Week 9: Transcription And Regulatory Networks Flashcards
What is the central dogma of molecular biology?
DNA → RNA → Protein
What enzyme carries out transcription?
RNA polymerase
What are the main subunits of RNA polymerase in E. coli?
- β, β’-subunits
- α-subunits
- ω-subunit
- σ-factor
What role do magnesium ions play in nucleic acid processing?
They are ubiquitous in enzymes that process nucleic acids.
How does RNA polymerase initially move to the promoter of a gene?
By diffusion (three-dimensional random walk)
What happens when RNA polymerase encounters DNA?
It binds unspecifically and slides along the DNA, transitioning to a one-dimensional random walk.
What triggers the start of RNA synthesis?
Consensus sequences such as TCTTGACA, AGAACTGT, TATAAT, ATATTA.
How does the strength of a promoter affect transcription?
The closer the promoter sequence resembles the consensus sequence, the stronger the interaction with RNA polymerase.
What are the two basic forms of transcriptional regulation in bacteria?
- Strength of the promoter
- Sigma factor involved
What is formed when a promoter is bound by RNA polymerase?
An open complex
What is the typical RNA synthesis rate by RNA polymerase?
Approximately 30 – 50 nt/s
What are the two main mechanisms for termination of transcription?
- GC hairpin formation
- Rho (ρ) factor interaction
What is the accuracy of transcription in vivo?
Approximately 1 × 10–5
What is the half-life of mRNA in bacteria?
Approximately 7 minutes
What happens during head-on collisions between replication forks and transcription complexes?
They create extremely stable complexes with a long half-life.
What is the role of activator proteins in transcription?
They help recruit RNA polymerase complexes.
What is Class I activation in transcription?
Binding of activator proteins near or at the promoter.
What is the role of repressor proteins in transcription?
They prevent binding of RNA polymerase complexes.
What is the significance of the lactose operon in gene expression regulation?
It is regulated on several levels including the binding of repressor proteins.
What happens when lactose is available to the cell?
Lactose is isomerised into allolactose, which binds to the repressor and changes its shape.
What is required for strong transcription of the lac operon?
Binding of CAP protein (catabolite activator protein).
What does cAMP indicate in the context of glucose levels?
cAMP levels are high when glucose is absent.
What is quorum sensing?
A regulatory network in bacteria such as Vibrio fischeri.
What is the function of LuxI in Vibrio fischeri?
It produces the auto-inducer AHL (acetyl-homoserine lactone).
Fill in the blank: The closer the actual promoter sequence resembles the consensus sequence, the _______.
stronger the interaction of RNA polymerase with the promoter.
What is the significance of the light organ in Euprymna scolopes for Vibrio fischeri?
The light organ is rich in nutrients for V. fischeri
This mutualistic relationship benefits both the squid and the bacteria.
What is the role of LuxI in Vibrio fischeri?
LuxI produces the auto-inducer AHL (acetyl-homoserine lactone)
AHL is a common autoinducer found in various bacteria.
What does AHL do in the context of Vibrio fischeri?
AHL diffuses freely between the inside and the outside of the bacterium
This allows communication between bacterial cells.
What is the function of the gene luxR in Vibrio fischeri?
The gene luxR codes for the transcription activator LuxR
LuxR requires AHL as a cofactor to function.
How does an increase in bacterial population affect AHL concentration?
An increased bacterial population increases the AHL concentration
This elevation in AHL concentration is crucial for quorum sensing.
What happens when AHL concentration reaches a certain level in Vibrio fischeri?
AHL allows LuxR to dimerise and bind to the activator site
This binding switches on strong transcription of the lux operon.
What is the consequence of luxI being part of the operon in Vibrio fischeri?
luxI is strongly expressed, flooding the environment with AHL
This creates a positive feedback loop for luminescence.
What occurs during the day regarding Vibrio fischeri luminescence?
The majority of bacteria are released by the squid, switching luminescence off
This is a regulatory mechanism based on the time of day.
What triggers the switch back on for luminescence in Vibrio fischeri at night?
Critical levels of bacteria are reached at night
This allows luminescence to be switched back on.
What is Pseudomonas aeruginosa known for?
It is an opportunistic pathogen that infects immunocompromised patients
Common conditions include AIDS and cystic fibrosis.
How does Pseudomonas aeruginosa utilize quorum sensing?
It waits until a certain threshold of cells is reached to switch on virulence factors
This strategy helps the pathogen evade the host immune system.
What disease does Vibrio cholerae cause?
Cholera
It is a Gram-negative, comma-shaped bacterium.
What happens when high bacterial numbers are reached in the small intestine for Vibrio cholerae?
Symptoms of cholera cause large numbers of bacteria to be excreted
This process is part of the bacterial life cycle and spread.
True or False: At low cell numbers, bacterial infections can easily be eradicated by the host immune system.
True
This is why pathogens like P. aeruginosa wait to express virulence factors.
Fill in the blank: The auto-inducer produced by LuxI is _______.
AHL (acetyl-homoserine lactone)
AHL plays a critical role in quorum sensing.
