GRE Subject Test: Biochemistry, Cell, and Molecular Biology : Help with Promoters
Study concepts, example questions & explanations for GRE Subject Test: Biochemistry, Cell, and Molecular Biology
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Example Questions
Example Question #1 : Gene Regulation
Where are promoters typically found in DNA?
In the 3' UTR
Downstream of the coding region of a gene
Upstream 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
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 #2 : Gene Regulation
__________ are regions of DNA, located __________ of a gene, that will increase its expression.
Silencers . . . upstream
Enhancers . . . either upstream or downstream
Silencers . . . either upstream or downstream
Enhancers . . . upstream
Enhancers . . . either upstream or downstream
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?
Bacteria rely on a single RNA polymerase
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
Transcription and translation are coupled in bacteria
Bacterial transcription occurs in the cytoplasm
Bacterial RNA polymerase has a number of subunits that interact with initiation factors to form a holoenzyme
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 #2 : Gene Regulation
What proteins enhance transcription by promoting the recruitment of transcription factors and stabilizing the RNA polymerase holoenzyme at the promoter?
Coactivators
Histone acetyltransferases
DNA methyltransferases
Corepressors
Histone acetyltransferases
Coactivators
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 #4 : 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?
TATA box
5' untranslated region
None of the other answers
3' untranslated region
Translation start site
TATA box
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.
Example Question #401 : Gre Subject Test: Biochemistry, Cell, And Molecular Biology
In a hypothetical situation, the enhancer region of gene X, which controls tail length in mice, is mutated such that transcription factors bind to the enhancer region at a much higher efficiency than if the region were wild-type. What is a reasonable phenotypic outcome possible from this mutation in gene X's enhancer region?
Tail length is increased due to increased activity of the gene's promoter.
There will be no phenotype because enhancers are not coding regions.
Tail length is not changed because the enhancer region does not dictate gene expression.
The mouse will be globally larger because increased transcription at the enhancer will impact any gene behind the enhancer.
Tail length is decreased because any mutation will cause a loss-of-function of these regulatory regions.
Tail length is increased due to increased activity of the gene's promoter.
This question is inspired by a real life example, in which if you put a bat enhancer region in front of the gene that controls limb development in mice, the limbs are longer due to changes in the enhancer activity, which increases the activity of the promoter. By permitting more transcription factor interaction with the regulatory region, one might expect that this type of mutation may increase the tail length of the mouse because more "pro-tail length" protein is being made.
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