When proteins are incubated with the detergent sodium dodecyl sulfate (SDS), they are partially denatured, losing much of their structure, and tend to take on a consistent mass-to-charge ratio (see Highlight 4-1). In SDS-polyacrylamide gel electrophoresis, proteins are separated almost entirely as a function of their mass. Histones are an exception. On these same gels, many histones migrate more slowly than they should, as though they were much larger than they actually are. Suggest an explanation for this behavior.

In eukaryotic chromatin, approximately what length of DNA is typically associated with a single histone octamer?

Which of the following protein modifications—acetylation, phosphorylation, and methylation—could change the net charge on the surface of a modified histone?

Within the histone structure, do protein modifications occur primarily near the N-terminus or near the C-terminus? What features distinguish the structure where modifications occur?

In bacteria, the transcription of a subset of genes is affected by DNA topology, with expression increasing or (more often) decreasing when the DNA is relaxed. When a bacterial chromosome is cleaved at a specific site by a restriction enzyme (one that cuts at a long, and thus rare, sequence), only nearby genes (within 10,000 bp) exhibit either an increase or a decrease in expression. The transcription of genes elsewhere in the chromosome is unaffected. Explain.

In different regions of chromatin, the ratio of histone H1 to histone H2A may vary, but the ratio of histone H2A to histone H2B is generally the same. If the amount of H1 increases in a region of chromatin, will transcription of genes in that region increase or decrease? Explain your answer.

In chromatin, nucleosomes are organized in higher-order structures: 30 nm filaments. Although the detailed structure is not known, which features of the 30 nm filament have been experimentally determined?

In eukaryotes, chromosomes are packaged into successively higher-order structures, such as the 30 nm filaments. In bacteria, DNA is not packaged into such stable proteinaceous structures, and histonelike proteins bind to the DNA less tightly. Suggest an explanation for this difference.

Describe at least three differences between chromatin regions that are transcriptionally active and those in which genes are transcriptionally silent.

How does epigenetic inheritance differ from Mendelian inheritance?

During replication, nucleosomes are partially displaced and distributed on the daughter DNA strands. New histone subunits are added to bring the entire complement of nucleosomes up to the required level. Nucleosomes on the DNA to be replicated may have modified histone subunits, but the new histones that appear after replication lack the modifications (at least transiently). Which of the following statements describes how the modified and unmodified histone subunits are distributed in nucleosomes after replication?

The human genome contains about 3.1 × 10⁹ bp of DNA. Assuming that the DNA is covered with nucleosomes spaced as described in this chapter, how many molecules of histone H2A are present in one somatic human cell? (Do not consider any reductions in H2A due to its replacement by H2A variants.) How would the number change after DNA replication but before cell division?

Roger Kornberg’s histone cross-linking experiments defined an H3-H4 heterotetramer as a nucleosome substructure (see the How We Know section for this chapter). Suppose nucleosomes actually contained two H3 subunits but only one H4 subunit, forming a stable H3-H3-H4 heterotrimer. How would the cross-linking results have been different?