Bio Chapter 8 Study
Label the following structures in Figure Q8-35. Figure Q8-35 A. activator protein B. RNA polymerase C. general transcription factors D. Mediator
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Which gene regulatory protein is bound in experiment 1 (the normal situation)? Explain.
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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 Q8-28. You hypothesize that there are two gene regulatory sites, A and B, in the upstream regulatory sequencethat 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 Q8-28 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?
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Which of these method(s) of controlling eukaryotic gene expression is NOT employed in prokaryotic cells? 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 E. controlling how rapidly proteins are destroyed once they are made
B,C
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. acetylase eukaryotic operator centrosome helicase peroxidase deacetylase heterochromatin prokaryotic deoxidase leucine zipper telomere enhancer Mediator viral
During transcription in eukaryotic cells, transcriptional regulators that bind to DNA thousands of nucleotides away from a gene's promoter can affect a gene's transcription. The Mediator 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 acetylases, 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 deacetylases. Sometimes, many contiguous genes can become transcriptionally inactive as a result of chromatin remodeling, like the heterochromatin found in interphase chromosomes.
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. 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 RISC, which searches the mRNAs in the cytoplasm for sequence complementary to that of the miRNA. When such a molecule is found, it is then targeted for destruction. RNAi is triggered by the presence of foreign double-stranded RNA molecules, which are digested by the Dicer enzyme into shorter fragments approximately 23 nucleotide pairs in length.
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 negatively positively constitutively operator promoter induced operon repressed
The genes of a bacterial operon are transcribed into a single mRNA. Many bacterial promoters contain a region known as an operator, to which a specific transcription regulator binds. Genes in which transcription is prevented are said to be repressed. The interaction of small molecules, such as tryptophan, with allosteric DNA-binding proteins, such as the tryptophan repressor, regulates bacterial genes. Genes that are being constitutively expressed are being transcribed all the time.
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. 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. 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 epigenetic inheritance. This type of inheritance is seen with the inheritance of the covalent modifications on histone 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 methylation, 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 feedback loops that can involve a transcription regulator activating its own transcription in addition to other genes. These mechanisms all allow for cell memory, a property involving the maintenance of gene expression patterns important for cell identity.
Experiment 1 in Figure Q8-21 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
a
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
a
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
b
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
b
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.
c
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.
d
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 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. V1 and V2 contain binding sites for the zinc finger protein, A, only. 2. V3 contains a binding site for the homeodomain protein, B, only. 3. 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
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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.
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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?
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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 signaldependent transcription pattern, how can such a small number of transcriptional regulatory proteins generate a much larger set of transcriptional patterns?
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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 Q8-7. Figure Q8-7 A. translation control B. transcriptional control C. RNA processing control D. protein activity control
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In the absence of glucose, E. coli can proliferate by using the pentose sugar arabinose. As shown in Figure Q8-27, 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 Q8-27 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 Q8-27.
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The CAP activator protein and the Lac repressor both control the Lac operon (see Figure Q8-14). 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 Q8-14 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
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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 Q8-66A shows the patterns of expression of these regulators. Figure Q8-66 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 Q8-66B. 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 Q8-66B, 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 Q8-66B 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 Q8-66C. 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 Q8-66B
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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 Q8-65 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 Q8-65 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].
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The yeast GAL4 gene encodes a transcriptional regulator that can bind DNA upstream of genes required for the metabolism of the sugar galactose and turn them on. Gal4 has a DNA-binding domain and an activation domain. The DNA-binding 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?
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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 Q8-16. Table Q8-16 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?
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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 testesdetermining 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.
a
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
a
The extent of complementarity of a miRNA with its target mRNA determines ___________________________. (a) whether the mRNA will be immediately degraded or whether the mRNA will first be transported elsewhere in the cell before degradation. (b) whether the mRNA will be transported to the nucleus. (c) whether RISC is degraded. (d) whether the miRNA synthesizes a complementary strand.
a
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.
a
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.
a
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 hold the double helix together.
a
Which proteins are likely to act as gene repressors? (a) G (b) H (c) J (d) both H and J
a
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.
a
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.
a
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.
b
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.
b
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'd like this project to succeed? (a) the presence of foreign double-stranded RNA (b) the presence of genes in the genome that code for RISC proteins (c) the presence of miRNA genes in the genome (d) the presence of single-stranded siRNAs within the cell
b
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.
b
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.
b
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
b
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.
b
Which of the following statements about iPS cells is false? (a) iPS cells are created by adding a combination of transcription regulators to a fibroblast. (b) iPS cells created from mouse cells can differentiate into almost any human cell type. (c) Stimulation by extracellular signal molecules causes iPS cells to differentiate. (d) During the de-differentiation process to become an iPS, the fibroblast will undergo changes to its gene expression profile.
b
Which of the following statements about mRNA half-life is false? (a) The half-life of mRNAs produced from different genes will vary more than the half-life of mRNAs produced from the same gene. (b) The half-life of most eukaryotic-cell mRNAs is >24 hours. (c) The half-life of most bacterial mRNAs is shorter than the half-life of a typical eukaryotic mRNA. (d) The 5′ and 3′ untranslated regions of an mRNA often contain specific sequences that determine the lifetime of the mRNA molecule.
b
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
b
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) 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.
c
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
c
In what tissue is factor Z normally present and bound to the DNA? (a) kidney (b) liver (c) heart (d) none of the above
c
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.
c
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 musclespecific 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.
c
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
c
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.
c
Which of the following is not involved in post-transcriptional control? (a) the spliceosome (b) Dicer (c) Mediator (d) RISC
c
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 the above
c
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.
c
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.
c
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
c
Which transcription factors 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
c
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
c
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
c
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 produced due to faster ribosome movement across the LacZ mRNA. (b) transcriptional repression, resulting in fewer mRNA molecules produced from this gene. (c) a longer half-life for the LacZ mRNA. (d) translational inhibition of the LacZ mRNA.
d
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-typespecific 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
d
Which of the following is not a good example of a housekeeping protein? (a) DNA repair enzymes (b) histones (c) ATP synthase (d) hemoglobin
d
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
d
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.
d
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.
d
Which proteins are likely to act as gene activators? (a) G (b) H (c) J (d) both H and J
d