Ch 8 Book Terms

Question 1

Nucleosome

Answer 1

The basic structural subunit of chromatin, consisting of approximately 200 bp of DNA and an octamer of histone proteins.

Question 2

Histones

Answer 2

Conserved DNA-binding proteins that form the basic subunit of chromatin in eukaryotes. H2A, H2B, H3, and H4 form an octameric core around which DNA coils to form a nucleosome. Linker histones are external to the nucleosome.

Question 3

Histone Tails

Answer 3

Flexible amino- or carboxy-terminal regions of the core histones that extend beyond the surface of the nucleosome; they are sites of extensive posttranslational modification.

Question 4

10-nm Fiber

Answer 4

A linear array of nucleosomes generated by unfolding from the natural condition of chromatin.

Question 5

Linker Histones

Answer 5

A family of histones (such as histone H1) that are not components of the nucleosome core; linker histones bind nucleosomes and/or linker DNA and promote 30-nm fiber formation.

Question 6

30-nm Fiber

Answer 6

A coil of nucleosomes. It is the basic level of organization of nucleosomes in chromatin.

Question 7

Nonhistones

Answer 7

Any structural protein found in a chromosome except one of the histones.

Question 8

Micrococcal Nuclease (MNase)

Answer 8

An endonuclease that cleaves DNA; in chromatin, DNA is cleaved preferentially between nucleosomes.

Question 9

Linker DNA

Answer 9

Nonnucleosomal DNA present between nucleosomes.

Question 10

Core DNA

Answer 10

Region of nucleosomal DNA that has an invariant length of 146 bp, the minimum length of DNA needed to form a stable monomeric nucleosome, and is relatively resistant to digestion by nucleases.

Question 11

Histone Octamer

Answer 11

The complex of two copies each of the four different core histones (H2A, H2B, H3, and H4); DNA wraps around this complex to form the nucleosome.

Question 12

Core Histones

Answer 12

One of the four types of histone (H2A, H2B, H3, and H4 and their variants) found in the core particle derived from the nucleosome. (This excludes linker histones.)

Question 13

Histone Fold

Answer 13

A motif found in all four core histones in which three α-helices are connected by two loops.

Question 14

Chromatosomes

Answer 14

Nucleosomes that contain linker histones.

Question 15

Histone Code

Answer 15

The hypothesis that combinations of specific modifications on specific histone residues act cooperatively to define chromatin function.

Question 16

Bromodomain

Answer 16

A domain of 110 amino acids that binds to acetylated lysines (often in histones).

Question 17

Chromodomain

Answer 17

Domains of approximately 60 amino acids that recognize various methylated states of lysines in histones and other
proteins; some have other functions, such as RNA binding.

Question 18

Plant Homeodomain (PHD)

Answer 18

Domain of approximately 50 to 80 amino acids. Many of these domains bind various methylation states of lysines in histones. Also called the PHD finger.

Question 19

Tudor Domain

Answer 19

A type of methyl-lysine binding domain characterized by a specific sequence of approximately 60 amino acids.

Question 20

Histone Variants

Answer 20

Any of a number of histones closely related to one of the core histones (H2A, H2B, H3, or H4) that can assemble into a nucleosome in the place of the related core histone; many have specialized functions or localization. There are also numerous linker variants.

Question 21

Linking Number Paradox

Answer 21

The discrepancy between the existence of –1.67 supercoils in the path of DNA on the nucleosome compared with the measurement of –1 supercoil released when the restraining protein is removed.

Question 22

Replication-Coupled Pathway

Answer 22

The pathway for assembling chromatin from an equal mix of old and new histones during the S phase of the cell cycle.

Question 23

Replication-Independent Pathway

Answer 23

Pathway for assembling nucleosomes during phases of the cell cycle that do not involve DNA synthesis; may be necessary due to damage to the DNA or because of displacement of the nucleosome during transcription.

Question 24

Nucleosome Positioning

Answer 24

The placement of nucleosomes at defined sequences of DNA instead of at random locations with regard to sequence.

Question 25

Indirect End Labeling

Answer 25

A technique for examining the organization of DNA by making a cut at a specific site and identifying all fragments containing the sequence adjacent to one side of the cut; it reveals the distance from the cut to the next break(s) in DNA.

Question 26

Rotational Positioning

Answer 26

The location of the histone octamer relative to turns of the double helix that determines which face of DNA is exposed on the nucleosome surface.

Question 27

Hypersensitive Sites

Answer 27

A short region of chromatin detected by its extreme sensitivity to cleavage by DNase I and other nucleases; it comprises an area from which nucleosomes are excluded.

Question 28

Chromosomal Domain

Answer 28

A region of altered chromosome structure that includes at least one active transcription unit.

Question 29

Locus Control Region (LCR)

Answer 29

The region that is required for the expression of several genes in a domain.

Question 30

Insulators

Answer 30

A sequence that prevents an activating or inactivating effect from passing from one side to the other.