Week 9: Transcription And Regulatory Networks

Question 1

What is the central dogma of molecular biology?

Answer 1

DNA → RNA → Protein

Question 2

What enzyme carries out transcription?

Answer 2

RNA polymerase

Question 3

What are the main subunits of RNA polymerase in E. coli?

Answer 3

• β, β’-subunits
• α-subunits
• ω-subunit
• σ-factor

Question 4

What role do magnesium ions play in nucleic acid processing?

Answer 4

They are ubiquitous in enzymes that process nucleic acids.

Question 5

How does RNA polymerase initially move to the promoter of a gene?

Answer 5

By diffusion (three-dimensional random walk)

Question 6

What happens when RNA polymerase encounters DNA?

Answer 6

It binds unspecifically and slides along the DNA, transitioning to a one-dimensional random walk.

Question 7

What triggers the start of RNA synthesis?

Answer 7

Consensus sequences such as TCTTGACA, AGAACTGT, TATAAT, ATATTA.

Question 8

How does the strength of a promoter affect transcription?

Answer 8

The closer the promoter sequence resembles the consensus sequence, the stronger the interaction with RNA polymerase.

Question 9

What are the two basic forms of transcriptional regulation in bacteria?

Answer 9

• Strength of the promoter
• Sigma factor involved

Question 10

What is formed when a promoter is bound by RNA polymerase?

Answer 10

An open complex

Question 11

What is the typical RNA synthesis rate by RNA polymerase?

Answer 11

Approximately 30 – 50 nt/s

Question 12

What are the two main mechanisms for termination of transcription?

Answer 12

• GC hairpin formation
• Rho (ρ) factor interaction

Question 13

What is the accuracy of transcription in vivo?

Answer 13

Approximately 1 × 10–5

Question 14

What is the half-life of mRNA in bacteria?

Answer 14

Approximately 7 minutes

Question 15

What happens during head-on collisions between replication forks and transcription complexes?

Answer 15

They create extremely stable complexes with a long half-life.

Question 16

What is the role of activator proteins in transcription?

Answer 16

They help recruit RNA polymerase complexes.

Question 17

What is Class I activation in transcription?

Answer 17

Binding of activator proteins near or at the promoter.

Question 18

What is the role of repressor proteins in transcription?

Answer 18

They prevent binding of RNA polymerase complexes.

Question 19

What is the significance of the lactose operon in gene expression regulation?

Answer 19

It is regulated on several levels including the binding of repressor proteins.

Question 20

What happens when lactose is available to the cell?

Answer 20

Lactose is isomerised into allolactose, which binds to the repressor and changes its shape.

Question 21

What is required for strong transcription of the lac operon?

Answer 21

Binding of CAP protein (catabolite activator protein).

Question 22

What does cAMP indicate in the context of glucose levels?

Answer 22

cAMP levels are high when glucose is absent.

Question 23

What is quorum sensing?

Answer 23

A regulatory network in bacteria such as Vibrio fischeri.

Question 24

What is the function of LuxI in Vibrio fischeri?

Answer 24

It produces the auto-inducer AHL (acetyl-homoserine lactone).

Question 25

Fill in the blank: The closer the actual promoter sequence resembles the consensus sequence, the _______.

Answer 25

stronger the interaction of RNA polymerase with the promoter.

Question 26

What is the significance of the light organ in Euprymna scolopes for Vibrio fischeri?

Answer 26

The light organ is rich in nutrients for V. fischeri ## Footnote This mutualistic relationship benefits both the squid and the bacteria.

Question 27

What is the role of LuxI in Vibrio fischeri?

Answer 27

LuxI produces the auto-inducer AHL (acetyl-homoserine lactone) ## Footnote AHL is a common autoinducer found in various bacteria.

Question 28

What does AHL do in the context of Vibrio fischeri?

Answer 28

AHL diffuses freely between the inside and the outside of the bacterium ## Footnote This allows communication between bacterial cells.

Question 29

What is the function of the gene luxR in Vibrio fischeri?

Answer 29

The gene luxR codes for the transcription activator LuxR ## Footnote LuxR requires AHL as a cofactor to function.

Question 30

How does an increase in bacterial population affect AHL concentration?

Answer 30

An increased bacterial population increases the AHL concentration ## Footnote This elevation in AHL concentration is crucial for quorum sensing.

Question 31

What happens when AHL concentration reaches a certain level in Vibrio fischeri?

Answer 31

AHL allows LuxR to dimerise and bind to the activator site ## Footnote This binding switches on strong transcription of the lux operon.

Question 32

What is the consequence of luxI being part of the operon in Vibrio fischeri?

Answer 32

luxI is strongly expressed, flooding the environment with AHL ## Footnote This creates a positive feedback loop for luminescence.

Question 33

What occurs during the day regarding Vibrio fischeri luminescence?

Answer 33

The majority of bacteria are released by the squid, switching luminescence off ## Footnote This is a regulatory mechanism based on the time of day.

Question 34

What triggers the switch back on for luminescence in Vibrio fischeri at night?

Answer 34

Critical levels of bacteria are reached at night ## Footnote This allows luminescence to be switched back on.

Question 35

What is Pseudomonas aeruginosa known for?

Answer 35

It is an opportunistic pathogen that infects immunocompromised patients ## Footnote Common conditions include AIDS and cystic fibrosis.

Question 36

How does Pseudomonas aeruginosa utilize quorum sensing?

Answer 36

It waits until a certain threshold of cells is reached to switch on virulence factors ## Footnote This strategy helps the pathogen evade the host immune system.

Question 37

What disease does Vibrio cholerae cause?

Answer 37

Cholera ## Footnote It is a Gram-negative, comma-shaped bacterium.

Question 38

What happens when high bacterial numbers are reached in the small intestine for Vibrio cholerae?

Answer 38

Symptoms of cholera cause large numbers of bacteria to be excreted ## Footnote This process is part of the bacterial life cycle and spread.

Question 39

True or False: At low cell numbers, bacterial infections can easily be eradicated by the host immune system.

Answer 39

True ## Footnote This is why pathogens like P. aeruginosa wait to express virulence factors.

Question 40

Fill in the blank: The auto-inducer produced by LuxI is _______.

Answer 40

AHL (acetyl-homoserine lactone) ## Footnote AHL plays a critical role in quorum sensing.