The sequences of promoters tend to be rich in A and T residues. Suggest why this is so.

The −10 and −35 sequences in bacterial promoters are separated by about two turns of the DNA double helix. How would transcription be affected if a deletion were introduced in the promoter region that moved the −35 sequence to the −29 position?

The gene encoding the E. coli enzyme β-galactosidase begins with the sequence ATGACCATGATTACG. What is the sequence of the mRNA transcript specified by this part of the gene?

The gene for β-galactosidase has 3,075 bp. How long would it take for the E. coli RNA polymerase to transcribe this gene, assuming initiation has occurred upstream prior to its encounter with the gene?

The sequence of the consensus −10 region is TATAAT. If two genes, tesA and tesB, have identical promoter sequences except in the −10 region, where the tesA sequence is TAATAT and the tesB sequence is TGTCGA, which gene do you expect to be more efficiently transcribed, and why?

If a Pol II promoter were replaced with a promoter specific for Pol III in a human cell, what do you expect would happen to the number of transcripts produced?

Name the three major steps in the transcription of a typical bacterial gene, and indicate their relative rates.

Working in a research lab, you wish to examine the kinetics of the initiation phase of bacterial RNA polymerase, as a function of promoter sequence. You want to prevent the reaction from entering the elongation phase. How many nucleotides can be added to an RNA polymer in the initiation phase? Suggest a simple reaction strategy to limit the reaction to initiation, based on the sequence of the template and the components added to the reaction mix. With your experimental design, what would the reaction products be? Assume you have an assay to measure the production of short RNA oligonucleotides (you do not need to describe the assay).

People who ingest A. phalloides (the source of α-amanitin) initially experience gastrointestinal distress caused by other toxins also produced by this mushroom. α-Amanitin shuts down the action of RNA polymerase II, but death does not occur until about 48 hours after ingestion and usually involves liver dysfunction. Suggest a reason for the delay in lethality.

A drug company has discovered a natural product, cupramycin, that efficiently intercalates into DNA. How might this compound affect transcription?

How might an investigator search for Pol II promoters in the DNA sequence of an entire organism? Is it possible to find all such promoters computationally?

Gene A encodes protein A. A genetic engineer excises a promoter sequence for gene A from the DNA and reinserts it at the other end of gene A, oriented so that an RNA polymerase binding at the promoter will transcribe across gene A. Will the mRNA synthesized by the RNA polymerase still possess a sequence that produces a functional protein A? Why or why not?

In most organisms, specialized DNA repair systems are closely linked to transcription. Suggest a biological rationale for this close relationship.

In bacteria, there are many examples of two (or even more) genes being transcribed from one promoter—for example, the promoter is followed by gene A and then gene B, with both genes transcribed into a single mRNA. In some cases, the first gene in the linear sequence is transcribed at much higher levels than the second gene (i.e., many but not all of the mRNAs do not include gene B). What kind of DNA sequences might be present between the first and second genes to account for the lower level of transcription of gene B?