the cycle repeats. The RNA–DNA fragments generated in this way are called Okazaki fragmentsafter their
discoverer.^47
The Okazaki fragments become joined up by DNA polymerase I, which possesses a 5–3exonuclease
activity that degrades the RNA primers and replaces them by DNA copied from the template strand. This
leaves a gap in the phosphodiester backbone (absence of a single phosphodiester bond), which is closed
by the enzyme DNA ligase.
6.6.4.5 Termination of DNA Replication. DNA replication terminates when another replication fork
or the telomere is reached (Section 6.4.4). In E. coli, a circular genome, replication always terminates within
a defined region roughly opposite oriC. This is mediated by DNA binding proteins called Replication
Terminator Proteins (TUS) that allow replicationforks to proceed through them in one direction only, thus
trapping them at the termination region.
6.6.5 Telomerases, Transposons and the Maintenance of Chromosome Ends
Eukaryotes have linear chromosomes that pose a problem for the DNA replication machinery. When the
DNA polymerase elongation complex reaches the end of the chromosome, the leading strand can perhaps
be completed in its entirety (assuming that the DNA polymerase is happy to replicate these final nucleotides
although it is falling off the end of the chromosome). However, the lagging strand must at least lack the
region corresponding to the template for the short RNA primer, and thus DNA replication cannot proceed
in the reverse direction by priming from beyond the telomere (Figure 6.30). Furthermore, the telomeres
are susceptible to degradation by nuclease action and have been shown to progressively shorten in somatic
(non-germ line) cells.
Almost all telomeres contain short tandemly repeated sequences (Section 6.4.4 and Figure 6.14).^28 In
most organisms, including all mammals, cells preserve the integrity of their telomeres by synthesis of fur-
ther copies of the repeated sequence by a special DNA polymerase called telomerase. The telomerase has
an RNA component that contains a short sequence that acts as a template for telomerase to extend the 3-end
of one DNA strand (Figure 6.31). This enzyme is thus a highly specialised reverse transcriptase, since it syn-
thesises DNA from an RNA template. Interestingly, in some other organisms, notably Drosophila, a dif-
ferent mechanism for telomere maintenance exists. In these species, a specialised long interspersed element
(LINE) transposable element(Section 6.8.3) transposes into the region and thus extends the telomere in
order to counteract degradation.
Genes and Genomes 235
Figure 6.30 DNA replication and Okazaki fragments. Synthesis of the leading strand of DNA is continuous and
discontinuous for the other strand, resulting in generation of Okazaki fragments