Lecture 12: Pt. 2 of Regulation of Gene Expression Flashcards
(42 cards)
1
Q
What are ways in which transcription is regulated?
A
Through:
- Repression (negative) and induction
- Activation (positive)
2
Q
What type of regulation is repression?
A
Negative regulation
3
Q
What type of regulation is activation?
A
Positive regulation
4
Q
What is an advantage of grouping genes in an operon?
A
It can get expression of both genes at once and it is faster/more efficient.
5
Q
What are the components of a bacterial gene? Define each.
A
- Promoter: where RNA polymerase binds upstream of coding region of gene to initiate transcription
- Coding region: where translation starts (AUG)
- Shine-Dalgarno Sequence: ribosome binding site (RBS)
6
Q
What occurs during repression in inhibiting transcription?
A
- The repressor inhibits transcription by blocking RNA polymerase from binding to the promoter. The operator s the region in which the repressor binds to.
- It stops making enzyme if its product is already present (if already have it, don’t need enzyme to make it)
7
Q
What happens in the absence of repressor?
A
It needs gene products. The RNA Polymerase binds promoter and initiates transcription, then transcription occurs.
8
Q
What happens with the presence of a repressor?
A
The repressor binds to operator and blocks RNA polymerase from initiating transcription.
9
Q
What occurs during induction in starting trascription?
A
- Induction turns on transcription of repressed genes. The inducer is a small molecule that binds to repressor, makes it fall off operator and genes can be expressed.
- Makes an enzyme only when substrate is present
10
Q
What is activation and what occurs during it when helping transciption?
A
- Activation is a form of positive regulation.
- Activators help recruit RNA polymerase to the promoter
- RNA P binds to some promoters better than others depending on sequence
- Activators help make enzymes only when the substrate is present
11
Q
What occurs during the repression of the lac operon when ONLY GLUCOSE is present?
A
- If no lactose present, cell doesn’t want to waste E making the lactose enzymes/transporter.
- The repressor protein, Lacl, binds to operator and blocks lac transcription and the cell uses glucose
12
Q
What occurs during the induction of the lac operaon?
A
- If lactose is present, the cell can sense it. Lactose (allolactose) is an inducer.
- Binds Lacl and stops it from binding to operator (allosteric inhibition) and RNA polymerase can do its thing.
13
Q
What occurs during the positive regulation of the lac operon?
A
- Even w/ lactose, cell doesn’t want to use it if glucose is there.
- Even if Lacl repressor is off, RNA P also needs lac activator CRP to help bind and initiate lac transcription. CRP only helps PNAP bind when glucose is low
- The cell senses glucose via cyclic AMP (cAMP) signal molecule: Low glucose -> lotta cAMP, High glucose -> low cAMP. cAMP binds CRP (the cAMP receptor protein) to turn it on
14
Q
What is the repressor protein during repression of lac operon when only glucose is present?
A
Lacl
15
Q
What is the inducer in the induction of lac operon if lactose is present?
A
Lactose/Allolactose
16
Q
What is the lac activator in the positive regulation of the lac operon?
A
CRP or cAMP receptor protein
17
Q
What occurs during the repression of lac operon when LACTOSE AND GLUCOSE are present?
A
- The lactose inducer (allolactose) indicates that the repressor is not bound, RNA polymerase also needs CRP activator to help it bind
- high glucose = low cAMP and the CRP activator is inactive. RNA Polymerase can’t initiate lac transcription.
- cell uses glucose instead of lactose.
When lactose is present, Lacl is inactive and high glucose indicates that CRP is inactive.
18
Q
What occurs during the repression of the lac operon in the presence of ONLY LACTOSE?
A
- low glucose = high cAMP = CRP activator is active
- CRP helps RNA polymerase bind and start lac transcription
- cell can use lactose
19
Q
What makes a sRNA?
A
- one type of cell RNA (like mRNA or tRNA)
- unlike mRNAs, most do not encode info to make proteins = non-coding RNAs (ncRNAs)
- huge roles in cell survival, health, and disease
20
Q
What are the roles of ncRNAs in health and disease?
A
- Stem and reproduction cells: keep stem cells undifferentiated; help egg cell maturation
- Proper formation of B & T cells: skeletal and cardiac muscle
- Cancer and heart disease: some sRNAs contribute; others help prevent/suppress
- Help viruses like Epstein-Barr and Kaposi’s Sarcoma cause disease
21
Q
How do most sRNAs act in terms of negative regulation?
A
- Negatively regulation sRNAs often block translation by inhibiting ribosome binding to the mRNA
- The sRNA specifically binds to the same nucleotides in the mRNA where ribosome binding site is
22
Q
How do most sRNAs act in terms of positive regulation?
A
- positively regulation sRNAs often enhance translation by stabilizing the mRNA or helping the ribosome bind
23
Q
What is Glucose-phosphate in terms of sRNA regulation?
A
- When some bacterial cells accumulate too much sugar, it stresses them out.
- utilizes PtsG to transport glucose into cell
- when glucose-phosphate accumulates, cell growth is inhibited
24
Q
What is the glucose-phosphate stress response?
A
- “SgrS” = sugar transport-related sRNA. It helps stop glucose-phosphate from coming into cell
- SgrR: protein regulator that activates transcription of SgrS in response to stress
- SgrS stops PtsG transporter synthesis and cell stops bringing sugar into cell and growth can resume
25
What is the two-component regulator system (TCS)?
- consist of a sensor kinase protein and a response regulator protein.
1. TCS sensor kinase
2. TCS respomse regulator
26
What is the sensor kinase in TCS?
- it detects environmental signal, then phosphorylates itself (autophosphorylation)
- Histidine kinase: a particular His amino acid residue in the protein is P-ated
- kinase then transfers P signal to the response regulator
27
What is the response regulator in TCS?
it is a DNA-binding protein (either activates or represses transcription)
- ex: phosphate starvation, pathogen virulence, changes in osmotic pressure
28
What is α2 sigma factor?
It assembles RNAP and recognizes regulatory factors
29
What is β sigma factor?
catalyzes synthesis of RNA (initiation/elongation)
30
What is β' sigma factor?
binds DNA non-specifically
31
What is ω sigma factor?
promotes assembly of RNAP
32
What is σ factor?
- Holoenzyme = core enzyme + 5th subunit
- recognizes specific DNA seq. in promoter (-10 & -35)
- required for initiation of RNA synthesis
- for E. coli "housekeeping" sigma, is σ^70
33
What are alternative sigmas?
recognize special promoters of genes that need to be transcribed only under certain conditions
34
What is included in the regulation of flagellar gene expression?
- Class I (early): FlhDC, master transcriptional activator
- Class II (middle) promoters: σ^70 PNAP + FlhDC, encodes hook-basal body, regulators FliA (σ^28) + FlgM
- Class III (late) promoters: FliA (σ^28), late flagellar assembly
35
What occurs during regulation by sigmas and anti-sigmas in flagellar gene expression?
- Late (class III) gene expression is couples to flagellum assembly and is not expressed until basal body is completed
- Anti-sigma factors: negative regulators; bind and sequester cognate sigmas, keep inactive until appropriate signal sensed
- FlgM is a cytoplasmic anti-sigma factors. It binds σ^28 (FliA) and prevents it from binding with the core RNAP
36
How can σ^28 help transcribe late (Class III) genes?
Once class III (hook & basal body) are assembled, FlgM is secreted out of cell, freeing up σ^28
37
What occurs in the regulation of endospore formation?
- Initiated due to unfavorable conditions (ex : starvation)
- In B. subtilis, sensor kinases monitor environment and relay signals via phosphate transfer called phosphorelay: Pi transfered to multiple proteins.
- If Spo0A is P-ated, sporulation occurs and activates transcription of sporulation genes
38
What occurs in the sigma regulation of endospore formation?
- remove anti-sigma SpoIIAB from σ^F, regulates genes needed for early endospore development. σ^G controls late endospore development
- σ^E and σ^K activate genes needed in the mother cell
- cellular cannibalism: cells with active Spo0A secrete toxin and lyses nearby cells
- "sacrificed" cells used as nutrient source for developing endospores
39
What is quorum sensing?
how bacteria sense population density
- ensures sufficient number of cells before starting an activity requiring high cell numbers (= not waste E)
- often transition from individual to group behaviors
40
What are the uses of quorum sensing?
- Pathogenesis: one pathogen cell producing a toxin will have no effect, but many cells together can attack and invade host
- forming biofilms is only worth it if enough cells are present to form them
- bioluminescence can only be seen if many cells are producing light
41
What are the mechanisms of quorum sensing?
- Autoinducer (AI): QS signal molecule produced by cell: diffuses freely in and out of cell, so can sense concentration. In gram (-), acyl homoserine lactones (AHLs), in gram (+), small peptides
- when many cells are nearby, AI concentration in cell is high
- AI binds to an activator protein and transcribes genes (need high concentration to sufficiently turn on)
42
What are examples of quorum sensing and bioluminescence?
- Vibrio fischeri, lux genes encode enzymes that allow it to emit light
- one cell emitting light is invisible, QS allows to only make light when enough cells are present
- Symbiosis: colonizes specialized light organ of Hawaiian bobtail squid
- Mutualism: mimics moonlight to help squid evade predators, bacteria get habitat and nutrients
