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Encyclopedia of Physical Science and Technology en010k-502 July 16, 2001 16:56

Nucleic Acid Synthesis 863

TABLE II Cellular DNA Polymerases form or RF) is the template for rolling circle synthesis
and is formed first by replication of the single-stranded
Prokaryote (E. coli) In vivo function
form. Such a single-stranded circular DNA template has

Pol I Nonreplicative removal of 5 primer of Okazaki
fragments been exploited in recombinant DNA techniques.
Small organisms (e.g., bacteria), as well as plasmids
Pol II Nonreplicative, damage responsive polymerase
and many viruses, have only one ori sequence per cellu-
Pol III Replicative synthesis
6
lar genome (4.7 × 10 nucleotide pairs in E. coli), which
Din B Lesion bypass DNA synthesis
is often an uninterrupted DNA molecule (Figs. 4A and
UmuC Lesion bypass DNA synthesis
4B). In complex organisms, with a much larger genome
Eukaryote
9
size (∼3 × 10 nucleotide pairs for mammals), which is
Pol α RNA primer synthesis
divided into multiple discrete chromosomes, thousands of
Pol β Repair synthesis
ori sequence are present (Fig. 4C), although not all of them
Pol δ Replicative (repair) synthesis
may be active in all cells; this requires that replication be
Pol ε Replicative (repair) synthesis
regulated and coordinated.
Pol ζ Damage bypass synthesis
Pol η Damage bypass synthesis
B. Regulation of DNA Replication
Pol θ Damage bypass synthesis
Pol ι Damage bypass synthesis Semi-conservative replication of the genome ensures that
Pol γ Mitochondrial DNA synthesis each daughter cell receives a full complement of the
genome prior to cell division. In eukaryotes, this is
achieved by the distinct phases of the cell cycle, namely,
subunits which may have distinct functions. These will G1 phase, during which cells prepare for DNA synthesis;
be discussed later. S phase, in which DNA replication is carried out; and G2-
M (mitosis), during which the replicated chromosomes
segregate into the two newly divided daughter cells. Un-
III. DNA REPLICATION AND like in eukaryotes, DNA replication in prokaryotes may
ITS REGULATION occur continuously during growth (in rich medium). Thus,
the copy number of genomes could exceed two in rapidly
A. DNA Replication growing cells. In the case of viruses, which multiply by
utilizing the host cell synthetic machinery and eventually
DNA replication is initiated at discrete sequences called
killing them, genome replication may be not controlled.
origin (ori) of replication to which DNA polymerase and
However, plasmid DNA, as well as the genomes of or-
accessoryproteinsbindandcopybothstrands,aspredicted
ganelles such as mitochondria and chloroplasts, is repli-
by the semi-conservative replication model (Fig. 2B). In
cated with some degree of regulation. In these cases the
contrasttounidirectional RNA synthesis, DNA replication
genomic copy number can vary within limits as a function
in most genomes occurs bidirectionally (Fig. 2B). This re-
of growth condition.
sults in both continuous and discontinuous synthesis of the
same strand on two sides of the origin of replication. Some
C. Regulation of Bacterial DNA Replication
circular genomes, such as mitochondrial DNA, are repli-
at the Level of Initiation
cated unidirectionally. In these cases, replication starting

at the ori proceeds continuously in the 5 → 3 direction, In all organisms, as well as autonomously replicating

followed by discontinuous synthesis of the complemen- DNA molecules of organelles and plasmids, replication
tary strand. Termination occurs at the same site as the ori is divided into three stages: initiation, chain elongation,
after the circle is completely traversed. During replication and termination. The control of replication occurs pri-
of the mitochondrial genome, elongation of the continuous marily at the level of initiation of DNA synthesis at the
strand pauses at some distance from the ori, resulting in a “origin” (ori site). Because DNA chains cannot be started
bubble (θ structure) structure named a D-(displacement) de novo and requires a primer, the initiation com-
loop (Fig. 4A). plex contains primase activity for synthesis of an RNA
The single-stranded DNA genomes of certain small primer. Discontinuous synthesis of Okazaki fragments
E. coli viruses (such as M13 and φX174) are replicated needs repeated primer synthesis for each fragment as
in the form of rolling circles in which unidirectional syn- an integral component of chain elongation. Initiation of
thesis of one (virus genome) strand occurs by continuous the primer at the ori sequence rather than elongation of
displacement from the template (complementary strand; initiated chains is the critical event in DNA replication
Fig. 4A). The initial duplex DNA (called the replicative control.