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asdfghjmak 2 > P1 L4 > Flashcards

P1 L4 Flashcards

1
Q

What is gene expression?

A

The transcription of genes to mRNA followed by their translation to protein

gene -> mRNA -> protein

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2
Q

Why is the regulation of gene expression important?

A

To save energy and resources - by controlling protein production.
Allows cells to react quickly - to signals like available nutrients and temperature.

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3
Q

Why is the regulation of transcription important?

A

Saves the most energy -> no mRNA synthesis
mRNA is very unstable

transcription is first step of gene expression that involves DNA -> mRNA

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4
Q

the 3 Different steps of RNA synthesis where regulation can occur

A

Initiation
elongation
termination

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5
Q

What is the role of transcriptional regulators?

A

They bind to DNA to control the transcription process at initiation

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6
Q

How is the initiation of transcription negatively regulated?

A

By transcriptional regulators that bind to the DNA
negatively:
- with the repressor (protein) that binds to the operator (DNA) and blocks transcription.
- with effectors that bind to the repressor and thus change its affinity to the DNA

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7
Q

What are effectors in the context of transcription regulation?

A

Small molecules that modulate the activity of repressors or activators by changing its affinity to DNA

COREPRESSORS or INDUCERS

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8
Q

Describe repression (decreasing expression)

A

In this process, a COREPRESSOR binds to the repressor and changes conformation so it can bind to operator easier and thus prevents transcription

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9
Q

Describe induction (increasing expression)

A

The INDUCER binds to the repressor, which leads to a structural change -> prevents the transcription from being cancelled

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10
Q

What is the role of allolactose in the lac operon?

A

It binds to the repressor, causing it to release from the operator and allowing transcription.

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11
Q

How is the initiation of transcription positively regulated?

A

with the ACTIVATOR (protein) that binds to the activator-binding (DNA) and transcription is activated:

  1. interaction with RNA polymerase
  2. alteration of the DNA structure at the promoter
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12
Q

What is the difference between negative and positive regulation in transcription?

A

Negative regulation: repressor blocks or induces transcription
Positive regulation: activator enhances or represses transcription

depends on effector molecule: inducer or corepressor

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13
Q

Negative mutations

A

A mutation that inactivates the regulating gene (repressor) and thus activates transcription.

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14
Q

Positive mutations

A

The inactivation of the regulating gene (activator) prevents transcription

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15
Q

Constitutive active mutation

A

Mutations that do not react to additional signals -> often in negative regulation but rarely in positive regulation.

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16
Q

How do mutations affect negative and positive regulation in transcription?

A

Mutations inactivating repressors (negative) allow transcription, while mutations inactivating activators (positive) prevent transcription. (opposite)

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17
Q

The lactose operon

A

-Regulates the degradation of lactose
-Catabolic operon
-Positive regulation: without glucose/allolactose
-Negative regulation: with lactose
-LacI acts as a repressor

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18
Q

Why is the lactose operon called catabolic or degradative?

A

Because it encodes enzymes that are involved in catabolism - expression induced only when substrate is available

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19
Q

What does the Lac promoter do?

A

-sigma 70 bacterial promoter with regions: -10 and -35

-Lac I is continuously expressed -> if no lactose, it binds to lacO, close to the promoter -> TC OFF
-With lactose: allolactose binds to repressor Lac I -> change of conformation -> TC ON

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20
Q

What is allolactose

A

Lactose isomer -> is produced by beta-glactosidase. and inducer

21
Q

How Lac I forms a tetramer

A

It binds 2 operator sites. -> The sites (o1,o2,o3)
If o2 + o3 are removed -> repression only 20-fold instead of 1000
-If Lac I binds o1 and o2 or o3 -> Folds DNA in promoter region and stabilises.
Prevents binding of RNA polymerase to promoter

22
Q

Does the repression require the folding of the DNA and the tetramerisation of Lac I on the DNA?

23
Q

What are the negative repressible systems?

A

Effectors bind to repressor, which in turn binds to the operator.

Repressors (that negatively control the biosynthetic operator) ->is inactivated when no effector (corepressor) is present ->aporepressor

24
Q

What is the tryptophan operon?

A

-In E.coli
-Negatively repressible system. The gene TrpR (constitutive expression) encodes it.
-TrpR acts as a repressor

25
Describe the negatively repressible system of the tryptophan operon.
-The TrpR repressor is expressed continuously and negatively regulates the operon. -Transcription continues if no tryptophan is present -> repressor does not bind to operator site. -If tryptophan is present: it binds to TrpR repressor -> conformational change and it binds to the operator site -> blocks RNA transcription
26
Describe the positive regulation.
Positive regulation of transcription initiation by activators. -Promoters, that are dependent on it, -> low affinity to RNA polymerase. -> leads to little transcription IN ABSENCE of activator -Transcriptional activators bind DNA immediately upstream of the RNA polymerase binding site -Inducers activate activators and corepressors deactivate them
27
What is the arabinose operon
-in E. coli -The genes in operon: araB,araA, araD -> are transcribed from the single promoter pBAD.
28
What is the function of the AraC protein in the arabinose operon?
AraC is a DNA binding protein that acts as an activator or antiactivator depending on the presence of arabinose. P1 - without bound arabinose - anti activator P2 - L-arabinose is bound to araC - binds to araI and recruits RNA polymerase
29
How can the activity of an activator be modified?
The activity of the activator can be activated by an inducer or inactivated by a corepressor.
30
What is the fab operon?
-bionsynthesis of fatty acids -Positive repressible regulation -FadR = transcriptional activator Fatty acyl-CoA inhibits FadR's binding to the activator site, preventing transcription activation. with acyl-CoA: binds to FadR = no activation = no TC = no biosynthesis -High levels of fatty acyl-CoA = induces expression of degredation enzymes
31
what is the fad operon?
-degradation of fatty acids -negative inducible regulation -FadR = repressor with acyl-CoA: binds to FadR = not able to repress = TC = degradation of fatty acids
32
What is transcription attenuation?
Transcription attenuation is control of transcription that functions by premature termination of mRNA synthesis. Transcription begins at promoter but terminates in leader region.
33
What influences the formation of the termination or antitermination helix?
Helix formation can be regulated by ribosome position, or binding: small molecules, a second RNA, or a protein.
34
How can transcription attenuation be prevented?
can be prevented by folding RNA into alternative RNA structure - anti-terminator
35
What is the role of the leader sequence in the tryptophan operon?
The leader sequence encodes a short mRNA with two Trp codons. contains 4 complementary regions: RNA can fold into 2 possible secondary structures 3/4 = terminator helix 2/3 = antiterminator helix = cont transcription
36
How does the position of the ribosome affect transcription in the tryptophan operon?
The position of the ribosome influences which RNA helices will form, affecting transcription termination.
37
What happens when tryptophan levels are low?
When tryptophan is low, the ribosome stalls, allowing the formation of the antitermination helix 2/3 and continuing transcription.
38
What occurs when tryptophan is present?
When tryptophan is present, the ribosome prevents the formation of the antitermination helix, allowing the termination helix 3/4 to form and stopping transcription.
39
What is the function of riboswitches?
-Riboswitches are RNA domains that bind molecules to control translation of mRNA. -directly sense regulatory signal -Located at 5' end of mRNA -control transcription attenuation and translation initiation.
40
tRNA-sensing riboswitches
codon-anticodon base pairing IF tRNA is not aminoacylated => 3' end of tRNA interacts with bulge in antiterminator => stablises => prevents termination
41
small molecule binding riboswitches
binding of molecule directly to leader RNA => influences RNA folding + formation of terminator structure.
42
How does the secondary structure of leader RNA influence gene expression?
some structures can protect RNA from degradation
43
What are the 3 types of RNA degradation mechanisms?
-3’-5’ exoribonucleases -5’-3’ exoribonucleases -endoribonucleases.
44
how do RNA degradation mechanisms work generally?
sequence and structure of RNA affects stability of RNA
45
What is the average half-life of mRNA in bacteria?
The average half-life of mRNA in bacteria is 1-3 minutes.
46
How do structured RNAs like tRNA and rRNA compare to mRNA in terms of stability?
Structured RNAs like tRNA and rRNA are very stable, while mRNAs are generally unstable.
47
What is the Expression of RNAse E enzyme regulated by?
degradation of its own mRNA by RNAse E. Autoregulation of expression by measuring activity of the enzyme. RNAse E too high => transcript rapidly degraded => prevents further synthesis
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