tymoczko3e

PROBLEMS

Question 37.1

1. Defining features. Identify three characteristics that differentiate eukaryotic transcription from bacterial transcription.

Question 37.2

2. Three of a kind. Differentiate among the three types of eukaryotic RNA polymerases.

Question 37.3

3. Promoting for two. Describe the major features of a promoter for RNA polymerase II.

Question 37.4

4. Distinguishing characteristic. What structural feature of RNA polymerase II distinguishes it from RNA polymerases I and III?

Question 37.5

5. Different sides of a bond? Explain the difference between cis-acting and trans-acting elements.

Question 37.6

6. Does it require spandex? What is an enhancer, and how does it function?

Question 37.7

7. Listening to its world. Why are promoters for RNA polymerase II necessarily more complex than promoters for RNA polymerases I and III? ✓ 3

Question 37.8

8. Making noncombustible matches. Pair the properties with the appropriate RNA polymerase.

RNA polymerase I RNA polymerase I RNA polymerase I RNA polymerase II RNA polymerase II RNA polymerase II RNA polymerase II RNA polymerase II RNA polymerase III RNA polymerase III RNA polymerase III	Located in the nucleoplasm Located in the nucleolus Very sensitive to α-amanitin Insensitive to α-amanitin Located in the nucleoplasm Synthesizes tRNA Moderately sensitive to α-amanitin TATA is a promoter sequence Synthesizes mRNA precursors Synthesized rRNA Contains a carboxyl-terminal domain
Correct Matches:

Question 37.9

9. A fitting end. Cordycepin inhibits RNA synthesis.

Cordycepin is an analog of which ribonucleotide? Why does it inhibit RNA synthesis?

Question 37.10

10. Leaving the station. What is the functional consequence of phosphorylation of the carboxyl-terminal domain of RNA polymerase II?

Question 37.11

11. Bubble translation. The lengths of the RNA–DNA hybrid and of the unwound region of DNA stay rather constant as RNA polymerase moves along the DNA template. What does this finding show about the rate of unwinding and rewinding of the DNA in the course of transcription?

Question 37.12

12. Like Harry Potter and Lord Voldemort. Match each term with its description.

Transcription factor

Enhancer

Mediator

Combinatorial control

Zinc-finger domain

Coactivator

Selective estrogen-receptor modulator

Histone acetyltransferase

Acetyllysine-binding domain

Chromatin-remodeling engine

DNA-binding domain in some proteins

Acts as a bridge between transcription factors and RNA polymerase II

Based on the fact that the regulatory properties of a protein depend on what other proteins are present

Shifts the location of nucleosomes

Tamoxifen

Bromodomain

Facilitates estrogen-receptor action

Binds to cis-acting elements

Depends on ATP-citrate lyase for its substrate

Cis-acting element that may be far from the gene regulated

Question 37.13

13. Teamwork. What is the relation between the nuclear hormone receptors and the coactivators? ✓ 3

Question 37.14

14. Creating complexity. What is the advantage of combinatorial control? ✓ 3

Question 37.15

15. Charge changes. In light of the fact that histones are highly basic proteins, how does acetylation affect these molecules? ✓ 3

Question 37.16

16. Destroying-angel toxin. α-Amanitin is a deadly poison and potent inhibitor of RNA polymerase II. The toxin is produced by a species of Amanita. Initial symptoms of α-amanitin poisoning are gastrointestinal distress, but these symptoms usually subside. Liver-cell cytolysis is evident by the fourth day after ingestion. Death caused by liver failure is within 10 days. Suggest some reasons why it takes days for this powerful poison to cause liver failure and death.

Question 37.17

17. Hybrid receptor. Through recombinant DNA methods, a modified steroid-hormone receptor was prepared that consists of an estrogen receptor with its ligand-binding domain replaced by the ligand-binding domain from the progesterone receptor. Predict the expected responsiveness of gene expression for cells treated with estrogen or with progesterone. ✓ 3

Chapter Integration Problems

Question 37.18

18. Hormone action. How does estradiol action differ from that of hormones that bind G-protein-coupled receptors? ✓ 3

Question 37.19

19. Specificity. If estradiol can diffuse through cell membranes, explain why all cell types are not sensitive to the presence of estradiol. ✓ 3

Question 37.20

20. RDA. The recommended daily allowance (RDA) for zinc is between 9 and 11 mg per day. Suggest one crucial use for zinc in human beings.

Data Interpretation and Challenge Problems

Question 37.21

21. Accessibility matters. Chromatin accessibility varies with cell type. For instance, if cells synthesizing globin mRNA are treated briefly with DNase (an enzyme that digests DNA), the genes that encode globin are destroyed but the gene for ovalbumin remains intact. Conversely, if the oviduct is similarly treated, the gene for ovalbumin is destroyed but the genes that encode globin are undamaged. Explain these results. ✓ 3

Question 37.22

22. Run-off experiment. Nuclei were isolated from the liver, muscle, and the brain. The nuclei were then incubated with α-[³²P]UTP under conditions that allow RNA synthesis, except that an inhibitor of RNA initiation was present. The radioactive RNA was isolated and annealed to various DNA sequences that had been attached to a gene chip (Chapter 41). In the adjoining graphs, the intensity of the shading indicates roughly how much RNA was attached to each DNA sequence. ✓ 3

(a) Why does the intensity of hybridization differ between genes?

(b) What is the significance of the fact that some of the RNA molecules display different hybridization patterns in different tissues?

(c) Some genes are expressed in all three tissues. What would you guess is the nature of these genes?

(d) Suggest a reason why an initiation inhibitor was included in the reaction mixture.

Selected Readings for this chapter can be found online at www.whfreeman.com/tymoczko3e.

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