Prokaryotic Gene Regulation Flashcards
In the bacterial genome, where does the RNA transcript begin?
- at the +1 position
- upstream of other RNA Polymerase DNA recognition sequences
Where are other RNA Polymerase DNA recognition sequences?
–10 and –35
Where does translation begin in bacteria?
ribosome binding site
What does translation induction require in bacteria?
ATG-coded Methionine must be present at the start of the structural gene, 6-10bps downstream
Where is the bacterial terminator?
3’ region
In what direction does bacterial translation occur?
5’ to 3’.
What a promotors?
- gene switches
- switch genes on
What are inducible promotors?
response is mediated by metabolite presence
How is transcription regulated (and gene expression activated)?
dimeric proteins bind to inverted DNA repeats, slotting neatly into the major groove
Describe the motifs exhibited by dimeric transcription regulation proteins in bacteria
helix turn helix
Describe the dimer monomers involved in transcription regulation in bacteria
two domains: the recognition and stabilising helices.
What is the main interactor between the proteins and the DNA?
recognition domain.
Describe transcription regulation
- negatively regulated (repression)
- promoted (induction)
What is a repressor?
protein that negatively regulates gene expression, blocking transcription, by binding to an operator site
Where are operators typically found?
downstream of promotor regions
How do operators work?
mechanical blockage of the repressor blocks RNA polymerase from transcribing
Describe end-product repression
- common in anabolic (biosynthetic) genes
- the corepressor (the end product of the reaction) must be present to activate the repressor
Describe the arg operon
- end-product repression
- repressor protein will only bind when the corepressor (arginine) is present
- arginine binds to repressor protein, allowing the repressor protein to bind to operator
- blocks movement of RNA polymerase down the DNA (mechanical inhibition)
- stops arginine synthesis once enough has been synthesised by
Describe catabolic (degradative) genes
- become induced by a starting substrate (the inducer), which renders the repressor inactive
- induction period: removing the repressor, transcribing and translating
Describe the lac operon
- negative regulation resulting in induction
- LacI Repressor protein is bound to an operator site mechanically preventing transcription
- inducer: allolactose (or IPTG in a laboratory setting)
- cyclic AMP must be bound to the activator site, using a carbon source
- inducer binds LacI; conformational change reduces affinity for LacI to the operator DNA, causing it to drop off the DNA and remove the mechanical hindrance blocking off transcription
Describe allolactose
a lactose isomer derivative formed in an hydrolysis isomerisation reaction of beta 1,4 to beta 1,6 by LacZ.
Describe LacY
necessary as a permase transport system that allows lactose into the cell
IPTG
- isoproylthiogalactoside
- non metabolisable lactose analogue
Describe LacA
- part of the lac operon
- adds an acetyl group to lactose
- importance of this function is unclear
- gene can be knocked out without impact
Describe E. coli
- feast and famine organism
- can grow on both glucose and lactose, with glucose being its preferred carbon source
- experiences a lag phase between resource depletion and induction
Describe ‘leaky expression’
low level transcription will occur, even in the absence of an inducer
Transcription will only ever occur when…
an activator is bound to the DNA.
What is an activator?
a protein that recruits RNA polymerases
Where must the activator binding site be?
- upstream (sometimes kbs)
- so that it does not mechanically block the RNA polymerase
- allows bending of the DNA, for RNA polymerase location.
Describe RNA polymerase recruitment
- bimodal
- can occur by either binding to the RNA polymerase, and ‘pulling’ it down onto the DNA
- or binding to the DNA, ‘capturing’ the RNA polymerase and then pulling it down
What is an operon?
a discrete entity when two or more genes are being cotranscribed by polycistronic RNA, which each have their own ribosome binding site.
What is a regulon?
a group of operons with regulatory proteins
Describe the Maltose regulon
- made up of operons 1 and 2 and a regulatory protein
- inducer (maltose) allows the maltose activator to bind to DNA
What is the regulatory protein in the Maltose regulon allowing?
Metabolite repression
Give an example set of regulatory proteins
alarmones: binosine and tetraphosphane
Describe the Pho regulon
- phosphate regulon
- composed of 100 different genes in multiple operons
Most bacteria have a preferred carbon source composed of
- organic acids such as succinate and methylate
- they do not rely on glucose
Give an example of a set of archaeal regulatory proteins
- nitrogen regulatory protein (NRP)
- measures alpha-ketoglutarate
- NRP binds to the TATA box under sufficient alpha-ketoglutarate exposure
- causes it to drop off
Describe alpha-ketoglutarate
(the ketoacid of glutamate, having lost its ammonia).
When is there lots of alphaketoglutarate?
`When nitrogen is limited
Binding to the TATA box can
- have both positive and negative control on different genes
- stop/promote transcription
Describe glutamate
- the central amino acid which transaminates other amino acids
- necessary for the final transamination reactions of leucine, valine, isoleucine, and other amino acids
