Genomes are typically divided into chromosomes, which are distinct DNA molecules together with all of the other molecules that associate with them in the cell. These associated molecules, primarily proteins, are involved in organizing the DNA, recognizing genes and initiating or inhibiting their expression. An organism can have one chromosome or many. Each chromosome has a unique sequence and specific genes are organized in the same order along a particular chromosome. For example, your chromosome 4 will have the same genes in the same sequence along its length as those of all (or at least the vast majority) of the people you will ever met. The difference is that you are likely to have different versions of those genes, different alleles. In this light, most macroscopic organisms (including humans) are diploid and so have two copies of each chromosome, with the exception of the chromosomes that determine sex, the X and Y chromosomes in humans. So you may have two different alleles for any particular gene. Most of these sequence differences will have absolutely no discernible effect on your molecular, physiological, or behavioral processes. However, some will have an effect, and these form the basis of genetic differences between organisms. That said, their effects will be influenced by the rest of your genome, so for most traits there is no simple link between genotype and phenotype.
In humans, only ~5% of the total genomic DNA is involved in encoding polypeptides. The amount of DNA used to regulate gene expression is more difficult to estimate, but it is clear that lots of the genome (including the 50% that includes dead transposons) is not directly functional. That said, gene organization can be quite complex. We can see an example of this complexity by looking at organisms with more “streamlined” genomes. While humans have an estimated ~25,000 genes in ~3.2 x 109 base pairs of DNA (about 1 gene per 128,000 base pairs of DNA), the single circular chromosome of the bacterium E. coli (K-12 strain) contains 4,377 genes in 4,639,221 base pairs of DNA, of which 4,290 encode polypeptides and the rest RNAs261. That is about one gene per 1000 base pairs of DNA.
In prokaryotes and eukaryotes, genes can be located on either strand of the DNA molecule, typically referred (arbitrarily) as the “+” and the “–“ strands of the molecule. Given that the strands are anti-parallel, a gene on the “+” strand runs in the opposite direction from a gene on the “–“ strand. We can illustrate this situation using the euryarchaea Picrophilus torridus. This archaea organism can grow under extreme conditions, around pH 0 and up to ~65°C. Its genome is 1,545,900 base pairs of DNA in length and it encodes 1,535 polypeptides (open reading frames), distributed fairly equally on the + and – strands262.
While most prokaryotic genes are located within a single major circular chromosome, the situation is complicated by the presence of separate, smaller circular DNA moleculesknown as plasmids. In contrast to the organism’s chromosome, plasmids can (generally) be gained or lost. That said, because plasmids contain genes it is possible for an organism to become dependent upon or addicted to a plasmid. For example, a plasmid can carry a gene that makes its host resistant to certain antibiotics. Given that most antibiotics have their origins as molecules made by one organism to kill or inhibit the growth of others, if an organism is living in the presence of an antibiotic, losing a plasmid that contains the appropriate antibiotic resistance gene will be lethal. Alternatively, plasmids can act selfishly. For example, suppose a plasmid carries the genes encoding an “addiction module” (which we discussed previously.) When the plasmid is present both toxin and anti-toxin are made. If, however, the plasmid is lost, the synthesis of the unstable anti-toxin ceases, while the stable toxin persists, becomes active (uninhibited), and kills the host. As you can begin to suspect, the ecological complexities of plasmids and their hosts are not simple.
Like the host chromosome plasmids have their own “origin of replication” sequence required for the initiation of DNA synthesis; this enables them to replicate independently of the main chromosome. Plasmids can be transferred from cell to cell either when the cell divides (vertical transmission) or between “unrelated” cells through what is known as horizontal transmission. If you think back to Griffith’s experiments on pneumonia, the ability of the DNA from dead S-type bacteria to transform R-type bacteria (and make them pathogenic) is an example of horizontal transmission.