In eukaryotic cells, DNA in the nucleus is packaged differently from DNA in bacteria. As discussed in Chapter 3, eukaryotic DNA is linear and each DNA molecule forms a single chromosome. In a chromosome, DNA is packaged with proteins to form a DNA-protein complex called chromatin. There are several levels of packaging. First, eukaryotic DNA is wrapped twice around a group of histone proteins called a nucleosome. A nucleosome is made up of eight histone proteins: two each of histones H2A, H2B, H3, and H4. The histone proteins are rich in the amino acids lysine and arginine, whose positive charges are attracted to the negative charges of the phosphates along the backbone of each DNA strand.

This first level of packaging of the DNA is sometimes referred to as “beads on a string,” with the nucleosomes the beads and the DNA the string. It is also called a 10-nm fiber in reference to its diameter, which is about five times the diameter of the DNA double helix (Fig. 13.12). In general, these are areas of the genome that are transcriptionally active.

The next level of packaging occurs when the chromatin is more tightly coiled, forming a 30-nm fiber (Fig. 13.12). As the chromosomes in the nucleus condense in preparation for cell division, each chromosome becomes progressively shorter and thicker as the 30-nm fiber coils onto itself to form a 300-nm coil, a 700-nm coiled coil, and finally a 1400-nm condensed chromosome in a manner that is still not fully understood. The progressive packaging constitutes chromosome condensation, an active, energy-consuming process requiring the participation of several types of proteins.

Greater detail of the structure of a fully condensed chromosome is revealed when the histones are chemically removed (Fig. 13.13). Without histones, the DNA spreads out in loops around a supporting protein structure called the chromosome scaffold. Each loop of relaxed DNA is 30 to 90 kb long and anchored to the scaffold at its base. Before removal of the histones, the loops are compact and supercoiled. Each human chromosome contains 2000–8000 such loops, depending on its size.

Despite intriguing similarities between the nucleoid model in Fig. 13.11 and the chromosome scaffold model in Fig. 13.13, the structures evolved independently and make use of different types of protein to bind the DNA and form the folded structure of DNA and protein. Furthermore, the size of the eukaryotic chromosome is vastly greater than the size of the bacterial nucleoid. To appreciate the difference in scale, keep in mind that the volume of a fully condensed human chromosome is five times larger than the volume of a bacterial cell.