Exam 4: Prokaryotic Gene Regulation

Question 1

Compare positive and negative regulator proteins (transcription factors).

Answer 1

Positive: The regulator protein is an activator; it activates gene expression through transcription. Transcription occurs only when regulator molecule directly stimulates RNA production.

Negative: The regulator protein is a repressor; it prevents gene expression through transcription. Genetic expression occurs unless shut off by regulator molecule

Question 2

Compare inducible and repressible gene expression.

Answer 2

Inducible: Transcription of the gene goes from low to high. (0 to 1) Bacteria adapt to environment by producing inducible
enzymes only when specific substrates are present.

Repressible: Transcription of the gene goes from high to low. (1 to 0) Presence of specific molecule inhibits gene expression. Abundance of end product in environment represses gene expression.

Question 3

Positive Repressible

Answer 3

-Activator regulator protein can trigger higher expression of operon.

-Since it’s repressible, it starts at some level of transcription and turns off.

-Feedback Repression: Activator will be turned off by product and become nonfunctional.

(Prevents you from having too much product)

Question 4

Positive Inducible

Answer 4

-Inactive activator protein

-Since it’s inducible, it starts off with a nonfunctional gene product, and then turns on.

-It needs a co-activator to turn it on.

Question 5

Negative Repressible

Answer 5

-The repressor regulator protein can prevent expression of the operon.

-HOWEVER, since it is repressible, transcription goes from high to low.

-That means that the protein must start off as nonfunctional and be turned on to repress the system.

-The product produced from the operon is a co-repressor that can make the regulator protein nonfunctional.

Ex: trp operon
Regulator protein can’t bind to operon without the co-repressor.

Question 6

Negative Inducible

Answer 6

-The repressor regulator protein prevents expression of the operon. (Think of it as creating a roadblock on the operator so that the RNA polymerase is stuck on the promoter.)

-Since it’s inducible, however, a substrate could make the repressor inactive.

Ex: The lac operon.
When lactose binds as allolactose to the repressor protein, it inactivates the repressor protein unblocking the operator. This is called substrate induction. It makes sense, because the genes for breaking down lactose would be unnecessary if there wasn’t any lactose. But when they are necessary, substrate induction will always be possible.

Question 7

In the presence of allolactose (the inducer), the regulator protein known as the lac repressor

Answer 7

cannot bind to the operator

Question 8

Given that the the trp operon is a negative repressible operon, what happens to the trp repressor in the absence of the tryptophan co-repressor?

Answer 8

It cannot bind to the operator and transcription takes place.

Question 9

Co-activator

Answer 9

Positive inducible (0 to 1):

Molecule (substrate) that interacts with the activator to make it functional (allowing transcription)

Question 10

Co-repressor

Answer 10

Negative repressible (1 to 0)

Molecule (product) interacts with the activator to make it functional (preventing transcription)

Question 11

In a negative repressible operon, the regulator protein is synthesized as an

Answer 11

inactive repressor

Question 12

Describe the components of prokaryotic gene regulation.

Answer 12

Regulator gene: This is separate and has its own promoter. It encodes for the regulator protein than affects gene regulation.

Regulator protein: Binds to DNA at the operator. Can be an activator or a repressor.

Promoter: This is where RNA polymerase binds.

Operator: This is where regulator protein binds.

Structural genes: Genes coding for something but not involved in the regulation process.

Question 13

Operon

Answer 13

A group of prokaryotic genes with a single promoter (transcribed as a single mRNA). The genes in an operon encode proteins that all function in a given process.

-promoter
-operator
-structural genes

Ex: the lac operon

Question 14

Catabolite-activating protein (CAP)

Answer 14

-Exerts positive control over lac operon

-Binds to CAP-binding site, facilitating RNA polymerase binding at promoter and facilitating transcription

-Lack of CAP binding diminishes expression of operon when glucose present (catabolite repression)

Question 15

A fellow student suggest that the lac operon will be expressed even in the presence of glucose. Is this true?

Answer 15

CAP (Catabolite-activating protein) diminishes expression of lac operon when glucose is present (catabolite repression).

Question 16

Define constitutive expression and its potential caveat.

Answer 16

Gene products are continuously expressed often at a
specific concentration produced regardless of chemical
makeup of environment.

-may be energetically expensive
-won’t allow for control in response to environment of the cell

Question 17

Describe the layered complexity of gene regulation.

Answer 17

Transcription:
-Promotors and enhancers

RNA Processing:
-Alternative splicing

Translation:
-Initiation factors
-RNAi?

-Feedback loops

Question 18

Describe how attenuation and riboswitches create gene regulation through RNA structure.

Answer 18

Attenuation and riboswitches are two mechanisms of gene regulation that operate at the level of RNA structure. These mechanisms involve the control of transcriptional termination or translation initiation based on the folding of the RNA molecule.

Attenuation:
-trp structural genes are preceded by leader sequence containing regulatory site called an attenuator.
-Based on the presence of trp on charged tRNAs mRNA has potential to fold into two different stem-loops (hairpins)
-Antiterminator hairpin: In absence of tryptophan, ribosome stalls on trp codons, allowing formation of 2-3 stem-loop. Transcription proceeds.
-Terminator hairpin: In presence of tryptophan, ribosome moves onto 1-2 stem-loop, preventing formation of 2-3 stem loop and terminating transcription.

Riboswitches: metabolite-sensing RNA sequence:
–Based on presence or absence of the metabolite, alternative forms of mRNA secondary structure
–Bind with small ligands; cause conformational change and induce second RNA domain
–Create anti-terminator or terminator structure that allow transcription to proceed or not, respectively
-Aptamer: Is bound to ligand
-Expression platform: Capable of forming terminator structure

Question 19

Why has E. coli gene regulation been studied so extensively?

Answer 19

Highly efficient genetic mechanisms have evolved that turn transcription of specific genes on and off
depending on metabolic need for gene products. Respond to changes in environment.

Question 20

Positive systems have activators. In an inducible system, the activator is_________ while in a repressible system, the activator is _________.

Answer 20

inactive

active

Question 21

Negative systems have repressors. In an inducible system, the repressor is __________, while in a repressible system, the repressor is __________.

Answer 21

active

inactive

Question 22

How does the concentration
of Glucose relate to the
concentration of cAMP?

Answer 22

cAMP: Cyclic adenosine monophosphate

– ATP is converted to cAMP by adenyly cyclase

– Glucose inhibits activity of adenylyl cyclase, which means a higher concentration of glucose will result in a lower concentration of cAMP.

– To bind to promoter, CAP must be bound to cAMP

– Lack of cAMP prevents CAP from binding when glucose is present

-CAP not binding will prevent expression of the lac operon.

-Glucose subsequently prevents metabolism of lactose; glucose favored

Question 23

Describe a lac operon repression loop

Answer 23

Binding of repressor to operators O1 and O3 creates repression loop.

Prevents access of RNA polymerase to promoter.

Question 24

Which of the 4 systems begin with nonfunctional regulatory proteins?

Answer 24

Positive inducible

Negative repressible

Question 25

Which of the 4 will be CA when the regulator protein is deleted?

Answer 25

Negative inducible

Negative repressible

Repressors when deleted will allow it to be constantly on

Question 26

Cis-acting vs trans-acting sites

Answer 26

Cis-acting elements are regulatory elements that are located on the same molecule of DNA as the genes they regulate.

Example: In the context of gene regulation, a promoter region is a cis-acting element because it is located on the same DNA strand as the gene it regulates. Enhancers and silencers are other examples of cis-acting elements.

Trans-acting elements are regulatory elements that can regulate the activity of genes located on different DNA molecules.

Example: Transcription factors are common examples of trans-acting elements. They can bind to specific DNA sequences in the promoter or enhancer regions of genes, even if those genes are on different chromosomes.

Question 27

Attenuation

Answer 27

-trp structural genes are preceded by leader sequence containing regulatory site called an attenuator

-Attenuation: transcription of leader region occurs even when operon is repressed in presence of tryptophan

Question 28

Attenuation can only happen in prokaryotes because

Answer 28

you need transcription to occur at the same time as translation, which is only possible for a prokaryote

Question 29

How do regulatory genes differ from regulatory elements?

Answer 29

Regulatory elements are not transcribed.

Question 30

What is the difference between a structural gene and a regulatory gene?

Answer 30

Structural genes encode proteins; regulator genes control the transcription of structural genes.

Question 31

Ara operon

Answer 31

Regulatory Genes (araC): The ara operon is regulated by the AraC protein, which is encoded by the araC gene. AraC can act both as an activator and a repressor, depending on its binding to specific DNA sequences. In the absence of arabinose, AraC acts as a repressor, preventing the transcription of ara genes. When arabinose is present, it binds to AraC, causing a conformational change in the protein, and allowing it to function as an activator.