1. Describe the molecular events that occur at the lac operon when E. coli cells are shifted from a glucose-containing medium to a lactose-containing medium.

2. The concentration of free glutamine affects transcription of the enzyme glutamine synthetase in E. coli. Describe the mechanism of this effect.

3. Recall that the trp repressor binds to a site in the operator region of tryptophan-producing genes when tryptophan is abundant, thereby preventing transcription. What would happen to the expression of the tryptophan biosynthetic enzyme genes in the following scenarios? Fill in the blanks with one of the following phrases:

never be expressed/always (constitutively) be expressed

4. Compare and contrast bacterial and eukaryotic gene expression mechanisms.

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5. What types of genes are transcribed by RNA polymerases I, II, and III? Design an experiment to determine whether a specific gene is transcribed by RNA polymerase II.

6. The CTD of the largest subunit of RNA polymerase II can be phosphorylated at multiple serine residues. What are the conditions that lead to the phosphorylated versus nonphosphorylated RNA polymerase II CTD?

7. What do TATA boxes, initiators, and CpG islands have in common? Which was the first of these to be identified? Why?

8. Describe the methods used to identify the location of transcription-control elements in promoter-proximal regions of genes.

9. What is the difference between a promoter-proximal element and a distal enhancer? What are the similarities?

10. Describe the methods used to identify the location of DNA-binding proteins in the regulatory regions of genes.

11. Describe the structural features of transcription activator and repressor proteins.

12. Give two examples of how gene expression may be repressed without altering the coding sequence.

13. Using CREB and nuclear receptors as examples, compare and contrast the structural changes that take place when these transcription factors bind to their co-activators.

14. What general transcription factors associate with an RNA polymerase II promoter in addition to the polymerase? In what order do they bind in vitro? What structural change occurs in the DNA when an “open” transcription initiation complex is formed?

15. Expression of recombinant proteins in yeast is an important tool for biotechnology companies that produce new drugs for human use. In an attempt to get a new gene X expressed in yeast, a researcher has integrated gene X into the yeast genome near a telomere. Will this strategy result in good expression of gene X? Why or why not? Would the outcome of this experiment differ if the experiment had been performed in a yeast line containing mutations in the H3 or H4 histone tails?

16. You have isolated a new protein called STICKY. You can predict from comparisons with other known proteins that STICKY contains a bHLH domain and a Sin3-interacting domain. Predict the function of STICKY and explain the importance of these domains in STICKY function.

17. Prokaryotes and lower eukaryotes such as yeast have transcription-control elements called upstream activating sequences. What are the comparable sequences found in higher eukaryotic species?

18. You are curious to identify the region of the gene X sequence that serves as an enhancer for gene expression. Design an experiment to investigate this issue.

19. Some organisms have mechanisms in place that will override transcription termination. One such mechanism using the Tat protein is employed by the HIV retrovirus. Explain why Tat is therefore a good target for HIV vaccination.

20. Upon identification of the DNA regulatory sequence responsible for translating a given gene, you note that it is enriched with CG sequences. Is the corresponding gene likely to be a highly expressed transcript?

21. Name four major classes of DNA-binding proteins that are responsible for controlling transcription, and describe their structural features.