Block B - Microbial Gene Regulation

Question 1

Which one is more stable, eukaryotic mRNA or bacterial mRNA?

Answer 1

eukaryotic mRNA

Question 2

What is the shine-dalgarno sequence and what process is it involved in? (3 marks)

Answer 2

its a specific region of nucleotide bases found in the mRNA of prokaryotes like bacteria. its rich in purines and guanine.
critical in translation initiation since it binds to the 16S rRNA of the 30S ribosome unit. The binding helps position the ribosome correctly at the start of the codon, ensuring translation begins at the correct site.

Question 3

What is an operon? (2 marks)

Answer 3

its a functional unit of DNA consisting of a group of genes under the control of a single promotor. these are transcribed together and usually encode proteins with related functions, often involved in shared metabolic pathways.

Question 4

What is the importance of operons? (3 marks)

Answer 4

-by grouping genes under a single promotor, operons ensure coordinated expression of genes that work together, saving energy and resources
-operons allow bacteria to adapt quickly to changes in the environment by turning gene sets on and off in response to external changes
-control of operon control expression of entire function

Question 5

in bacteria, transcription is catalysed by?

Answer 5

RNA polymerase

Question 6

Describe the structure of RNA polymerase?

Answer 6

its a multi-subunit enzyme, composed of core enzyme which is made up of five subunits; α (alpha), β (beta), β’ (beta prime), and ω (omega). also has a sigma factor.

Question 7

What is the role of a sigma factor in RNA polymerase?

Answer 7

a detachable subunit that helps the core enzyme recognize and bind to the promotor regions of DNA.

Question 8

What are the 3 main stages of transcription?

Answer 8

initiation, elongation and termination

Question 9

What does the sigma factor interact with to form holoenzyme at the beginning of transcription initiation?

Answer 9

RNAP

Question 10

What is a closed complex in terms of transcription?

Answer 10

when the RNA polymerase binds to the promotor, but the DNA remains double stranded

Question 11

What is a open complex in terms of transcription?

Answer 11

when DNA unwinds aka DNA duplex opening, forming the transcription bubble

Question 12

In bacteria, where does transcription usually begin and why? (3 marks)

Answer 12

usually begins near the pribnow box in bacterial promotors, where the DNA is rich is adenine and thymine, which have fewer hydrogen bonds and are easier to seperate

Question 13

What happens in trancription elongation? (1 mark)

Answer 13

RNA polymerase synthesizes an RNA molecule by adding ribonucleotides which are complementry to the DNA template strand. it maintains the transcription bubble until transcription has been terminated

Question 14

Name some elongation factors and its affects (3 marks)

Answer 14

Pause sites-certain DNA sequences cause the RNAP to pause, which can regulate elongation speed
Proteins such as NusA, NusG and DksA associate with RNAP can reduce the likelihood of pauses by modulating RNAP interactions with DNA
Supercoiling also influences elongation, positive supercoiling makes the DNA duplex tighter and harder, while negative supercoiling loosens the DNA duplex

Question 15

Tell me about intrinsic termination? (3 marks)

Answer 15

it is when the RNA transcript forms a hairpin structure because of base pairing in the GC rich region, the hairpin is followed by a stretch of uracil bases in the RNA transcript the weak A-U base paring causes RNAP to detach

Question 16

Tell me about Rho-dependant termination (5 marks)

Answer 16

it requires the rho protein, which binds to a rho utilisation site in the mRNA. it catches up to RNAP and when the RNAP pauses at a termination site, rho disrupts the RNA-DNA hybrid using its helicase activity, causing RNAP to release the transcript to release and dissociate

Question 17

What are transcription factors?

Answer 17

these are proteins that regulate the transcription of specific genes by binding to nearby DNA sequences. they are essential for controlling the rate of transcription by activating or repressing gene expression.

Question 18

Most activator proteins only bind to DNA poorly unless their _____ is present

Answer 18

inducer

Question 19

Name 2 examples of alternative gene regulatory strategies (4 marks)

Answer 19

-DNA methylation of the promotor of the CDKN2A gene (which encodes the tumour suppressor p16) can silence its expression in many cancers, enabling uncontrolled cell proliferation
-in the bacteriophage lambda, anti-termination is used to control the switch between the lysogenic and lytic cycles, allowing the virus to dynamically regulate gene expression based on its host environment

Question 20

Explain how PrfA thermometer regulates genes in Listeria monocytogenes

Answer 20

-at temperatures below 30°C, the RBS is inaccessible due to secondary structures
-At 37°C (host conditions), the structure unfolds, initiating translation of PrfA, which activates virulence factors for infection

Question 21

For Listeria monocytogenes, why are virulence factors only expressed at 37°C? (3 marks)

Answer 21

this is because this temperature is the typical core body temp of mammals. this regulation ensures that virulence factors, which are energetically costly to produce, are only expressed when the pathogen is in a host and can cause infection

Question 22

Tell me about transcriptional attenuation in trp operon?

Answer 22

controls gene expression based on the availability of tryptophan in the cell. if trp is high, the ribosome translates the leader peptide, allowing it to move past the two tryptophan codons. this exposes regions 3 and 4 which form the terminator hairpin, halting transcription of the operon. if trp is low, ribosomes stall at the tryptophan codons because tryptophan-charged tRNA is scarce. this prevents the 3:4 hairpin from forming and promotes the 2:3 anti-terminator hairpin allowing transcription to continue

Question 23

Tell me about riboswitches (5 marks)

Answer 23

These are regulatory RNA elements, these directly sense small molecules or ions to regulate gene expression. they act as molecular switches, modulating processes based on the presence of specific ligands. they do not require proteins for their regulatory function. for example the thiamine pyrophosphate (TPP) riboswitch in bacillus subtilis stabilizes a terminator hairpin, halting transcription of the thiamine biosynthesis genes.