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Discontinuous model of DNA replication. Lagging-strand replication requires Okazaki fragments to form going backward, away from the Y-junction.
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the proofreading function of DNA polymerase. In addition, exonuclease activity can remove the RNA primers of Okazaki fragments.
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DNA polymerase I is a polymerase when it adds nucleotides, one at a time, and an exonuclease when it removes nucleotides one at a time. To complete the Okazaki fragment, DNA polymerase I acts in both capacities. (DNA polymerase I mutants cannot properly connect Okazaki fragments.) DNA polymerase I completes the Okazaki fragment by removing the previous RNA primer and replacing it with DNA nucleotides ( g. 9.29). When DNA polymerase I has completed its nuclease and polymerase activity, the two previous Okazaki fragments are almost complete. All that remains is for a single phosphodiester bond to form.
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DNA polymerase I cannot make the nal bond to join two Okazaki fragments. The con guration needing completion is shown in gure 9.30. An enzyme, DNA ligase,
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Tamarin: Principles of Genetics, Seventh Edition
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9. Chemistry of the Gene1
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The McGraw Hill Companies, 2001
Nine
Chemistry of the Gene
3 5 Continuous replication 3 RNA primer Last Okazaki 3 fragment 5 5 5 3
Continuous replication on leading strand
3 5 New Okazaki fragment 3 5 Continuous replication on leading strand 5 3 5 5 3 Primase acts here 3 RNA primer formation on lagging strand
3 5 New Okazaki fragment 5 3 3 5 Figure 9.28 Another new primer 5 3 5 3 5 3 DNA polymerase III results in Okazaki fragment synthesis on lagging strand
Primer formation and elongation create an Okazaki fragment during discontinuous DNA replication.
completes the task by making the nal phosphodiester bond in an energy-requiring reaction. A question of evolutionary interest is why RNA is used to prime DNA synthesis. Why not use DNA directly and avoid the exonuclease and resynthesis activity seen in gure 9.29 Probably, making use of RNA primers lowers the error rate of DNA replication. That is, priming is an inherently error-prone process since nucleotides are initially added without a stable primer con guration. To prevent long-term errors in the DNA, an RNA primer is put in that can later be recognized and removed. Resynthesis by polymerase I is in a much more stable primer con guration (a long primer) and thus makes very few errors. Another question of evolutionary interest is why DNA synthesis cannot take place in the 3 5 direc-
tion. Probably, the answer has to do with proofreading and the exonuclease removal of mismatched nucleotides. When an incorrect nucleotide is found and removed, the next nucleotide brought in, in the 5 3 direction, has a triphosphate end available to provide the energy for its own incorporation (see g. 9.25). Consider what would happen if the polymerase were capable of adding nucleotides in the opposite direction. The energy for the phosphodiester bond would be coming from the triphosphate already attached in the growing 3 5 strand (see g. 9.25). Then, if an error in complementarity were detected and the polymerase removed the most recently added nucleotide from the 3 5 strand, the last nucleotide in the double helix would no longer have a triphosphate available to provide energy for the diester bond with the next nu-
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
9. Chemistry of the Gene1
The McGraw Hill Companies, 2001
DNA Replication The Enzymology
3 3 Leading strand 5 Previous Okazaki fragment 3
3 Primer Okazaki fragment Primer 5
5 3
5 Removed primer fragments DNA polymerase I
3 5
3 3 5
5 3
3 5
3 Nick 3 5
5 Figure 9.29
The completion of an Okazaki fragment requires that DNA polymerase I replace the RNA primer base by base with DNA nucleotides. A nal nick in the DNA backbone remains (arrow).
cleotide. Continued polymerization would thus require additional enzymatic steps to provide the energy needed for the process to continue. This could stop or slow the process down considerably. As it is, the process incorporates about four hundred nucleotides per second with an error rate of about one incorrect pairing per 109 bases. (Other repair systems further improve this error rate see chapter 12.)
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