A researcher engineers a lac operon on a plasmid, but inactivates all parts of the Lac operator (lacO) and the Lac promoter, replacing them with the binding site for the LexA repressor (which acts in the SOS response) and a promoter regulated by LexA. The plasmid is introduced into E. coli cells that have a lac operon with an inactive lacZ gene. Under what conditions will these transformed cells produce β-galactosidase?

Describe the probable effects on the expression of lac genes of mutations that (a) relocate the Lac operator so that it is on the other side of the operon, (b) inactivate the binding site for CRP, and (c) alter the promoter sequence around position −10.

In the ara operon, the AraC protein can act as either an activator or a repressor. If AraC remains bound to the DNA in the absence of arabinose, why does the protein not always function as an activator?

E. coli cells are growing in a medium with glucose as the sole carbon source. Tryptophan is suddenly added. The cells continue to grow, and they divide every 30 minutes. Describe (qualitatively) how the levels of tryptophan synthase (an enzyme produced by the trp operon) change with time under the following conditions:

How would the SOS response in E. coli be affected by mutations in the lexA gene that (a) prevented autocatalytic cleavage of the LexA protein or (b) weakened the interaction of LexA with its normal binding site?

A typical bacterial repressor protein discriminates between its specific DNA binding site (operator) and nonspecific DNA by a factor of 10⁴ to 10⁶. About 10 molecules of repressor per cell are sufficient to ensure a high level of repression. Assume that a very similar repressor existed in a human cell, with a similar specificity for its binding site. How many copies of the repressor would be required to elicit a level of repression similar to that in the bacterial cell? (Hint: The E. coli genome contains about 4.6 × 10⁶ bp; the human haploid genome has about 3.2 × 10⁹ bp.)

The dissociation constant for a particular repressor-operator complex is very low, about 10⁻¹³ m. An E. coli cell (volume 2 × 10⁻¹² mL) contains 10 copies of the repressor. Calculate the cellular concentration of the repressor protein. How does this value compare with the dissociation constant of the repressor-operator complex? What is the significance of this answer?

E. coli cells are growing in a medium containing lactose but no glucose. Indicate whether each of the following changes or conditions would increase, decrease, or not change expression of the lac operon. It may be helpful to draw a model depicting what is happening in each situation.

How would transcription of the E. coli trp operon be affected by the following manipulations of the leader region of the trp mRNA?

Many riboswitches have been characterized in bacteria, including one that binds to thiamine pyrophosphate (TPP) and another that binds to glucosamine 6-phosphate. Compare and contrast the mechanisms by which these two riboswitches inhibit translation of their RNAs.

A mutation is found in the gene encoding the translational repressor of an r-protein operon. The mutation increases the affinity of the repressor protein for mRNA and decreases its affinity for rRNA. What is the likely effect of such a mutation?

A λ phage lysogen (an E. coli cell with a λ prophage integrated into its genome) is largely immune to lysis by λ phages introduced into the cell later. Explain.

Mutant versions of CRP have been isolated that bind DNA normally but do not activate transcription. What does the existence of these mutants indicate about the mechanism of CRP-mediated transcription activation, and what phenotype would you expect to observe for cells expressing one of these mutant CRP alleles?

How does the organization of related genes into operons enable the coordinated production of proteins? Suggest a way that would allow different genes in an operon to be expressed at different levels.

Name one advantage and one disadvantage to using RNA structures such as riboswitches to regulate gene expression in response to small-molecule effectors.

What general principle of gene regulation is illustrated by transcription attenuation?

Would you expect the mechanism of transcription attenuation described for the trp operon to function similarly in eukaryotic cells? Why or why not?

Name three properties of riboswitch-regulated mRNAs.

How would a large increase in the intracellular concentration of ppGpp affect the growth of bacterial cells in a nutrient-rich medium?