Control of Gene Expression in Prokaryotes

Choose one of the models in the activity. What conditions would need to be present in the cell in order to reverse the regulatory conditions in the model. (turn "off" once its been turned "on")

My model of choice: 2 In this model, the first diagram the operon is "on" until in diagram B the protein represses(stops/ turns "off") the activities. The presence of the compressor molecule activates the protein. If we wanted to reverse the process then the molecule would have to be removed from the environment.

Consider the nonscience meaning of the following terms. Match the purpose with each of the sections in the operon in terms of the gene transcription.

-Promoter--Spot where transcription starts -Operator--On/Off Switch -Terminator--Spot where transcription ends

Describe the 4 combinations of active or inactive regulatory proteins that could be present at any time in the cell.

Active repressor Active activator Inactive activator Inactive repressor

In which diagram of model 3 is transcription occurring successfully, A or B? Justify your answer with evidence from model 3.

Diagram B is showing transcription occurring successfully.

Can the protein produced by the regulatory gene in model 3 bind to the operon itself? If no, describe what must occur in order for it to bind.

No, the activator protein doesn't have a signal from the ligand to bind to the operon. In order for the protein to bind, it must have the message from the ligand.

Consider the operon In Model 1. Other than the gene that regulates the operon, how many genes are contained within the operon?

Three

Operator

on/off switch

What compound could serve as the corepressor of the TRP operon in E. coli based on the description provided?

A corepressor is, by definition, In the field of molecular biology, "a substance that inhibits the expression of genes. In prokaryotes, corepressors are small molecules whereas in eukaryotes, corepressors are proteins." In the case of E. coli, the corepressor is the Tryptophan.

What protein does the regulatory gene in model 1 produce?

A repressor protein

What type of operon is illustrated in Model 1?

An inductible operon

Which type of operon, inducible or repressible, would an organism likely use to produce enzymes and other proteins required to metabolize a nutrient in its environment? Justify your answer based on models 1 and 2.

An organism would most likely be using a repressible operon for things it requires. Observing model 2, we see how the operon will continue to produce those proteins and enzymes until the organism has plenty and the corepressor molecule activates the repressor protein and the processes temporarily stop.

Compare and contrast the positive control mechanism of model 3 with the negative control mechanism in models 1 and 2.

Bigger meaning: In negative mechanisms, a repressor protein binds to an operator and prevents/allows a gene to be expressed. In positive control, a transcription factor is required to bind at the promoter in order to enable RNA polymerase to initiate transcription.

Propose an explanation for why the regulatory protein in model 3 is called an "activator" protein.

It is called an activator protein because the operon will not be activated unless the protein is binded.

Which direction is the RNA polymerase moving in model 1?

Left to right From 3' to 5' end

Explain what would happen within the lac operon in each of the following scenarios: LOW lactose

Not enough allolactose is present. The repressor protein binds to the operator, not allowing transcription of the operon genes. Without those genes producing the correct enzymes, lactose is not metabolized

Describe the role of the compressor molecule in the repressible operon system shown in model 2.

The compressible molecule activates the repressor protein and prevents the promoter from making proteins.

Propose an explanation for why transcription is not occuring in diagram A but is occuring in diagram B.

The model is demonstrating an inducible operon, therefore it needs the protein to bind in order to complete its function. In diagram B the ligand is present and has delivered the message to the protein but in diagram A the ligand is not present.

Some mutations can disable genes. What might be the result of such a mutation within the LAC regulatory region of the LAC operon (model 1)?

The monomers won't break up.

In model 3, where on the DNA strand does RNA polymerase bind to start transcription?

The promoter is (in most cases) where RNA polymerase binds to start operon processes.

To what section of the operon does this protein bind?

The repressor protein binds to the operator site.

In model 2, Where on the DNA strand does RNA polymerase bind to start transcription?

To the promoter

In which diagram of model 1 is transcription and translation occurring successfully, diagram A or diagram B? Justify your answer with evidence from model 1.

Transcription is occurring in diagram B. That diagram shows the mRNA and proteins being made from the DNA.

Which type of operon, inducible or repressible, would an organism likely use to produce enzymes and other proteins required to manufacture a molecule needed from smaller molecules in the environment? Justify your answer based on models 1 and 2.

An organism would most likely be using an inducible operon because the molecules are not necessary for daily processes.

How does the change identified in part A allow transcription of the genes in operon to occur?

The repressor protein no longer binds to the operator and is no longer blocking RNA polymerase, so transcription can occur.

Does the regulatory gene in model 2 produce a protein that is an active or inactive repressor naturally?

The regulatory gene produces a naturally inactive repressor protein because in the absence of the activator molecule the protein will not prevent normal operon activities.

Propose an exclamation for why transcription is not occurring in diagram A.

The repressor protein blocks RNA polymerase so transcription of genes X, Y, and Z cannot occur.

When an inducer molecule attaches to the repressor protein, what happens to the repressor protein?

The repressor protein changes shape.

Explain what would happen with the LAC operon in each of the following scenarios: HIGH lactose.

When there are high levels of lactose present (and some allolactose) the operon is switched "on". This initiates several proteins to be produces that move the lactose into the cell and break down the lactose into its monomers (glucose and galactose).

Compare and contrast an inducible operon and a repressible operon.

Simply, a repressible operon can be repressed or "turned off," it is naturally "on". Contrarily, the inducible operon is naturally "off" but can be turned "on".

Promoter

Spot where transcription begins

Terminator

Spot where transcription ends

In model one, where on the DNA strand does RNA polymerase bind to start transcription, the promoter, the operator or the terminator?

The RNA polymerase binds to the promoter.

Propose an explanation for why RNA polymerase is not bound to the promoter in diagram A of model 3.

The RNA polymerase cannot initiate its functions unless the ligand (messenger) tells the activator protein to attach to the promoter.

In which diagram of model 2 is transcription and translation occurring successfully, diagram A or B? Justify your answer based on evidence from model 2.

Diagram A properly shows translation and transcription happening. The repressor protein in this model is not activated by the corepressor molecule, therefore not preventing the proper operon function.

To what section of the operon does this protein bind?

The activator protein binds to the promoter, like all other operons.

Describe, in complete sentences, the cellular environment(s) that would turn the operon "on".

The answers all depend on the kind of operon being studied.

What protein does the regulatory gene in model 3 produce?

The regulator gene produces an activator protein. We can compare model 3 to model 1 and observe that the proteins have the same function which is to activate the operons processes.

Propose an explanation for why operons evolved in prokaryotes. What advantage do organisms have when they group genes together with a regulatory system?

When an operon is transcribed, all of the genes on the operon are on the same mRNA. Operons occur in prokaryotes, but not eukaryotes. In eukaryotes, each gene is made on individual mRNAs and each gene has its own promoter. Cells can't afford to waste energy making genes if they don't need them. However, prokaryotes can spend the energy to reproduce genes. Prokaryotes also need the products produced by the operons and the regulatory system allows the organism to continue its functions constantly.