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Microbio > Lecture 12: Pt. 2 of Regulation of Gene Expression > Flashcards

Lecture 12: Pt. 2 of Regulation of Gene Expression Flashcards

1
Q

What are ways in which transcription is regulated?

A

Through:

  • Repression (negative) and induction
  • Activation (positive)
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2
Q

What type of regulation is repression?

A

Negative regulation

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3
Q

What type of regulation is activation?

A

Positive regulation

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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.

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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)
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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)
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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.

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8
Q

What happens with the presence of a repressor?

A

The repressor binds to operator and blocks RNA polymerase from initiating transcription.

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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
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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
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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
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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.
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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
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14
Q

What is the repressor protein during repression of lac operon when only glucose is present?

A

Lacl

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15
Q

What is the inducer in the induction of lac operon if lactose is present?

A

Lactose/Allolactose

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16
Q

What is the lac activator in the positive regulation of the lac operon?

A

CRP or cAMP receptor protein

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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
Q

What is the two-component regulator system (TCS)?

A
  • consist of a sensor kinase protein and a response regulator protein.
    1. TCS sensor kinase
    2. TCS respomse regulator
26
Q

What is the sensor kinase in TCS?

A
  • 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
Q

What is the response regulator in TCS?

A

it is a DNA-binding protein (either activates or represses transcription)
- ex: phosphate starvation, pathogen virulence, changes in osmotic pressure

28
Q

What is α2 sigma factor?

A

It assembles RNAP and recognizes regulatory factors

29
Q

What is β sigma factor?

A

catalyzes synthesis of RNA (initiation/elongation)

30
Q

What is β’ sigma factor?

A

binds DNA non-specifically

31
Q

What is ω sigma factor?

A

promotes assembly of RNAP

32
Q

What is σ factor?

A
  • 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
Q

What are alternative sigmas?

A

recognize special promoters of genes that need to be transcribed only under certain conditions

34
Q

What is included in the regulation of flagellar gene expression?

A
  • 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
Q

What occurs during regulation by sigmas and anti-sigmas in flagellar gene expression?

A
  • 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
Q

How can σ^28 help transcribe late (Class III) genes?

A

Once class III (hook & basal body) are assembled, FlgM is secreted out of cell, freeing up σ^28

37
Q

What occurs in the regulation of endospore formation?

A
  • 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
Q

What occurs in the sigma regulation of endospore formation?

A
  • 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
Q

What is quorum sensing?

A

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
Q

What are the uses of quorum sensing?

A
  • 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
Q

What are the mechanisms of quorum sensing?

A
  • 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
Q

What are examples of quorum sensing and bioluminescence?

A
  • 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

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