barcode reader using vb net source code The Origin of DNA Replication in Software

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The Origin of DNA Replication
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Each replicon (e.g., the E. coli chromosome, or a segment of a eukaryotic chromosome with an origin of replication) must have a region where DNA replication initiates. In E. coli, this region is referred to as the genetic locus oriC; it occurs at map location 84 minutes (see g. 7.27). For DNA replication to begin, several steps must occur.
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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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Chemistry of the Gene
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First, the appropriate initiation proteins must recognize the speci c origin site.Then the site must be opened and stabilized. And, nally, a replication fork must be initiated in both directions, involving continuous and discontinuous DNA replication. Although most of the proteins involved are known, there are still a few gaps in our knowledge. OriC, the origin of replication in E. coli, is about 245 base pairs long and is recognized by initiator proteins. These proteins, the product of the dnaA locus, open up
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the double helix. (Other DNA-binding proteins are also involved here.) The initiator proteins then take part in the attachment of DNA helicase, the product of the dnaB gene, which unwinds DNA at the Y-junction. Helicase is then responsible for recruiting (binding) the rest of the proteins that form the replication initiation complex. First is primase, which creates RNA primers. Together, the helicase and primase comprise a primosome, attached to the lagging-strand template. As the primosomes move along, they create RNA primers that
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Previous Okazaki fragment P O Base Base P
Gap P HO O
New Okazaki fragment P O
Base
Base
Base
Base
DNA ligase
Previous Okazaki fragment P O Base Base O O P O P
Base
Base
P Figure 9.30
After DNA polymerase I removes the RNA primer to complete an Okazaki fragment, a nal gap remains. DNA ligase closes it.
O P New Okazaki fragment P O Base Base O P
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
9. Chemistry of the Gene1
The McGraw Hill Companies, 2001
DNA Replication The Enzymology
DNA polymerase III uses to initiate leading-strand synthesis. As primers are being laid down on the laggingstrand template, Okazaki fragment synthesis begins, and Y-junction activity then proceeds as outlined earlier (see gs. 9.28, 9.29, and 9.30). DNA polymerase III holoenzyme is a very large protein composed of ten subunits (table 9.4). Three of the subunits, , , and , form the polymerization core, with both 5 3 polymerase activity and 3 5 exonuclease activity. One subunit, the subunit, is a processivity clamp. As a dimer (two identical copies attached head to tail), the protein forms a doughnut around the DNA so it can move freely on the DNA. When it is attached to the core enzyme, the polymerase is held tightly to the DNA and shows high processivity ( g. 9.31): the leading strand is usually synthesized entirely without the enzyme leaving the template ( g. 9.32). The remaining subunits
are involved in processivity control and replisome formation. They allow the polymerase to move off and on the DNA of the lagging-strand template as Okazaki fragments are completed (a process known as polymerase cycling). Eukaryotes have evolved at least nine DNA polymerases, named DNA polymerase , , , , , , , , and . DNA polymerase seems to be the major replicating enzyme in eukaryotes, forming replisomes as in E. coli. In eukaryotes, the polymerase -primase complex adds the Okazaki fragment primers, rst adding an RNA primer and then a short length of DNA nucleotides. Polymerase may be involved in repair or in normal DNA replication, as is polymerase . DNA polymerase appears to replicate mitochondrial DNA. The remaining polymerases are probably involved in DNA repair, with polymerase being the major repair polymerase, as polymerase I is in
Table 9.4 Summary of the Enzymes Involved in DNA Replication in E. coli
Enzyme or Protein DNA polymerase I DNA polymerase II DNA polymerase III subunit subunit subunit subunit subunit subunit subunit subunit subunit subunit Helicase Primase Initiator protein DNA ligase Ssb protein DNA topoisomerase I DNA topoisomerase type II (DNA Gyrase) subunit subunit Topoisomerase IV Termination protein gyrA gyrB parE tus Relaxes supercoiled DNA; ATPase Relaxes supercoiled DNA Unconcatenates DNA circles Binds at termination sites dnaE dnaQ holE dnaN dnaX dnaX holA holB holC holD dnaB dnaG dnaA lig ssb topA Polymerization core; 5 3 polymerase Polymerization core; 3 5 exonuclease Polymerization core Processivity clamp (as a dimer) Preinitiation complex; dimerization of core Preinitiation complex; loads clamp Processivity core Processivity core Processivity core Processivity core Primosome; unwinds DNA Primosome; creates Okazaki fragment primers Binds at origin of replication Closes Okazaki fragments Binds single-stranded DNA Relaxes supercoiled DNA Genetic Locus polA polB Function Gap lling and primer removal Replicating damaged templates
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