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Exam 7: Control of Gene Expression

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Question 1

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Stimulated B lymphocytes switch from the synthesis of membrane-bound to secreted antibody molecules by increasing the concentration of a subunit of the trimeric CstF complex that cleaves and polyadenylates mRNAs. How does this up-regulation of CstF bring about the production of soluble antibodies?

A) It favors a strong polyadenylation site in the immunoglobulin primary transcript, creating a longer antibody molecule that is secreted.
B) It activates a weak polyadenylation site in the immunoglobulin primary transcript and prevents splicing, creating a shorter molecule that is secreted.
C) It favors a strong polyadenylation site in the immunoglobulin primary transcript, creating a shorter antibody molecule that is secreted.
D) It activates a weak polyadenylation site in the immunoglobulin primary transcript, creating a longer antibody molecule that is secreted.
E) It favors a strong polyadenylation site in the immunoglobulin primary transcript, aborting translation and creating a shorter antibody molecule that is secreted.

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Question 2

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What is the function of RNA-dependent RNA polymerases in RNAi?

A) They prevent the spread of the RNAi pathway by replicating the target RNAs.
B) They help amplify the RNAi response by replicating the target RNAs.
C) They produce additional copies of the siRNAs to ensure that the RNAi response is sustained and spread.
D) They are viral proteins that prevent the spread of RNAi by preferentially replicating siRNA sponges.

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Question 3

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The schematic diagram below shows the processing of a class of small RNAs that are involved in RNA interference (RNAi). Which of the following is true regarding these RNAs?

Some viruses encode a protease that cleaves the translation initiation factor eIF4G, rendering it unable to bind to eIF4E. What is the consequence of this cleavage?

Indicate true (T) and false (F) statements below regarding gene control. Your answer would be a four-letter string composed of letters T and F only, e.g. TTFT. ( ) Development of multicellular organisms from a fertilized egg only rarely involves DNA rearrangements in specialized cells. ( ) A typical human cell expresses less than 1% of its approximately 30,000 genes at any given time. ( ) Genes that are expressed in all cell types usually vary in their level of expression in different cell types. ( ) Many differentiated plant cells can be fully de-differentiated and give rise to an entire plant.

Protein subunits that interact specifically with DNA sequences …

The majority of transcription regulators make sequence-specific contacts with DNA in the major groove. In the two diagrams below, where are the contact surfaces that are exposed in the major groove?

Consider the two feed-forward loops below containing three transcription regulators A, B, and C, where A receives the input signal and C generates the output. In the so-called coherent loop (left), A activates C both directly and indirectly, whereas in an incoherent loop (right), A activates C via one route and inactivates it via the other. Answer the following question(s) based on these network motifs. -Considering coherent and incoherent feed-forward loops, eight different designs are possible using three components and involving activation (positive) and inhibition (negative) regulation only. In all such loops, A would regulate both B and C, and B would regulate only C. How many of these designs constitute a coherent loop? Write down your answer as a number, e.g. 7.

Expression of the Even-skipped (Eve) gene in early Drosophila embryos is under the control of several transcription regulators. In one example, one of the Eve stripes is positioned near the anterior region of the embryo, and its regulatory module contains binding sites for Bicoid and Hunchback (activators) as well as Giant and Krüppel (inhibitors) such that the gene is expressed only in the region where concentrations of the two activators are high and the concentrations of the two inhibitors are low. A reporter gene can be placed under the control of this module, and it can be shown to form a stripe in the same place in the embryo as the corresponding stripe of Eve. Answer the following question(s) based on these findings. -In the following schematic diagrams of an early Drosophila embryo, in which region would you expect to find the reporter protein put under the control of the regulatory module mentioned above?

Which of the following is directed by transcription activators in eukaryotic cells in order to provide a more accessible DNA for the transcription machinery?

Considering the diagrams below that show hydrogen-bond donors and acceptors as well as hydrophobic groups in four DNA base pairs, which of the following do you think is the most difficult to accomplish by DNA-binding proteins?

You have engineered the X chromosomes in female mice such that one X chromosome expresses green fluorescent protein when active, while the other expresses red fluorescent protein. You have used these mice to study cancer in females. You know that each tumor is a clonal cellular proliferation, meaning all of its proliferating cells are descendants of a single original cancer-causing cell. It follows that, unless X-chromosome inactivation is perturbed in tumors, …

Consider the two feed-forward loops below containing three transcription regulators A, B, and C, where A receives the input signal and C generates the output. In the so-called coherent loop (left), A activates C both directly and indirectly, whereas in an incoherent loop (right), A activates C via one route and inactivates it via the other. Answer the following question(s) based on these network motifs. -Would you expect a coherent (C) or an incoherent (I) loop to generate the following response pattern? In this example, A is stimulated by the input, and the transcription of C is measured as the output. Write down C or I as your answer.

Which strand in an miRNA precursor will serve as the guide strand in the RNA-induced silencing complex (RISC)? Analysis of miRNA sequences has revealed an asymmetry in the stability of the double-stranded RNA precursor. The strand showing lower thermodynamic stability near its 5? end (nucleotides 2 to 6 in the mature guide strand) is normally selected as the guide strand, and the other strand is usually degraded. In the following miRNA precursor, which strand (1 or 2) do you think will be incorporated into the active RISC? Write down 1 or 2 as your answer.

Which of the following classes of noncoding RNAs is NOT directly involved in RNA interference?

The Trp operon in Escherichia coli encodes the components necessary for tryptophan biosynthesis. In the presence of the amino acid in a bacterium, …

Under which of the following conditions is the Lac operon in Escherichia coli fully turned on?

The alternative splicing of a certain transcript can result in the production of two mRNA isoforms, one predominant in muscle cells and the other in neurons. The gene contains an exon that is skipped in muscle cells but retained in neurons. You create a mutant version of the gene in which the 3? splice site near this exon is deleted. However, when you introduce this into a culture of neural cells, an even longer pre-mRNA is produced, consistent with the activation of a secondary splice site located near the deleted one. Is the secondary splice site within the exon (E) or its neighboring intron (I)? Write down E or I as your answer.

You have transfected HeLa cells with a gene encoding the human immunodeficiency virus (HIV) protein Rev and have induced the expression of the protein. You incubate the cell culture in the presence or absence of leptomycin B and later measure the localization of Rev inside the cells by immunofluorescence microscopy. Leptomycin B specifically inhibits the cellular Crm1 protein, a nuclear transport receptor that is essential for the normal function of Rev in the HIV life cycle. Your results are tabulated below. Which condition (1 or 2) do you think corresponds to the presence of leptomycin B?

What determines the time and place that a certain gene is transcribed in the cell?