The synthesis of any macromolecule proceeds in three stages: initiation, elongation and termination. This is true for DNA replication as well. During initiation, DNA synthesis begins at a specific site, called an origin of replication. The circular E. coli chromosome has a single origin, called oriC. Many bacteria have circular chromosomes with single origins of replication. However, other chromosomes, especially those in eukaryotes, can have multiple origins. During elongation, nucleotides are added to the growing DNA strand as the replication fork moves along the chromosome. Termination are the final steps that occur when all or an appropriate portion (replicon, see below) of the chromosome has been replicated.
The primary control of replication is exerted during initiation. This is economical, of course, since little benefit would come from initiating replication that will never be completed. As will be covered later in this chapter, an examination of the DNA structures, proteins and enzymes needed for initiation show that it is highly regulated. Initiation is an active process, requiring the accumulation of ATP-bound DNA binding proteins at a specific site prior to the start of replication. Both the activity of the initiator proteins and the state of covalent modification of the DNA at the origin are part of the control process.