Chromosomes, eukaryotic chromatin

As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the remainder of this chapter fall under the heading of secondary structure. The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure this is discussed in Chapter 24. 

The eukaryotic cell cycle (see Fig. 12-41) produces remarkable changes in the structure of chromosomes (Fig. 24-25). In nondividing eukaryotic cells (in GO) and those in interphase (Gl, S, and G2), the chromosomal material, chromatin, is amorphous and appears to be randomly dispersed in certain parts of the nucleus. In the S phase of interphase the DNA in this amorphous state replicates, each chromosome producing two sister chromosomes (called sister chromatids) that remain associated with each other after replication is complete. The chromosomes become much more condensed during prophase of mitosis, taking the form of a species-specific number of well-defined pairs of sister chromatids (Fig. 24-5). 

Bacterial chromosomes are also extensively compacted into the nucleoid, but the chromosome appears to be much more dynamic and irregular in structure than eukaryotic chromatin, reflecting the shorter cell cycle and very active metabolism of a bacterial cell. 

Shioda et al. [43,44] visualized by electron microscopy both regions of naked DNA and of DNA covered with particles in the chromosome of Halobacterium salinarium isolated from gently lysed cells. In a control experiment, they did not detect such particles in E. coli. They also reported the existence of nucleosome-like structures in S. acidocaldarius and methanogens (unpublished results cited in ref. [43]). The size of the particles detected in H. salinarium (9.5 nm) is similar to that of eukaryotic nucleosomes (10.3 nm) however, this putative archaebacterial chromatin is not as regular as eukaryotic chromatin, since not all of the DNA is covered with nucleosomes and since the length of the DNA spacer between the particles is not uniform. In contrast to these results, Bohrmann and coworkers [45] did not visualize nucleosome-like structures in isolated chromosome fibers of Thermoplasma acidophilum. These authors also reported that in situ the nucleoid of T. acidophilum appears to be highly dispersed in the cytoplasm. 

The Physical Organization of Eukaryotic DNA Chromosomes and Chromatin Chromosomes Chromatin (Table 28.1)... 

Topoisomerases are recruited for enabling topological motions to occur. In condensed eukaryotic chromatin, loops of 300 A fiber are attached to a scaffold. Topoisomerases are a major component of the proteins that make up the chromosome scaffold. Although the DNA of mammalian chromosomes is linear, these frequent attachment points make each constrained loop into topologically circular. 

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

The DNA in a eukaryotic cell nucleus during the interphase between cell divisions exists as a nucleoprotein complex called chromatin. The proteins of chromatin fall into two classes histones and nonhistone chromosomal proteins. 

CHROMATIN IS THE CHROMOSOMAL MATERIAL EXTRACTED FROM NUCLEI OF CELLS OF EUKARYOTIC ORGANISMS... 

Bacteria normally harbour a single, circular chromosome that tends to be tethered to the bacterial plasma membrane and tends to have few if any closely associated proteins. Many bacteria also contain extra-chromosomal DNA in the form of plasmids, as will be discussed later. Eukaryotes (plants, animals and yeasts) posses multiple linear chromosomes contained within a cell nucleus, and these chromosomes are normally closely associated with proteins termed histones (the pro-tein-DNA complex is termed chromatin). Eukaryotes also invariably possess DNA sequences within mitochondria and in chloroplasts in plants. The (usually circular) DNA molecules are much... 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

Endonuclease activation and chromatin fr mentation are characteristic features of eukaryotic cell death by apoptosis. Which of the following chromosome structures would most likely be degraded first in an apoptotic cell ... 

Daban, J.R. (2000) Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures. Biochemistry 39, 3861-3866. 

In the nuclei of eukaryotes (see p. 196), DNA is closely associated with proteins and RNA. These nucleoprotein complexes, with a DNA proportion of approximately one-third, are known as chromatin. It is only during cell division (see p. 394) that chromatin condenses into chromosomes that are visible under light microscopy. During interphase, most of the chromatin is loose, and in these conditions a morphological distinction can be made between tightly packed heterochromatin and the less dense euchromatin. Euchro-matin is the site of active transcription. 

The effects of chromosome structure on gene regulation in eukaryotes have no clear parallel in prokaryotes. In the eukaryotic cell cycle, interphase chromosomes appear, at first viewing, to be dispersed and amorphous (see Figs 12-41, 24-25). Nevertheless, several forms of chromatin can be found along these chromosomes. About 10% of the chromatin in a typical eukaryotic cell is in a more condensed form than the rest of the chromatin. This form, heterochromatin, is transcriptionally inactive. Heterochromatin is generally associated... 

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