Genetics Chapter 17 Questions

C14. What is a histone variant?

A histone variant is a histone with an amino acid sequence that is slightly different from a core histone. Histone variants play specialized roles with regard to chromatin structure and function.

C20. What is DNA methylation? When we say that DNA methylation is heritable, what do we mean? How is it passed from a mother to a daughter cell?

DNA methylation is the attachment of a methyl group to a base within the DNA. In many eukaryotic species, this occurs on cytosine at a CG sequence. After de novo methylation has occurred, it is passed from mother to daughter cell. Because DNA replication is semiconservative, the newly made DNA contains one strand that is methylated and one that is not. DNA methyltransferase recognizes this hemimethylated DNA and methylates the cytosine in the unmethylated DNA strand; this event is called maintenance methylation.

C29. With regard to RNAi, what are three possible sources for doublestranded RNA?

First, the double-stranded miRNA could come from the transcription of a gene, as pre-miRNA. Second, it could come from a virus. Third, multiple insertions of the same gene in the genome may lead to both DNA strands being transcribed, thereby forming double-stranded RNA.

C7. Describe the steps that occur for the glucocorticoid receptor to bind to a GRE.

For the glucocorticoid receptor to bind to a GRE, a steroid hormone must first enter the cell. The hormone then binds to the glucocorticoid receptor, which releases HSP90. The release of HSP90 exposes a nuclear localization signal (NLS) within the receptor, which enables it to dimerize and then enter the nucleus. Once inside the nucleus, the dimer binds to a GRE, which activates transcription of the adjacent genes.

C11. An enhancer, located upstream from a gene, has the following sequence: 5ʹ-GTAG-3ʹ 3ʹ-CATC-5ʹ This enhancer is orientation-independent. Which of the following sequences also works as an enhancer? A. 5ʹ-CTAC-3ʹ 3ʹ-GATG-5ʹ B. 5ʹ-GATG-3ʹ 3ʹ-CTAC-5ʹ C. 5ʹ-CATC-3ʹ 3ʹ-GTAG-5ʹ

The enhancer found in A would work, but the ones found in B and C would not. The sequence that is recognized by the transcriptional activator is 5'-GTAG- 3' in one strand and 3'-CATC-5' in the opposite strand. This is the same arrangement found in A. In B and C, however, the arrangement is 5'-GATG-3' and 3'-CATC-5'. In the arrangement found in B and C, the two middle bases (i.e., A and T) are not in the correct order.

C23. What is the function of a splicing factor? Explain how splicing factors can regulate the tissue-specific splicing of mRNAs.

The function of splicing factors is to influence the selection of splice sites in RNA. In certain cell types, the concentration of particular splicing factors is higher than in other tissues. The high concentration of particular splicing factors, and the regulation of their activities, may promote the selection of particular splice sites and thereby lead to tissue-specific splicing.

C16. What is meant by the term histone code? With regard to gene regulation, what is the proposed role of the histone code?

The histone code hypothesis is the idea that the patterns of covalent modifications of histones are recognized by proteins that affect chromatin structure and function. In this way, the modification of histones plays a role in gene regulation.

C30. What is the relationship between mRNA stability and mRNA concentration? What factors affect mRNA stability?

If mRNA stability is low, this means that it is degraded more rapidly. Therefore, low stability results in a low mRNA concentration. The length of the polyA tail is one factor that affects stability. A longer tail makes mRNA more stable. Certain mRNAs have sequences that affect their half-lives. For example, AU-rich elements (AREs) are found in many short-lived mRNAs. The AREs are recognized by cellular proteins that cause the mRNAs to be rapidly degraded.

C21. Let's suppose that a vertebrate organism carries a mutation that causes some cells that normally differentiate into nerve cells to differentiate into muscle cells. A molecular analysis of this mutation revealed that it was in a gene that encodes a methyltransferase. Explain how an alteration in a methyltransferase could produce this phenotype.

Perhaps the methyltransferase is responsible for methylating and inhibiting a gene that causes a cell to become a muscle cell. The methyltransferase is inactivated by the mutation.

C1. Discuss the common points of control in eukaryotic gene regulation.

1. DNA−chromatin structure. This includes gene amplification, an increase in copy number; gene rearrangement, as in immunoglobulin genes; DNA methylation, attachment of methyl groups, which inhibits transcription; locus control regions, sites that control chromatin conformation. 2. Transcription. This includes transcription factors/regulatory elements, interactions that can activate or inhibit transcription. 3. RNA level. This includes RNA processing, regulation of splicing via SR proteins; RNA stability, regulation of RNA half-life and RNA translation via RNA binding proteins; regulation via miRNA. 4. Protein level. This includes feedback inhibition, small molecules that modulate enzyme activity; and posttranslational modification-covalent changes to protein structure that affect protein activity.

C8. Let's suppose a mutation in the glucocorticoid receptor does not prevent the binding of the glucocorticoid hormone to the protein but prevents the ability of the receptor to activate transcription. Make a list of all the possible defects that may explain why transcription cannot be activated.

1. It could be in the DNA-binding domain, so that the receptor would not recognize GREs. 2. It could be in the HSP90 domain, so that HSP90 would not be released when the hormone binds. 3. It could be in the dimerization domain, so that the receptor would not dimerize. 4. It could be in the nuclear localization domain, so that the receptor would not travel into the nucleus. 5. It could be in the domain that activates RNA polymerase, so that the receptor would not activate transcription, even though it could bind to GREs.

C22. What is a CpG island? Where would you expect one to be located? How does the methylation of CpG islands affect gene expression?

A CpG island is a stretch of 1,000 to 2,000 base pairs in length that contains a high number of CpG sites. CpG islands are often located near promoters. When the island is methylated, this inhibits transcription. This inhibition may be the result of the inability of the transcriptional activators to recognize the methylated promoter and/or the effects of methyl-CpG-binding proteins, which may promote a closed chromatin conformation.

C26. In response to potentially toxic substances (e.g., high levels of iron), eukaryotic cells often use translational or posttranslational regulatory mechanisms to prevent cell death, rather than using transcriptional regulatory mechanisms. Explain why.

A cell may need to respond rather quickly to a toxic substance in order to avoid cell death. Translational and posttranslational mechanisms are much faster than transcriptional activation, in which it is necessary to up regulate the gene, synthesize the mRNA, and then translate the mRNA to make a functional protein.

C17. What is a nucleosome-free region? Where are they typically found in a genome? How are nucleosome-free regions thought to be functionally important?

A nucleosome-free region (NFR) is a location in the genome where nucleosomes are missing. They are typically found at the beginning and ends of genes. An NFR at the beginning of a gene is thought to be important so that genes can be activated. The NFR at the end of a gene may be important for its proper termination.

C18. Nucleosomes are thought to be displaced as RNA polymerase is transcribing a gene. What would be the potentially harmful consequences if nucleosomes were not put back into a gene after RNA polymerase had passed?

A potentially harmful consequence would be that transcription may be initiated a multiple points within a gene, thereby producing many nonfunctional transcripts. This would be waste of energy.

C6. Transcription factors usually contain one or more motifs that play key roles in their function. What is the function of the following motifs? A. Helix-turn-helix B. Zinc finger C. Leucine zipper

A. DNA binding. B. DNA binding. C. Protein dimerization.

C5. Are the following statements true or false? A. An enhancer is a type of regulatory element. B. A core promoter is a type of regulatory element. C. Regulatory transcription factors bind to regulatory elements. D. An enhancer may cause the down regulation of transcription.

A. True. B. False. C. True. D. False, it causes up regulation.

C13. Briefly describe three ways that ATP-dependent chromatinremodeling complexes may change chromatin structure.

ATP-dependent chromatin remodeling complexes may change the positions of nucleosomes, evict histones, and/or replace histones with histone variants.

C19. What is an insulator? Describe two different ways that insulators may exert their effects.

An insulator is a segment of DNA that functions as a boundary between two adjacent genes. An insulator may act as a barrier to changes in chromatin structure or block the effects of a neighboring enhancer.

C24. Figure 17.17 shows the products of alternative splicing for the α-tropomyosin pre-mRNA. Let's suppose that smooth muscle cells produce splicing factors that are not produced in other cell types. Explain where you think such splicing factors bind and how they influence the splicing of the α-tropomyosin pre-mRNA.

As shown in Figure 17.17, the unique feature of the smooth muscle mRNA for α-tropomyosin is that it contains exon 2. Splicing factors that are only found in smooth muscle cells may recognize the splice junction at the 3' end of intron 1 and the 5' end of intron 2 and promote splicing at these sites. This would cause exon 2 to be included in the mRNA. Furthermore, because smooth muscle mRNA does not contain exon 3, a splicing suppressor may bind to the 3' end of intron 2. This would promote exon skipping, so that exon 3 would not be contained in the mRNA.

C9. The glucocorticoid receptor is an example of a transcriptional activator that binds to response elements and activates 408 CHA P T E R 1 7 : : GENE REGULATION IN EUKARYOTES transcription. (Note: The answer to this question is not directly described in this chapter. You have to rely on your understanding of the functioning of other proteins that are modulated by the binding of effector molecules, such as the lac repressor.) How would the function of the glucocorticoid receptor be shut off?

Eventually, the glucocorticoid hormone will be degraded by the cell. The glucocorticoid receptor binds the hormone with a certain affinity. The binding is a reversible process. Once the concentration of the hormone falls below the affinity of the hormone for the receptor, the receptor will no longer have the glucocorticoid hormone bound to it. When the hormone is released, the glucocorticoid receptor will change its conformation, and it will no longer bind to the DNA.

C28. What is the phenomenon of RNA interference (RNAi)? During RNAi, explain how the double-stranded RNA is processed and how it leads to the silencing of a complementary mRNA.

RNA interference refers to the phenomenon in which the presence of a double-stranded RNA molecule leads to the silencing of a complementary mRNA. For this to occur, the double-stranded RNA is processed by Dicer into small RNA fragments (miRNA or siRNA). The miRNA or siRNA associates with a complex called the RNAinduced silencing complex (RISC). The RISC complex then binds to a complementary mRNA. This either leads to mRNA degradation or inhibits translation.

C2. Discuss the structure and function of regulatory elements. Where are they located relative to the core promoter?

Regulatory elements are relatively short genetic sequences that are recognized by regulatory transcription factors. After the regulatory transcription factor has bound to the regulatory element, it will affect the rate of transcription, either activating it or repressing it, depending on the action of the regulatory protein. Regulatory elements are typically located in the upstream region near the promoter, but they can be located almost anywhere (i.e., upstream and downstream) and even quite far from the promoter.

C15. Explain how the acetylation of core histones may loosen chromatin packing.

The attraction between DNA and histones occurs because the histones are positively charged and the DNA is negatively charged. The covalent attachment of acetyl groups decreases the amount of positive charge on the histone proteins and thereby may decrease the binding of the DNA. In addition, histone acetylation may attract proteins to the region that loosen chromatin compaction.

C12. Solved Problem S4 shows the locations of domains in the glucocorticoid receptor relative to the amino- and carboxylterminal ends of the protein. Make a drawing that illustrates the binding of a glucocorticoid receptor dimer to the DNA. In your drawing, label the amino- and carboxyl-terminal ends, the hormone-binding domains, the DNA-binding domains, the dimerization domains, and the transactivation domains.

This is one hypothetical drawing of the glucocorticoid receptor. As discussed in your textbook, the glucocorticoid receptor forms a homodimer. The dimer shown here has rotational symmetry. If you flip the left side around, it has the same shape as the right side. The hormone-binding, DNA-binding, dimerization, and transactivation domains are labeled. The glucocorticoid hormone is shown in orange.

C3. What is meant by the term transcription factor modulation? List three general ways this can occur.

Transcription factor modulation refers to different ways that the function of transcription factors can be regulated. The three general ways are the binding of an effector molecule, protein-protein interactions, and covalent modifications.

C4. What are the functions of transcriptional activator proteins and repressor proteins? Explain how they work at the molecular level.

Transcriptional activation occurs when a regulatory transcription factor binds to a regulatory element and activates transcription. Such proteins, called activators, may interact with TFIID and/or mediator to promote the assembly of RNA polymerase and general transcription factors at the promoter region. They also could alter the structure of chromatin so that RNA polymerase and transcription factors are able to gain access to the promoter. Transcriptional inhibition occurs when a regulatory transcription factor inhibits transcription. Such repressors also may interact with TFIID and/or mediator to inhibit RNA polymerase.

C27. What are the advantages and disadvantages of mRNAs with a short half-life compared with mRNAs with a long half-life?

A disadvantage of mRNAs with a short half-life is that the cells probably waste a lot of energy making them. If a cell needs the protein encoded by a short-lived mRNA, the cell has to keep transcribing the gene that encodes the mRNA because the mRNAs are quickly degraded. An advantage of short-lived mRNAs is that the cell can rapidly turn off protein synthesis. If a cell no longer needs the polypeptide encoded by a short-lived mRNA, it can stop transcribing the gene, and the mRNA will be quickly degraded. This will shut off the synthesis of more proteins rather quickly. With most long-lived mRNAs, it will take much longer to shut off protein synthesis after transcription has been terminated.

C25. Let's suppose a person is homozygous for a mutation in the IRP gene that changed the structure of the IRP in such a way that it could not bind iron, but it could still bind to IREs. How would this mutation affect the regulation of ferritin and transferrin receptor mRNAs? Do you think such a person would need more iron in his or her diet than normal individuals? Do you think that excess iron in the diet would be more toxic than it would be for normal individuals? Explain your answer.

This person would be unable to make ferritin, because the IRP would always be bound to the IRE. The amount of transferrin receptor mRNA would be high, even in the presence of high amounts of iron, because the IRP would always remain bound to the IRE and stabilize the transferrin receptor mRNA. Such a person would not have any problem taking up iron into his/her cells. In fact, this person would take up a lot of iron via the transferrin receptor, even when the iron concentrations were high. Therefore, this person would not need more iron in the diet. However, excess iron in the diet would be very toxic for two reasons. First, the person cannot make ferritin, which prevents the toxic buildup of iron in the cytosol. Second, when iron levels are high, the person would continue to synthesize the transferrin receptor, which functions in the uptake of iron.