The DNA molecules inside cells are highly convoluted. They have to be because DNA molecules in cells have a length far greater than the diameter of the cell itself. The DNA of a bacterium known as Mycoplasma, for example, if stretched to its full linear extent would be about 1000 times longer than the diameter of the bacterial cell. Many of the double-stranded DNA molecules in prokaryotic cells are circular and form supercoils in which the circular molecule coils upon itself, much like what happens to a rubber band when you twist it between your thumb and forefinger (Fig. 3.12). Supercoiling is caused by enzymes called topoisomerases that cleave, partially unwind, and reattach a DNA strand, which puts strain on the DNA double helix. Supercoils then relieve the strain and help to preserve the 10 base pairs per turn in the double helix.

In eukaryotic cells, most DNA molecules in the nucleus are linear, and each individual molecule forms one chromosome. There is a packaging problem here, too, which you can appreciate by considering that the length of the DNA molecule contained in a single human chromosome is roughly 6000 times greater than the average diameter of the cell nucleus. Double-stranded DNA molecules in eukaryotes are usually packaged with proteins called histones, and others, to form a complex of DNA and proteins referred to as chromatin (Chapter 13).

Histone proteins are found in all eukaryotes, and they interact with double-stranded DNA without regard to sequence. The reason for this ability is that these proteins are evolutionarily conserved, which means that they are very similar in sequence from one organism to the next. Conserved DNA, RNA, or protein sequences indicate that they serve an essential function and therefore have not changed very much over long stretches of evolutionary time. The more distantly related two organisms are that share conserved sequences, the more highly conserved the sequence is.