Regulation of transcription Flashcards
What are cis acting sequences
- 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
What are trans acting sequences
- does not necessarily have to be close to the sequence that they regulate
- have to be expressed as regulatory proteins to regulate target sequence
What is operator?
a cis acting sequnce where regulatory proteins bind
what does negative regulation mean?
when DNA/protein interaction decrease transcription
what does positive regulation mean?
when DNA/protein interaction increase transcription
Genes can be repressible or inducible, what do they mean?
- repressible: transcription is ON by default
- inducible: transcription is OFF by default
what is an activator protein?
regulatory protein that recruit RNAP to DNA
what is a repressor protein
regulatory protein that inhibits RNAP binding or initiation
What is a corepressor?
small molecule whose presence help reduce transcription through causing allosteric change in regulatory protein
what is an inducer?
- small molecule whose presence help increase transcription through causing allosteric change in regulatory protein
- induces transcription
what does positive repressible regulation mean?
- activator protein bound to DNA by default and activates transcription
- when corepressor binds activator, activator is prevented from binding the DNA => prevents transcription
What does negative repressible regulation mean?
- Transcription is ON by default
- when corepressor binds repressor, repressor/corepressor complex binds DNA and prevents transcription
What does positive inducible mean?
- transcription of is OFF by default
- when inducer binds to activator, activator activates trancription
what does negative inducible mean
- Repressor protein bound to DNA by default and prevents transcription
- When inducer binds repressor ,repressor is prevented from binding DNA, and activates transcription
what are transcription factors
- DNA binding proteins encoded by trans acting sequences
- can repress or activate transcription
DNA sequences (cis acting sequences) bound by TFs can be high level assemblies or low level sequences, what are they?
- 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
suggest some eukaryotic high level assemblies
- promoter
- enhancer
- silencer
- insulator
suggest some eukaryotic low level sequences
- TATA box
- CAAT box
- BRE
Suggest some prokaryotic high level assemblies
- promoter
- operator
suggest a bacterial low level sequence
pribnow box (“TATAAT”)
What is an operon?
a cluster of structural genes its adjacent regulatory sequences
What do polycistronic and monocistronic mRNA mean?
- polycistronic mRNA: codes for more than one gene, common in prokaryotes
- monocistronic mRNA: codes for one gene, common in eukaryotes
What is TRP operon
- the operon that codes for enzymes that catalyses tryptophan synthesis
- polycistronic
what kind of regulation is TRP operon under?
negative repressible
what is the repressor protein of TRP operon?
TrpR, coded for by regulatory gene trpR (gene name of a protein is italised and its first letter have to be lower case)
what is the corespressor for TRP operon
tryptophan
describe how TRP operon is turned OFF
- 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
Describe when TRP operon is ON
- Not enough tryptophan available for TrpR to be in DNA-binding form
- No TrpR + tryptophan blocking the operator, so RNAP can transcribe operon
TRP operon is also regulated by attenuation, describe attenuation
- 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
What is trpL
- 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
what is the lac operon
lac operon code for lactose degrading enzymes and lactose importer proteins
how is the lac operon regulated?
negative inducible
What is the repressor protein of lac operon
LacI
what is the inducer of lac operon
lactose
how is lac operon switched OFF?
- LacI binds to operator, loops the DNA
- making DNA inacessible to RNAP
how is lac operon switched ON?
- LacI inactivated by binding lactose
- No LacI blocking the operator, so RNAP can transcribe operon
lac operon is also under postive control by catabolite activator protein (CAP), how?
- 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
What is the purpose of controlling lac operon with CAP?
- 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
(eukaryotes) what are enhancers?
- 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
what are silencers?
- cis acting sequence
- when bind to transcription factors, inhibits the transcription of a gene
regulatory proteins can be regulated by autologus regulation, how?
- 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
transcription is also regulated by gene activation cascades, what is a gene activation cascade?
- where the activation or repression of a gene activates or repress a cascade of other genes
- initiated by external gradients or factors
