Chapter 37

1. (1) Eukaryotes have more complex transcriptional regulation than that of bacteria. (2) RNA, especially mRNA, is more highly processed in eukaryotes than in bacteria. (3) In eukaryotes, RNA synthesis is localized to a particular organelle—the nucleus. As a result, transcription and translation take place in different cellular compartments.

2. RNA polymerase I catalyzes the synthesis of all ribosomal RNA except 5S RNA and is located in the nucleolus. RNA polymerase I is insensitive to α-amanitin inhibition. RNA polymerase II makes mRNA, is located in the nucleoplasm, and is very sensitive to α-amanitin inhibition. RNA polymerase III, also located in the nucleoplasm, synthesizes tRNA and 5S RNA. RNA polymerase III can be inhibited by high concentrations of α-amanitin. The polymerases also differ in their subunit composition and the mass of the holoenzyme.

3. Three common elements are found in the promoter for RNA polymerase II: (1) the TATA box, (2) the initiator element (Inr), and (3) a downstream promoter element (DPE). Additional elements, such as the CAAT box and GC box may be present.

4. RNA polymerase II has a domain called the carboxyl-terminal domain that plays a key role in the regulation of RNA polymerase II activity.

5. Cis-acting elements are DNA sequences that regulate the expression of a gene located on the same molecule of DNA. Transacting elements, also called transcription factors or transcription activators, are proteins that bind to cis-acting elements and regulate RNA synthesis.

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6. Enhancers are DNA sequences that have no promoter activity of their own; yet they can stimulate promoters located several thousand base pairs away. They can be upstream, downstream, or even in the midst of a transcribed gene and are effective when present on either DNA strand. Enhancers are bound by proteins that participate in the regulation of transcription.

7. RNA polymerases I and III produce the same products in all cells. RNA polymerase II, however, must respond to changes in environmental conditions. Thus, the promoters for the genes transcribed by RNA polymerase II must be complex enough to respond to a variety of signals.

8. Complete the interactive matching exercise to see answers.

9. Cordycepin (3′-deoxyadenosine) is an adenosine analog and, when phosphorylated, is an adenylate nucleotide analog. The absence of a 3′-hydroxyl group means that it cannot form a phosphodiester linkage with another nucleotide. If cordycepin is incorporated, RNA synthesis will cease.

10. Phosphorylation of the CTD marks the transition from initiation to elongation. The phosphorylated CTD facilitates elongation by RNA polymerase II and serves as a binding site for RNA-processing enzymes that act in the course of elongation.

11. This finding indicates that DNA is rewound at about the same rate at the rear of RNA polymerase as it is unwound at the front of the enzyme, locking the genomic information away again.

12. Complete the interactive matching exercise to see answers.

13. Nuclear hormone receptors bind to appropriate response elements in the DNA. When a nuclear hormone receptor binds a hormone, the receptor’s structure changes so that the receptor can bind a coactivator (or corepressor), which in turn activates (or inhibits) RNA polymerase.

14. A given regulatory protein may have different effects, depending on the other regulatory proteins in the environment. Therefore, complex regulatory patterns leading to differentiation and development can be obtained with a smaller number of regulatory proteins.

15. The acetylation reduces the number of positive charges while introducing a negative charge and thus reduces the affinity for the negatively charged DNA.

16. Although RNA polymerase II might be rapidly inhibited, there are still many functional mRNAs and proteins in the liver. However, as they are damaged and replacements cannot be provided, the liver fails and death results.

17. Gene expression is not expected to respond to the presence of estrogen. However, genes for which expression normally responds to estrogen will respond to the presence of progesterone.

18. Estradiol, because of its hydrophobic nature, can diffuse into the cell, where it can bind to its receptor. The complex can bind directly to DNA. The ligands for G-protein-coupled receptors do not enter the cell. Moreover, these receptors themselves are confined to the membrane. Any effect on gene regulation must include other components of a signal-transduction pathway.

19. Estradiol exerts its effect only in the presence of the estradiol receptor. Thus, only tissues having the receptor recognize the presence of estradiol.

20. Zinc is a component of zinc fingers, the DNA-binding motifs of nuclear hormone receptors.

21. These results suggest that chromatin structure varies, depending on the transcription status of the gene. If the gene is being transcribed, chromatin packing is loosened to allow access to the DNA for transcription factors and RNA polymerase. In the presence of DNase, these regions are susceptible to digestion.

22. 1. Different amounts of RNA are present for the various genes.

    2. Although all of the tissues have the same genes, the genes are expressed to different extents in different tissues.

    3. These genes are called housekeeping genes—genes expressed by most tissues. They might include genes for glycolysis or for citric acid cycle enzymes.

    4. The point of the experiment was to determine which genes are initiated in vivo. The initiation inhibitor was added to prevent initiation at start sites that may have been activated during the isolation of the nuclei.