Biochemistry : Regulating Transcription

Study concepts, example questions & explanations for Biochemistry

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Example Questions

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Example Question #1 : Regulating Transcription

Which statement about transcription is false?

Possible Answers:

None of the other statements is false

Corepressor proteins can play an inhibitory role in gene expression even without directly binding to DNA

Normally, proteins which activate histone acetyl-transferase have an inhibitory role in transcription

A promoter is typically upstream of the gene for which it initiates transcription

Multiple proteins are required to interact in regulating eukaryotic gene RNA transcription

Correct answer:

Normally, proteins which activate histone acetyl-transferase have an inhibitory role in transcription

Explanation:

Among the proteins needed for RNA transcription are RNA polymerase, activators, and repressors. Corepressor proteins indeed bind to repressors, rather than DNA, in order to inhibit gene expression. Promoters are located toward the 5’ region of the sense strand (i.e., upstream). Normally, however, histone acetylation increases, rather than inhibits, gene expression (and hence transcription), by removing positive charges on the histone, thus decreasing the attractive interaction between the positively charged histones and negatively charged DNA. The decreased attraction allows room for transcription factors and RNA polymerase to bind promoter regions, increasing the incidence of transcription.

Example Question #47 : Nucleic Acid Synthesis

Which of the following is true about transcriptional regulation?

Possible Answers:

Spliceosomes splice DNA

The 3’ end of pre-RNA is capped, while the 5’ end of pre-RNA is modified by poly-A tails

The 3’ untranslated region is where protein kinases attach, regulating different intra and extra-cellular signaling pathways

None of these

Correct answer:

None of these

Explanation:

Untranslated regions never yield proteins, and thus do not attach to protein kinases. The 5’ end of pre-RNA is capped, and the 3’ end modified by poly A tails. Pre-RNA is, indeed, spliced when introns are removed. This is performed by spliceosomes, which only splice RNA, not DNA.

Example Question #2 : Regulating Transcription

Which of the following is true regarding bacterial transcription?

Possible Answers:

It involves addition of methyl cap at the end of transcription

It is immediately followed by translation

It utilizes reverse transcriptase

It occurs in the same location as eukaryotic transcription

Correct answer:

It is immediately followed by translation

Explanation:

Transcription is the process of utilizing information in DNA molecules to make RNA molecules. It can occur in eukaryotes (such as humans) and in prokaryotes (such as bacteria). In eukaryotic transcription, the DNA is transcribed to RNA inside the nucleus. Upon completion, the synthesized RNA undergoes further post-transcriptional modifications such as addition of methyl cap, poly-A tail, and removal of introns. After these modifications, the RNA molecule leaves the nucleus, enters the cytoplasm, and undergoes translation (process of synthesizing proteins).

In contrast, bacterial transcription occurs in the cytoplasm and does not involve any of the post-transcriptional modifications. As a result, the transcribed RNA can immediately be used to synthesize proteins; therefore, translation immediately follows transcription in bacteria.

Recall that reverse transcriptase is a special enzyme that converts RNA to DNA (‘reverse’ of transcription). It is found in some viruses such as HIV.

Example Question #51 : Nucleic Acid Synthesis

During which of the following phase(s) of the cell cycle does transcription occur?

Possible Answers:

More than one of these are true

G1 phase

G2 phase

S phase

Correct answer:

More than one of these are true

Explanation:

Transcription is the process of transcribing RNA molecules from DNA. This is a normal cellular process that is required for cells to grow and function properly (because these RNA molecules are eventually converted to proteins, the building blocks of cells). Growth of cells occurs in G1 and G2 phases; therefore, transcription occurs during both of these phases.

Note that DNA replication occurs during S phase; therefore, no DNA molecules will be available for transcription during S phase and transcription will be halted.

Example Question #3 : Regulating Transcription

A bacteria is known to have a defect in a protein that codes for the sigma factor. What will you most likely observe in this bacteria?

Possible Answers:

Complete halt of transcription because there is an increased degradation of RNA polymerase

Increased post-transcriptional modifications

Complete halt of transcription because RNA polymerase stays as a holoenzyme

Complete halt of DNA replication and transcription because there is an increased degradation of both DNA and RNA polymerase

Correct answer:

Complete halt of transcription because RNA polymerase stays as a holoenzyme

Explanation:

Sigma factor is a special molecule in bacteria that is used to initiate transcription. In a bacterial cell, RNA polymerase is typically kept in its inactive form, called holoenzyme. When it is needed for transcription, RNA polymerase is converted to its active form by sigma factor. Sigma factor facilitates the binding of RNA polymerase to the gene sequence on the corresponding DNA molecule. Upon binding, RNA polymerase will carry out transcription and generate a new mRNA strand.

Example Question #53 : Nucleic Acid Synthesis

Promoter regions on DNA templates bind RNA polyermase and determine where transcription will begin.  Which of the following could be part of a promoter region in bacteria?

Possible Answers:

5' - CCGGTTAACCGG - 3'

5' - CGCTATAATGCT - 3'

5' - TACGTGCGAATAG - 3'

3' - TTCGTAGCATAACG - 5'

3' - CTAGCGTAGCAGCA - 5'

Correct answer:

5' - CGCTATAATGCT - 3'

Explanation:

A Pribnow box is a type of promoter region in bacteria that contains a sequence similar to the eukaryotic TATA box.  5'- TATAAT -3' will be found in the Pribnow box and signifies that the particular section of DNA is a promoter region.  The eukaryotic TATA box typically contains the sequence 5'- TATAAA -3' and also serves as a promoter region, typically found upstream of a gene.

Example Question #54 : Nucleic Acid Synthesis

Genetic variety is accomplished in eukaryotes via which of the following mechanisms?

I. Pieces of DNA can move around spontaneously within the genome

II. Multiple, distinct proteins can be translated from a single coding region of mRNA

III. Segments of DNA can spontaneously switch to become new DNA coding regions

Possible Answers:

I and II

I, II, and III

I and III

I only

II and III

Correct answer:

I, II, and III

Explanation:

Transposable elements are those that can move around within the genome, which increases genetic diversity. Also, due to alternative splicing of introns, multiple distinct proteins can be synthesized from the same exact mRNA transcript. One example of this is antibody production. Segments of DNA can spontaneously switch to become new DNA coding regions (mutation). This also increases genetic diversity, if this occurs in the germ-line cells.

Example Question #55 : Nucleic Acid Synthesis

Inhibition of RNA polymerase II would disrupt which of the following processes?

Possible Answers:

Synthesis of protein

Synthesis of rRNA

Synthesis of mRNA

Synthesis of tRNA

Synthesis of DNA

Correct answer:

Synthesis of mRNA

Explanation:

RNA polymerase II is the polymerase that catalyzes the synthesis of mRNA from a coding strand of DNA. Therefore, mRNA synthesis would be greatly affected by an inhibition of RNA polymerase II.

Example Question #56 : Nucleic Acid Synthesis

How does the action of histone acetyltransferases affect transcription?

Possible Answers:

It decreases the rate of transcription by removing positive charge from histones

It increases the rate of transcription by removing positive charge from histones

It decreases the rate of transcription by adding positive charge to histones

It increases the rate of transcription by adding positive charge to histones

Correct answer:

It increases the rate of transcription by removing positive charge from histones

Explanation:

For this question, we need to consider how histone acetyltransferases affect histones. Then, we need to determine how these modified histones affects the expression of genes.

First, it's important to note that histones are proteins that mostly contain positive charges. As a result of this, histones are able to associate with DNA very well, since DNA contains a negatively charged backbone. When histones associate with DNA in this way, the DNA molecule becomes tightly coiled around the histones. In this tightly bound conformation, the collection of DNA and proteins are referred to as hererochromatin. What's more is that when the DNA is tightly bound like this, the transcription machinery in the cell is physically blocked from associating with genes. Thus, gene expression is lowered.

Histone acetyltransferases are enzymes that attach acetyl groups to the positively charged lysine residues that are part of histones. Remember, the positive charge of these lysine residues is what allows the histones to associate with the DNA. When acetyl groups are added, the positive charge on these histones becomes neutralized. As a result, the histones are no longer able to associate with the DNA. What this means is that the transcription machinery in the cell is now able to physically access the genes, allowing gene expression to increase.

Example Question #4 : Regulating Transcription

An inhibition of RNA polymerase III would directly affect which of the following processes?

Possible Answers:

Synthesis of mRNA

Synthesis of rRNA

Synthesis of DNA

Synthesis of protein

Synthesis of tRNA

Correct answer:

Synthesis of tRNA

Explanation:

RNA polymerase III catalyzes the synthesis of tRNA - RNA that is responsible for carrying amino acids during translation. So, synthesis of protein will be affected down the line, however the direct effect of an inhibition of RNA polymerase III would be the inability to create tRNA.

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