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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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9. Chemistry of the Gene1
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The McGraw Hill Companies, 2001
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Chemistry of the Gene
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Stereo view of sliding clamp, DNA polymerase, and DNA from bacteriophage RB69. The clamp (red, blue, green) surrounds the DNA (brown) like a doughnut. The clamp is attached to the proximal segment of the DNA polymerase (gray ). (From Yousif Shamoo and
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Thomas A. Steitz, Building a replisome from interacting pieces in Cell, 99:155 166, October 15. Reprinted by permission of Cell.)
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E. coli. Several of the polymerases most likely both replicate and repair DNA. Eukaryotes also have a clamp-loader complex, called replication factor C, and a six-unit clamp called the proliferating cell nuclear antigen. The RNA primers are removed during Okazaki fragment completion (maturation) by mechanisms similar to those in prokaryotes. In eukaryotes, RNAase enzymes remove the RNA primers in Okazaki fragments; a repair polymerase lls gaps; and a DNA ligase forms the nal seal. Helicases, topoisomerases, and single-strand binding proteins play roles similar to those they play in prokaryotes.The completion of the replication of linear eukaryotic chromosomes involves the formation of specialized structures at the tips of the chromosomes, which we discuss in chapter 15. Thus, all of the enzymatic processes are generally the same in prokaryotes and eukaryotes. DNA replication developed in prokaryotes and was re ned as prokaryotes evolved into eukaryotes. T. Steitz and his colleagues have done much X-ray crystallography work that has given us an excellent look at the structure of a polymerase. (Most work has actually been done on a fragment of DNA polymerase I called the Klenow fragment.) The enzyme is shaped like a cupped right hand with enzymatic activity taking place in two places, separated by a distance of about
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two to three nucleotides ( g. 9.33). It is proposed that when the polymerization site senses a mismatch, the DNA is moved so that the 3 end enters the exonuclease site, where the incorrect nucleotide residue is then cleaved. Polymerization then continues. There may be a general mode of polymerase action among diverse polymerases. The replication of the E. coli chromosome may be controlled by the methylation state of several sequences within oriC. As we discuss in chapter 13, certain enzymes add methyl groups to speci c DNA bases, and the presence or absence of these methyl groups can serve as signals to other enzymes.
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Events at the Y-Junction
We now have the image of DNA replication proceeding as a primosome moves along the lagging-strand template, opening up the DNA (helicase activity), and creating RNA primers (primase activity) for Okazaki fragments. One DNA polymerase III moves along the leading-strand template, generating the leading strand by continuous DNA replication, whereas a second DNA polymerase III moves backward, away from the Y-junction, creating Okazaki fragments. Single-strand binding proteins (ssb proteins) keep single-stranded DNA stabilized (open) during
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
9. Chemistry of the Gene1
The McGraw Hill Companies, 2001
DNA Replication The Enzymology
oriC
Initiator proteins attach Initiator proteins
Primosome
Helicase attaches
Primosomes form
Helicase Primase
Primosomes move down DNA and initiate primers (5
3 Primer
3 5
Leading-strand synthesis begins DNA polymerase III 5 3 Clamp DNA polymerase III 3
Primers for Okazaki fragments created
5 Okazaki primer 3
3 Okazaki primer 5 3
Events at the origin of DNA replication in E. coli. The DNA opens up at oriC to create two moving Y-junctions. Initiator proteins attach and then bind helicase. The helicase then binds primase, forming a primosome. After the primer forms and two copies of DNA polymerase III are bound, the polymerization process begins.
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
9. Chemistry of the Gene1
The McGraw Hill Companies, 2001
Nine
Chemistry of the Gene
Clamp
DNA polymerase III
Leading strand
3 E Editing mode Figure 9.33
Exonuclease domain
E Polymerizing mode Helicase
DNA polymerase (P) and exonuclease (E) activities of the Klenow fragment of DNA polymerase I in E. coli. On the right, 5 3 polymerization is occurring. On the left, the 3 end of the nascent strand has been backed up into the exonuclease site, presumably when a mismatch was detected.
(With permission from the Annual Review of Biochemistry, Volume 63. 1994 by Annual Reviews. www.AnnualReviews.org.)
Primase Lagging strand
ssb proteins
this process, and DNA polymerase I and ligase connect Okazaki fragments ( g. 9.34). This simple picture is slightly complicated by the fact that the lagging- and leading-strand synthesis is coordinated. B. Alberts suggested an explanation: the replisome model, in which both copies of DNA polymerase III are attached to each other and work in concert with the primosome at the Y-junction ( g. 9.35). According to this model, a single replisome, consisting of two copies of DNA polymerase III, a helicase, and a primase, moves along the DNA. The leading-strand template is immediately fed to a polymerase, whereas the lagging-strand template is not acted on by the polymerase until an RNA primer has been placed on the strand, meaning that a long ( fteen-hundred base) single strand has been opened up ( g. 9.35a). As the replisome moves along, another singlestranded length of the lagging-strand template forms. At about the time that the Okazaki fragment is completed, a new RNA primer has been created ( g. 9.35b).The Okazaki fragment is released ( g. 9.35c), and a new Okazaki fragment is begun (polymerase cycling), starting with the latest primer ( g. 9.35d). This takes the replisome back to the same con guration as in gure 9.35a, but one Okazaki fragment farther along. Figure 9.36 gives us a closer look at the details of the Y-junction at the moment of polymerase cycling. Primase, which is not highly processive, must be in touch with an ssb protein to stay attached to the DNA when forming a primer. At the appropriate moment, after the primer is formed, the clamp loader contacts the ssb, dis-
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