Structures such as these can create distinct biochemical environments by immobilizing select groups of macromolecules, as can other networks of proteins and RNA molecules associated with nuclear pores and with the nuclear envelope. In principle, this allows other molecules that enter these spaces to be processed with great efficiency through complex reaction pathways. Highly permeable, 1 µm fibrous networks of this sort can thereby impart many of the kinetic advantages of compartmentalization (see p. 164) to reactions that take place in subregions of the nucleus (Figure 4–58A). However, unlike the membrane-bound compartments in nuclear subcompartments. The large the cytoplasm (discussed in Chapter 12), these nuclear subcompartments—lack sphere here is a Cajal body. The smaller ing a lipid bilayer membrane—can neither concentrate nor exclude specific small darker sphere is an interchromatin granule molecules. cluster, also known as a speckle (see also Figure 6–46). These “subnuclear
The cell has a remarkable ability to construct distinct environments to per- organelles” are from the nucleus of a form complex biochemical tasks efficiently. Those that we have mentioned in the
Xenopus oocyte. (From k.E. Handwerger nucleus facilitate various aspects of gene expression, and will be further discussed and J.g. gall, Trends Cell Biol. 16:19–26, in Chapter 6. These subcompartments, including the nucleolus, appear to form 2006. with permission from Elsevier.) only as needed, and they create a high local concentration of the many different enzymes and RNA molecules needed for a particular process. In an analogous way, when DNA is damaged by irradiation, the set of enzymes needed to carry out DNA repair are observed to congregate in discrete foci inside the nucleus, creating “repair factories” (see Figure 5–52). And nuclei often contain hundreds of discrete foci representing factories for DNA or RNA synthesis (see Figure 6–47).
It seems likely that all of these entities make use of the type of tethering illustrated in Figure 4–58B, where long flexible lengths of polypeptide chain and/or long noncoding RNA molecules are interspersed with specific binding sites that concentrate the multiple proteins and other molecules that are needed to catalyze a particular process. Not surprisingly, tethers are similarly used to help to speed biological processes in the cytoplasm, increasing specific reaction rates there (for example, see Figure 16–18).
Is there also an intranuclear framework, analogous to the cytoskeleton, on which chromosomes and other components of the nucleus are organized? The nuclear matrix, or scaffold, has been defined as the insoluble material left in the nucleus after a series of biochemical extraction steps. Many of the proteins and RNA molecules that form this insoluble material are likely to be derived from the fibrous subcompartments of the nucleus just discussed, while others may be proteins that help to form the base of chromosomal loops or to attach chromosomes to other structures in the nucleus.
Having discussed the dynamic structure of interphase chromosomes, we now turn to mitotic chromosomes. The chromosomes from nearly all eukaryotic cells become readily visible by light microscopy during mitosis, when they coil up to form highly condensed structures. This condensation reduces the length of a typical interphase chromosome only about tenfold, but it produces a dramatic change in chromosome appearance.
Figure 4–59 depicts a typical mitotic chromosome at the metaphase stage of mitosis (for the stages of mitosis, see Figure 17–3). The two DNA molecules produced by DNA replication during interphase of the cell-division cycle are separately folded to produce two sister chromosomes, or sister chromatids, held together at their centromeres, as mentioned earlier. These chromosomes are normally covered with a variety of molecules, including large amounts of RNA–protein