Prokaryotic Gene Regulation

Question 1

In the bacterial genome, where does the RNA transcript begin?

Answer 1

• at the +1 position
• upstream of other RNA Polymerase DNA recognition sequences

Question 2

Where are other RNA Polymerase DNA recognition sequences?

Answer 2

–10 and –35

Question 3

Where does translation begin in bacteria?

Answer 3

ribosome binding site

Question 4

What does translation induction require in bacteria?

Answer 4

ATG-coded Methionine must be present at the start of the structural gene, 6-10bps downstream

Question 5

Where is the bacterial terminator?

Answer 5

3’ region

Question 6

In what direction does bacterial translation occur?

Answer 6

5’ to 3’.

Question 7

What a promotors?

Answer 7

• gene switches
• switch genes on

Question 8

What are inducible promotors?

Answer 8

response is mediated by metabolite presence

Question 9

How is transcription regulated (and gene expression activated)?

Answer 9

dimeric proteins bind to inverted DNA repeats, slotting neatly into the major groove

Question 10

Describe the motifs exhibited by dimeric transcription regulation proteins in bacteria

Answer 10

helix turn helix

Question 11

Describe the dimer monomers involved in transcription regulation in bacteria

Answer 11

two domains: the recognition and stabilising helices.

Question 12

What is the main interactor between the proteins and the DNA?

Answer 12

recognition domain.

Question 13

Describe transcription regulation

Answer 13

• negatively regulated (repression)
• promoted (induction)

Question 14

What is a repressor?

Answer 14

protein that negatively regulates gene expression, blocking transcription, by binding to an operator site

Question 15

Where are operators typically found?

Answer 15

downstream of promotor regions

Question 16

How do operators work?

Answer 16

mechanical blockage of the repressor blocks RNA polymerase from transcribing

Question 17

Describe end-product repression

Answer 17

• common in anabolic (biosynthetic) genes
• the corepressor (the end product of the reaction) must be present to activate the repressor

Question 18

Describe the arg operon

Answer 18

• 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

Question 19

Describe catabolic (degradative) genes

Answer 19

• become induced by a starting substrate (the inducer), which renders the repressor inactive
• induction period: removing the repressor, transcribing and translating

Question 20

Describe the lac operon

Answer 20

• 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

Question 21

Describe allolactose

Answer 21

a lactose isomer derivative formed in an hydrolysis isomerisation reaction of beta 1,4 to beta 1,6 by LacZ.

Question 22

Describe LacY

Answer 22

necessary as a permase transport system that allows lactose into the cell

Question 23

IPTG

Answer 23

• isoproylthiogalactoside
• non metabolisable lactose analogue

Question 24

Describe LacA

Answer 24

• part of the lac operon
• adds an acetyl group to lactose
• importance of this function is unclear
• gene can be knocked out without impact

Question 25

Describe E. coli

Answer 25

• 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

Question 26

Describe ‘leaky expression’

Answer 26

low level transcription will occur, even in the absence of an inducer

Question 27

Transcription will only ever occur when…

Answer 27

an activator is bound to the DNA.

Question 28

What is an activator?

Answer 28

a protein that recruits RNA polymerases

Question 29

Where must the activator binding site be?

Answer 29

• upstream (sometimes kbs)
• so that it does not mechanically block the RNA polymerase
• allows bending of the DNA, for RNA polymerase location.

Question 30

Describe RNA polymerase recruitment

Answer 30

• 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

Question 31

What is an operon?

Answer 31

a discrete entity when two or more genes are being cotranscribed by polycistronic RNA, which each have their own ribosome binding site.

Question 32

What is a regulon?

Answer 32

a group of operons with regulatory proteins

Question 33

Describe the Maltose regulon

Answer 33

• made up of operons 1 and 2 and a regulatory protein
• inducer (maltose) allows the maltose activator to bind to DNA

Question 34

What is the regulatory protein in the Maltose regulon allowing?

Answer 34

Metabolite repression

Question 35

Give an example set of regulatory proteins

Answer 35

alarmones: binosine and tetraphosphane

Question 36

Describe the Pho regulon

Answer 36

• phosphate regulon
• composed of 100 different genes in multiple operons

Question 37

Most bacteria have a preferred carbon source composed of

Answer 37

• organic acids such as succinate and methylate
• they do not rely on glucose

Question 38

Give an example of a set of archaeal regulatory proteins

Answer 38

• nitrogen regulatory protein (NRP)
• measures alpha-ketoglutarate
• NRP binds to the TATA box under sufficient alpha-ketoglutarate exposure
• causes it to drop off

Question 39

Describe alpha-ketoglutarate

Answer 39

(the ketoacid of glutamate, having lost its ammonia).

Question 40

When is there lots of alphaketoglutarate?

Answer 40

`When nitrogen is limited

Question 41

Binding to the TATA box can

Answer 41

• have both positive and negative control on different genes
• stop/promote transcription

Question 42

Describe glutamate

Answer 42

• the central amino acid which transaminates other amino acids
• necessary for the final transamination reactions of leucine, valine, isoleucine, and other amino acids