In most differentiated tissues, daughter cells retain a memory of gene expression

In terms of the way it interacts with DNA, the helixloophelix motif is more closely related to the leucine zipper motif than it is to the helixturnhelix motif.

Once cells have differentiated to their final specialized forms, they never again alter expression of their genes.

CG islands are thought to have arisen during evolution because they were associated with portions of the genome that remained unmethylated in the germ line.

In most differentiated tissues, daughter cells retain a memory of gene expression patterns that were present in the parent cell through mechanisms that do not involve changes in the sequence of their genomic DNA.

A small portion of a two-dimensional display of proteins from human brain is shown in Figure Q71. These proteins were separated on the basis of size in one dimension and electrical charge (isoelectric point) in the other. Not all protein spots on such displays are products Figure 7-1 Problem 7-8 acidic basic larger smaller Figure Q71 Twodimensional separation of proteins from the human brain (Problem 75). The proteins were displayed using two-dimensional gel electrophoresis. Only a small portion of the protein spectrum is shown. (Courtesy of Tim Myers and Leigh Anderson, Large Scale Biology Corporation.) of different genes; some represent modified forms of a protein that migrate to different positions. Pick out a couple of sets of spots that could represent proteins that differ by the number of phosphates they carry. Explain the basis for your selection.

Comparisons of the patterns of mRNA levels across different human cell types show that the level of expression of almost every active gene is different. The patterns of mRNA abundance are so characteristic of cell type that they can be used to determine the tissue of origin of cancer cells, even though the cells may have metastasized to different parts of the body. By definition, however, cancer cells are different from their noncancerous precursor cells. How do you suppose then that patterns of mRNA expression might be used to determine the tissue source of a human cancer?

What are the two fundamental components of a genetic switch?

The nucleus of a eukaryotic cell is much larger than a bacterium, and it contains much more DNA. As a consequence, a transcription regulator in a eukaryotic cell must be able to select its specific binding site from among many more unrelated sequences than does a transcription regulator in a bacterium. Does this present any special problems for eukaryotic gene regulation? Consider the following situation. Assume that the eukaryotic nucleus and the bacterial cell each have a single copy of the same DNA binding site. In addition, assume that the nucleus is 500 times the volume of the bacterium, and has 500 times as much DNA. If the concentration of the transcription regulator that binds the site were the same in the nucleus and in the bacterium, would the regulator occupy its binding site equally as well in the eukaryotic nucleus as it does in the bacterium? Explain your answer.

Some transcription regulators bind to DNA and cause the double helix to bend at a sharp angle. Such bending proteins can affect the initiation of transcription without directly contacting any other protein. Can you devise a plausible explanation for how such proteins might work to modulate transcription? Draw a diagram that illustrates your explanation.

How is it that proteinprotein interactions that are too weak to cause proteins to assemble in solution can nevertheless allow the same proteins to assemble into complexes on DNA?

Imagine the two situations shown in Figure Q72. In cell 1, a transient signal induces the synthesis of protein A, which is a transcription activator that turns on many genes including its own. In cell 2, a transient signal induces the synthesis of protein R, which is a transcription repressor that turns off many genes including its own. In which, if either, of these situations will the descendants of the original cell remember that the progenitor cell had experienced the transient signal? Explain your reasoning.

Examine the two pedigrees shown in Figure Q73. One results from deletion of a maternally imprinted autosomal gene. The other pedigree results from deletion of a paternally imprinted autosomal gene. In both pedigrees, affected individuals (red symbols) are heterozygous for the deletion. These individuals are affected because one copy of the chromosome carries an imprinted, inactive gene, while the other carries a deletion of the gene. Dotted yellow symbols indicate individuals that carry the deleted locus, but do not display the mutant phenotype. Which pedigree is based on paternal imprinting and which on maternal imprinting? Explain your answer.

If you insert a -galactosidase gene lacking its own transcription control region into a cluster of piRNA genes in Drosophila, you find that -galactosidase expression from a normal copy elsewhere in the genome is strongly inhibited in the flys germ cells. If the inactive -galactosidase gene is inserted outside the piRNA gene cluster, the normal gene is properly expressed. What do you suppose is the basis for this observation? How would you test your hypothesis?