Chapter 8: Gene regulation

The image shows cells from the same organism. Which of the following statements is correct regarding these two human cells?

Both cells contain the same genes, but they are expressed differently. If both cells come from the same human organism, then they are both descendants of the initial cell that was created at fertilization and therefore contain the same genome.

The maltose operon contains genes that code for proteins that catabolize the disaccharide maltose. Similar to the Lac operon, which is only efficiently transcribed in the presence of lactose, the maltose operon is only efficiently transcribed in the presence of maltose. How might induction of the maltose operon in response to maltose be achieved?

Maltose removes a repressor from an operon with an efficient promoter. Maltose causes an activator to bind an operon with an inefficient promoter.

Which of the following mutations would be least likely to disrupt the function of the leucine zipper protein? The structures of relevant amino acids are provided below.

Mutation of a leucine to valine in the dimerization domain of the protein. This would be least likely of the choices to disrupt the function of the leucine zipper protein. Dimerization of the two subunits occurs through tight packing of the hydrophobic side chains. Since both leucine and valine have hydrophobic side chains, dimerization is likely to still occur.

Which of the following describes the Lac operon in E. coli when both lactose and glucose are present in the culture medium?

Neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the Lac operon is not expressed. Under these conditions, neither CAP nor the Lac repressor is bound to the Lac operon's regulatory DNA, and the operon is not expressed.

Researchers have created plasmids that only allow expression of inserted genes in response to a metabolite. Researchers can add these plasmids to E. coli cells and increase the expression of the inserted gene by adding the appropriate metabolite to the culture media. Plasmids containing which combination of operator and promoter allow activation of gene expression in response to an added metabolite?

Operator recognized by Lac repressor protein and strong promoter The combination of a strong promoter and the operator sequence from the Lac operon allows transcription in response to lactose.

Which protein complex mediates the RNAi silencing process by inhibiting RNA polymerase via histone methylation and heterochromatin formation?

RITS: siRNAs can form a complex with different protein complexes to lead to different effects on gene expression. siRNAs that form a complex with RITS will bind to the RNA coming from RNA polymerase and will lead to the formation of repressive chromatin structures at the gene region.

Which of these is an evolutionarily ancient defense mechanism that protects a variety of organisms from viral infection?

RNA interference (RNAi) RNA interference is an evolutionary ancient defense mechanism that protects a variety of organisms from viral infection by triggering the degradation of foreign RNA.

Which of the following is considered a housekeeping protein?

RNA polymerase Proteins that are common to all the cells of a multicellular organism are called housekeeping proteins. All cells are involved in gene expression and are therefore undergoing transcription, which requires RNA polymerase.

Many transcriptional regulators function together to decide the expression level of a particular gene. This describes the concept of

combinatorial control Transcriptional regulators work as a committee to determine the level of expression of a gene; this is called combinatorial control. Operons, on the other hand, are a set of genes under the control of a specific transcriptional regulator, a typical control mechanism in prokaryotes.

Which is the main point of control for regulating gene expression levels?

Transcription While the expression of gene products can be regulated at many different steps as the information moves from DNA to RNA to protein, the main point of control is the level of transcription. Inhibiting the transcription of genes that are not currently needed help keep unnecessary intermediates from being synthesized.

Determine whether the following statement is true or false: Differentiated cells in multicellular organisms require hormonal input to "remember" what type of cell they should be.

false The expression of specific transcriptional regulators can determine a cell's differentiation and be maintained through successive rounds of cell division.

Determine whether the following statement is true or false: When a transcription regulator binds to DNA, it typically disrupts the hydrogen bonding between base pairs.

false When a transcription regulator binds to DNA, it does not typically disrupt the hydrogen bonding between base pairs, even though it does form hydrogen bonds with atoms in the base pairs.

A housekeeping gene is a gene whose cellular function is

important for process found in all cell types. Housekeeping genes encode proteins that play critical roles in basic cellular processes that are found in all cell types. They include the genes that encode the enzymes of glycolysis, gene expression, metabolism and basic cell structure.

MicroRNAs regulate the activity of protein-coding genes by doing which of the following?

inhibiting the translation of mRNAs, promoting the degradation of mRNAs. microRNAs regulate the activity of protein-coding genes by inhibiting the translation of mRNAs and promoting the degradation of mRNAs. Taken together, these mechanisms impact the level of translation that is possible from a transcript.

In the cell, enhancer sequence functions are limited in their range of action by the formation of ___________ that hold specific genes and enhancers in close proximity.

loops Enhancers act at a distance from their target gene, so they are prevented from inappropriately activating the transcription of other nearby genes by the formation of chromosome loops that restrict the engagement of the enhancers to just the genes within the same loop.

Which of these is not a type of noncoding RNA?Choose one: miRNA tRNA mRNA rRNA

mRNA mRNA codes for proteins. Thus, mRNA is not considered a noncoding RNA. Noncoding RNAs, by definition do not encode proteins and are therefore not translated by the ribosome.

MicroRNAs block the expression of a specific gene product by binding to the ___________ and inhibiting ___________.

mRNA, translation MicroRNAs form a complex with RISC proteins and once the miRNA forms a complementary base-paired duplex with target RNA, it either targets the mRNA for destruction or reduces the efficiency of translation.

A transcriptional regulator that activates expression of additional transcriptional regulators that induce production of a particular cell type or organ is called a

master regulator Master transcription regulators drive the development of a particular cell type and even whole organs by turning on specific genes. The master regulator turns on the expression of other regulators that regulate other genes in a cascade of expression, coordinating the formation of an organized group of cells.

When a transcription regulator binds to DNA, its most important interactions occur with which of the following?

nucleotide pairs in the major groove of the double helix. Proteins that recognize a specific nucleotide sequence do so because the surface of the protein fits tightly against the surface features of the DNA double helix in that region.

The figure depicts which of the following mechanisms that cells use to maintain their identity through cell divisions?

positive feedback a master transcription regulator that controls its own expression, as well as the expression of other cell type specific genes, can create a positive feedback loop. Because the regulator is present in the precursor cell before division, the protein will be present in the progeny cells, and thus will drive further expression of the regulator.

Mutations in which of the following elements would abrogate RNA polymerase's ability to activate gene expression?

promoter

Researchers assayed the activity of enzyme F in three different types of tissue from the same mouse by determining the amount of enzyme product produced per milligram of tissue per unit time. As shown in the graph below, results indicate more product generation in the liver compared to the kidney and muscle samples.

promoting the formation of heterochromatin

Long noncoding RNA (lncRNA) can function as a(n)

protein scaffold lncRNAs are known to have functions in regulating gene activity but can also act as a scaffold for protein complex assembly. A prominent example is a lncRNA that helps the telomerase complex assemble.

In eukaryotes, where do transcription regulators bind?

upstream, downstream, or within the genes they control In eukaryotes, transcription regulators bind upstream, downstream, or within the genes they control. More common in eukaryotes than prokaryotes, gene activation can occur at a distance.

Generally, bacterial promoters that are regulated by transcriptional activators bind ___________ to RNA polymerase on their own, but promoters that are regulated with transcriptional repressors bind ___________ to RNA polymerase.

weakly, strongly Transcriptional activators in bacteria bind to an activator binding site to help the RNA polymerase bind to the promoter. Without this aid, the binding of the polymerase to the promoter is weak and does not activate transcription at high frequency. Genes controlled by transcriptional repressors have promoters that strongly bind polymerase, and this binding can be blocked by the binding of the repressor in the region

The transcription initiation site of a eukaryotic gene is found at which location?

where RNA synthesis begins The transcription initiation site of a eukaryotic promoter is where RNA synthesis first begins, and this location is "Downstream" of the core promoter region.

Which of the following statements is/are true of long noncoding RNAs?

- They can regulate the translation and stability of mRNAs.-They are involved in X chromosome inactivation. Long noncoding RNAs are involved in X chromosome inactivation and can regulate the translation and stability of mRNAs.

Clinicians and the public are excited about the prospects of replacing damaged and diseased tissues with patient-derived (autologous) cells. Using autologous cells, as opposed to cells from a donor, avoids complications such as immune rejection. What series of steps could lead to the production of smooth muscle cells from the fibroblasts of a patient?

1. obtain fibroblasts 2. use transcription factors to convert fibroblasts to iPS cells 3. Grow iPS cells in culture 4. Use transcription factors to convert iPS cells to smooth muscle cells.

Which of the following statements concerning leucine zipper protein dimerization and DNA binding is correct?

A leucine zipper proteins function as a dimer with the sequence-specific DNA site. The leucine and other hydrophobic side chains in the first portion of the helices dimerize along the length of the two helices. The second portion of the helices forms the DNA-binding domain, where amino acid side chains hydrogen-bond with specific bases in the DNA, leading to sequence-specific binding.

What is an operon?

A set of genes transcribed as a single mRNA from a single promoter.

Which of the following statements about eukaryotic activator proteins is false? A. They stimulate transcriptional initiation by opening up the double helix.B. They stimulate transcription initiation by promoting the assembly of a transcription initiation complex at the promoter.C. They stimulate transcription initiation by aiding in the assembly of general transcription factors and RNA polymerase at the promoter.D. They stimulate transcription initiation by recruiting proteins that modify chromatin structure.

A. They stimulate transcriptional initiation by opening up the double helix. Eukaryotic activator proteins do not open up the double helix. Rather, eukaryotic transcriptional activators can recruit chromatin-modifying proteins to help initiate gene transcription

Which of the following describes the Lac operon in E. coli when lactose, but not glucose, is present in the culture medium?

CAP, but not the Lac repressor, is bound to the Lac operon's regulatory DNA, and the Lac operon is expressed. Under these conditions, only CAP (and not the lac repressor protein) is bound to the Lac operon's regulatory DNA. Therefore, the Lac operon is expressed.

Determine whether the following statement is true or false: The general transcription factors that assemble at a eukaryotic promoter are different, depending on the specific gene being transcribed by polymerase II.

False The general transcription factors that assemble at a eukaryotic promoter are not different, depending on the specific gene being transcribed by polymerase II.

Determine whether the following statement is true or false: Different cell types that respond to the same hormone usually turn on the same sets of genes.

False Different cell types can respond in different ways to the same extracellular signals.

Determine whether the following statement is true or false: Once a cell has become specialized to produce the set of proteins that are responsible for its distinctive properties, its gene expression patterns remain fixed.

False Even though cells in a multicellular organism become specialized, their gene expression patterns do not remain fixed. Cells must also respond to cues from the environment, which often requires a change in gene expression.

Determine whether the following statement is true or false: In the laboratory, transcription regulators can be used to convert one differentiated cell type into another cell type, but not to convert differentiated cells into a less differentiated, pluripotent stem cells.

False This approach is actively being used by researchers to produce "induced pluripotent stem cells" that can potentially be coaxed into producing a population of differentiated cells useful for the study or even treatment of disease.

Determine whether the following statement is true or false: In eukaryotes, individual transcription regulators are often involved in controlling the expression of multiple genes. Thus, their interactions with DNA must be weak and relatively non-specific.

False Transcription regulators recognize nucleotide sequences by fitting tightly to the surface features of the DNA double helix, allowing multiple weak interactions such as hydrogen bonds to form, yet resulting in a tight interaction.

What type of molecule triggers RNA interference (RNAi)?

Foreign-double stranded RNA. Double-stranded RNAs are produced by many viruses and transposable elements, and are thus recognized as "foreign". This makes them valid target for elimination by RNAi.

Using powerful new sequencing technologies, investigators can now catalog every RNA molecule made by a cell and determine at what quantities these RNAs are present. In an experiment, researchers measured the relative quantities of two different mRNAs—one transcribed from gene A, the other from gene B—in two different cell types. Gene B is expressed in both the liver and the brain whereas gene A is expressed in the brain but not in the liver. Which most likely encodes a housekeeping protein?

Gene B only Because gene B is expressed in both the liver and the brain, it could encode a housekeeping protein, which is the term given to genes that are expressed in all cells of a multicellular organism.

If lactose and glucose are both available to a bacterial cell, which carbon source(s) will be used?

Glucose Bacteria prefer to use glucose whenever it is present. When glucose is present, it will be the only sugar used and expression of the Lac operon genes will be reduced. When only lactose is present, the production of lactose-breakdown enzymes will increase to enable the usage of this alternative carbon source.

In terms of the Trp operon, where would the Trp operon repressor protein most likely bind? Drag the "Trp repressor" label to the location where that repressor protein is most likely to bind and exert its effect on the system.

The Trp repressor is an allosteric protein that blocks transcription. As such, this protein does not bind to the 5' end of the mRNA transcript. To repress transcription, where must this protein bind?

In bacterial cells, the tryptophan operon encodes the genes needed to synthesize tryptophan. What happens when the concentration of tryptophan inside a cell is high?

It activates the tryptophan repressor, which shuts down expression of the tryptophan operon. In bacterial cells, when the concentration of tryptophan is high, it activates the tryptophan repressor, which binds to the Top operator and shuts down expression of the tryptophan operon.

c-Met is an oncogene that contributes to the development of certain cancers by triggering cell division and tumor growth. In a 2009 article, Yan and colleagues found regions in the 3' untranslated region of c-Met mRNA complementary to microRNA-1/206. In addition, higher levels of microRNA-1/206 were associated with slower cell proliferation. What is a likely explanation for the inverse correlation between microRNA-1/206 and cell proliferation?

MicroRNA-1/206 targets c-Met mRNA for destruction via RISC. MicroRNAs are noncoding regulatory RNAs that regulate gene expression by binding complementary mRNAs, leading to the destruction of the targeted mRNAs.

The control of a gene product's levels or activity after transcription has taken place is called

Post-transcriptional Control: The level of expression of a gene can be regulated by changing the level at which the transcript is produced but the levels can be altered after the point of transcription.

Eukaryotic repressor proteins can decrease transcription using which of the following mechanisms?

Preventing the assembly of the transcription initiation complex

In eukaryotes, multiple genes can be expressed simultaneously by

The binding of a specific transcriptional regulator to several genes.

Which of the following statements most accurately describes the expression of the repressor protein of the tryptophan operon?

The gene for the tryptophan repressor is expressed constitutively. The gene for the tryptophan repressor is expressed constitutively. The Trp repressor protein must always be present so as to constantly respond to the levels of tryptophan in the cell.

What would happen to the helix-3 interaction with DNA if a mutation occurred that altered this adenine (as shown) to guanine?

The integrity of the interaction would decrease because one of the two hydrogen bonds would not be able to form. If guanine replaced adenine, the integrity of the protein-DNA interaction would decrease because one of the two hydrogen bonds would not be able to form. This is because adenine contains an amino group that interacts with the asparagine carbonyl group; however, this interaction would not form if guanine were present in place of adenine.

What is the ultimate fate of an mRNA that is targeted by a microRNA (miRNA)?

The mRNA will be destroyed by nucleases.

Excess amounts of the amino acid tryptophan result in downregulation of the expression of the enzymes required for its synthesis due to

The repressor binding to the operator.

In bacteria, what would be the consequence of a protein binding to and blocking the ribosomal binding site on an mRNA?

The small ribosomal subunit will not be able to bind to the mRNA and translation will be inhibited. When the ribosomal binding site is covered by a protein, translation is inhibited.

Which of the following statements is not true about the differences between liver cells and kidney cells in the same organism?

They contain different genes.

Determine whether the following statement is true or false: Intense exercise can change gene expression.

True A cell can change its pattern of gene expression in response to external signals. Those signals can include environmental cues, such as starvation, prolonged stress, or intense exercise.

Determine whether the following statement is true or false: A single transcription regulator, if expressed in the appropriate precursor cell, can trigger the formation of a specialized cell type or even an entire organ.

True A single transcription regulator, if expressed in the appropriate precursor cell, can trigger the formation of a specialized cell type or even an entire organ, as demonstrated by developmental studies using artificial expression of these types of genes in Drosophila.

Determine whether the following statement is true or false: Even though control of eukaryotic gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off.

True Although the control of eukaryotic gene expression is combinatorial, a single transcription regulator can activate or repress a gene by completing the "combination" needed to control that gene's activity.

Determine whether the following statement is true or false: A cell can change the expression of its genes in response to external signals.

True Different cell types often respond in different ways to the same extracellular signals, contributing to the specialization that gives each cell type its distinctive character.

Determine whether the following statement is true or false: Master regulators such as Ey in Drosophila are so powerful that they can even activate their regulatory networks outside the normal location.

True In Drosophila, master regulators such as Ey induce the expression of other regulatory genes, which can result in the development of organs such as the eye outside of their normal location.

Determine whether the following statement is true or false: Small interfering RNAs bind to the same RISC proteins that take up miRNAs.

True: small interfering RNAs bind to the same RISC proteins that take up miRNAs. They are generated from larger, double-stranded foreign RNA precursor molecules by some of the same enzymes that process miRNAs.

Transplanting the nucleus of an epithelial cell into an egg cell lacking genetic information leads to the formation of

a normally developing embryo Nuclear transplantation experiments took different types of adult body cells and placed them in egg cells without any DNA and these cells developed into normal embryos and then into a normal animal. This showed that differentiated cells contain all the genetic information for making any other type of cell.

How or where do most transcription regulators bind?

as dimers Dimerization roughly doubles the area of contact with the DNA, making the interaction tighter and more specific.

What must many activator proteins do before they can interact with DNA?

bind to a metabolite or other small molecule Before they can interact with DNA, many activator proteins must first bind to a metabolite or other small molecule, which causes a conformational change in the activator protein.

What are two types of noncoding regulatory RNAs?

siRNAs and miRNAs

Although all of the steps involved in expressing a gene can in principle be regulated, what is the most important stage of control for most genes?

transcription initiation Because transcriptional control is the first step in gene expression, regulation at this level has the most dramatic effects. If an RNA transcript is never synthesized, there is no way for that gene to ever be expressed.

Which form of control directly influences which mRNAs are selected by ribosomes for the synthesis of proteins?

translational control If an mRNA fails to associate with the ribosome, then that mRNA will not be translated into protein.