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Molecular biology > Regulation of transcription > Flashcards

Regulation of transcription Flashcards

1
Q

What are cis acting sequences

A
  • non protein coding regulatory sequences in DNA that are usually physcially close/connected to the sequences they regulate
  • regulates genes by binding to regulatory proteins
  • e.g. promoters
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2
Q

What are trans acting sequences

A
  • does not necessarily have to be close to the sequence that they regulate
  • have to be expressed as regulatory proteins to regulate target sequence
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3
Q

What is operator?

A

a cis acting sequnce where regulatory proteins bind

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4
Q

what does negative regulation mean?

A

when DNA/protein interaction decrease transcription

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5
Q

what does positive regulation mean?

A

when DNA/protein interaction increase transcription

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6
Q

Genes can be repressible or inducible, what do they mean?

A
  • repressible: transcription is ON by default
  • inducible: transcription is OFF by default
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7
Q

what is an activator protein?

A

regulatory protein that recruit RNAP to DNA

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8
Q

what is a repressor protein

A

regulatory protein that inhibits RNAP binding or initiation

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9
Q

What is a corepressor?

A

small molecule whose presence help reduce transcription through causing allosteric change in regulatory protein

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10
Q

what is an inducer?

A
  • small molecule whose presence help increase transcription through causing allosteric change in regulatory protein
  • induces transcription
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11
Q

what does positive repressible regulation mean?

A
  • activator protein bound to DNA by default and activates transcription
  • when corepressor binds activator, activator is prevented from binding the DNA => prevents transcription
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12
Q

What does negative repressible regulation mean?

A
  • Transcription is ON by default
  • when corepressor binds repressor, repressor/corepressor complex binds DNA and prevents transcription
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13
Q

What does positive inducible mean?

A
  • transcription of is OFF by default
  • when inducer binds to activator, activator activates trancription
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14
Q

what does negative inducible mean

A
  • Repressor protein bound to DNA by default and prevents transcription
  • When inducer binds repressor ,repressor is prevented from binding DNA, and activates transcription
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15
Q

what are transcription factors

A
  • DNA binding proteins encoded by trans acting sequences
  • can repress or activate transcription
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16
Q

DNA sequences (cis acting sequences) bound by TFs can be high level assemblies or low level sequences, what are they?

A
  • high level assemblies are cis acting regulatory DNA that is made up of many low level sequences
  • low level sequences (response elements) are short sequences that are recognised by regulatory proteins (e.g. TFs). they are within high level assemblies
  • e.g. promoter is a high level assembly that includes the low level sequence TATA box
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17
Q

suggest some eukaryotic high level assemblies

A
  • promoter
  • enhancer
  • silencer
  • insulator
18
Q

suggest some eukaryotic low level sequences

A
  • TATA box
  • CAAT box
  • BRE
19
Q

Suggest some prokaryotic high level assemblies

A
  • promoter
  • operator
20
Q

suggest a bacterial low level sequence

A

pribnow box (“TATAAT”)

21
Q

What is an operon?

A

a cluster of structural genes its adjacent regulatory sequences

22
Q

What do polycistronic and monocistronic mRNA mean?

A
  • polycistronic mRNA: codes for more than one gene, common in prokaryotes
  • monocistronic mRNA: codes for one gene, common in eukaryotes
23
Q

What is TRP operon

A
  • the operon that codes for enzymes that catalyses tryptophan synthesis
  • polycistronic
24
Q

what kind of regulation is TRP operon under?

A

negative repressible

25
Q

what is the repressor protein of TRP operon?

A

TrpR, coded for by regulatory gene trpR (gene name of a protein is italised and its first letter have to be lower case)

26
Q

what is the corespressor for TRP operon

A

tryptophan

27
Q

describe how TRP operon is turned OFF

A
  • when tryptophan is abundant
  • a lot can bind to repressor, allosterically changing the TrpR => activating it
  • TrpR + tryptophan complex stops transcription by binding operator and blocking RNAP
28
Q

Describe when TRP operon is ON

A
  • Not enough tryptophan available for TrpR to be in DNA-binding form
  • No TrpR + tryptophan blocking the operator, so RNAP can transcribe operon
29
Q

TRP operon is also regulated by attenuation, describe attenuation

A
  • possible because translation and transcription are concurrent in bacteria
  • High [tRNAtrp]:
    • Ribosome reads through domain 1 easily & shields domain 2
    • domain 3&4 form transcription terminator hairpin
  • Low [tRNAtrp]:
    • Ribosome stalls in 1 waiting for tRNAtrp
    • 2 binds 3
    • 3&4 cannot form transcription terminator hairpin
    • RNAP can proceed transcribing the TRP operon
  • As a result:
    • when trp is abundant, trp synthesis is slowed
    • but when trp is not abundant, trp synthesis occurs as normal
30
Q

What is trpL

A
  • a leader sequence: codes for the mRNA that will either form hairpin or not depending on the abundancy of tRNAtrp
  • translated but its peptide is degraded
  • role in fine tuning regulation of trp operon
31
Q

what is the lac operon

A

lac operon code for lactose degrading enzymes and lactose importer proteins

32
Q

how is the lac operon regulated?

A

negative inducible

33
Q

What is the repressor protein of lac operon

A

LacI

34
Q

what is the inducer of lac operon

A

lactose

35
Q

how is lac operon switched OFF?

A
  • LacI binds to operator, loops the DNA
  • making DNA inacessible to RNAP
36
Q

how is lac operon switched ON?

A
  • LacI inactivated by binding lactose
  • No LacI blocking the operator, so RNAP can transcribe operon
37
Q

lac operon is also under postive control by catabolite activator protein (CAP), how?

A
  • When [glucose] is low, [cAMP] will be high
  • cAMP is the inducer that binds to CAP and allow it to bind to CBS (CAP binding site) of DNA
  • CAP/cAMP complex actively recruits RNAP
  • transcription turns ON
38
Q

What is the purpose of controlling lac operon with CAP?

A
  • allows cells to express preference of what sugars to breakdown
  • cells prefer glucose over lactose
  • but when glucose is scarce, CAP allows cell to turn on lac operon => break down lactose
39
Q

(eukaryotes) what are enhancers?

A
  • cis acting sequences
  • encodes regulatory sequences that help recruit RNAP
  • can be located near, within, upstream or downstream of a gene (sometimes by 1000s of nts away)
  • binds transcription factors
40
Q

what are silencers?

A
  • cis acting sequence
  • when bind to transcription factors, inhibits the transcription of a gene
41
Q

regulatory proteins can be regulated by autologus regulation, how?

A
  • some regulatory proteins can regulate themselves: autologus
    • ​e.g. LacI inhibits the expression of its own gene lacI => when there’s too much LacI, expresson of lacI is repressed
42
Q

transcription is also regulated by gene activation cascades, what is a gene activation cascade?

A
  • where the activation or repression of a gene activates or repress a cascade of other genes
  • initiated by external gradients or factors

Molecular biology (8 decks)

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