Before taking a closer look at replication, we make a short digression into the use of abbreviations in naming genes and proteins — you will encounter many of these in this and later chapters. Bacterial genes generally are named using three italicized, lowercase letters that often reflect a gene’s apparent function. For example, the dna, uvr, and rec genes affect DNA replication, resistance to the damaging effects of UV radiation, and recombination, respectively. Where several genes affect the same process, the letters A, B, C, and so forth, are added — as in dnaA, dnaB, dnaQ, for example — usually reflecting their order of discovery rather than the order of their gene products in a reaction sequence. Similar conventions exist for naming eukaryotic genes, although the exact form of the abbreviations may vary with the species, and no single convention applies to all eukaryotic systems. For example, in the budding yeast Saccharomyces cerevisiae, gene names are generally three uppercase letters followed by a number, all italicized (e.g., the gene COX1 encodes a subunit of cytochrome oxidase). Gene names that predate current conventions may differ in format.

The use of abbreviations in naming proteins is less straightforward. During genetic investigations, the protein product of each gene is usually isolated and characterized. Many bacterial genes were identified and named before the roles of their protein products were understood in detail. Sometimes the gene product was found to be a previously isolated protein, and some renaming occurred. Often, however, the product turned out to be an as yet unknown protein, with an activity not easily described by a simple enzyme name.

Bacterial proteins often retain the name of their genes. When referring to the protein product of an E. coli gene, we use roman type and capitalize the first letter: for example, the dnaA and recA gene products are the DnaA and RecA proteins, respectively. Conventions for eukaryotic proteins are again complex. For yeast, some proteins have long common names (such as cytochrome oxidase). Others have the same name as the gene, in which case the protein name usually has one uppercase and two lowercase letters, followed by a number and the letter “p,” all in roman type (such as Rad51p). The “p” is to emphasize that this is a protein and to prevent confusion with naming conventions for other organisms.