Deck 8: Control of Gene Expression

Question 1

Which of the following is not a good example of a housekeeping protein?

A)DNA repair enzymes
B)histones
C)ATP synthase
D)hemoglobin

Answer 1

D

Question 2

Which of the following statements about the Lac operon is FALSE?

A)The Lac repressor binds when lactose is present in the cell.
B)Even when the CAP activator is bound to DNA, if lactose is not present, the Lac operon will not be transcribed.
C)The CAP activator can only bind DNA when it is bound to cAMP.
D)The Lac operon only produces RNA when lactose is present and glucose is absent.

Answer 2

A
A constitutively active phospholipase C will lead to the constitutive production of IP₃ and diacylglycerol, leading to activation of PKC in a signal-independent manner; thus, Rafty activation and the lipid modification will be signal-independent.A mutation in the GPCR that bind the signal more tightly and a Ca²⁺ channel with an increased affinity for IP will increase activity of the signal transduction pathway in a signal-dependent manner.A mutation that renders Rafty such that it can no longer by phosphorylated by PKC will prevent PKC from activating Rafty and will thus prevent the lipid modifications.

Question 3

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table 8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$
$\begin{array}{lcccc}\text { Binding sites present } & \begin{array}{l}\text { No } \mathrm{Ca}^{2+} \\\text { or } \mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Ca}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \mathrm{Ca}^{2+} \\\text { and } \mathrm{Mg}^{2 *}\end{array} \\\hline \text { A, B, and C } & - & - & - & ++ \\\hline \text { none } & - & - & - & - \\\hline \text { A only } & - & - & + & + \\\hline \text { B only } & - & - & - & - \\\hline \text { C only } & - & + & - & + \\\hline \text { A and B only } & - & - & - & + \\\hline \text { A and C only } & - & + & + & ++ \\\hline \text { B and C only } & - & - & - & +\end{array}$

$\text {For this table: -= no transcription of Pst,}$
$\text {\( += \) low level of transcription of Psf, and}$
$\text {\( ++= \) high levels of transcription of Pst.}$
Table 8-12
Which of the following proteins are likely to act as gene repressors?

A)MetA only
B)MetB only
C)MetC only
D)both MetA and MetC

Answer 3

MetB only

Question 4

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table 8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$
$\begin{array}{lcccc}\text { Binding sites present } & \begin{array}{l}\text { No } \mathrm{Ca}^{2+} \\\text { or } \mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Ca}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \mathrm{Ca}^{2+} \\\text { and } \mathrm{Mg}^{2 *}\end{array} \\\hline \text { A, B, and C } & - & - & - & ++ \\\hline \text { none } & - & - & - & - \\\hline \text { A only } & - & - & + & + \\\hline \text { B only } & - & - & - & - \\\hline \text { C only } & - & + & - & + \\\hline \text { A and B only } & - & - & - & + \\\hline \text { A and C only } & - & + & + & ++ \\\hline \text { B and C only } & - & - & - & +\end{array}$

$\text {For this table: -= no transcription of Pst,}$
$\text {\( += \) low level of transcription of Psf, and}$
$\text {\( ++= \) high levels of transcription of Pst.}$

Table 8-12
Which transcription regulator(s) are normally bound to the Psf promoter in the presence of Mg²⁺ only?

A)none
B)MetA only
C)MetA and Met B
D)MetA, MetB, and MetC

Question 5

Which of the following statements about differentiated cells is TRUE?

A)Cells of distinct types express nonoverlapping sets of transcription regulators.
B)Once a cell has differentiated, it can no longer change its gene expression.
C)Once a cell has differentiated, it will no longer need to transcribe RNA.
D)Some of the proteins found in differentiated cells are found in all cells of a multicellular organism.

Question 6

You are interested in understanding the gene regulation of Lkp1, a protein that is normally produced in liver and kidney cells in mice.Interestingly, you find that the LKP1 gene is not expressed in heart cells.You isolate the DNA upstream of the LKP1 gene, place it upstream of the gene for green fluorescent protein (GFP), and insert this entire piece of recombinant DNA into mice.You find GFP expressed in liver and kidney cells but not in heart cells, an expression pattern similar to the normal expression of the LKP1 gene.Further experiments demonstrate that there are three regions in the promoter, labeled A, B, and C in Figure 8-16, that contribute to this expression pattern.Assume that a single and unique transcription factor binds each site such that protein X binds site A, protein Y binds site B, and protein Z binds site C.You want to determine which region is responsible for tissue-specific expression, and create mutations in the promoter to determine the function of each of these regions.In Figure 8-16, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor. Figure 8-16
In what tissue is factor Z normally present and bound to the DNA?

A)kidney
B)liver
C)heart
D)none of these answers are correct.

Question 7

Which of the following statements about transcriptional regulators is FALSE?

A)Transcription regulators interact only with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix.
B)Transcription regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA.
C)The DNA-binding motifs of transcription regulators usually bind in the major groove of the DNA helix.
D)The binding of transcription regulators generally does not disrupt the hydrogen bonds that hold the double helix together.

Question 8

You are interested in understanding the gene regulation of Lkp1, a protein that is normally produced in liver and kidney cells in mice.Interestingly, you find that the LKP1 gene is not expressed in heart cells.You isolate the DNA upstream of the LKP1 gene, place it upstream of the gene for green fluorescent protein (GFP), and insert this entire piece of recombinant DNA into mice.You find GFP expressed in liver and kidney cells but not in heart cells, an expression pattern similar to the normal expression of the LKP1 gene.Further experiments demonstrate that there are three regions in the promoter, labeled A, B, and C in Figure 8-16, that contribute to this expression pattern.Assume that a single and unique transcription factor binds each site such that protein X binds site A, protein Y binds site B, and protein Z binds site C.You want to determine which region is responsible for tissue-specific expression, and create mutations in the promoter to determine the function of each of these regions.In Figure 8-16, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor. Figure 8-16
Which of the following proteins are likely to act as gene activators?

A)factors X and Y
B)factors X and Z
C)factors Y and Z
D)factor X only

Question 9

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table Q8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$
$\begin{array}{lcccc}\text { Binding sites present } & \begin{array}{l}\text { No } \mathrm{Ca}^{2+} \\\text { or } \mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Ca}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \mathrm{Ca}^{2+} \\\text { and } \mathrm{Mg}^{2 *}\end{array} \\\hline \text { A, B, and C } & - & - & - & ++ \\\hline \text { none } & - & - & - & - \\\hline \text { A only } & - & - & + & + \\\hline \text { B only } & - & - & - & - \\\hline \text { C only } & - & + & - & + \\\hline \text { A and B only } & - & - & - & + \\\hline \text { A and C only } & - & + & + & ++ \\\hline \text { B and C only } & - & - & - & +\end{array}$

$\text {For this table: -= no transcription of Pst,}$
$\text {\( += \) low level of transcription of Psf, and}$
$\text {\( ++= \) high levels of transcription of Pst.}$


Table 8-12
Which transcription factors are normally bound to the Psf promoter in the presence of both Mg²⁺ and Ca²⁺?

A)MetA and MetB
B)MetB and MetC
C)MetA and MetC
D)MetA, MetB, and MetC

Question 10

The human genome encodes about 21,000 protein-coding genes.Approximately how many such genes does the typical differentiated human cell express at any one time?

A)21,000-all of them
B)between 18,900 and 21,000-at least 90% of the genes
C)between 5000 and 15,000
D)less than 2100

Question 11

You are interested in the regulation of gene Q.Proteins G, H, and J are proteins that are important for regulating gene Q, and bind to its promoter region in a sequence-specific fashion.Proteins G and H both bind to site "A" but cannot bind to site "A" at the same time.Protein J binds to site "B" on the promoter.The promoter region is diagrammed in Figure 8-20. Figure 8-20
You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q.Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced.When you add these proteins to the system, you get the results shown in Table 8-20. $\text { experiment }$$\text { reaulator protein added }$$\text { Q mRNA }$
$\begin{array}{ccccc}\text { number } &\quad\quad\quad\text { G } & H & J & \quad\quad\text { made? } \\\hline 1 &\quad\quad - & - & - & \text { no } \\\hline 2 & \quad\quad+ & - & - & \text { no } \\\hline 3 & \quad\quad- & + & - & \text { yes } \\\hline 4 &\quad\quad - & - & + & \text { yes } \\\hline 5 &\quad\quad + & + & - & \text { no } \\\hline 6 &\quad\quad + & - & + & \text { yes } \\\hline 7 & \quad\quad- & + & + & \text { yes } \\\hline 8 & \quad\quad+ & + & + & \text { yes }\end{array}$

Table 8-20
Which proteins are likely to act as gene activators?

A)G
B)H
C)J
D)both H and J

Question 12

A neuron and a white blood cell have very different functions.For example, a neuron can receive and respond to electrical signals, while a white blood cell defends the body against infection.This is because

A)all of the proteins found in a neuron are completely different from the proteins found in a white blood cell.
B)the neuron and the white blood cell within an individual have the same genome.
C)the neuron expresses some mRNAs that the white blood cell does not.
D)neurons and white blood cells are differentiated cells and thus no longer need to transcribe and translate genes.

Question 13

You are interested in understanding the gene regulation of Lkp1, a protein that is normally produced in liver and kidney cells in mice.Interestingly, you find that the LKP1 gene is not expressed in heart cells.You isolate the DNA upstream of the LKP1 gene, place it upstream of the gene for green fluorescent protein (GFP), and insert this entire piece of recombinant DNA into mice.You find GFP expressed in liver and kidney cells but not in heart cells, an expression pattern similar to the normal expression of the LKP1 gene.Further experiments demonstrate that there are three regions in the promoter, labeled A, B, and C in Figure 8-16, that contribute to this expression pattern.Assume that a single and unique transcription factor binds each site such that protein X binds site A, protein Y binds site B, and protein Z binds site C.You want to determine which region is responsible for tissue-specific expression, and create mutations in the promoter to determine the function of each of these regions.In Figure 8-16, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor. Figure 8-16
Experiment 1 in Figure 8-18 is the positive control, demonstrating that the region of DNA upstream of the gene for GFP results in a pattern of expression that we normally find for the LKP1 gene.Experiment 2 shows what happens when the sites for binding factors X, Y, and Z are removed.Which experiment above demonstrates that factor X alone is sufficient for expression of LPK1 in the kidney?

A)experiment 3
B)experiment 5
C)experiment 6
D)experiment 7

Question 14

The distinct characteristics of different cell types in a multicellular organism result mainly from the differential regulation of the

A)replication of specific genes.
B)transcription of genes transcribed by RNA polymerase II.
C)transcription of housekeeping genes.
D)proteins that directly bind the TATA box of eukaryotic genes.

Question 15

The tryptophan operator

A)is an allosteric protein.
B)binds to the tryptophan repressor when the repressor is bound to tryptophan.
C)is required for production of the mRNA encoded by the tryptophan operon.
D)is important for the production of the tryptophan repressor.

Question 16

You are interested in understanding the gene regulation of Lkp1, a protein that is normally produced in liver and kidney cells in mice.Interestingly, you find that the LKP1 gene is not expressed in heart cells.You isolate the DNA upstream of the LKP1 gene, place it upstream of the gene for green fluorescent protein (GFP), and insert this entire piece of recombinant DNA into mice.You find GFP expressed in liver and kidney cells but not in heart cells, an expression pattern similar to the normal expression of the LKP1 gene.Further experiments demonstrate that there are three regions in the promoter, labeled A, B, and C in Figure 8-16, that contribute to this expression pattern.Assume that a single and unique transcription factor binds each site such that protein X binds site A, protein Y binds site B, and protein Z binds site C.You want to determine which region is responsible for tissue-specific expression, and create mutations in the promoter to determine the function of each of these regions.In Figure 8-16, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor. Figure 8-16
Which of the following proteins is likely to act as a gene repressor?

A)factor X
B)factor Y
C)factor Z
D)none of these answers are correct.

Question 17

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table 8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$
$\begin{array}{lcccc}\text { Binding sites present } & \begin{array}{l}\text { No } \mathrm{Ca}^{2+} \\\text { or } \mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Ca}^{2+}\end{array} & \begin{array}{l}\text { With } \\\mathrm{Mg}^{2+}\end{array} & \begin{array}{l}\text { With } \mathrm{Ca}^{2+} \\\text { and } \mathrm{Mg}^{2 *}\end{array} \\\hline \text { A, B, and C } & - & - & - & ++ \\\hline \text { none } & - & - & - & - \\\hline \text { A only } & - & - & + & + \\\hline \text { B only } & - & - & - & - \\\hline \text { C only } & - & + & - & + \\\hline \text { A and B only } & - & - & - & + \\\hline \text { A and C only } & - & + & + & ++ \\\hline \text { B and C only } & - & - & - & +\end{array}$

$\text {For this table: -= no transcription of Pst,}$
$\text {\( += \) low level of transcription of Psf, and}$
$\text {\( ++= \) high levels of transcription of Pst.}$
Table 8-12
Which of the following proteins are likely to act as gene activators?

A)MetA only
B)MetB only
C)MetC only
D)both MetA and MetC

Question 18

Operons

A)are commonly found in eukaryotic cells.
B)are transcribed by RNA polymerase II.
C)contain a cluster of genes transcribed as a single mRNA.
D)can only be regulated by gene activator proteins.

Question 19

What do you predict would happen if you replace the Lac operator DNA from the Lac operon with the DNA from the operator region from the tryptophan operon?

A)The presence of lactose will not cause allosteric changes to the Lac repressor.
B)The Lac operon will not be transcribed when tryptophan levels are high.
C)The lack of glucose will no longer allow CAP binding to the DNA.
D)RNA polymerase will only bind to the Lac promoter when lactose is present.

Question 20

Investigators performed nuclear transplant experiments to determine whether DNA is altered irreversibly during development.Which of the following statements about these experiments is TRUE?

A)Because the donor nucleus is taken from an adult animal, the chromosomes from the nucleus must undergo recombination with the DNA in the egg for successful development to occur.
B)The cells in the embryo that develop from the nuclear transplant experiment have DNA that is identical to the donor of the nucleus.
C)The meiotic spindle of the egg must interact with the chromosomes of the injected nuclei for successful nuclear transplantation to occur.
D)Although nuclear transplantation has been successful in producing embryos in some mammals with the use of foster mothers, evidence of DNA alterations during differentiation has not been obtained for plants.

Question 21

Enhancers can act over long stretches of DNA, but are specific about which genes they affect.How do eukaryotic cells prevent these transcription regulators from looping in the wrong direction and inappropriately turning on the transcription of a neighboring gene?

A)The cell uses histone acetyltransferase to prevent enhancer binding to the DNA.
B)The cell will group neighboring genes into operons so that they are transcribed as a single unit, regulated by a single enhancer.
C)Chromosome loop-forming proteins arrange the DNA into topological associated domains such that individual genes and their associated enhancer binding regions are in proximity.
D)There is no mechanism to prevent inappropriate enhancer action on neighboring genes.The cells will degrade inappropriately produced mRNA molecules.

Question 22

How are most eukaryotic transcription regulators able to affect transcription when their binding sites are far from the promoter?

A)by binding to their binding site and sliding to the site of RNA polymerase assembly
B)by looping out the intervening DNA between their binding site and the promoter
C)by unwinding the DNA between their binding site and the promoter
D)by attracting RNA polymerase and modifying it before it can bind to the promoter

Question 23

You are interested in the regulation of gene Q.Proteins G, H, and J are proteins that are important for regulating gene Q, and bind to its promoter region in a sequence-specific fashion.Proteins G and H both bind to site "A" but cannot bind to site "A" at the same time.Protein J binds to site "B" on the promoter.The promoter region is diagrammed in Figure 8-20. Figure 8-20
You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q.Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced.When you add these proteins to the system, you get the results shown in Table 8-20. $\text { experiment }$$\text { reaulator protein added }$$\text { Q mRNA }$
$\begin{array}{ccccc}\text { number } &\quad\quad\quad\text { G } & H & J & \quad\quad\text { made? } \\\hline 1 &\quad\quad - & - & - & \text { no } \\\hline 2 & \quad\quad+ & - & - & \text { no } \\\hline 3 & \quad\quad- & + & - & \text { yes } \\\hline 4 &\quad\quad - & - & + & \text { yes } \\\hline 5 &\quad\quad + & + & - & \text { no } \\\hline 6 &\quad\quad + & - & + & \text { yes } \\\hline 7 & \quad\quad- & + & + & \text { yes } \\\hline 8 & \quad\quad+ & + & + & \text { yes }\end{array}$


Table 8-20
Which proteins are likely to act as gene repressors?

A)G
B)H
C)J
D)both H and J

Question 24

Which of the following statements about DNA methylation in eukaryotes is FALSE?

A)Appropriate inheritance of DNA methylation patterns involves maintenance methyltransferase.
B)DNA methylation involves a covalent modification of cytosine bases.
C)Methylation of DNA attracts proteins that block gene expression.
D)Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.

Question 25

Which of the following statements about the Ey transcriptional regulator is FALSE?

A)Expression of Ey in cells that normally form legs in the fly will lead to the formation of an eye in the middle of the legs.
B)The Ey transcription factor must bind to the promoter of every eye-specific gene in the fly.
C)Positive feedback loops ensure that Ey expression remains switched on in the developing eye.
D)A homolog of Ey is found in vertebrates; this homolog is also used during eye development.

Question 26

Which of the following statements about iPS cells is FALSE?

A)iPS cells can be made by adding a combination of transcription regulators to a fibroblast.
B)iPS cells made from mouse cells can differentiate into almost any human cell type.
C)Stimulation by extracellular signal molecules causes iPS cells to differentiate.
D)A cell that is dedifferentiated to become an iPS cell will undergo changes to its gene expression profile.

Question 27

The MyoD transcriptional regulator is normally found in differentiating muscle cells and participates in the transcription of genes that produce muscle-specific proteins, such as those needed in contractile tissue.Amazingly, expression of MyoD in fibroblasts causes these cells derived from skin connective tissue to produce proteins normally only seen in muscles.However, some other cell types do not transcribe muscle-specific genes when MyoD is expressed in them.Which of the following statements below is the best explanation of why MyoD can cause fibroblasts to express muscle-specific genes?

A)Unlike some other cell types, fibroblasts have not lost the muscle-specific genes from their genome.
B)The muscle-specific genes must be in heterochromatin in fibroblasts.
C)During their developmental history, fibroblasts have accumulated some transcriptional regulators in common with differentiating muscle cells.
D)The presence of MyoD is sufficient to activate the transcription of muscle-specific genes in all cell types.

Question 28

You are interested in the regulation of gene Q.Proteins G, H, and J are proteins that are important for regulating gene Q, and bind to its promoter region in a sequence-specific fashion.Proteins G and H both bind to site "A" but cannot bind to site "A" at the same time.Protein J binds to site "B" on the promoter.The promoter region is diagrammed in Figure 8-20. Figure 8-20
You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q.Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced.When you add these proteins to the system, you get the results shown in Table 8-20. $\text { experiment }$$\text { reaulator protein added }$$\text { Q mRNA }$
$\begin{array}{ccccc}\text { number } &\quad\quad\quad\text { G } & H & J & \quad\quad\text { made? } \\\hline 1 &\quad\quad - & - & - & \text { no } \\\hline 2 & \quad\quad+ & - & - & \text { no } \\\hline 3 & \quad\quad- & + & - & \text { yes } \\\hline 4 &\quad\quad - & - & + & \text { yes } \\\hline 5 &\quad\quad + & + & - & \text { no } \\\hline 6 &\quad\quad + & - & + & \text { yes } \\\hline 7 & \quad\quad- & + & + & \text { yes } \\\hline 8 & \quad\quad+ & + & + & \text { yes }\end{array}$


Table 8-20
Your colleague looks at your data above and predicts that protein G will bind more strongly to the DNA at site A, compared to protein H.Which experiment above is critical for this prediction?

A)#2
B)#3
C)#5
D)#6

Question 29

In principle, how many different cell types can an organism having four different types of transcription regulators and thousands of genes create?

A)up to 4
B)up to 8
C)up to 16
D)thousands

Question 30

You are interested in studying the transcriptional regulation of the Gip1 promoter.The Gip1 promoter contains a binding site for the Jk8 protein that overlaps with the binding site for the Pa5 protein.Jk8 and Pa5 cannot bind DNA at the same time, but both proteins are present at high levels in adult liver cells.The binding sites for Jk8 and Pa5 are shown in Figure 8-24. Figure 8-24
Jk8 binds to site A while Pa5 binds to site B.You create mutations that remove the nonoverlapping sequences of either binding site A or B, and examine Gip1 mRNA production in adult liver cells that contain these mutations.The data you obtain from these experiments are shown in Table 8-24. $\begin{array}{c}\begin{array}{c} \text {experiment}\\ \text { number}\\\hline 1 \\ \hline 2 \\ \hline 3 \\ \hline 4 \end{array}\begin{array}{cc}\text { binding site } \\ \text { A } \quad\text { B } \\ \hline+\quad+\\ \hline+ \quad-\\ \hline-\quad+\\ \hline-\quad-\\\end{array}\begin{array}{c} \text {Gip 1 mRNA}\\ \text {levels}\\\hline \text {high}\\\hline \text {high}\\\hline \text {none}\\\hline \text {none}\\\end{array}\end{array}$

Table 8-24
You know that Gip1 is only expressed in adult liver cells and not in the liver of embryos.You also know that Jk8 and Pa5 behave similarly on other promoters in the embryo or in the adult, in terms of whether they act as repressors or gene activators.Given the data, use of which of the following mechanisms would make the most sense for regulating the Jk8 and Pa5 proteins:

A)Jk8 is ubiquitylated and targeted for destruction in adult cells.
B)Jk8, but not Pa5, is transcribed in embryonic liver cells.
C)Jk8 binds to the promoter of the gene that encodes Jk8 in embryonic liver cells.
D)Pa5 binds to the promoter of the gene that encodes Jk8 in embryonic liver cells.

Question 31

The modular nature of the Eve gene's regulatory region means that

A)there are seven regulatory elements and each element is sufficient for driving expression in a single stripe.
B)all the regulatory elements for each stripe use the same transcriptional activators.
C)the E.coli LacZ gene is normally only expressed in a single stripe-unlike Eve, which is expressed in seven stripes.
D)transcription regulators only bind to the stripe 2 regulatory DNA segment in stripe 2.

Question 32

You are interested in the regulation of gene Q.Proteins G, H, and J are proteins that are important for regulating gene Q, and bind to its promoter region in a sequence-specific fashion.Proteins G and H both bind to site "A" but cannot bind to site "A" at the same time.Protein J binds to site "B" on the promoter.The promoter region is diagrammed in Figure 8-20. Figure 8-20
You develop a cell-free transcriptional system to study the effects of proteins G, H, and J on the transcription of gene Q.Using this system, you can examine the effects of adding these proteins to the transcriptional system in equal amounts and measuring how much gene Q is produced.When you add these proteins to the system, you get the results shown in Table 8-20. $\text { experiment }$$\text { reaulator protein added }$$\text { Q mRNA }$
$\begin{array}{ccccc}\text { number } &\quad\quad\quad\text { G } & H & J & \quad\quad\text { made? } \\\hline 1 &\quad\quad - & - & - & \text { no } \\\hline 2 & \quad\quad+ & - & - & \text { no } \\\hline 3 & \quad\quad- & + & - & \text { yes } \\\hline 4 &\quad\quad - & - & + & \text { yes } \\\hline 5 &\quad\quad + & + & - & \text { no } \\\hline 6 &\quad\quad + & - & + & \text { yes } \\\hline 7 & \quad\quad- & + & + & \text { yes } \\\hline 8 & \quad\quad+ & + & + & \text { yes }\end{array}$


Table 8-20
Which proteins do you predict are bound to the promoter in experiment #8?

A)only H and J
B)only G and H
C)only G and J
D)only J

Question 33

In mammals, individuals with two X chromosomes are female, and individuals with an X and a Y chromosome are male.It had long been known that a gene located on the Y chromosome was sufficient to induce the gonads to form testes, which is the main male-determining factor in development, and researchers sought the product of this gene, the so-called testes-determining factor (TDF).For several years, the TDF was incorrectly thought to be a zinc finger protein encoded by a gene called BoY.Which of the following observations would most strongly suggest that BoY might NOT be the TDF?

A)Some XY individuals that develop into females have mutations in a different gene, SRY, but are normal at BoY.
B)BoY is not expressed in the adult male testes.
C)Expression of BoY in adult females does not masculinize them.
D)A few of the genes that are known to be expressed only in the testes have binding sites for the BoY protein in their upstream regulatory sequences, but most do not.

Question 34

From the sequencing of the human genome, we believe that there are approximately 21,000 protein-coding genes in the genome, of which 1500-3000 are transcription factors.If every gene has a tissue-specific and signal-dependent transcription pattern, how can such a small number of transcriptional regulatory proteins generate a much larger set of transcriptional patterns?

Question 35

Which of the following statements about how fruit flies can develop an eye in the middle of a leg is TRUE?

A)When the Ey gene is expressed in adult leg cells, these cells dedifferentiate and become eye cells.
B)The Ey gene encodes a transcription regulator that is the only transcription regulator used to produce a fruit fly eye.
C)When the Ey gene is introduced into cells that would normally give rise to a leg, the transcription regulators used to control its expression in the leg are different from those that are normally used to control Ey expression in the eye.
D)All the eye cells found in the adult leg are a single cell type and have identical characteristics.

Question 36

You are studying a set of mouse genes whose expression increases when cells are exposed to the hormone cortisol, and you believe that the same cortisol-responsive transcriptional activator regulates all of these genes.If your hypothesis is correct, which of the following statements below should be TRUE?

A)The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-responsive transcriptional activator.
B)The cortisol-responsive genes must all be in an operon.
C)The transcriptional regulators that bind to the regulatory regions of the cortisol-responsive genes must all be the same.
D)The cortisol-responsive genes must not be transcribed in response to other hormones.

Question 37

Combinatorial control of gene expression

A)involves every gene using a different combination of transcriptional regulators for its proper expression.
B)involves groups of transcription regulators working together to determine the expression of a gene.
C)involves only the use of gene activators used together to regulate genes appropriately.
D)is seen only when genes are arranged in operons.

Question 38

Which of the following statements about nucleosomes is TRUE?

A)Nucleosomes activate transcription when bound to the promoter.
B)Although RNA polymerase can access DNA packed within nucleosomes, the general transcription factors and transcriptional regulators cannot.
C)Histone acetyltransferases affect transcription by both altering chromatin structure to allow accessibility to the DNA and by adding acetyl groups to histones that can bind proteins that promote transcription.
D)Histone deacetylases remove lysines from histone tails.

Question 39

The expression of the BRF1 gene in mice is normally quite low, but mutations in a gene called BRF2 lead to increased expression of BRF1.You have a hunch that nucleosomes are involved in the regulation of BRF1 expression and so you investigate the position of nucleosomes over the TATA box of BRF1 in normal mice and in mice that lack either the BRF2 protein (BRF2^-) or part of histone H4 (HHF^-) (histone H4 is encoded by the HHF gene).Table 8-27 summarizes your results.A normal functional gene is indicated by a plus sign (+). $\begin{array}{c}\begin{array}{lll}\text { Mouse }\\\hline\text {\(B R F 2^{+}\quad \mathrm{HHF}^{+} \) }\\ \hline\text {\(B R F 2^{-}\quad H H F^{+}\)}\\\hline\text {\(\mathrm{BRF2}^{+}\quad \mathrm{HHF}^{-}\)}\\\hline\text {\(B R F 2^{-} \quad H H F^{-}\)}\\ \end{array}\begin{array}{c} \text {Nucleosome positioning}\\\hline \text {specific pattern}\\\hline \text {random}\\\hline \text {random}\\\hline \text {random}\\\end{array}\begin{array}{c}\text { Relative level of BRF1 mRNA }\\\hline 1 \\\hline 100 \\\hline 1 \\\hline 100 \end{array}\end{array}$
Table 8-27
Which of the following conclusions CANNOT be drawn from your data?

A)BRF2 is required for the repression of BRF1.
B)BRF2 is required for the specific pattern of nucleosome positions over the BRF1 upstream region.
C)The specific pattern of nucleosome positioning over the BRF1 upstream region is required for BRF1 repression.
D)The part of histone H4 missing in HHF^- mice is not required for the formation of nucleosomes.

Question 40

Which of the following is NOT a general mechanism that cells use to maintain stable patterns of gene expression as cells divide?

A)a positive feedback loop, mediated by a transcriptional regulator that activates transcription of its own gene in addition to other cell-type-specific genes
B)faithful propagation of condensed chromatin structures as cells divide
C)inheritance of DNA methylation patterns when cells divide
D)proper segregation of housekeeping proteins when cells divide

Question 41

The gene for a hormone necessary for insect development contains binding sites for three transcription regulators called A, B, and C. Because the binding sites for A and B overlap, A and B cannot bind simultaneously. You make mutations in the binding sites for each of the proteins and measure hormone production in cells that contain equal amounts of the A, B, and C proteins. Figure 8-52 summarizes your results. In each of the following sentences, fill in the blank one of the phrases within square brackets to make the statement consistent with the results.


-Protein A binds to its DNA binding site __________ [more tightly/less tightly] than protein B binds to its DNA binding site.

Question 42

Which of the following examples does NOT describe a mechanism of post-transcriptional control of gene expression?

A)the alternative splicing of a gene, leading to the production of a muscle-specific protein
B)the action of the RNA component of telomerase
C)the activation of a protein when it is phosphorylated by a protein kinase
D)translational inhibition of an mRNA by the binding of a protein at the 5′ untranslated region of the message.

Question 43

Which of the following is NOT involved in post-transcriptional control?

A)the spliceosome
B)Dicer
C)Mediator
D)RISC

Question 44

Using genetic engineering techniques, you remove the sequences that code for the ribosome-binding sequences of the bacterial LacZ gene.The removal of these sequences will lead to

A)more LacZ protein being produced due to faster ribosome movement across the LacZ mRNA.
B)transcriptional repression, resulting in fewer mRNA molecules being produced from this gene.
C)a longer half-life for the LacZ mRNA.
D)translational inhibition of the LacZ mRNA.

Question 45

The owners of a local bakery ask for your help in improving a special yeast strain they use to make bread.They would like you to help them design experiments using RNA interference to turn off genes, to allow them to test their hypothesis that certain genes are important for the good flavors found in their bread.Of the components in the following list, which is the most important to check for in this yeast strain if you would like this project to succeed?

A)foreign double-stranded RNA
B)genes in the genome that code for RISC proteins
C)miRNA genes in the genome
D)single-stranded siRNAs within the cell

Question 46

An allosteric transcription regulator called HisP regulates the enzymes for histidine biosynthesis in the bacterium E.coli.Histidine modulates HisP activity.On binding histidine, HisP alters its conformation, markedly changing its affinity for the regulatory sequences in the promoters of the genes for the histidine biosynthetic enzymes.
A.If HisP functions as a gene repressor, would you expect that HisP would bind more tightly or less tightly to the regulatory sequences when histidine is abundant? Explain your answer.
B.If HisP functions as a gene activator, would you expect that HisP would bind more tightly or less tightly to the regulatory sequences when histidine levels are low? Explain your answer.

Question 47

MicroRNAs

A)are produced from a precursor miRNA transcript.
B)are found only in humans.
C)control gene expression by base-pairing with DNA sequences.
D)can degrade RNAs by using their intrinsic catalytic activity.

Question 48

In the absence of glucose, E.coli can proliferate by using the pentose sugar arabinose.As shown in Figure 8-57, the arabinose operon regulates the ability of E.coli to use arabinose.The araA, araB, and araD genes encode enzymes for the metabolism of arabinose.The araC gene encodes a transcription regulator that binds adjacent to the promoter of the arabinose operon.To understand the regulatory properties of the AraC protein, you engineer a mutant bacterium in which the araC gene has been deleted and look at the effect of the presence or absence of the AraC protein on the AraA enzyme.
Figure 8-57
A.If the AraC protein works as a gene repressor, would you expect araA RNA levels to be high or low in the presence of arabinose in the araC^- mutant cells? What about in the araC^- mutant cells in the absence of arabinose? Explain your answer.
B.Your findings from the experiment are summarized in Table 8-57.
Table 8-57
Do the results in Table 8-57 indicate that the AraC protein regulates arabinose metabolism by acting as a gene repressor or a gene activator? Explain your answer.

Question 49

Which of the following statements about RNAi is TRUE?

A)The RNAi mechanism is found only in plants and animals.
B)RNAi is induced when double-stranded, foreign RNA is present in the cell.
C)RISC uses the siRNA duplex to locate complementary foreign RNA molecules.
D)siRNAs bind to miRNAs to induce RNAi.

Question 50

The gene for a hormone necessary for insect development contains binding sites for three transcription regulators called A, B, and C. Because the binding sites for A and B overlap, A and B cannot bind simultaneously. You make mutations in the binding sites for each of the proteins and measure hormone production in cells that contain equal amounts of the A, B, and C proteins. Figure 8-52 summarizes your results. In each of the following sentences, fill in the blank one of the phrases within square brackets to make the statement consistent with the results.


-Protein C is able to prevent activation by __________ [protein A only/protein B only/both protein A and protein B].

Question 51

You are interested in studying the transcriptional regulation of the Gip1 promoter.The Gip1 promoter contains a binding site for the Jk8 protein that overlaps with the binding site for the Pa5 protein.Jk8 and Pa5 cannot bind DNA at the same time, but both proteins are present at high levels in adult liver cells.The binding sites for Jk8 and Pa5 are shown in Figure 8-24.
Figure 8-24
Jk8 binds to site A while Pa5 binds to site B.You create mutations that remove the nonoverlapping sequences of either binding site A or B, and examine Gip1 mRNA production in adult liver cells that contain these mutations.The data you obtain from these experiments are shown in Table 8-24.
Table 8-24
Which transcription regulatory protein is bound in experiment #1 (the normal situation)? Explain.

Question 52

The gene for a hormone necessary for insect development contains binding sites for three transcription regulators called A, B, and C. Because the binding sites for A and B overlap, A and B cannot bind simultaneously. You make mutations in the binding sites for each of the proteins and measure hormone production in cells that contain equal amounts of the A, B, and C proteins. Figure 8-52 summarizes your results. In each of the following sentences, fill in the blank one of the phrases within square brackets to make the statement consistent with the results.


-Protein A is a __________ [stronger/weaker] activator of transcription than protein B.

Question 53

The CAP activator protein and the Lac repressor both control the Lac operon (see Figure 8-53).You create cells that are mutant in the gene coding for the Lac repressor so that these cells lack the Lac repressor under all conditions.For these mutant cells, state whether the Lac operon will be switched on or off in the following situations, and explain why.
Figure 8-53
A.in the presence of glucose and lactose
B.in the presence of glucose and the absence of lactose
C.in the absence of glucose and the absence of lactose
D.in the absence of glucose and the presence of lactose

Question 54

You have discovered an operon in a bacterium that is turned on only when sucrose is present and glucose is absent.You have also isolated three mutants that have changes in the upstream regulatory sequences of the operon and whose behavior is summarized in the Table 8-58.You hypothesize that there are two gene regulatory sites, A and B, in the upstream regulatory sequence that are affected by the mutations.For this question, a plus (+) indicates a normal site and a minus (-) indicates a mutant site that no longer binds its transcription regulator.
Table 8-58
A.If mutant 1 has sites A^- B⁺, which of these sites is regulated by sucrose and which by glucose?
B.Give the state (+ or-) of the A and B sites in mutants 2 and 3.
C.Which site is bound by a repressor and which by an activator?

Question 55

miRNAs, tRNAs, and rRNAs all

A)do not code for proteins.
B)act in the nucleus.
C)are packaged with other proteins to form RISC.
D)form base pairs with mRNA molecules.

Question 56

Which of the following statements about miRNAs is FALSE?

A)One miRNA can regulate the expression of many genes.
B)miRNAs are transcribed in the nucleus from genomic DNA.
C)miRNAs are produced from rRNAs.
D)miRNAs are made by RNA polymerase.

Question 57

Bacterial cells can take up the amino acid tryptophan from their surroundings, or, if the external supply is insufficient, they can synthesize tryptophan by using enzymes in the cell.In some bacteria, the control of glutamine synthesis is similar to that of tryptophan synthesis, such that the glutamine repressor inhibits the transcription of the glutamine operon, which contains the genes that code for the enzymes required for glutamine synthesis.On binding to cellular glutamine, the glutamine repressor binds to a site in the promoter of the operon.
A.Why is glutamine-dependent binding to the operon a useful property for the glutamine repressor?
B.What would you expect to happen to the regulation of the enzymes that synthesize glutamine in cells expressing a mutant form of the glutamine repressor that cannot bind to DNA?
C.What would you expect to happen to the regulation of the enzymes that synthesize glutamine in cells expressing a mutant form of the glutamine repressor that binds to DNA even when no glutamine is bound to it?

Question 58

Fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; each word or phrase should be used only once.
The genes of a bacterial __________ are transcribed into a single mRNA.Many bacterial promoters contain a region known as a/an __________, to which a specific transcription regulator binds.Genes in which transcription is prevented are said to be __________.The interaction of small molecules, such as tryptophan, with __________ DNA-binding proteins, such as the tryptophan repressor, regulates bacterial genes.Genes that are being __________ expressed are being transcribed all the time.
allosteric negatively positively
constitutively operator promoter
induced operon repressed

Question 59

Which method or methods of controlling eukaryotic gene expression is NOT employed in prokaryotic cells? Select all that apply.

A)controlling how often a gene is transcribed
B)controlling how an RNA transcript is spliced
C)controlling which mRNAs are exported from the nucleus to the cytosol
D)controlling which mRNAs are translated into protein by the ribosomes

Question 60

The long noncoding RNA Xist

A)is important for the formation of highly condensed heterochromatin on the X chromosome.
B)binds to foreign RNAs in the cell to promote their destruction.
C)catalyzes miRNA maturation.
D)acts with the RTS complex to bind to complementary RNA molecules.

Question 61

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; use each word or phrase only once.
acetylation methylation riboswitch
destruction mitochondria RISC
Dicer mRNA rRNA
DNA phosphorylation single-stranded RNA
double-stranded RNA prokaryotic tRNA
MicroRNAs are noncoding RNAs that are incorporated into a protein complex called __________, which searches the __________s in the cytoplasm for sequence complementary to that of the miRNA.When such a molecule is found, it is then targeted for __________.RNAi is triggered by the presence of foreign __________ molecules, which are digested by the __________ enzyme into shorter fragments approximately 23 nucleotide pairs in length.

Question 62

In principle, a eukaryotic cell can regulate gene expression at any step in the pathway from DNA to the active protein.Place the types of control listed below at the appropriate places on the diagram in Figure 8-67.
Figure 8-67
A.translation control
B.transcriptional control
C.RNA splicing
D.RNA degradation
E.protein degradation

Question 63

Label the following structures in Figure 8-51.
Figure 8-51
A.activator protein
B.RNA polymerase
C.general transcription factors
D.Mediator

Question 64

For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; use each word or phrase only once.
combinatorial feedback phosphorylation
deacetylation histone pluripotency
differential leucine zipper proliferation
epigenetic memory receptor
expression methylation unwinding
The transmission of information important for gene regulation from parent to daughter cell, without altering the actual nucleotide sequence, is called __________ inheritance.This type of inheritance is seen with the inheritance of the covalent modifications on __________ proteins bound to DNA; these modifications are important for reestablishing the pattern of chromatin structure found on the parent chromosome.Another way to inherit chromatin structure involves DNA __________, a covalent modification that occurs on cytosine bases that typically turns off the transcription of a gene.Gene transcription patterns can also be transmitted across generations through positive __________ loops that can involve a transcription regulator activating its own transcription in addition to other genes.These mechanisms all allow for cell __________, a property involving the maintenance of gene expression patterns important for cell identity.

Question 65

For each of the following sentences, fill in the blanks with the best word or phrase in the list below.Not all words or phrases will be used; use each word or phrase only once.
During transcription in __________ cells, transcription regulators that bind to DNA thousands of nucleotides away from a gene's promoter can affect a gene's transcription.The __________ is a complex of proteins that links distantly bound transcription regulators with the proteins bound closer to the transcription start site.Transcription activators can also interact with histone __________s, which alter chromatin by modifying lysines in the tail of histone proteins to allow greater accessibility to the underlying DNA.Gene repressor proteins can reduce the efficiency of transcription initiation by attracting histone __________s.Sometimes, many contiguous genes can become transcriptionally inactive as a result of chromatin remodeling, like the __________ found in interphase chromosomes.
acetyltransferase eukaryotic operator
centrosome helicase peroxidase
deacetylase heterochromatin prokaryotic
deoxidase leucine zipper telomere
enhancer Mediator viral

Question 66

The Drosophila Eve gene has a complex promoter containing multiple binding sites for four transcription regulators: Bicoid, Hunchback, Giant, and Krüppel.Bicoid and Hunchback are activators of Eve transcription, whereas Giant and Krüppel repress Eve transcription.Figure 8-66A shows the patterns of expression of these regulators.
Figure 8-66
The Eve promoter contains modules that control expression in various stripes.You construct a reporter gene that contains the DNA 5 kb upstream of the Eve gene, so that this reporter contains the stripe 3 module, the stripe 2 module, the stripe 7 module, and the TATA box, all fused to the LacZ reporter gene (which encodes the β-galactosidase enzyme), as shown in Figure 8-66B.This construct results in expression of the β-galactosidase enzyme in three stripes, which correspond to the normal positions of stripes 3, 2, and 7.
A.By examining the overlap of sites on the stripe 2 module, as depicted in Figure 8-66B, what is the biological effect of having some of the transcription regulator binding sites overlap?
B.You make two mutant versions in which several of the binding sites in the Eve stripe 2 module have been deleted, as detailed in items (i) and (ii) below.Refer to Figure 8-66B for the positions of the binding sites.(Note, however, that because many of the binding sites overlap, it is not possible to delete all of one kind of site without affecting some of the other sites.) Match the appropriate mutant condition with the most likely pattern of Eve expression shown in Figure 8-66C.Explain your choices.
i.deletion of the Krüppel-binding sites in stripe 2
ii.deletion of the two Bicoid-binding sites in the stripe 2 module that are marked with an asterisk (*) in Figure 8-66B

Question 67

Fill in the blanks with the best word or phrase selected from the list below.Not all words or phrases will be used; each word or phrase should be used only once.
allosteric negatively positively
constitutively operator promoter
induced operon repressed
The genes of a bacterial __________ are transcribed into a single mRNA.Many bacterial promoters contain a region known as a/an __________, to which a specific transcription regulator binds.Genes in which transcription is prevented are said to be __________.The interaction of small molecules, such as tryptophan, with __________ DNA-binding proteins, such as the tryptophan repressor, regulates bacterial genes.Genes that are being __________ expressed are being transcribed all the time.

Question 68

For each of the following sentences, fill in the blanks with the best word or phrase in the list below.Not all words or phrases will be used; use each word or phrase only once.
acetyltransferase eukaryotic operator
centrosome helicase peroxidase
deacetylase heterochromatin prokaryotic
deoxidase leucine zipper telomere
enhancer Mediator viral
During transcription in __________ cells, transcription regulators that bind to DNA thousands of nucleotides away from a gene's promoter can affect a gene's transcription.The __________ is a complex of proteins that links distantly bound transcription regulators with the proteins bound closer to the transcription start site.Transcription activators can also interact with histone __________s, which alter chromatin by modifying lysines in the tail of histone proteins to allow greater accessibility to the underlying DNA.Gene repressor proteins can reduce the efficiency of transcription initiation by attracting histone __________s.Sometimes, many contiguous genes can become transcriptionally inactive as a result of chromatin remodeling, like the __________ found in interphase chromosomes.