Chapter 10 - Bacterial Gene Expression Control Flashcards
Promoter
Eukaryotes and Prokaryotes can diff ones.
This is where transcription begins.
It is a region on DNA when RNA polymerase binds to start transcription
Sigma Factor
a protein that binds to specific DNA sequences at the promoter to initiate transcription.
binds to two regions
What two regions does the sigma factor bind to
Pribnow Box (-10 element): TATAAT
helps find the start point
-35 element: sequence TTGACA
helps stabilize
RNA polymerase recruitment
sigma factor recruits RNA polymerase to the promoter and transcription begins
then sigma factor falls off
Termination Sequence
The sequence where transcription stops, typically containing a GC-rich region and a series of uracils (U) in the RNA.
Hairpin Loop
The GC-rich sequence in the RNA forms a hairpin structure that causes RNA polymerase to dissociate and terminate transcription.
RNA Polymerase Detachment
RNA polymerase dissociates from the DNA after transcribing the terminator sequence, releasing the newly synthesized RNA molecule.
In bacteria ___ is favored over ___
Efficiency, complexity
Many genes are ____
Constitutive - always on
The basic transcriptional control system is the
Operon - a cluster of genes on a DNA strand that are transcribed together as a single unit
Operon regulation (Prokaryotes)
regulated by single on/off switches for transcription
Polycistronic mRNA
The genes within an operon are transcribed as a single polycistronic mRNA (one long RNA molecule) that contains the coding information for multiple genes (or ORFs - Open Reading Frames).
Promoter
The DNA region where sigma factor (σ) and RNA polymerase bind to initiate transcription.
Operator
binding site. Operators regulate the transcription of nearby genes by controlling whether RNA polymerase can access the promoter region to start transcription
IRES (Internal Ribosome Entry Sites)
Sequences in the mRNA that allow ribosomes to bind at multiple sites, enabling translation of several proteins from one mRNA molecule.
Inducible Operon
An operon that is normally off but can be turned on by an inducer molecule (e.g., the lac operon for lactose metabolism).
Repressible Operon
An operon that is usually on but can be turned off by a corepressor molecule (e.g., the trp operon for tryptophan synthesis).
Lac Operon
An inducible operon involved in lactose metabolism. It is turned on when lactose (or allolactose) is present and inactivates the repressor.
Trp Operon
A repressible operon involved in tryptophan biosynthesis. usually on. It is turned off when tryptophan (the corepressor) is abundant.
Repressor
A protein that binds to the operator of an operon to block transcription by preventing RNA polymerase from transcribing the operon.
Singletons
Genes in bacteria that are regulated individually, not grouped into operons.
Lac Operon
An inducible operon that is usually off, but can be turned on in the presence of lactose.
Lactose
A milk sugar (glucose + galactose) that bacteria metabolize.
β-galactosidase (lactase)
Enzyme encoded by lacZ that cleaves lactose into galactose and glucose.
Permease
Enzyme encoded by lacY that transports lactose into the bacterial cell.
Galactoside Acetyltransferase (GAT)
Enzyme encoded by lacA that is involved in modifying galactosides (role is less understood).
Promoter
The DNA sequence where RNA polymerase binds to initiate transcription of the lac operon genes.
Operator
The region near the promoter where the lac repressor binds to block transcription in the absence of lactose.
Lac Repressor (lacI)
A protein encoded by the lacI gene that binds to the operator to prevent transcription of the lac operon in the absence of lactose.
Inducer (Allolactose)
The molecule that inactivates the lac repressor when lactose is present. Allolactose, a form of lactose, binds to the repressor, causing it to detach from the operator.
Lac Operon Activation
When allolactose binds to the repressor, it removes the repressor from the operator, allowing RNA polymerase to transcribe the lacZYA genes.
LacI Gene
Encodes the lac repressor. It is not part of the lac operon but regulates the operon by binding to the operator to prevent transcription.
Lac Operon and Glucose
The lac operon is regulated by glucose levels. High glucose = lac operon off, low glucose = lac operon on.
cAMP
Cyclic AMP (cAMP) is a signaling molecule whose levels are inversely proportional to glucose levels.
cAMP and CRP Complex
When glucose is low, high cAMP binds to CRP (cAMP receptor protein), forming a complex that binds to the lac promoter to enhance RNA polymerase binding.
CRP Binding
CRP-cAMP complex binds to the lac promoter and aids the recruitment of RNA polymerase to increase transcription of the lac operon genes.
Effect of High Glucose on cAMP
High glucose = low cAMP, which means CRP cannot bind to the lac promoter, resulting in low transcription of the lac operon (even if lactose is present).
Low Glucose and Lac Operon Activation
Low glucose = high cAMP → CRP-cAMP complex binds to the lac promoter, promoting transcription of the lac operon.
Glucose Override System
The “glucose override” ensures that bacteria use glucose preferentially. When glucose is high, the lac operon is off, even if lactose is present.
Transcription of LacZYA
Transcription of lac operon genes (lacZYA) is promoted when glucose is low (cAMP is high) and inhibited when glucose is high (cAMP is low).
low glucose
high cAMP
High glucose
low cAMP
Tryptophan
One of the 20 amino acids. Bacteria synthesize tryptophan, but humans must obtain it from food.
Key Genes in Trp Operon
trpE, trpD, trpC, trpB, trpA – genes that encode the enzymes for tryptophan synthesis.
Polycistronic mRNA
The genes trpE, trpD, trpC, trpB, trpA are transcribed together into one long polycistronic mRNA (trpEDCBA).
Trp Repressor (trpR)
Encoded by the trpR gene (outside the operon), the trp repressor prevents transcription of the operon when tryptophan is present.
Trp Repressor Mechanism
When tryptophan is present, it binds to the trp repressor, activating it and allowing it to bind to the operator, blocking transcription of the operon.
Repression of Trp Operon
High tryptophan levels activate the trp repressor, which binds to the operator and blocks transcription, saving energy and resources.
When Trp is Low
When tryptophan is low, the trp repressor is inactive, allowing the operon to be on and transcription to occur for tryptophan production.
Repressible vs. Inducible Operons
The trp operon is repressible (usually on, turned off when enough tryptophan is made), while the lac operon is inducible (usually off, turned on when lactose is present).
Attenuation in Trp Operon
Attenuation regulates transcription after it has started, in response to tRNA^Trp levels. It can abort transcription midway through.
TrpL Leader Sequence
The trpL leader sequence is a 130 bp region upstream of the trpEDCBA genes that contains an attenuator sequence capable of forming a hairpin structure.
TrpL Peptide
The trpL leader sequence encodes a short peptide of 14 amino acids, including two adjacent tryptophans, which are rare and crucial for attenuation regulation.
Transcription and Translation Coupling
In bacteria, transcription and translation are coupled. The ribosome begins translating the mRNA as it is transcribed.
Attenuation Mechanism
Low tRNA^Trp causes the ribosome to stall at tryptophan codons in the trpL sequence, preventing hairpin formation and allowing transcription to continue.
Effect of High tRNA^Trp
High tRNA^Trp allows the ribosome to pass over the tryptophan codons in trpL, enabling the formation of the hairpin terminator, halting transcription.
Trp Operon Attenuation vs. TrpR Repression
TrpR repression blocks transcription initiation based on tryptophan levels, while attenuation aborts transcription midway based on tRNA^Trp levels.
When Attenuation Causes Transcription to Stop
High tRNA^Trp → ribosome moves past codons → hairpin forms → transcription terminates early.
When Attenuation Allows Transcription to Continue
Low tRNA^Trp → ribosome stalls → hairpin does not form → transcription proceeds to trpEDCBA genes.
