GRE Subject Test: Biochemistry, Cell, and Molecular Biology : Gene Regulation and Genomics

Study concepts, example questions & explanations for GRE Subject Test: Biochemistry, Cell, and Molecular Biology

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Example Questions

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Example Question #1 : Gene Regulation And Genomics

In regards to the lac operon in the presence of lactose, will the genes be transcribed in large amounts?

Possible Answers:

Maybe; it depends on the concentration of glucose

No; the lac operon does not utilize lactose sugars in its regulatory mechanism

Yes; the lactose sugars remove the repressor and the genes will be transcribed rigorously 

Yes; the lactose sugars bind transcription factors that turn on transcription

Correct answer:

Maybe; it depends on the concentration of glucose

Explanation:

Activation of the lac operon is necessary for the transport and metabolism of lactose sugars by E. coli. Lactose sugars actively work to remove a repressor that statically inhibits transcription; however, high concentrations of glucose (and, thus, low concentrations of cAMP) will prevent these genes from being transcribed rigorously. In order for the lac operon to be active at high levels, lactose must be present and glucose must be absent.

Example Question #1 : Gene Regulation And Genomics

Which of the following conditions are crucial to maintain high activation of the lac operon?

Possible Answers:

Large concentrations of cAMP and large concentrations of glucose

Low concentrations of cAMP and large concentrations of lactose

Large concentrations of cAMP and large concentrations of lactose

Large concentrations of glucose and large concentrations of lactose

Correct answer:

Large concentrations of cAMP and large concentrations of lactose

Explanation:

The lac operon is a system designed to only express particular proteins when the concentration of glucose is low and the concentration of lactose is high. The common cellular response to a low concentration of glucose is to increase the concentration of cAMP in order to activate various alternative metabolic pathways. Both a high concentration of cAMP and a high concentration of lactose are necessary to get sustained expression of the lac operon. When glucose levels begin to rise, the cAMP concentration will begin to fall and the operon function will deteriorate.

Example Question #1 : Gene Regulation

Which of the following choices best represents the phenotype of a cell containing a mutation in the lac I gene?

Possible Answers:

Lactose cannot enter the cell

No expression of the operon; RNA polymerase cannot bind properly

Constitutive expression of the lac operon

Lactose can enter the cell, but cannot be broken down

Correct answer:

Constitutive expression of the lac operon

Explanation:

lac I is the gene that encodes for the repressor of the lac operon. If there is no repressor, the cell will constantly express the genes present in the lac operon whether or not the typical conditions are present.

A mutation of the gene encoding -galactosidase permease (lac Y) would prevent lactose from entering the cell. A mutation in the gene encoding -galactosidase (lac Z) would prevent the breakdown of lactose. A mutation in the promoter region would prevent RNA polymerase from binding.

Example Question #1 : Gene Regulation

In prokaryotes, functionally related genes are sometimes position adjacent to each other in the genome and can under the control of the same regulatory machinery. What are these called?

Possible Answers:

Repressors

Promoters

Activators

Operators

Operons

Correct answer:

Operons

Explanation:

Prokaryotic organisms often have functionally related genes joined together on the chromosome under the direction of a single promoter. These structures are called operons. Operons have additional sequences, called operators that can be bound by either repressor or activator proteins, which will repress or activate transcription of the operon. One commonly studied example is the lac operon, whose genes encodes products required for lactose metabolism.

Example Question #1 : Gene Regulation And Genomics

Inducible operons are bound by a repressor and turned off under normal conditions. How are these operons turned on? 

Possible Answers:

A second repressor protein binds to and represses the repressor

An inducer molecule binds to and inactivates the repressor

An activator protein displaces the repressor on the operator

An inducer molecule competes with the repressor for binding to the operator

The transcription of the repressor protein is inactivated

Correct answer:

An inducer molecule binds to and inactivates the repressor

Explanation:

Negatively regulated operons that are said to be inducible have their operator sequence bound by a repressor molecule normally. That leads to these operons being off normally. For these operons to be turned on and transcribed, a small molecule called an inducer has to bind to and inactivate the repressor protein.

Example Question #1 : Gene Regulation

Where are promoters typically found in DNA?

Possible Answers:

Downstream of the coding region of a gene

In the middle of the coding region of a gene

Upstream of the coding region of a gene

In the 3' UTR

Correct answer:

Upstream of the coding region of a gene

Explanation:

Promoters are the sites where transcription factors and RNA polymerase bind to initiate transcription. It makes sense that the promoter would be found upstream of a gene (i.e. before a gene). "Downstream of the coding region" and "in the middle of the coding region" are redundant answers, and neither describes a location where a promoter would normally be located. The 3' UTR describes a region of mRNA and, thus, has nothing to do with promoters.

Example Question #1 : Gene Regulation

__________ are regions of DNA, located __________ of a gene, that will increase its expression. 

Possible Answers:

Enhancers . . . upstream

Enhancers . . . either upstream or downstream

Silencers . . . upstream

Silencers . . . either upstream or downstream

Correct answer:

Enhancers . . . either upstream or downstream

Explanation:

As the name suggests, enhancers enhance the expression of a gene; they increase the number of mRNA transcripts produced from said gene. Silencers do the opposite, and repress the expression of a gene by serving as a binding site for repressors. It does not matter exactly how far enhancers are from the gene (either upstream or downstream) as long as they are geometrically close.

Example Question #1 : Gene Regulation

Which of the following does not represent a feature of bacterial transcription that is not found in eukaryotic transcription?

Possible Answers:

Bacterial transcription occurs in the cytoplasm

Transcription and translation are coupled in bacteria

The bacterial genome utilizes 3 kinds of promoter elements

Bacterial RNA polymerase has a number of subunits that interact with initiation factors to form a holoenzyme

Bacteria rely on a single RNA polymerase

Correct answer:

Bacterial RNA polymerase has a number of subunits that interact with initiation factors to form a holoenzyme

Explanation:

Bacterial RNA polymerase is very similar to eukaryotic RNA Polymerase II in that both have many subunits and form a holoenzyme with cofactors. The rest of the answers are in fact unique to bacterial transcription.

Example Question #1 : Gene Regulation

What proteins enhance transcription by promoting the recruitment of transcription factors and stabilizing the RNA polymerase holoenzyme at the promoter?

Possible Answers:

Corepressors

DNA methyltransferases

Coactivators

Histone acetyltransferases

Histone acetyltransferases

Correct answer:

Coactivators

Explanation:

Coactivators increase gene expression by binding to a transcription factor, recruiting other transcription factors and cofactors, and stabilizing the RNA polymerase holoenzyme to ensure that it can pass the promoter and begin transcribing coding sequence. Corepressors repress transcription, while histone methyl/acetlytransferases act on histone proteins. DNA methyltransferases methylate DNA to establish epigenetic marks that generally inhibit transcription. 

Example Question #2 : Gene Regulation

What regulatory element promotes RNA polymerase II binding as well as binding of factors that facilitate the unwinding of DNA prior to translation? 

Possible Answers:

3' untranslated region 

None of the other answers 

TATA box

Translation start site

5' untranslated region

Correct answer:

TATA box

Explanation:

The correct answer is TATA box. Found in about 24% of human gene promoters, this regulatory element is mostly found in genes transcribed by RNA polymerase II, and as such, recruits this enzyme to the promoter. Additionally, the TATA binding protein aids in unwinding DNA. 

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