Exam 8: Control of Gene Expression

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

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

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

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

Which of the following statements about RNAi is TRUE?

MicroRNAs

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

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

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

Which of the following statements about differentiated cells is TRUE?

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table Q8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$ Binding sites present No or With With With and A, B, and C - - - ++ none - - - - A only - - + + B only - - - - C only - + - + A and B only - - - + A and C only - + + ++ B and C only - - - + $\text {For this table: -= no transcription of Pst,}$ $\text { += low level of transcription of Psf, and}$ $\text { ++= high levels of transcription of Pst.}$ Table 8-12 Which transcription factors are normally bound to the Psf promoter in the presence of both Mg²⁺ and Ca²⁺?

The long noncoding RNA Xist

The tryptophan operator

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

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

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

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

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

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?

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