The DNA polymerases (DNA pols) responsible for copying the DNA templates are only able to read the parental nucleotide sequences in the 3′→5′ direction, and they synthesize the new DNA strands only in the 5′→3′ (antiparallel) direction. Therefore, beginning with one parental double helix, the two newly synthesized stretches of nucleotide chains must grow in opposite directions, one in the 5′→3′ direction toward the replication fork and one in the 5′→3′ direction away from the replication fork (Fig. 30.14). This feat is accomplished by a slightly different mechanism on each strand.
1.
Leading strand: The strand that is being copied in the direction of the advancing replication fork is synthesized continuously and is called the leading strand.
2.
Lagging strand: The strand that is being copied in the direction away from the replication fork is synthesized discontinuously, with small fragments of DNA being copied near the replication fork. These short stretches of discontinuous DNA, termed Okazaki fragments, are eventually joined (ligated) by ligase to become a single, continuous strand. The new strand of DNA produced by this mechanism is termed the lagging strand.
D. RNA primer
DNA pols cannot initiate synthesis of a complementary strand of DNA on a totally single-stranded template. Rather, they require an RNA primer, which is a short piece of RNA base-paired to the DNA template, thereby forming a double-stranded DNA–RNA hybrid. The free hydroxyl group on the 3′end of the RNA primer serves as the first acceptor of a deoxynucleotide by action of a DNA pol (Fig. 30.15). [Note: Recall that glycogen synthase also requires a primer (see p. 126).] 1.
Primase: A specific RNA polymerase, called primase (DnaG), synthesizes the short stretches of RNA (~10 nucleotides long) that are complementary and antiparallel to the DNA template. In the resulting hybrid duplex, the U (uracil) in RNA pairs with A in DNA. As shown in Figure 30.16, these short RNA sequences are constantly being synthesized at the replication fork on the lagging strand, but only one RNA sequence at the origin of replication is required on the leading strand. The substrates for this process are 5′-ribonucleoside triphosphates, and pyrophosphate is released as each ribonucleoside monophosphate is added through formation of a 3′→5′-phosphodiester bond. [Note: The RNA primer is later removed, as described in F. below.] 2.
Primosome: The addition of primase converts the prepriming complex of proteins required for DNA strand separation (see p. 415) to a primosome. The primosome makes the RNA primer required for leading-strand synthesis and initiates Okazaki fragment formation in discontinuous lagging-strand synthesis. As with DNA synthesis, the direction of synthesis of the primer is 5′→3′.
E. Chain elongation
Prokaryotic (and eukaryotic) DNA pols elongate a new DNA strand by adding deoxyribonucleotides, one at a time, to the 3′-end of the growing chain (see Fig. 30.16). The sequence of nucleotides that are added is dictated by the base sequence of the template strand with which the incoming nucleotides are paired.