Completion of DNA replication requires a set of specific events. These events am different for circular versus linear chromosomes. For a circular chromosome, the conventional replication fork machinery can replicate the entire molecule, but the resulting daughter molecules are topologically linked to one another. In contrast, replication of the very ends of linear chromosomes cannot be completed by the replication fork machinery we have discussed so far. Therefore, organisms containing linear chromosomes have developed novel strategies to overcome this end replication problem.
Type II Topoisomerases Are Required to Separate Daughter DNA Molecules
After replication of a circular chromosome is complete, the resulting daughter DNA molecules remain linked together as catenanes (Figure 8-33). Catenane is the general term for two circles that are linked (similar to links in a chain). To segregate these chromosomes into separate daughter cells, the two circular DNA molecules must be disengaged from one another. This separation is accomplished by the action of type 11 topoisomerases. As we saw in Chapter 6, these enzymes have the ability to break a double-stranded DNA molecule and pass a second double-stranded DNA molecule through this break. Thus, type 11 topoisomerases catalyze a break in one of the two daughter molecules and allow the second daughter molecule to pass through the break. This reaction decatenates the two daughter chromosomes, allowing their segregation into separate cells.
Although the importance of this activity for the separation of circulai chromosomes is most clear, the activity of type 11 topoisomerases is also critical to the segregation of large linear molecules. Although there is no inherent topological linkage after the replication of a linear molecule, the large size of eukaryotic chromosomes necessitates the intricate folding of the DNA into loops attached to a protein scaffold. These attachments lead to many of the same problems that circular chromosomes have when (he two daughter chromosomes must be separated.
Lagging Strand Synthesis Is Unable to Copy the Extreme Ends of Linear Chromosomes
The requirement for an KNA primer to initiate all new DNA synthesis creates a dilemma for the replication of the ends of linear chromosomes. This is called the end replication problem (Figure 8-34). This difficulty is not observed during the duplication of the leading strand template. In that case, a single internal RNA primer can direct the initiation of a DNA strand that can be extended to the extreme 5' terminus of its template. In contrast, the requirement for multiple primers to complete lagging strand synthesis means that a complete copy of its template cannot be made. Even if the end of the last RNA primer for Okazaki fragment synthesis anneals to the final base pairs of the lagging strand template, once this KNA molecule is removed, there will remain a short region of unreplicated ssDNA at the end of the chromosome. This means that each round of DNA replication would result in the shortening of one of the two daughter DNA molecules. Obviously,
incompletely replicated DNA
chromosome is Shorter
^ last Okazaki fragment chromosome is Shorter incompletely replicated DNA
FIGURE 8-34 The end replication problem. As the lagging strand replication machinery reaches the end of die chromosome, 3\ some point pntnasc no longer has sufficient space to synthesize a new RNA primer, this results in incomplete replication and a short ssDNA region at the 3' end of the lagging strand DNA product. When this DNA product is replicated in the next round, one of the two products will be shortened and will Ijck the region that was not fully copied in the previous round of replication.
FIGURE 8-35 Protein priming as a solution to the end replication problem.
By binding to (be DMA polymerase and to the 3' end of the template, a protein provides the priming hydroxyl group to initiated DMA synthesis, In the example shown, the protein primes ail DNA synthesis as is seen for many viruses. For longer DNA molecules, this method combines with conventional origin function to replicate the chromosomes.
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