was the conclusion of putting a wild type copy of the lac region in O- mutants?
LacI binds to the operator to stop transcription
109
How was it discovered that LacI binds to the operator?
When the operator was mutated and LacI was expressed, the system remained constitutively active
110
What happens when a cell is under stressed conditions (such as high temperature)?
Heat shock proteins are produced to help the cell survive
111
What are regulons?
Groups of operons coordinated to respond to the same regulatory systems
112
What is an example of global control?
Regulation by glucose
113
How does glucose act as a global control?
It is involved in catabolite repression to shut down other pathways
114
In E. coli, how many operons does CRP regulate?
100
115
What environmental stresses can damage DNA?
UV radiation and chemicals
116
What is the SOS response?
A regulon that allows the cell to recognize and respond to serious DNA damage
117
What was used for the experimental evidence for the existence of regulons?
Bacteriophages treated with UV light
118
What two E. coli cultures were used to prove the existence of regulons?
One that was preexposed to UV, and another that was untreated
119
What happened when E. coli untreated with UV were mixed with the phages?
There was a low number of phages, and no increase in mutations
120
What happened when E. coli treated with UV were mixed with the phages?
There was a greater number of phages, with an increase in phage mutations
121
What did the experiments with UV light on E. coli show?
That DNA repair is error prone (generates mutations)
122
What does chloramphenicol do?
It is an antibiotic that blocks protein synthesis in bacteria
123
What happened when chloramphenicol was added to E. coli?
DNA repair was also blocked
124
What was the conclusion from adding chloramphenicol to E. coli?
DNA repair required protein synthesis
125
How were the genes expressed for DNA repair identified?
Through a lacZ promoter probe transposon
126
What is a lacZ promoter probe transposon?
A promoter-less lacZ reporter gene that can insert into DNA
127
How does lacZ get expressed in a lacZ promoter probe transposon?
It must insert within an actively transcribed gene
128
How can the lacZ in the lacZ promoter probe transposon be identified?
By using X-gal to see if there is LacZ activity
129
What happens if LacZ inserts into an active gene?
It will show up blue in the presence of X-gal
130
What happens if LacZ inserts into an inactive gene?
It will show up white in the presence of X-gal
131
What DNA damaging agent was used to study the SOS regulon?
Mitomycin C
132
In the experiments with Mitomycin C, which cells had genes that were part of the SOS regulon?
Those that were blue in the presence of Mitomycin C, but white in the absence of Mitomycin C
133
What does din stand for?
Damage induced gene
134
What are din genes?
Genes part of the SOS regulon that respond to DNA damage
135
How do cells sense DNA damage?
They detect single stranded DNA (a result of damage)
136
Which genes can alter the SOS response?
lexA and recA
137
What is recA involved in?
Recombination
138
What does RecA do?
Binds to single stranded DNA to regulate the SOS regulon
139
What is RecA activated?
When it is bound to single stranded DNA
140
What does LexA do?
It is a repressor that binds to the operator of the SOS regulon
141
What does RecA do when it is bound to single stranded DNA?
It cleaves LexA
142
What happens when LexA is cleaved?
It can no longer bind to the operator, so the SOS genes are expressed
143
How many genes in E. coli are part of the SOS regulon?
40
144
Besides regulons, how can global gene regulation be achieved?
Through alternative sigma factors
145
What is a sigma factor and what does it do?
A polypeptide that allows RNA polymerase to identify promoter for initiation of transcription
146
What is a primary sigma factor?
The sigma factor responsible for recognizing the most promoters
147
What is the primary sigma factor in E. coli?
Sigma-70
148
What does Sigma-54 do?
Regulates nitrogen utilization genes
149
What is required for Sigma-54 to function?
An activating protein and ATP to initiate transcription
150
True or false: Sigma-70 requires an activating protein and ATP to initiate transcription
False: Sigma-54 requires this, not Sigma-70
151
What does Sigma-32 do?
Regulates heat shock proteins
152
What does Sigma-38 do?
It is a general stress response gene regulator
153
Which sigma factor is a general stress response gene regulator?
Sigma-38
154
Which sigma factor regulates heat shock proteins?
Sigma-32
155
Which sigma factor regulates nitrogen utilization?
Sigma-54
156
What RNAs are encoded in the genome?
rRNA, tRNA, and regulatory RNAs
157
What is sRNA?
Small noncoding RNAs
158
How big are sRNAs?
50-400 nt
159
What do sRNAs do?
Affect gene expression by interacting with existing mRNA
160
How do sRNAs silence a gene?
By preventing transcription from completing or by blocking translation
161
What are some types of sRNA?
miRNA, siRNA, and asRNA
162
What does miRNA stand for?
MicroRNA
163
What does siRNA stand for?
Small interfering RNA
164
What does asRNA stand for?
Antisense RNA
165
What is another name for Sigma-38?
rpoS
166
What does rpoS stand for?
RNA polymerase S
167
How do asRNAs work?
They use complementary base pairing to interact with specific mRNA molecules
168
What does rpoS do in the absence of asRNA?
It inhibits translation through its 5' leader sequence
169
What is the structure of rpoS?
A 5' leader sequence that forms a hairpin stem loop structure
170
What happens when cells are exposed to different stresses?
They accumulate different sRNAs
171
What is DsrA?
A sRNA
172
When is DsrA produced?
When the cell is exposed to low temperatures
173
What does DsrA do?
It binds with Hfq, which binds to rpoS
174
What is Hfq?
An RNA-binding protein for DsrA
175
What happens when DsrA and Hfq bind to RpoS?
They disrupt the inhibitory secondary structure, which allows translation to proceed
176
What are riboswitches?
Regulatory molecules that bind to RNA and alter its shape
177
What is quorum sensing?
A chemical signaling system used to detect presence and number of other organisms in a population
178
What is a quorum?
The number of members that must be present at a meeting to conduct business
179
What does quorum sensing involve?
Release of specific signaling molecules called autoinducers
180
What does an autoinducer do?
It acts as a signaling molecule that increases in concentration as density of bacterial population increases
181
How can bacteria assess population density?
By detecting autoinducer concentration
182
What happens when population density changes?
Gene expression may also change
183
What is special about Vibrio fischeri?
They can produce light
184
Which organism does Vibrio fischeri live inside?
The Hawaiian bobtail squid
185
What does the light organ in bobtail squid do?
It luminesces when colonized by V. fischeri
186
What was the first quorum sensing system described?
The lux system
187
What does luciferase do?
Produces light
188
When do V. fischeri cells emit light?
When they are at a high density
189
What is the autoinducer in the lux system?
AHL
190
What does AHL stand for?
N-acyl-homoserine lactone
191
True or false: AHL is only used for intracellular signaling in V. fischeri
False: it is seen in many other types of bacteria
192
What protein synthesizes AHL?
LuxL
193
What does LuxL do?
Synthesizes AHL
194
At low cell density, what is the concentration of AHL?
Low
195
How come AHL concentration is low at low cell density?
It diffuses away from the cell
196
At high cell density, what is the concentration of AHL?
High
197
What happens when there is a high concentration of AHL?
It binds to LuxR
198
What is LuxR?
A transcriptional activator protein
199
What happens when LuxR is activated?
It binds to the lux box to promote transcription
200
What is the lux box?
A regulatory DNA site for the lux operon
201
What is encoded by the lux operon?
LuxA, LuxB, and LuxL
202
What does LuxA and LuxB do?
Encode luciferase
203
True or false: the lux system is a positive feedback mechanism
True: LuxL is produced, which creates more AHL
204
How is the lux system a positive feedback loop?
LuxL is produced, which creates more AHL to regulate the lux operon further
205
What processes can be controlled by quorum sensing?
Motility, conjugation, biofilm formation, pathogenesis, and secondary metabolite production
206
How can quorum sensing control pathogenesis?
By producing cholera toxin when enough cells are present (V. cholera)
207
How can autoinducers play a role in competition?
They may interrupt or inhibit a control pathway in other organisms in the environment
208
How to cells commonly react to the environment?
Through a two component regulatory system
209
What are the components of a two component regulatory system?
A sensor protein, and a protein that regulates transcription
210
What happens when the two components of a two component regulatory system interact?
It creates signal transduction
211
What are the most common regulatory systems in bacteria?
A two component system
212
What is a commonly used sensor?
HPK
213
What does HPK stand for?
Histidine protein kinase
214
What does RR stand for?
Response regulator
215
What does HPK do?
It becomes phosphorylated and phosphorylates RR
216
What happens when RR is phosphorylated?
It changes confirmation and regulates gene expression
217
What is chemotaxis?
The movement of motile bacteria in response to a chemical stimulus
218
Why is chemotaxis important in bacteria?
It is important to swim towards the highest concentration of food or run away from detrimental chemicals
219
In which organism is regulation of chemotaxis best understood?
In E. coli
220
What is the flagella structure of E. coli?
Peritrichous (several flagella all around the cell)
221
What happens during counterclockwise rotation?
The cell propels forward
222
What happens during clockwise rotation?
It causes a tumble (change of direction)
223
What happens to flagellar rotation in the absence of an attractant or repellant?
It alternates between clockwise and counterclockwise rotation
224
What is the rate of rotation switching in E. coli?
Once per sec
225
What happens to flagellar rotation in the presence of an attractant or repellent?
The ratio of clockwise to counterclockwise rotation changes
226
What did researchers use to understand chemotaxis?
Mutants where chemotaxis was disrupted
227
How were mutants where chemotaxis was disrupted isolated?
By using a capillary tube with semi-solid agar and higher concentration of attractant than surrounding media
228
In the apparatus to isolate chemotaxis mutants, where would wild-type E. coli be found?
In the capillary tube
229
How come wild type E. coli would be in the capillary tube?
There is a higher concentration of attractant there
230
In the apparatus to isolate chemotaxis mutants, where would the mutants be?
In the surrounding media
231
How come chemotaxis mutants would be in the surrounding media?
Because they would not move to the capillary tube with higher concentration
232
Mutations in which genes result in counterclockwise rotation?
cheA, cheY, cheW, or cheR
233
Mutations in which genes result in clockwise rotation?
cheB or cheZ
234
What happens if cheA is mutated?
Counterclockwise rotation
235
What happens if cheY is mutated?
Counterclockwise rotation
236
What happens if cheW is mutated?
Counterclockwise rotation
237
What happens if cheR is mutated?
Counterclockwise rotation
238
What happens if cheB is mutated?
Clockwise rotation
239
What happens if cheZ is mutated?
Clockwise rotation
240
What does the regulation of chemotaxis involve?
Protein switches
241
What proteins are found in all chemotactic bacteria?
CheA and CheY
242
What does CheA do?
Acts as the sensor kinase in the system
243
How does CheA work?
It is phosphorylated at a histidine residue in response to the presence or absence of a particular attractant or repellant
244
What does CheY do?
Acts as a RR in the system
245
What does pCheA do?
It phosphorylates CheY at a specific aspartic residue
246
What does pCheY do?
It interacts with the flagellar motor to determine direction of rotation
247
True or false: phosphorylation circuit is typical in a 2 component regulatory system
True: phosphorylation is very common in cell signaling
248
In the absence of an attractant, what state is CheA in?
Phosphorylated state
249
What phosphorylates CheA?
CheW
250
What does CheW do?
Phosphorylates CheA in the absence of an attractant
251
What direction does pCheY lead to?
Clockwise rotation (tumble)
252
When does a cell tumble?
Clockwise rotation
253
What does a cell run?
Counterclockwise rotation
254
What happens when pCheY is dephosphorylated?
It cannot interact with the flagellar motor, leading to counterclockwise rotation (run)
255
How does CheY get dephosphorylated?
By CheZ
256
What does CheZ do?
Dephosphorylates CheY
257
In the presence of an attractant, what state is CheA in ?
Dephosphorylated state
258
What happens to CheY in the presence of an attractant?
It cannot be phosphorylated by CheA, so it stays dephosphorylated
259
What is the result of CheY being dephosphorylated in the presence of an attractant?
The cell run towards that attractant (counterclockwise rotation)
260
True or false: the chemotaxis system is a two component regulatory system
True: it has a sensor kinase (CheA) and an RR (CheY)
261
True or false: the chemotaxis system involves transcriptional or translation regulation
False: it involves protein switches
262
What is the most common promoter sequence?
The consensus sequence
263
What is the least common method of gene expression?
Controlling mRNA expression (after transcription, before translation)
264
What does virB do?
Has virulence genes involved in DNA transfer form bacteria to plant
265
How many structural genes are in the virB operon?
11
266
What bacteria has virB?
Agrobacterium
267
What does nifHDK do?
Nitrogenase enzyme involved in nitrogen fixation
268
How many structural genes are in the nifHDK operon?
3
269
What bacteria has nifHDK?
Klebsiella pneumoniae
270
What does S10 do?
Ribosome structure
271
How many structural genes are in the S10 operon?
11
272
What bacteria has S10?
Conserved throughout bacteria
273
Where are the genes encoding regulatory proteins for the operon found?
They can be adjacent to the operon, or located elsewhere on the chromosome
274
How did researchers figure out what genes did what in the lac operon?
By using radioactive lactose
275
What happens if lacA is mutated?
There is no effect on lactose utilization or transport
276
What mutations defined the promoter of the lac operon?
Mutations where no LacZ or LacY was produced
277
Who investigated lambda phages and E. coli in the DNA damage pathway?
Jean-Jacques Weigle
278
What correlation was seen in the E. coli and lambda phage UV experiments?
A correlation between infectivity and mutagenesis
279
What was the conclusion of the UV experiments on E. coli and lambda phages?
UV treatment of host cells enhanced their ability to repair UV-induced damage of lambda phages, but this system was error-prone
280
What does the cell detect to determine DNA damage?
Single stranded DNA
281
What does the SOS repair system use to repair DNA?
An alternative DNA polymerase that lacks proof-reading ability
282
How come the SOS repair system is error prone?
The DNA polymerase used lacks the ability to proofread to fill in the missing DNA
283
What does umuDC do?
Error-prone DNA polymerase V
284
What are some genes in the E. coli SOS regulon?
umuDC, dinB, polB, uvrA, uvrB, uvrD, sbmC, ruvAB, lexA, recA, dinI, recN, ssb, dinG, sulA, ftsK, and pcsA
285
What does dinB do?
Error-prone DNA polymerase IV
286
What does polB do?
DNA polymerase II, repair of DNA interstrand crosslinks
287
What does uvrA do?
Nucleotide excision repair
288
What does uvrB do?
Nucleotide excision repair
289
What does uvrD do?
DNA helicase, involved in DNA repair
290
What does sbmC do?
DNA gyrase inhibitor
291
What does ruvAB do?
Homologous recombination, Holliday junction resolution
292
What does dinI do?
DNA damage inducible protein, regulation of RecA protease activity
293
What does recN do?
DNA recombinational repair protein
294
What does ssb do?
Single stranded DNA binding protein
295
What does dinG do?
ATP-dependent DNA helicase
296
What does sulA do?
SOS cell division inhibitor
297
What does ftsK do?
Cell division protein
298
What does pcsA do?
Phosphatidylcholine synthesis
299
What is another name for sigma-70?
RpoD
300
How many alternative sigma-70 family members does E. coli have?
6
301
How many alternative sigma-70 family members does Streptomyces coelicolor have?
60
302
What is another name for sigma-54?
RpoN
303
True or false: sigma-54 can recognize promoter regions at different distances from the initiation of transcription
True: sigma-70 cannot do this
304
True or false: sigma-70 can recognize promoter regions at different distances from the initiation of transcription
False: sigma-54 can, not sigma-70
305
What is another name for sigma-32?
RpoH
306
What happens to sigma-32 under normal conditions?
It is degraded very rapidly
307
What happens to sigma-32 under higher temperatures?
Other proteins unfold and compete with sigma-32 for proteases. This increases the concentration of sigma-32
308
What are some examples of situations where rpoS would be activated?
High cell density, nutrient starvation, low temperature, high osmolarity, and oxidative stress
309
What are some genes that respond to RpoS?
Protein processing, general stress adaptation, membrane stability and transport, and metabolism
310
What do anti-sigma factors do?
They bind to the sigma factor to prevent RNA polymerase from binding to the promoters (thus turning off genes it controls)
311
What are anti-sigma factors useful for?
Controlling the timing of global gene expression
312
What is an example of an anti-sigma factor?
FlgM
313
What does FlgM interact with?
Sigma-28
314
What does sigma-28 do?
It is responsible for the timing of expression of the genes involved with the assembly of the flagella
315
What asRNAs regulate RpoS?
DsrA and RprA
316
When is DsrA activated?
When there are low temperatures
317
When is RprA activated?
Where there are high cell surface stresses
318
What is attenuation?
Regulatory mechanisms that involve interacts between transcription and translation
319
How was attenuation first discovered?
By deletion mutations in the upstream regulatory region of the trp operon
320
What happened when there were deletion mutations in the upstream regulatory region of the trp operon?
There was an increase in transcription, regardless of whether repressor was activated or not
321
When does regulation by attenuation occur?
After the initiation of transcription, but before transcription of the operon has been completed
322
What causes attenuation in the trp operon?
A short translated leader sequence of the mRNA coded by trpL
323
Where is trpL found?
Following the operator, but before the 5 structural genes
324
How come the 5' end of the leader sequence can be translated before the transcript is finished?
Transcription and translation is coupled in bacteria and archaea
325
What is the consequence of transcription and translation being coupled for attentuation?
The 5' end of the leader sequence can be translated before the transcript is finished
326
What does the leader sequence of trpL contain?
Tryptophan codons, and base pair complementary
327
What happens if tryptophan is abundant for the leader sequence?
The leader will be translated completely
328
What happens if tryptophan is scare for the leader sequence?
It is difficult for the leader to be translated completely
329
What region of trpL has the tryptophan codons?
Region 1
330
What is the consequence of base pair complementary in trpL?
It can form stem loops
331
Which regions of trpL can form stem loops?
Region 2 and Region 3, and Region 3 and Region 4 (not both)
332
In trpL, what is after Region 4, and what does it do?
A uracil-rich attenuator sequence that can interact with the 3-4 stem loop
333
What happens if the attenuator interacts with the 3-4 stem loop in trpL?
It will form a transcription termination structure, causing termination to occur before reaching the structural genes
334
If tryptophan is plentiful, how will trpL stop transcription?
The ribosome will reach the stop codon, blocking formation of the stem loop between Region 2 and 3. Thus, the 3-4 stem loop is formed, terminating transcription
335
If tryptophan is scare, how will trpL continue transcription?
The ribosome pauses at Region 1, which allows Region 2 to bind to Region 3. This prevents the attenuator from interacting with the 3-4 stem loop, continuing transcription
336
What can riboswitches bind to to regulate gene expression?
Effector molecules, such as vitamins and amino acids
337
True or false: riboswitches can affect both transcription and translation
True: they can be involved in either process
338
Which phylum uses AHL as an autoinducer?
Proteobacteria
339
What do Gram-positive bacteria use for quorum sensing?
Small peptides
340
How do small peptides function in quorum sensing?
They are transported outside the cell, and can bind to specific cell-surface receptors, triggering a cell-signaling pathway that affects gene expression
341
How can organisms use multiple quorum sensing signals?
By using AHLs with different lengths and chemical modifications
342
True or false: quorum sensing can only affect one particular species
False: they may also affect gene expression in other species (biofilms)
343
What is signal transduction?
A cellular response to an external stimulus
344
True or false: two-component systems can have several HPK and RR proteins
True: this is seen in Bacillus subtilis endospore formation
345
What does the transfer of tDNA from the bacterium to the plant require?
vir genes
346
When are the vir genes activated in agrobacterium?
In conditions similar to the plant wound site (acidic pH, and certain phenolic compounds like acetosyringone)
347
What is the HPK for the vir genes?
VirA
348
What is the RR for the vir genes?
VirG
349
What happens when VirA senses the phenolic compounds?
It becomes phosphorylated (activated)
350
What happens when VirA is phosphorylated?
It phosphorylates VirG
351
What happens when VirG is phosphorylated?
It is an activate transcription factor
352
What happens to VirA when VirG is phosphorylated?
VirA becomes dephosphorylated
353
What system uses phosphotransfer mechanisms?
The vir system
354
What do MCPs do in the chemotaxis pathway?
Sensory proteins or transducers, methylated by CheR
355
What does MCP stand for?
Methyl-accepting chemotaxis protein
356
What does CheR do?
Methylates MCP
357
What does CheA do?
Sensor kinase
358
What does CheY do?
Response regulator, controls direction of flagellar movement
359
What does CheB do?
Response regulator, demethylates MCP
360
What does CheZ do?
Dephosphorylates pCheY
361
What does CheW do?
Involved in the transduction of signal from MCP to CheA
362
What does methylation of MCP result in?
Adaptation
363
What does methylation of MCP do?
Decreases ability to respond to attractant
364
When does CheB demethylate MCP?
What is is phosphorylated by pCheA
