Exam 8: Control of Gene Expression

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

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 are likely to act as gene repressors?

Combinatorial control of gene expression

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

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

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

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

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

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.

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

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?

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table 8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$ 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 of the following proteins are likely to act as gene activators?

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

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?

You are interested in studying the transcriptional regulation of the Gip1 promoter.The Gip1 promoter contains a binding site for the Jk8 protein that overlaps with the binding site for the Pa5 protein.Jk8 and Pa5 cannot bind DNA at the same time, but both proteins are present at high levels in adult liver cells.The binding sites for Jk8 and Pa5 are shown in Figure 8-24. Figure 8-24 Jk8 binds to site A while Pa5 binds to site B.You create mutations that remove the nonoverlapping sequences of either binding site A or B, and examine Gip1 mRNA production in adult liver cells that contain these mutations.The data you obtain from these experiments are shown in Table 8-24. experiment number 1 2 3 4 binding site A B ++ +- -+ -- Gip 1 mRNA levels high high none none Table 8-24 You know that Gip1 is only expressed in adult liver cells and not in the liver of embryos.You also know that Jk8 and Pa5 behave similarly on other promoters in the embryo or in the adult, in terms of whether they act as repressors or gene activators.Given the data, use of which of the following mechanisms would make the most sense for regulating the Jk8 and Pa5 proteins:

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

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

You are interested in examining the Psf gene.It is known that Psf is normally produced when cells are exposed to high levels of both calcium (Ca²⁺) and magnesium (Mg²⁺).MetA, MetB, and MetC are important for binding to the promoter of the Psf gene and are involved in regulating its transcription.MetA binds to the "A" site in the promoter region, MetB to the "B" site, and MetC to the "C" site.You create binding-site mutations in the A, B, and C sites and observe what happens to transcription of the Psf gene.Your results are summarized in Table 8-12. $\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\quad$$\underline{\text { Transcription in the presence of } \mathrm{Ca}^{2+} \text { and/or } \mathrm{Mg}^{2+}}$ 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 regulator(s) are normally bound to the Psf promoter in the presence of Mg²⁺ only?

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

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?