Page 249 - Color Atlas of Biochemistry
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240 Molecular genetics
Replication theprocesses taking placeinthis typeoffork,
and only the most important are shown here.
For genetic information to be passed on dur- The two strands of the initial DNA (1)are
ing cell division, a complete copy of the ge- shown in blue and violet, while the newly
nome has to be produced before each mitosis. formed strands are pink and orange.
This processisknown as DNA replication. Each fork (2) contains two molecules of
DNA polymerase III and a number of helper
proteins. The latter include DNA topoisomer-
A. Mechanism of DNA polymerases
ases and single–strand-binding proteins.
Replication is catalyzed by DNA–dependent Topoisomerases are enzymes that unwind
DNA polymerases. Theseenzymes requirea the superhelical DNA double strand (gyrase,
single strand of DNA, known as the tem- topoisomerase II) and then separate it into the
plate. Beginning at a short starting sequence two individual strands (helicase, topoisomer-
of RNA (the primer), they synthesize a second ase I). Since the template strand is always read
complementary strand on the basis of this from 3 to 5 (see above), only one of the
template, and thus create a complete DNA strands (known as the leading strand; violet/
double helix again. The substrates of the pink) can undergo continuous replication. For
DNA polymerases are the four deoxynucleo- the lagging strand (light blue), the reading
side triphosphates dATP, dGTP, dCTP,and direction is the opposite of the direction of
dTTP. In each step, base pairing first binds movement of the fork. In this matrix, the
the nucleotide that is complementary to the new strand is first synthesized in individual
current base in the template strand. The pieces, which are known as Okazaki frag-
α–phosphate residue of the newly bound nu- ments after their discoverer (green/orange).
cleoside triphosphate is then subjected to nu- Each fragment starts with a short RNA pri-
cleophilic attack by the 3 –OH group of the mer (green), which is necessary for the func-
nucleotide incorporated immediately previ- tioning of the DNA polymerase and is synthe-
ously. This is followed by the elimination of sized by a special RNA polymerase (“primase,”
diphosphate and the formation of a new not shown). The primer is then extended by
phosphoric acid diester bond. These steps DNA polymerase III (orange). After 1000–2000
are repeated again for each nucleotide. The nucleotides have been included, synthesis of
mechanism described means that the matrix the fragment is interrupted and a new one is
can only be read in the 3 5 direction. In begun, starting with another RNA primer that
other words, the newly synthesized strand has been synthesized in the interim. The in-
always grows in the 5 3 direction.The dividual Okazaki fragments are initially not
same mechanism is also used in transcription bound to one another and still have RNA at
by DNA-dependent RNA polymerases (see the 5 end (3). At some distance from the fork,
p. 242). Most DNAand RNApolymerases con- DNA polymerase I therefore starts to remove
sist of more than 10 subunits, the role of the RNA primer and replace it with DNA com-
which is still unclear to some extent. ponents. Finally, the gaps still remaining are
closed by a DNA ligase. In DNA double helices
formed in this way, only one of the strands has
B. Replication in E. coli
been newly synthesized—i. e., replication is
Although replication in prokaryotes is now semiconservative.
well understood, many details in eukaryotes In bacteria, some 1000 nucleotides are re-
are still unclear. However, it is certain that the plicated per second. In eukaryotes, replication
process is in principle similar. A simplified takes place more slowly (about 50 nucleotides
–1
scheme of replicationinthe bacterium s )and thegenomeis larger. Thousands of
Escherichia coli is shown here. replication forks are therefore active simulta-
In bacteria, replication starts at a specific neously in eukaryotes.
point in the circular DNA—the origin of repli-
cation—and proceeds in both directions. This
results in two diverging replication forks,in
which the two strands are replicated simulta-
neously. Numerous proteins are involved in
Koolman, Color Atlas of Biochemistry, 2nd edition © 2005 Thieme
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