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The following mRNA sequence is taken from the middle of exon 3 in a mature mRNA that has 12 exons. Knowing that this mRNA does not undergo nonsense-mediated decay, which of the reading frames shown is the correct one for this mRNA? Write down 1, 2, or 3 as your answer.

1

On the ribosome, the mRNA is read from ..., and the polypeptide chain is synthesized from...

5' to 3'; N-to-C-terminus

This complex uses ATP and forms an "isolation chamber" for its misfolded protein substrates, allowing them to fold to their native conformation. It is called...

A chaperonin

The following schematic drawing represents the activation of transcription for a eukaryotic gene (gene X). Indicate what component (A to D) in the drawing corresponds to each of the following.

A-A general transcription factor; B-cis-regulatory sequence; C-"Spacer" DNA that may encode lncRNAs; D-Mediator

Indicate which of the following enzymatic activities corresponds to A, B, or C in the following schematic drawing of DNA methylation events in the human genome.

A. Maintenance methyl transferase enzyme. B. De novo methyl transferase enzyme. C. DNA demethylating enzyme

What determines the time and place that a certain gene is transcribed in the cell? -The type of cis-regulatory sequences associated with it. -The arrangement of various cis-regulatory sequences associated with it. -The specific combination of transcription regulators present in the nucleus

All of them

What is the function of the 19S cap in the proteasome complex? -Unfolding the proteins that will be degraded and threading them into the central 20S cylinder for digestion -Recognizing the proteins that will be degraded -Removing the polyubiquitin chain from the proteins that will be degraded and hydrolyzing ATP to make the digestion process highly efficient

All of them

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 Eve regulatory modules, the binding sites for Giant and Krüppel are usually close to, or even overlapping with, those of Bicoid and Hunchback. This implies that Eve expression is regulated by ... between the activators and regulators.

Competition

In the following qualitative histogram, which two curves better correspond to human exon and intron length distributions, respectively?

Curves 1 & 2

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?

Distinguishing between C-G and G-C in the minor groove.

Protein subunits that interact specifically with DNA sequences...

Do so via hydrogen bonds, ionic bonds, and hydrophobic interactions.

A typical human cell expresses less than 1% of its approximately 30000 genes at any given time.

False

CG islands are nonpermissive for RNA polymerase assembly.

False

DNA looping for gene regulation is the rule in bacteria but the exception in eukaryotes.

False

DNA methylation at the promoter region is usually an indication of active transcription.

False

DNA methylation makes repression of gene expression "leakier".

False

Dimerization of transcription regulators increases the chance of binding to nonspecific sequences.

False

Methylation of adenines is the most common DNA methylation in humans.

False

Which of the following nucleotides is hydrolyzed in both transcription and in translation elongation?

GTP

In the following schematic diagram of a region of a mammalian genome, genes A to D (triangles) are located in between a number of insulator elements (white squares) and barrier sequences (black squares). If the cis-regulatory sequence (oval) is bound by an abundant repressor protein, which gene would you expect to be expressed at a higher rate in this cell?

Gene C

In the following schematic graph of a hypothetical set of RNA-seq data, the number of reads is plotted for a region of chromosome containing two genes, from samples obtained from two different tissues. Which gene (X or Y) do you think is more likely a "housekeeping" gene? Which region (1 or 2) within gene Y most likely corresponds to an exon?

Gene Y; region 1

Which of the following better describes a typical, actively translated mRNA in its journey from the nucleus to the cytosol?

Initially linear, the mRNA enters the cytosol (5' end first), and adopts a circular conformation.

Which of the following is true regarding genomic imprinting? -It can "unmask" recessive alleles but cannot "mask" dominant ones. -It occurs in most animals -It is an epigenetic phenomenon -All of them

It is an epigenetic phenomenon

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?

It shuts down most host-cell protein synthesis and diverts the translation machinery to IRES-dependent initiation, thus favoring viral protein synthesis.

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. What would you expect to happen to the pattern of reporter expression in flies that lack the gene encoding Giant?

It would expand to cover a broad anterior region of the embryo

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. What would you expect to happen to the pattern of reporter expression in flies that lack the gene encoding Bicoid?

It would fail to express efficiently in the stripe 2 region

How many ATP molecules must be hydrolyzed by the proteasome for the digestion of a protein that has been tagged for degradation with a polyubiquitin chain?

Many; the number depends on the specific protein

Of the following proteins or protein complexes, which on e does NOT typically interact with an elongating RNA polymerase II?

Mediator complex

In humans, nearly 80% of proteins are acetylated on their N-terminal residue, a modification known to be recognized by a specific E3 enzyme, which directs the ubiquitylation of the protein for rapid degradation. Does this mean that all of these proteins are actively degraded at any given time?

No; the destruction signal can be buried in the interior of the protein or bound to other proteins.

Which of the following DNA-binding motifs uses b sheets to recognize DNA bases? -The helix-helix motif -The zinc finger motif -The leucine zipper

None of them

Beckwith-Wiedemann syndrome in humans is characterized by "overgrowth" in childhood, sometimes leading to unusually large parts of the body. An imprinted gene cluster on chromosome 11 is associated with this disease. The cluster contains several genes including Igf2 and H19. Igf2 encodes an insulin-like growth factor that is maternally imprinted, i.e. the maternal copy is not expressed. However, the DNA methylation pattern of this locus is not different between the two homologous chromosomes. On the other hand, H19 is also imprinted and its methylation pattern does differ between the two parental chromosomes. H19 is transcribed into a noncoding RNA that appears to silence the transcription of the Igf2 gene in cis. Would you expect the H19 locus to be hypermethylated in the maternally inherited chromosome (M) or paternally inherited chromosome (P)?

Patternally inhereted chromosome (P)

In analysis using two-dimensional gel electrophoresis of the proteins expressed in different cell types, the number of spots that are different in different cells usually exceeds the number of common spots, and even the common spots can still have different intensities. The spots representing which of the following proteins would you expect to be among the common spots when compared across several cell types? -Insulin (a hormone) -HBA1 (a hemoglobin subunit) -RPL10 (a ribosomal subunit)

RPL10 (a ribosomal subunit)

This large and complex general transcription factor has a DNA helicase activity that exposes the template for RNA polymerase II transcription. It also has a kinase activity that phosphorylates the C-terminal domain of the polymerase on Ser5 leading to promoter clearance. It is...

TFIIH

When unfolded proteins accumulate in the lumen of the endoplasmic reticulum due to inefficient folding conditions, a membrane-bound protein kinase is activated and phosphorylates a subunit of the translation initiation factor eIF2. Indicate which of the following events would occur as a result.

The GDP-bound form of eIF2 accumulates

An elongating ribosome is bound to appropriate tRNAs in both the A and the P sites and is ready for peptidyl transfer. What happens next?

The carboxyl end of the polypeptide chain is released from the P-site tRNA and joined to the free amino group of the amino acid linked to the A-site tRNA.

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, ...

The cells in any tumor should all express the same fluorescent protein (either red or green), but independently derived tumors in the same mouse can show either green or red fluorescence.

Consider a cis-regulatory enhancer sequence in the Escherichia coli chromosome that is located thousands of nucleotide pairs upstream of the gene that it regulates. If the regulatory sequence is mutated to become nonfunctional, the introduction of the wild-type enhancer on a plasmid fails to regulate the gene. This implies that ...

The regulation of the target gene involves looping out of the intervening DNA, and the promoter of the cis-regulatory sequence must be on the same chromosome.

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

The tryptophan operator is bound to the tryptophan repressor.

Which of the following features is common between the bacterial and eukaryotic ribosomes in translation initiation?

They both interact with various translation initiation factors.

Studying the expression of a transcription regulatory protein in two cell types, you have performed experiments showing that the mRNA encoding the protein is present at comparable levels in the cytosol of both cell types. However, based on the expression of its target genes, you suspect that the protein activity might be significantly different in the two cell types. Which of the following steps in expression of the gene encoding this protein is more likely to be differentially controlled in these cell types?

Translation

About 10% of the protein-coding genes in most organisms encode transcription regulators.

True

Cytosine methylation often occurs within a 5'-CG-3' sequence.

True

Development of multicellular organisms from a fertilized egg only rarely involves DNA rearrangements in specialized cells

True

Genes that are expressed in all cell types usually vary in their level of expression in different cell types.

True

Many differentiated plant cells can be fully de-differentiated and give rise to an entire plant.

True

Methylated cytosine can be accidentally deaminated to produce thymine, leading to a C-to-T transition.

True

RNA editing can change the pattern of pre-mRNA splicing

True

RNA editing in coding regions can result in changes in the protein sequence

True

The transcript for which of the following noncoding RNA in our cells is expected to undergo 5' cap addition after transcription?

miR-21 (a microRNA)

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?

B

To prevent spurious transcription from a gene, acetylation of histones—which is carried out by histone acetyl transferases ahead of a moving RNA polymerase II—is quickly reversed by histone deacetylases and histone methyl transferases in the wake of the polymerase, leaving a trail of specific methylated histones. Which of the following curves do you think better represents the distribution of this specific histone methylation mark with respect to a gene?

Curve B

Most bacterial genes are regulated individually, whereas most eukaryotic genes are regulated in clusters.

False

The default state of both bacterial and eukaryotic genomes is transcriptionally active.

False

Transcription regulators in both bacteria and eukaryotes usually bind directly to RNA polymerase.

False

A researcher studying the human immunodeficiency virus (HIV) has infected human T cells with wild-type or Rev-deficient viruses. She extracts cytoplasmic RNA from the cells and separates each isolated RNA mixture by agarose-gel electrophoresis. She then uses northern analysis using HIV-specific probes to identify those bands that contain viral RNA. The results are presented in the following schematic drawing. Which lane (1 or 2) corresponds to cells infected with the Rev-deficient virus? What is the size of the full-length HIV genome? Note: Rev is required for the export of the full-length viral RNA.

Lane 2; about 9000 nucleotides

Rna editing in animal cells mainly taje place through adenine or cytosine deamination

True

Shortly after fertilization, a genome-wide wave of demethylation takes place.

True

Some DNA-binding proteins can induce bends and kinks in their target DNA.

True

The rate of transcription for eukaryotic gene can vary in a much wider range than for a bacterial gene (which is, at most, only about 1000-fold)

True

The enzyme poly-A polymerase is responsible for adding 3' poly-A tails to eukaryotic mRNAs. This enzyme...

Uses ATP as a substrate