1.  The process of recording. Define transcription. ✓ 1

2.  Different strands. Explain the difference between the coding strand and the template strand in DNA. ✓ 1

3.  True of many endeavors. What are the three stages of RNA synthesis? ✓ 1

4.  Necessary ingredients. What components does RNA polymerase require for the synthesis of RNA? ✓ 1

5.  Location, location, location. What is the function of the sigma subunit in transcription? ✓ 1

6.  Like stalagmites and stalactites. Match each term with its description. ✓ 1

7.  Comparisons. Compare transcription with replication.

8.  A gene advocate. What is a promoter?

9.  Cerrada/Abierta. Distinguish between a closed promoter complex and an open promoter complex.

10.  Complements. The sequence of part of an mRNA is

5′-AUGGGGAACAGCAAGAGUGGGGCCCUGUCCAAGGAG-3′

What is the sequence of the DNA coding strand? Of the DNA template strand?

11.  Checking for errors. Why is RNA synthesis not as carefully monitored for errors as is DNA synthesis?

12.  Speed is not of the essence. Why is it advantageous for DNA synthesis to be more rapid than RNA synthesis?

13.  A loose cannon. The σ protein by itself does not bind to promoter sites. Predict the effect of a mutation enabling σ to bind to the −10 region in the absence of other subunits of RNA polymerase. ✓ 1

14.  Stuck sigma. What would be the likely effect of a mutation that would prevent σ from dissociating from the RNA polymerase core? ✓ 1

15.  Transcription time. What is the minimum length of time required for the synthesis by E. coli polymerase of an mRNA encoding a 100-kDa protein? ✓ 1

16.  Between bubbles. How far apart are transcription bubbles on E. coli genes that are being transcribed at a maximal rate?

17.  Anything like Robocop? Define riboswitch, and explain its role in the regulation of RNA synthesis. ✓ 2

18.  Missing genes. Predict the effects of deleting the following regions of DNA: (a) the gene encoding lac repressor; (b) the lac operator; (c) the gene encoding CAP. ✓ 2

19.  Unavailable resources. Lac operon mutants that lack permease activity exist. Even though the gene for β-galactosidase is intact, the enzyme is not induced when lactose is added to the bacterial growth medium. Why? ✓ 2

20.  Not such a random walk. RNA polymerase is a large enzyme, and one of its substrates, DNA, is a large biomolecule with thousands to millions of bases. Yet, RNA polymerase can locate a promoter sequence in DNA faster than two small molecules can collide in solution. Explain this apparent paradox. ✓ 1

21.  Alterations. What are the three types of tRNA modifications seen in E. coli?

22.  Christmas trees. The adjoining image depicts several bacterial genes undergoing transcription. Identify the DNA. What are the strands of increasing length? Where is the beginning of transcription? The end of transcription? On the page, what is the direction of RNA synthesis? What can you conclude about the number of enzymes participating in RNA synthesis on a given gene? ✓ 1

23.  Potent inhibitor. Heparin, a glycosaminoglycan, inhibits transcription by binding to RNA polymerase. What properties of heparin allow it to bind so effectively to RNA polymerase?

24.  Minimal concentration. Calculate the concentration of lac repressor, assuming that one molecule is present per cell. Assume that each E. coli cell has a volume of 10⁻¹² cm³. Would you expect the single molecule to be free or bound to DNA? The dissociation constant for the repressor–DNA complex is 10⁻¹³ M. ✓ 2

25.  The opposite direction. Some compounds, called anti-inducers, bind to repressors such as the lac repressor and inhibit the action of inducers; that is, transcription is repressed and higher concentrations of inducer are required to induce transcription. Propose a mechanism of action for anti-inducers. ✓ 2

26.  Abortive cycling. Di- and trinucleotides are occasionally released from RNA polymerase at the very start of transcription, a process called abortive cycling. This process requires the restart of transcription. Suggest a plausible explanation for abortive cycling. ✓ 1

27.  Scientist at work. You have just performed an experiment in which you investigated RNA synthesis in vitro. Interestingly, the RNA molecules synthesized in vitro by RNA polymerase acting alone are longer than those made in vivo. Being the bright scientist that you are, you hypothesized that something was missing from the in vitro system that was present in vivo. To check for this possibility, you added some cell extract and found that the correct termination took place. You purified this protein, which you named “boat” after your interest in sailing. You performed an experiment in which boat was added to the RNA synthesis mixture at various times after the initiation of RNA synthesis. The results are illustrated below. Explain these results. ✓ 2