bio chapter 8

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) do not code for proteins.

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) #5

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.

(c) During their developmental history, fibroblasts have accumulated some transcriptional regulators in common with differentiating muscle cells.

Which of the following is not involved in post-transcriptional control? (a) the spliceosome (b) Dicer (c) Mediator (d) RISC

(c) Mediator

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) translational inhibition of the LacZ mRNA.

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?

A. Site A is regulated by sucrose, and site B by glucose. B. Mutant 2 (A+ B-); mutant 3 (A- B-) or (A- B+). C. Site A is bound by an activator, and site B by a repressor.

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].

A. more tightly B. weaker C. both protein A and protein B

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. controlling how an RNA transcript is spliced C. controlling which mRNAs are exported from the nucleus to the cytosol

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.

RISC mRNA destruction double-stranded RNA Dicer

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?

Transcription regulators are generally used in combinations, thereby increasing the possible regulatory repertoire of gene expression with a limited number of proteins.

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.

epigenetic histone methylation feedback memory

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 Q8-29. Table Q8-29 8-29 Which proteins are likely to act as gene repressors? (a) G (b) H (c) J (d) both H and J

(a) G

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.

(a) Some XY individuals that develop into females have mutations in a different gene, SRY, but are normal at BoY.

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) The Lac repressor binds when lactose is present in the cell.

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. 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) The cortisol-responsive genes share a DNA sequence in their regulatory regions that binds the cortisol-responsive transcriptional activator.

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) 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.

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) are produced from a precursor miRNA transcript.

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) experiment 3

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) factors X and Y

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) there are seven regulatory elements and each element is sufficient for driving expression in a single stripe.

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) whether the mRNA will be immediately degraded or whether the mRNA will first be transported elsewhere in the cell before degradation.

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) MetB only

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) RNAi is induced when double-stranded, foreign RNA is present in the cell.

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.

(b) The Ey transcription factor must bind to the promoter of every eye- specific gene in the fly.

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) The Lac operon will not be transcribed when tryptophan levels are high.

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 embryo that develops from the nuclear transplant experiment is genetically identical to the donor of the nucleus.

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) The half-life of most eukaryotic-cell mRNAs is >24 hours.

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) binds to the tryptophan repressor when the repressor is bound to tryptophan.

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) by looping out the intervening DNA between their binding site and the promoter

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) iPS cells created from mouse cells can differentiate into almost any human cell type.

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) involves groups of transcriptional regulators working together to determine the expression of a gene.

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 presence of genes in the genome that code for RISC proteins

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) transcription of genes transcribed by RNA polymerase II.

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) 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.

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) MetA and Met B

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) MetA and MetC

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 Q8-37 summarizes your results. A normal functional gene is indicated by a plus sign (+). Table Q8-37 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) The specific pattern of nucleosome positioning over the BRF1 upstream region is required for BRF1 repression.

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 de- differentiate 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) 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.

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) between 5000 and 15,000

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) contain a cluster of genes transcribed as a single mRNA.

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) factor Z

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) heart

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) miRNAs are produced from rRNAs.

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) only G and J

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) the neuron expresses some mRNAs that the white blood cell does not.

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) up to 16

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) Both MetA and MetC

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) Immediately after DNA replication, each daughter helix contains one methylated DNA strand, which corresponds to the newly synthesized strand.

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) Pa5 binds to the promoter of the gene that encodes Jk8 in embryonic liver cells.

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) Some of the proteins found in differentiated cells are found in all cells of a multicellular organism.

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 Q8-29. Table Q8-29 8-29 Which proteins are likely to act as gene activators? (a) G (b) H (c) J (d) both H and J

(d) both H and J

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) hemoglobin

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

(d) proper segregation of housekeeping proteins when cells divide

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.

eukaryotic Mediator acetylases deacetylases hetrochromatin

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.

operon operator repressed allosteric constitutively