C
8
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2009 Garland Science Publishing
8-1 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) packing of DNA into nucleosomes in some cells and not others
8-2 The human genome encodes about 24,000 genes. Approximately how many genes does the typical differentiated human cell express at any one time?
(a) 24,000—all of them
(b) between 21,500 and 24,000—at least 90% of the genes
(c) between 5000 and 15,000
(d) less than 2500
8-3 Which of the following statements about differentiated cells is true ?
(a) Cells of distinct types express nonoverlapping sets of transcription factors.
(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.
8-4 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 embryo that develops from the nuclear transplant experiment is genetically 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.

8-5 In principle, a eucaryotic 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 Q8-5.
Figure Q8-5
A. translation control
B. transcriptional control
C. RNA processing control
D. protein activity control
8-6 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(n) __________________, 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 constitutively induced negatively operator operon positively promoter repressed
8-7 Which of the following statements about transcriptional regulators is false ?
(a) Transcriptional regulators usually interact with the sugar-phosphate backbone on the outside of the double helix to determine where to bind on the DNA helix.
(b) Transcriptional regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA.

(c) The DNA-binding motifs of transcriptional regulators usually bind in the major groove of the DNA helix.
(d) The binding of transcriptional regulators generally does not disrupt the hydrogen bonds that holds the double helix together.
8-8 Operons ___________________________.
(a) are commonly found in eucaryotic 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
8-9 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
8-10 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.
8-11 You are interested in examining the regulation of the gene that encodes an enzyme, Tre-ase, important in metabolizing trehalose into glucose in bacteria.
Trehalose is a disaccharide formed of two glucose units. It is known that two
DNA binding proteins, TreA and TreB, are important for binding to the promoter of the Tre-ase gene and are involved in regulating the transcription of the Tre-ase gene: TreA binds to the “A” site in the promoter region, and TreB binds to the
“B” site. You make mutations in the TreA and TreB genes to create cells lacking these genes, observe what happens to transcription of the Tre-ase gene, and obtain the results in Table Q8-11.
Table Q8-11
A. What is the role for TreA in controlling Tre-ase expression? Explain.

B. What is the role for TreB in controlling Tre-ase expression? Explain.
C. From these data, what do you predict will happen to Tre-ase transcription
(compared with that in normal cells) in the presence of trehalose if you were to create a version of the TreA protein that will constitutively bind to the “A” site in the Tre-ase promoter?
Note: Questions 8-12 to 8-15 use the following information and the data in Table
Q8-12. These questions may be used independently, or as a group.
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 (Ca
2+
) and magnesium (Mg
2+
).
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.
Table Q8-12
For this table: -, no transcription of Psf ; +, low level of transcription of Psf ; ++, high levels of transcription of Psf .
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
8-13 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

8-14 Which transcription factors are normally bound to the Psf promoter in the presence of Mg
2+
only?
(a) none
(b) MetA only
(c) MetA and Met B
(d) MetA, MetB, and MetC
8-15 Which transcription factors are normally bound to the Psf promoter in the presence of both Mg
2+
and Ca
2+
?
(a) MetA and MetB
(b) MetB and MetC
(c) MetA and MetC
(d) MetA, MetB, and MetC
Note: Questions 8-16 to 8-19 use the following information and the data in Figure
Q8-16. These questions may be used independently, or as a group.
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 Q8-16, 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 Q8-16, if the site is missing, it is mutated such that it cannot bind its corresponding transcription factor.
Figure Q8-16

8-16 Which of the following proteins are likely to act as gene repressors?
(a) factor X
(b) factor Y
(c) factor Z
(d) none of the above
8-17 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
8-18 Experiment 1 in Figure Q8-16 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
8-19 In what tissue is factor Z normally present and bound to the DNA?
(a) kidney
(b) liver
(c) heart
(d) none of the above
8-20 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.
8-21 Bacterial cells can take up the amino acid tryptophan from their surroundings, or, if the external supply is insufficient, they can synthesize trytophan 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?
8-22 In the absence of glucose, E. coli can proliferate by using the pentose sugar arabinose. As shown in Figure Q8-22, 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 Q8-22
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 Q8-22.
Table Q8-22
Do the results in Table Q8-22 indicate that the AraC protein regulates arabinose metabolism by acting as a gene repressor or a gene activator?
Explain your answer.
8-23 The CAP activator protein and the Lac repressor both control the Lac operon (see
Figure Q8-23). 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 Q8-23
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
8-24 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 Q8-24. You hypothesize that there are two gene regulatory sites in the upstream regulatory sequence, A and B, which 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 Q8-24
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?
8-25 Label the following structures in Figure Q8-25.

Figure Q8-25
A. activator protein
B. RNA polymerase
C. general transcription factors
D. mediator
8-26 How are most eucaryotic 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
8-27 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 Q8-27 summarizes your results. A normal functional gene is indicated by a plus sign (+).
Table Q8-27

Which of the following conclusions cannot be drawn from your data? Explain your answer.
(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.
8-28 The yeast GAL4 gene encodes a transcriptional regulator that can bind DNA upstream of genes required for the metabolism of the sugar galactose and turns them on. Gal4 has a DNA-binding domain and an activation domain. The DNAbinding domain allows it to bind to the appropriate sites in the promoters of the galactose metabolism genes. The activation domain attracts histone-modifying enzymes and also binds to a component of the RNA polymerase II enzyme complex, attracting it to the promoter so that the regulated genes can be turned on when Gal4 is also bound to the DNA. When Gal4 is expressed normally, the genes can be maximally activated. You decide to try to produce more of the galactose metabolism genes by overexpressing the Gal4 protein at levels fiftyfold greater than normal. You conduct experiments to show that you are overexpressing the Gal4 protein and that it is properly localized in the nucleus of the yeast cells. To your surprise, you find that too much Gal4 causes the galactose genes to be transcribed only at a low level. What is the most likely explanation for your findings?
8-29 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, transcriptional 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 transcriptional start site. Transcriptional 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. viral acetylase centrosome

helicase procaryotic mediator telomere eucaryotic peroxidase deoxidase enhancer operator deacetylase heterochromatin leucine zipper
8-30 In principle, how many different cell types can an organism having four different types of transcription regulator and thousands of genes create?
(a) up to 4
(b) up to 8
(c) up to 16
(d) thousands
8-31 From the sequencing of the human genome, we believe that there are approximately 24,000 protein-coding genes in the genome, for which there are an estimated 1500–3000 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?
8-32 Combinatorial control of gene expression __________________________.
(a) involves every gene using a different combination of transcriptional regulators for its proper expression
(b) involves groups of transcriptional 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
8-33 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 cortisolresponsive transcriptional activator regulates all of these genes. Which of the following statements below should be true if your hypothesis is correct?
(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.
8-34 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 musclespecific genes in all cell types.
8-35 A virus produces a protein X that activates only a few of the virus’s own genes
(V1, V2, and V3) when it infects cells. The cellular proteins A (a zinc finger protein) and the cellular protein B (a homeodomain protein) are known to be repressors of the viral genes V1, V2, and V3. You examine the complete upstream gene regulatory sequences of these three viral genes and find the following:
1.
2.
3.
V1 and V2 contain binding sites for the zinc finger protein A only.
V3 contains a binding site for the homeodomain protein B only.
The only sequence that all three genes have in common is the TATA box.
Label each of the choices below as likely or unlikely as an explanation for your findings. For each choice you label as unlikely , explain why.
A. Protein X binds nonspecifically to the DNA upstream of V1, V2, and V3 and activates transcription.
B. Protein X binds to a repressor and prevents the repressor from binding upstream of V1, V2, and V3.
C. Protein X activates transcription by binding to the TATA box.
D. Protein X activates transcription by binding to and sequestering proteins A and B.
E. Protein X represses transcription of the genes for proteins A and B.
8-36 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? Explain your answer.
(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.
8-37 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
8-38 Which of the following statements about DNA methylation in eucaryotes 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.
8-39 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 eyespecific 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.
8-40 Which of the following statements about riboswitches is false ?
(a) Riboswitches can block the production of mRNAs.
(b) Riboswitches can control the translation of mRNAs.
(c) Riboswitches are made from rRNAs.
(d) Riboswitches can bind metabolites.
8-41 Which of the following is not involved in post-transcriptional control?
(a) the spliceosome
(b) dicer
(c) mediator
(d) RISC

8-42 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
8-43 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.
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. tRNA
RISC procaryotic phosphorylation riboswitch destruction methylation double-stranded RNA mRNA single-stranded RNA rRNA acetylation
DNA dicer mitochondria
8-44 The extent of complementarity of a miRNA with its target mRNA determines
___________________________.
(a) whether the mRNA will be degraded or transported elsewhere in the cell
(b) whether the mRNA will be transported to the nucleus
(c) whether RISC is degraded
(d) whether the miRNA synthesizes a complementary strand
8-45 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.
8-46 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 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.

Eve
8-47 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 Q8-47 summarizes your results. In each of the following sentences, choose one of the phrases within square brackets to make the statement consistent with the results.
Figure Q8-47
A. Protein A binds to its DNA-binding site [ more tightly / less tightly ] than protein B binds to its DNA-binding site.
B. Protein A is a [ stronger / weaker ] activator of transcription than protein B.
C. Protein C is able to prevent activation by [ protein A only / protein B only / both protein A and protein B ].
8-48 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 Q8-48A shows the patterns of expression of these regulators.

Figure Q8-48
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 Q8-50B. 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 Q8-48B, 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 Q8-48B 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 Q8-48C. 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 Q8-48B