Bacterial chromosome - Almost all of the DNA of a typical prokaryote like E. coli is contained in a single, large, supercoiled circular DNA molecule, with a minor fraction present in small plasmids. It is complexed with proteins and exists free in the cytosol, although it is attached at one or more points to the cell membrane.

Eukaryotic chromosomes - The typical eukaryotic cell's genome is divided into several or many chromosomes, each of which contains a single, very large, linear DNA molecule. These DNA molecules are commonly of the order of 10⁷ to 10⁹ bp in length, though the size does vary. The number of eukaryotic chromosomes ranges from 1 (in an Australian ant) to 190 (in a species of butterfly). In nondividing cells, the chromosomes are segregated within the nucleus as an entangled mass of fibers of a DNA–protein complex called chromatin. During mitosis, the nuclear envelope breaks down and the diploid chromosomes condense into compact structures.

Ploidy - Most prokaryotes are haploid, containing only one copy of their chromosome, but most eukaryotic cells are diploid, carrying two copies of each chromosome. Some eukaryotic cells are highly polyploid, carrying many copies of each chromosome. The polytene chromosomes of the salivary glands of fruit flies provide a dramatic way to visualize the linearity of gene arrangements. In a polytene chromosome, multiple copies of the DNA, and its associated proteins, are arranged side by side in exact register. The linear array of light-staining and dark-staining bands can be correlated with the linear arrangement of genes on the chromosome.

Considerations in eukaryotic chromosomes - The enormous amount of DNA in eukaryotic cells poses the following obstacles to cells:

1. Compaction - The length of the total DNA content of a human cell is nearly 3 meters, yet it must be packed into a nucleus about 10^-5 m in diameter.

2. Selective transcription - In a typical differentiated eukaryotic cell, only a small fraction of the DNA (5%-10%) is ever transcribed. Much is nontranscribable. Many genes that do undergo transcription do so only in certain cell lines in particular tissues, and then often only under special circumstances. To maintain and regulate such complex programs of selective transcription, the accessibility of the DNA to RNA Polymerases must be under strict control.

Both compaction and the control of gene expression in eukaryotes are achieved by having the DNA complexed with a set of special proteins to form the protein-DNA complex called chromatin.