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862 Nucleic Acid Synthesis

DNA. This is then integrated into the host cell genome leading strand, while the 5 → 3 strand is copied after a

as proviral DNA, from which the progeny viral RNA is brief delay when separation of the strands occur, so this
eventuallytranscribed.Thus,thereversetranscriptaseisan nascent strand is called the lagging strand (Fig. 2). The
unusual polymerase because it can utilize both RNA and leading strand can be synthesized continuously without
DNA templates (Fig. 5). There is strong evidence that such interruption, while the lagging strand is synthesized dis-
reverse transcription was involved in synthesis of “retro- continuously after the leading strand is synthesized. The
transposons,” a special class of mobile genetic elements, discontinuous fragments are also called Okazaki frag-
during the evolution of mammalian genomes. These mo- ments, named after its discoverer.
bile genetic elements, also known as transposons, when
identified in bacteria and lower eukaryotes, consist of spe-
C. Multiplicity of DNA and RNA Polymerases
cific DNA sequences which can be relocated randomly in
the genome. The transposition is mediated by enzymes Multiple DNA and RNA polymerases are present in both
called transposase, usually synthesized by a gene in the eukaryotes and prokaryotes, which evolved to fulfill dis-
transposon. During transposition of retransposons, certain tinct roles in the cell. In E. coli, DNA polymerases I (Pol
mRNAsarereversetranscribedandthenintegratedintothe I), II (Pol II), and III (Pol III) account for most DNA poly-
genome like the proviral sequence. The presence of spe- merase activity. Pol I has the highest enzymatic activity
cific flanking sequences allows these elements to relocate and was the first DNA polymerase to be discovered by
to other sites in the genome. A Kornberg. However, Pol III is responsible for cellular
DNA replication, while Pol I is involved in gap filling nec-
essary during normal DNA replication (to fill in the space
B. DNA Replication vs Transcription:
Enzymatic Processes of degraded RNA primers) and also during repair of DNA
damage. Pol II and two other DNA polymerases, Din B
The broad chemical steps in DNA and RNA synthesis and UmuD/C, are responsible for replication of damaged
are quite similar, in that both processes represent reading DNA when it remains unrepaired.
of a DNA strand as the template. However, while both Eukaryotic cells express five different DNA poly-
strands of DNA have to be copied, transcription is po- merases, α, β, γ , δ, and ε, for normal DNA replication
lar because only one strand is normally copied into RNA and repair. Pol α is involved in synthesis of primers for
whose sequence is identical to the other strand (except for DNA replication; Pol β and possibly Pol ε are involved
replacement of thymidine by uridine). This is achieved in repair replication of damaged DNA. Pol δ (and possi-
by the presence of discrete start and stop signals brack- bly Pol ε) are responsible for replication of the nuclear
eting “transcription units” corresponding to each gene genome. Pol γ found in the mitochondria is responsible
containing unique sequences, called promoters; their se- for replication of the mitochondrial genome. Several ad-
quences provide the recognition motif for RNA poly- ditional DNA polymerases recently identified and charac-
merase to bind and start RNA synthesis unidirectionally. terized are involved in replication of unrepaired damaged
Similarly, the stop sequences are recognition motifs for bases, like the E. coli DinB and UmuD/C (Table II).
the transcription machinery to stop and fall off the DNA E. coli has only one RNA polymerase, while eukary-
template. otes have three distinct RNA polymerases, Pol I, Pol II,
As mentioned before, the two strands of a DNA dou- and Pol III, which transcribe different types of genes. RNA
ble helix are of opposite polarity, i.e., one strand is in the Pol I makes only ribosomal RNAs, which constitute the
5 → 3 orientation and its complementary strand in the largest fraction of total RNA and, in fact, a significant frac-

3 → 5 orientation. Furthermore, the fact that all nucleic tion of the cellular mass. Pol III transcribes small RNAs,

acid polymerases can polymerize nucleotide monomers including transfer RNAs, which function as carriers of

only in the 5 → 3 direction as guided by base pairing cognate amino acids and are required for protein synthe-

with a template does not pose a problem for RNA syn- sis. RNA Pol II transcribes all genes to generate mRNA,
thesis because only the 3 → 5 strand of the DNA tem- which encodes all proteins. Thus, this enzyme recognizes

plate is copied. However, DNA replication, where both the most diverse group of genes. All of these RNA classes
strands have to be copied in the same 5 → 3 direction of are initially synthesized as longer precursors that require

the duplex template, introduces a complication situation extensive, often regulated, processing to yield the mature

(Figs. 2 and 5). The 3 → 5 strand is copied like RNA, RNA product.

while the 5 → 3 strand has to be copied in the opposite RNA and DNA polymerases encoded by virus and other

direction. It has been observed in all cases that simul- episomal genomes are, in general, smaller and have fewer
taneous replication of both strands is accomplished by subunits than the cellular polymerases. Cellular poly-
continuous copying of the 3 → 5 strand, also called the merase holoenzymes are rather complex with multiple