Module 6 - Regulation of Gene Expression Flashcards
What is gene expression?
A process where information from a gene is used in the synthesis of a functional gene product (often a protein)
How do cells conserve energy?
Not all the genes are expressed all the time
What are constitutive genes?
Genes that are constantly on
What are some examples of constitutive genes?
Genes involved in glycolysis, transcription, and translation
What are inducible genes?
Genes that are needed when a substrate is present
What are the three levels of gene expression?
Transcriptional, translational, and post-translational
What is transcriptional control of gene expression?
Binding of RNA polymerase to the promoter and initiating transcription
What is translational control of gene expression?
Binding of the ribosome to mRNA for continued translation
What is post-translational control of gene expression?
Modification of the protein to activate, inhibit, or degrade it
What are enzymes?
Biological catalysts
How can the activity of an enzyme be altered?
By changing its confirmation due to modifications, or by using inhibitors
What modifications can be done to an enzyme to alter its function?
Phosphorylation, acetylation, methylation, and glycosylation
What is a competitive inhibitor?
An inhibitor that competes directly with the substrate for the active site of the enzyme
What is a non-competitive inhibitor?
An inhibitor that binds to an allosteric site
What is an allosteric site?
A site other than the active site on the enzyme
What is another name for allosteric inhibition?
Feedback inhibition
What happens when the enzyme activity is modified?
The biochemistry of the cell is changed
True or false: modifying an enzyme is a conservative process
False: it does not save much energy
How come modifying an enzyme is not a conservative process?
It still takes a lot of energy to create the enzyme in the first place
What is a better way for the cell to save energy?
By only producing the enzyme when it is needed
How do most of the control mechanisms in bacteria work?
By preventing transcription (and thus translation) of genes when not required
What does the operon mechanism suggest?
A method where regulatory genes can direct cell metabolism by altering rates of transcription of functional genes
What is an operon?
A transcriptional unit with a series of structural genes and their transcriptional regulatory elements
If a cell requires three proteins for a single process, how should they be regulated?
They should either all be produced or not produced at the same time
When was the first eukaryotic operon found?
In the 1990s
True or false: operons are only found in prokaryotes
False: while this was originally thought to be true, eukaryotic operons have been discovered
What does expression of prokaryotic operons lead to?
Polycistronic mRNA
What is polycistronic mRNA?
mRNA that encodes for 2 or more proteins
What is the majority of mRNA in eukaryotic cells?
Monocistronic mRNA
What is monocistronic mRNA?
mRNA that encodes for one protein
What are the structural genes of the lac operon?
lacZ, lacY, and lacA
What is another name for LacY?
Permease
What does LacY do?
Facilitates the uptake of lactose
What is another name for LacZ?
Beta-galactosidase
What does LacZ do?
Breaks down lactose enzymatically
What is another name for LacA?
Beta-galactosidase transacetylase
What does LacA do?
It is not well understood currently
Where does RNA polymerase bind to?
The promoter
Where do regulatory proteins bind to?
The operator
What do regulatory proteins do?
Modulate the ability of RNA polymerase to bind to the promoter
What does LacI do?
Inhibits the lac operon
What is negative control?
When regulatory proteins inhibit operon transcription
What is positive control?
When regulatory proteins facilitate operon transcription
What happens when lactose enters the cell?
It gets metabolized to glucose and galactose by beta-galactosidase
What two simple sugars make up lactose?
Glucose and galactose
What is allolactose?
An isomer of lactose
What reaction produced allolactose?
Beta-galactosidase converts lactose into allolactose
What does allolactose do?
It acts as an inducer of the lac operon (it turns it on)
What is a promoter?
The site on the DNA bound by RNA polymerase
What is an activator?
A protein that binds to a site on the DNA
What does a promoter do?
It directs initiation of transcription
What does an activator do?
It assists binding of RNA polymerase to the promoter
What is an activator binding site?
A site on the DNA bound by an activator
What is a repressor?
A protein that binds to the operator site to inhibit transcription
What is an operator?
A site on the DNA bound by a repressor
What is an effector?
A small molecule that binds to an activator or a repressor
What does an effector do?
Modifies gene regulation activity by being an inducer or corepressor
What is an inducer?
An effector than increases transcription
How does an inducer work?
It either enables an activator or disables a repressor
What is a corepressor?
An effector that decreases transcription
How does a corepressor work?
By enabling a repressor
What is LacI?
A repressor molecule
What does LacI do?
Binds to the operator as a dimer to interfere with the binding of RNA polymerase
What is the effector of the lac operon?
Allolactose
What type of proteins are usually effectors?
Intermediates of the related metabolic pathway
What happens to the lac operon in the absence of lactose?
Transcription is off due to LacI binding to the operator
What happens to the lac operon in the presence of lactose?
Allolactose acts as an inducer by inhibiting LacI, thus promoting transcription
What type of effector is allolactose?
An inducer (it inhibits LacI)
How does allolactose work?
It inactivates LacI by changing its shape so it can’t bind to the operator
What types of reactions are usually done by negative control?
Catabolic pathways in the absence of substrates
How many structural genes are in the trp operon?
6
What happens to the trp operon in the absence of tryptophan?
The repressor cannot bind to the operator, and the structural genes are transcribed
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
What is the effector molecule in the trp operon?
Tryptophan
What type of effector is tryptophan?
A corepressor
What type of control is the lac operon (considering lactose)?
Negative control
What type of control is the lac operon (considering glucose)?
Positive control
What type of control is the trp operon?
Negative control
True or false: the activator protein always binds directly to the activator site
False: there could be another protein involved
What is the activator protein in the lac operon?
CRP
What does CRP stand for?
cAMP receptor protein
What is the co-activator of CRP?
cAMP
How does CRP work?
When bound to cAMP, it binds to the activator site to promote binding of RNA polymerase to the promoter
What do E. coli cells grow best in?
Glucose (as opposed to lactose)
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
What is needed for the lac operon to be transcriped?
The repressor (LacI) must be unbound, and the activator (CRP) must be bound
When there is glucose present, what are the cAMP levels?
Low
Where glucose is absent, what are the cAMP levels?
High
What is catabolite repression?
When a catabolite is preferred over another, so there is repression of the catabolism of the nonpreferred catabolite
What happens when glucose is absent and lactose is present in a cell?
The operon has the activator, and there is transcription
What happens when glucose and lactose is absent in a cell?
The operon has the activator and the repressor, so there is low transcription
What happens when glucose is present and lactose is absent in a cell?
The operon has the repressor, so there is no transcription
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
What happens when glucose and lactose are available (in terms of sugar availability)?
Glucose is used first, and then lactose is used
What is a diauxic growth curve?
A growth curve caused by the use of two metabolites
When does a diauxic growth curve occur?
When a cell has both glucose and lactose available
What is the shape of a diauxic growth curve?
Logistic (steep at the ends, flat in the middle)
What happens when glucose becomes depleted in diauxic growth?
Beta-galactosidase and permease must be produced before the cells can use lactose
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
What happens during the lag phase of diauxic growth?
The cells are not growing because they are producing LacZ and LacY
What did scientists use to understand the role of LacI?
Mutants that constitutively expressed beta-galactosidase (even in absence of lactose)
What does I- refer to?
Inducer negative mutants (mutants that constitutively expressed beta-galactosidase)
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
What was the conclusion of putting a wild type copy of the lac region in I- mutants?
LacI was diffusable
How was it discovered that LacI was diffusable?
It was able to complement a lac mutant, even on a separate piece of DNA (plasmid)
What does O- refer to?
Mutants that had a mutation at the operator site
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
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
How was it discovered that LacI binds to the operator?
When the operator was mutated and LacI was expressed, the system remained constitutively active
What happens when a cell is under stressed conditions (such as high temperature)?
Heat shock proteins are produced to help the cell survive
What are regulons?
Groups of operons coordinated to respond to the same regulatory systems
What is an example of global control?
Regulation by glucose
How does glucose act as a global control?
It is involved in catabolite repression to shut down other pathways
In E. coli, how many operons does CRP regulate?
100
What environmental stresses can damage DNA?
UV radiation and chemicals
What is the SOS response?
A regulon that allows the cell to recognize and respond to serious DNA damage
What was used for the experimental evidence for the existence of regulons?
Bacteriophages treated with UV light
What two E. coli cultures were used to prove the existence of regulons?
One that was preexposed to UV, and another that was untreated
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
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
What did the experiments with UV light on E. coli show?
That DNA repair is error prone (generates mutations)
What does chloramphenicol do?
It is an antibiotic that blocks protein synthesis in bacteria
What happened when chloramphenicol was added to E. coli?
DNA repair was also blocked
What was the conclusion from adding chloramphenicol to E. coli?
DNA repair required protein synthesis
How were the genes expressed for DNA repair identified?
Through a lacZ promoter probe transposon
What is a lacZ promoter probe transposon?
A promoter-less lacZ reporter gene that can insert into DNA
How does lacZ get expressed in a lacZ promoter probe transposon?
It must insert within an actively transcribed gene
How can the lacZ in the lacZ promoter probe transposon be identified?
By using X-gal to see if there is LacZ activity
What happens if LacZ inserts into an active gene?
It will show up blue in the presence of X-gal
What happens if LacZ inserts into an inactive gene?
It will show up white in the presence of X-gal
What DNA damaging agent was used to study the SOS regulon?
Mitomycin C
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
What does din stand for?
Damage induced gene
What are din genes?
Genes part of the SOS regulon that respond to DNA damage
How do cells sense DNA damage?
They detect single stranded DNA (a result of damage)
Which genes can alter the SOS response?
lexA and recA
What is recA involved in?
Recombination
What does RecA do?
Binds to single stranded DNA to regulate the SOS regulon
What is RecA activated?
When it is bound to single stranded DNA
What does LexA do?
It is a repressor that binds to the operator of the SOS regulon
What does RecA do when it is bound to single stranded DNA?
It cleaves LexA
What happens when LexA is cleaved?
It can no longer bind to the operator, so the SOS genes are expressed
How many genes in E. coli are part of the SOS regulon?
40
Besides regulons, how can global gene regulation be achieved?
Through alternative sigma factors
What is a sigma factor and what does it do?
A polypeptide that allows RNA polymerase to identify promoter for initiation of transcription
What is a primary sigma factor?
The sigma factor responsible for recognizing the most promoters
What is the primary sigma factor in E. coli?
Sigma-70
What does Sigma-54 do?
Regulates nitrogen utilization genes
What is required for Sigma-54 to function?
An activating protein and ATP to initiate transcription
True or false: Sigma-70 requires an activating protein and ATP to initiate transcription
False: Sigma-54 requires this, not Sigma-70
What does Sigma-32 do?
Regulates heat shock proteins
What does Sigma-38 do?
It is a general stress response gene regulator
Which sigma factor is a general stress response gene regulator?
Sigma-38
Which sigma factor regulates heat shock proteins?
Sigma-32
Which sigma factor regulates nitrogen utilization?
Sigma-54
What RNAs are encoded in the genome?
rRNA, tRNA, and regulatory RNAs
What is sRNA?
Small noncoding RNAs
How big are sRNAs?
50-400 nt
What do sRNAs do?
Affect gene expression by interacting with existing mRNA
How do sRNAs silence a gene?
By preventing transcription from completing or by blocking translation
What are some types of sRNA?
miRNA, siRNA, and asRNA
What does miRNA stand for?
MicroRNA
What does siRNA stand for?
Small interfering RNA
What does asRNA stand for?
Antisense RNA
What is another name for Sigma-38?
rpoS
What does rpoS stand for?
RNA polymerase S
How do asRNAs work?
They use complementary base pairing to interact with specific mRNA molecules
What does rpoS do in the absence of asRNA?
It inhibits translation through its 5’ leader sequence
What is the structure of rpoS?
A 5’ leader sequence that forms a hairpin stem loop structure
What happens when cells are exposed to different stresses?
They accumulate different sRNAs
What is DsrA?
A sRNA
When is DsrA produced?
When the cell is exposed to low temperatures
What does DsrA do?
It binds with Hfq, which binds to rpoS
What is Hfq?
An RNA-binding protein for DsrA
What happens when DsrA and Hfq bind to RpoS?
They disrupt the inhibitory secondary structure, which allows translation to proceed
What are riboswitches?
Regulatory molecules that bind to RNA and alter its shape
What is quorum sensing?
A chemical signaling system used to detect presence and number of other organisms in a population
What is a quorum?
The number of members that must be present at a meeting to conduct business
What does quorum sensing involve?
Release of specific signaling molecules called autoinducers
What does an autoinducer do?
It acts as a signaling molecule that increases in concentration as density of bacterial population increases
How can bacteria assess population density?
By detecting autoinducer concentration
What happens when population density changes?
Gene expression may also change
What is special about Vibrio fischeri?
They can produce light
Which organism does Vibrio fischeri live inside?
The Hawaiian bobtail squid
What does the light organ in bobtail squid do?
It luminesces when colonized by V. fischeri
What was the first quorum sensing system described?
The lux system
What does luciferase do?
Produces light
When do V. fischeri cells emit light?
When they are at a high density
What is the autoinducer in the lux system?
AHL
What does AHL stand for?
N-acyl-homoserine lactone
True or false: AHL is only used for intracellular signaling in V. fischeri
False: it is seen in many other types of bacteria
What protein synthesizes AHL?
LuxL
What does LuxL do?
Synthesizes AHL
At low cell density, what is the concentration of AHL?
Low
How come AHL concentration is low at low cell density?
It diffuses away from the cell
At high cell density, what is the concentration of AHL?
High
What happens when there is a high concentration of AHL?
It binds to LuxR
What is LuxR?
A transcriptional activator protein
What happens when LuxR is activated?
It binds to the lux box to promote transcription
What is the lux box?
A regulatory DNA site for the lux operon
What is encoded by the lux operon?
LuxA, LuxB, and LuxL
What does LuxA and LuxB do?
Encode luciferase
True or false: the lux system is a positive feedback mechanism
True: LuxL is produced, which creates more AHL
How is the lux system a positive feedback loop?
LuxL is produced, which creates more AHL to regulate the lux operon further
What processes can be controlled by quorum sensing?
Motility, conjugation, biofilm formation, pathogenesis, and secondary metabolite production
How can quorum sensing control pathogenesis?
By producing cholera toxin when enough cells are present (V. cholera)
How can autoinducers play a role in competition?
They may interrupt or inhibit a control pathway in other organisms in the environment
How to cells commonly react to the environment?
Through a two component regulatory system
What are the components of a two component regulatory system?
A sensor protein, and a protein that regulates transcription
What happens when the two components of a two component regulatory system interact?
It creates signal transduction
What are the most common regulatory systems in bacteria?
A two component system
What is a commonly used sensor?
HPK
What does HPK stand for?
Histidine protein kinase
What does RR stand for?
Response regulator
What does HPK do?
It becomes phosphorylated and phosphorylates RR
What happens when RR is phosphorylated?
It changes confirmation and regulates gene expression
What is chemotaxis?
The movement of motile bacteria in response to a chemical stimulus
Why is chemotaxis important in bacteria?
It is important to swim towards the highest concentration of food or run away from detrimental chemicals
In which organism is regulation of chemotaxis best understood?
In E. coli
What is the flagella structure of E. coli?
Peritrichous (several flagella all around the cell)
What happens during counterclockwise rotation?
The cell propels forward
What happens during clockwise rotation?
It causes a tumble (change of direction)
What happens to flagellar rotation in the absence of an attractant or repellant?
It alternates between clockwise and counterclockwise rotation
What is the rate of rotation switching in E. coli?
Once per sec
What happens to flagellar rotation in the presence of an attractant or repellent?
The ratio of clockwise to counterclockwise rotation changes
What did researchers use to understand chemotaxis?
Mutants where chemotaxis was disrupted
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
In the apparatus to isolate chemotaxis mutants, where would wild-type E. coli be found?
In the capillary tube
How come wild type E. coli would be in the capillary tube?
There is a higher concentration of attractant there
In the apparatus to isolate chemotaxis mutants, where would the mutants be?
In the surrounding media
How come chemotaxis mutants would be in the surrounding media?
Because they would not move to the capillary tube with higher concentration
Mutations in which genes result in counterclockwise rotation?
cheA, cheY, cheW, or cheR
Mutations in which genes result in clockwise rotation?
cheB or cheZ
What happens if cheA is mutated?
Counterclockwise rotation
What happens if cheY is mutated?
Counterclockwise rotation
What happens if cheW is mutated?
Counterclockwise rotation
What happens if cheR is mutated?
Counterclockwise rotation
What happens if cheB is mutated?
Clockwise rotation
What happens if cheZ is mutated?
Clockwise rotation
What does the regulation of chemotaxis involve?
Protein switches
What proteins are found in all chemotactic bacteria?
CheA and CheY
What does CheA do?
Acts as the sensor kinase in the system
How does CheA work?
It is phosphorylated at a histidine residue in response to the presence or absence of a particular attractant or repellant
What does CheY do?
Acts as a RR in the system
What does pCheA do?
It phosphorylates CheY at a specific aspartic residue
What does pCheY do?
It interacts with the flagellar motor to determine direction of rotation
True or false: phosphorylation circuit is typical in a 2 component regulatory system
True: phosphorylation is very common in cell signaling
In the absence of an attractant, what state is CheA in?
Phosphorylated state
What phosphorylates CheA?
CheW
What does CheW do?
Phosphorylates CheA in the absence of an attractant
What direction does pCheY lead to?
Clockwise rotation (tumble)
When does a cell tumble?
Clockwise rotation
What does a cell run?
Counterclockwise rotation
What happens when pCheY is dephosphorylated?
It cannot interact with the flagellar motor, leading to counterclockwise rotation (run)
How does CheY get dephosphorylated?
By CheZ
What does CheZ do?
Dephosphorylates CheY
In the presence of an attractant, what state is CheA in ?
Dephosphorylated state
What happens to CheY in the presence of an attractant?
It cannot be phosphorylated by CheA, so it stays dephosphorylated
What is the result of CheY being dephosphorylated in the presence of an attractant?
The cell run towards that attractant (counterclockwise rotation)
True or false: the chemotaxis system is a two component regulatory system
True: it has a sensor kinase (CheA) and an RR (CheY)
True or false: the chemotaxis system involves transcriptional or translation regulation
False: it involves protein switches
What is the most common promoter sequence?
The consensus sequence
What is the least common method of gene expression?
Controlling mRNA expression (after transcription, before translation)
What does virB do?
Has virulence genes involved in DNA transfer form bacteria to plant
How many structural genes are in the virB operon?
11
What bacteria has virB?
Agrobacterium
What does nifHDK do?
Nitrogenase enzyme involved in nitrogen fixation
How many structural genes are in the nifHDK operon?
3
What bacteria has nifHDK?
Klebsiella pneumoniae
What does S10 do?
Ribosome structure
How many structural genes are in the S10 operon?
11
What bacteria has S10?
Conserved throughout bacteria
Where are the genes encoding regulatory proteins for the operon found?
They can be adjacent to the operon, or located elsewhere on the chromosome
How did researchers figure out what genes did what in the lac operon?
By using radioactive lactose
What happens if lacA is mutated?
There is no effect on lactose utilization or transport
What mutations defined the promoter of the lac operon?
Mutations where no LacZ or LacY was produced
Who investigated lambda phages and E. coli in the DNA damage pathway?
Jean-Jacques Weigle
What correlation was seen in the E. coli and lambda phage UV experiments?
A correlation between infectivity and mutagenesis
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
What does the cell detect to determine DNA damage?
Single stranded DNA
What does the SOS repair system use to repair DNA?
An alternative DNA polymerase that lacks proof-reading ability
How come the SOS repair system is error prone?
The DNA polymerase used lacks the ability to proofread to fill in the missing DNA
What does umuDC do?
Error-prone DNA polymerase V
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
What does dinB do?
Error-prone DNA polymerase IV
What does polB do?
DNA polymerase II, repair of DNA interstrand crosslinks
What does uvrA do?
Nucleotide excision repair
What does uvrB do?
Nucleotide excision repair
What does uvrD do?
DNA helicase, involved in DNA repair
What does sbmC do?
DNA gyrase inhibitor
What does ruvAB do?
Homologous recombination, Holliday junction resolution
What does dinI do?
DNA damage inducible protein, regulation of RecA protease activity
What does recN do?
DNA recombinational repair protein
What does ssb do?
Single stranded DNA binding protein
What does dinG do?
ATP-dependent DNA helicase
What does sulA do?
SOS cell division inhibitor
What does ftsK do?
Cell division protein
What does pcsA do?
Phosphatidylcholine synthesis
What is another name for sigma-70?
RpoD
How many alternative sigma-70 family members does E. coli have?
6
How many alternative sigma-70 family members does Streptomyces coelicolor have?
60
What is another name for sigma-54?
RpoN
True or false: sigma-54 can recognize promoter regions at different distances from the initiation of transcription
True: sigma-70 cannot do this
True or false: sigma-70 can recognize promoter regions at different distances from the initiation of transcription
False: sigma-54 can, not sigma-70
What is another name for sigma-32?
RpoH
What happens to sigma-32 under normal conditions?
It is degraded very rapidly
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
What are some examples of situations where rpoS would be activated?
High cell density, nutrient starvation, low temperature, high osmolarity, and oxidative stress
What are some genes that respond to RpoS?
Protein processing, general stress adaptation, membrane stability and transport, and metabolism
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)
What are anti-sigma factors useful for?
Controlling the timing of global gene expression
What is an example of an anti-sigma factor?
FlgM
What does FlgM interact with?
Sigma-28
What does sigma-28 do?
It is responsible for the timing of expression of the genes involved with the assembly of the flagella
What asRNAs regulate RpoS?
DsrA and RprA
When is DsrA activated?
When there are low temperatures
When is RprA activated?
Where there are high cell surface stresses
What is attenuation?
Regulatory mechanisms that involve interacts between transcription and translation
How was attenuation first discovered?
By deletion mutations in the upstream regulatory region of the trp operon
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
When does regulation by attenuation occur?
After the initiation of transcription, but before transcription of the operon has been completed
What causes attenuation in the trp operon?
A short translated leader sequence of the mRNA coded by trpL
Where is trpL found?
Following the operator, but before the 5 structural genes
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
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
What does the leader sequence of trpL contain?
Tryptophan codons, and base pair complementary
What happens if tryptophan is abundant for the leader sequence?
The leader will be translated completely
What happens if tryptophan is scare for the leader sequence?
It is difficult for the leader to be translated completely
What region of trpL has the tryptophan codons?
Region 1
What is the consequence of base pair complementary in trpL?
It can form stem loops
Which regions of trpL can form stem loops?
Region 2 and Region 3, and Region 3 and Region 4 (not both)
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
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
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
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
What can riboswitches bind to to regulate gene expression?
Effector molecules, such as vitamins and amino acids
True or false: riboswitches can affect both transcription and translation
True: they can be involved in either process
Which phylum uses AHL as an autoinducer?
Proteobacteria
What do Gram-positive bacteria use for quorum sensing?
Small peptides
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
How can organisms use multiple quorum sensing signals?
By using AHLs with different lengths and chemical modifications
True or false: quorum sensing can only affect one particular species
False: they may also affect gene expression in other species (biofilms)
What is signal transduction?
A cellular response to an external stimulus
True or false: two-component systems can have several HPK and RR proteins
True: this is seen in Bacillus subtilis endospore formation
What does the transfer of tDNA from the bacterium to the plant require?
vir genes
When are the vir genes activated in agrobacterium?
In conditions similar to the plant wound site (acidic pH, and certain phenolic compounds like acetosyringone)
What is the HPK for the vir genes?
VirA
What is the RR for the vir genes?
VirG
What happens when VirA senses the phenolic compounds?
It becomes phosphorylated (activated)
What happens when VirA is phosphorylated?
It phosphorylates VirG
What happens when VirG is phosphorylated?
It is an activate transcription factor
What happens to VirA when VirG is phosphorylated?
VirA becomes dephosphorylated
What system uses phosphotransfer mechanisms?
The vir system
What do MCPs do in the chemotaxis pathway?
Sensory proteins or transducers, methylated by CheR
What does MCP stand for?
Methyl-accepting chemotaxis protein
What does CheR do?
Methylates MCP
What does CheA do?
Sensor kinase
What does CheY do?
Response regulator, controls direction of flagellar movement
What does CheB do?
Response regulator, demethylates MCP
What does CheZ do?
Dephosphorylates pCheY
What does CheW do?
Involved in the transduction of signal from MCP to CheA
What does methylation of MCP result in?
Adaptation
What does methylation of MCP do?
Decreases ability to respond to attractant
When does CheB demethylate MCP?
What is is phosphorylated by pCheA
