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Genes and Genomics- Em > Prokaryotic Gene Regulation > Flashcards

Prokaryotic Gene Regulation Flashcards

1
Q

Where does gene expression occur?

A

There is no nucleus to separate processes so transcription and translation are coupled.

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2
Q

Describe the gene architecture in prokaryotes.

A

-have operons- mRNAs often polycistronic- not a single promoter for every gene- separate ribosome binding sites between each gene so that each gene is translated separately

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3
Q

What is an operon comprised of?

A

A promoter sequence, followed by an operator, followed by several structural genes.

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4
Q

How are operons controlled?

A

By regulatory genes found elsewhere on the chromosome which regulates the expression of the structural genes in response to an environmental change.

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5
Q

What is σs used for?

A

Needed in starvation or hyperosmolarity- can put cells in stationary phase.

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6
Q

What is σ 32 used for?

A

Needed during heat shock and nutrient starvation. Produces heat shock proteins which prevent protein unfolding at high temperatures.

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7
Q

How are the -35/-10 sites different in σ 32?

A

They are slightly closer together than in σ 70 and σs.

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8
Q

What is σ 54 used for?

A

Needed during nitrogen and nutrient starvation.

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9
Q

What are the binding sites of σ 54 to the promoter?

A

-24/-12

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10
Q

What does σ 54 need to initiate transcription?

A

ATP and an enhancer protein to bend the DNA into a loop.

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11
Q

What is σ 70 used for?

A

Control of the expression of most genes needed to survive.

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12
Q

What are the genes encoded for by the arabinose operon?

A

AraA, AraB, AraD

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13
Q

What are the cis elements in the arabinose operon?

A

AraO1, AraO2, AraI binding site, CAP binding site.

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14
Q

What are the trans elements in the arabinose operon?

A

AraC, cAMP and CAP.

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15
Q

Describe the negative regulation of the arabinose operon.

A

If arabinose is absent, AraC binds to AraO2 and AraI, forming a DNA loop ahead of the promoter, meaning that RNAP can’t access the promoter and there is no transcription.

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16
Q

Describe the positive regulation of the arabinose operon.

A

If arabinose is present, AraC binds to AraI1 and AraI2, meaning there is no DNA looping, allowing promoter access and transcription.

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17
Q

Describe the role of catabolite repression in the arabinose operon.

A

If glucose is absent, adenylate cyclase activity increases, cAMP binds to CAP, activating transcription. Positive regulation.

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18
Q

Describe the autoregulation of the arabinose operon.

A

If there are high levels of AraC, AraC binds to AraO1. RNAP can’t access Parac promoter, meaning there is no transcription of AraC.

19
Q

Why is the autoregulation of the arabinose operon necessary?

A

To regulate the level of positive/negative regulation of the operon.

20
Q

What does the tryptophan operon consist of?

A

Transcription regulatory region and 5 structural genes.

21
Q

Describe how the trp operon can be repressed by a repressor.

A

TrpR produces the repressor protein. At high levels of trp, trp binds to the repressor which can then bind to the operator- blocks transcription.

22
Q

To what extent does the repressor repress the trp operon?

A

70-fold repression.

23
Q

What is attenuation?

A

Post-transcriptional control of gene regulation, involving the formation of two different stem loops in the leader mRNA (trpL).

24
Q

To what extent does attenuation repress the trp operon?

A

An additional 10-fold repression. (Overall repression is 700-fold)

25
Q

Why is attenuation only possible in prokaryotes?

A

Transcription and translation are only coupled in prokaryotes.

26
Q

Give an example of another operon where attenuation occurs.

A

His operon.

27
Q

What happens when [trp] is low?

A

Ribosome stalls at 2 trp codons in region 1 as charged tRNA(trp) is in short supply. Stem loop forms between regions 2+3- does not affect transcription. Region 3 is not available to form a stem loop with region 4. Get transcription of all genes and trp production.

28
Q

Why is the 2/3 stem loop not an intrinsic terminator?

A

Stem loop is followed by Gs/Cs and is not a U-rich region (would release transcript due to weak A-U bonds).

29
Q

What happens when [trp] is high?

A

Ribosome quickly translates region 1, covering region 2. Region 2 can’t bind to region 3, leaves region 3 available form a stem loop with region 4- terminating transcription. No transcription, no trp production.

30
Q

What is lacI?

A

A separate transcript that encodes a lac repressor protein.

31
Q

Describe the structure of the lac repressor protein?

A

Multimeric protein of 4 subunits. 3° structure is a helix-turn-helix motif so it can bind to major groove of DNA.

32
Q

What does the lac repressor protein do?

A

Binds to the lac operator (O1 and O2 sites) to inhibit transcription.

33
Q

When can the lac repressor protein not bind to the lac operator?

A

If it is bound to an inducer.

34
Q

Describe the lac operator.

A

An imperfect inverted repeat region of DNA that lies partly in the promoter region. Consists of O1, O2 and O3.

35
Q

What happens when lactose is absent?

A

LacI binds to the operator. No lac genes are expressed.

36
Q

What happens when lactose is present?

A

Small amounts of allolactose are formed and acts as an inducer. Allolactose binds to the lac repressor and prevents it from binding to the operator. RNAP binds to promoter- genes are transcribed.

37
Q

Describe the feedback control mechanism of the lac operon.

A

Production of lacZ/lacY/lacA- break down lactose and allolactose, causing the eventual release of the repressor as lactose is absent. Stops additional lac mRNA synthesis.

38
Q

Describe the role of catabolite repression in the regulation of the lac operon.

A

If glucose is absent, adenylate cyclase activity increases and more cAMP is produced. cAMP binds to CAP, activating transcription. Positive regulation.

39
Q

When does maximal transcription of the lac operon occur?

A
  • glucose is absent - lactose is present - there has been interaction of CAP and cAMP- allolactose binds to lacI and the repressor is released
40
Q

What is the role of cAMP in catabolite repression?

A
  • cAMP acts as a positive regulator- binds to CAP and causes a conformational change in CAP that allows CAP/cAMP to bind to the operon as a dimer
41
Q

How does CAP interact with operons?

A
  • binds upstream of the promoter- increases the affinity of RNAP for the DNA- bends DNA to increase promoter accessibility
42
Q

What happens to the lac/ara operon if glucose is present?

A

The structural genes are not transcribed.

43
Q

What protein motif does CAP adopt and how does this allow CAP to bind to DNA?

A

Helix-turn-helix, binding to the major groove of DNA.

Genes and Genomics- Em (19 decks)

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