In eukaryotes, most genes are normally turned off, and RNA polymerases do not function without activation. In bacteria, RNA polymerase can transcribe almost any gene in the absence of bound inhibitors. Suggest a few reasons for this difference between bacteria and eukaryotes.

The regulatory proteins in eukaryotes bind to DNA sequences of about the same length as those bound by bacterial regulatory proteins. However, the genomes of eukaryotes are generally orders of magnitude larger than those of bacteria. What effect does this have on the strategy of eukaryotes for regulating a particular gene?

A histone acetyltransferase (HAT) is activated, transferring acetyl groups to histones in a particular region of the genome. What amino acid residues in histones are generally modified by HATs? What is the likely effect of the modifications on the transcription levels of genes in that region? What enzymes reverse the effects of HATs?

Optimal activation of transcription of the GAL genes in yeast requires the function of two proteins: Gal4p and Gal11p. Elimination of either protein decreases activation of the GAL promoters. However, inactivation of Gal11p has the additional and dramatic effect of cell lethality. Why might elimination of Gal11p have a greater effect than elimination of Gal4p?

What is the phosphorylation state of the yeast protein Mig1 when: (a) glucose and galactose are absent; (b) galactose is present and glucose is absent; (c) glucose is present and galactose is absent; and (d) both glucose and galactose are present?

Perhaps 3,000 or more transcription factors participate in the activation of human genes. However, this is far fewer than the number of genes in the human genome (∼20,000 to 25,000). Explain how specific gene activation is achieved when genes outnumber gene activators by 10:1.

If mice are engineered with a homozygous gene knockout (inactivation) for the gene encoding CTC-binding factor (CTCF), they exhibit an embryonic lethal phenotype. Explain.

Enhanceosomes consist of multiple transcription factors that activate transcription at particular genes. The enhanceosomes also often include HMG proteins (see Figure 21-6). Suggest a function for the HMG proteins.

Housekeeping genes are those that must be expressed at all times, providing a protein or RNA that is essential for general cellular metabolism. They are often expressed at a low but constant level. If an essential housekeeping gene were experimentally moved from euchromatin to a region of heterochromatin, what would be the likely effect on the cell?

Certain genes expressed on the X chromosome in mammals must be expressed at the same levels in males and females. However, there are two copies of each gene in females and only one copy in males. How is X-chromosome gene dosage controlled in mammals?

A scientist is studying the function of a type of nuclear steroid receptor protein in mouse cells. She introduces various mutations into the gene encoding the receptor protein and transfers the genes into mice. If mutations are introduced that (a) eliminate the nuclear import signal in the receptor protein or (b) alter the receptor protein surface so that the receptor can no longer interact with Hsp70 protein, how will the molecular pathway of hormone-receptor interaction be altered?