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(a) Autoradiograph of E. coli DNA during replication. (b) Diagram has labels on the three segments, A, B, and C, created by the existence of two forks, X and Y, in the DNA. Forks are created when the circle opens for replication. Length of the chromosome is about 1,300 m. ([a] From J.
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Cairns, The chromosome of E. coli , Cold Spring Harbor Symposia on Quantitative Biology, 28. Copyright 1963 by Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Reprinted by permission.)
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9. Chemistry of the Gene1
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Origin
Observable stages in the DNA replication of a circular chromosome, assuming bidirectional DNA synthesis. The intermediate gures are called theta structures.
Origin
Origin
Origin
Origin
Unidirectional
Radioactive label at only one Y-junction
Origin
Bidirectional
Radioactive label at both Y-junctions
Radioactive labels distinguish unidirectional from bidirectional DNA replication. In these hypothetical experiments, DNA replication was allowed to begin, and then a radioactive label was added. After a short period of time, the process was stopped and the autoradiographs prepared. In bidirectional replication (the actual case), the label appears at both Yjunctions.
5 kb
had already begun forming. Figure 9.23 illustrates hypothetical outcomes for either unidirectional or bidirectional replication. By counting silver grains in autoradiographs, Cairns found growth to be bidirectional. Both autoradiographic and genetic analysis have subsequently veri ed this nding. In eukaryotes, the DNA molecules (chromosomes) are larger than in prokaryotes and are not circular; there are also usually multiple sites for the initiation of replication. Thus, each eukaryotic chromosome is composed of many replicating units, or replicons stretches of DNA with a single origin of replication. In comparison, the E. coli chromosome is composed of only one replicon. In eukaryotes, these replicating units form bubbles (or eyes ) in the DNA during replication ( g. 9.24).
(b) Figure 9.24
Replication bubbles. (a) Formation of bubbles (eyes) in eukaryotic DNA because of multiple DNA synthesis sites of origin. (b) Electron micrograph (and explanatory line drawing) of replicating Drosophila DNA showing these bubbles.
([b] H. Kreigstein and D. Hogness, Mechanism of DNA replication in Drosophila chromosomes: Structure of replication forks and evidence for bidirectionality, Proceeding of the National Academy of Sciences USA, 71 (1974):135 39. Reproduced by permission.)
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
9. Chemistry of the Gene1
The McGraw Hill Companies, 2001
DNA Replication The Enzymology
D N A R E P L I C AT I O N _ THE ENZYMOLOGY
Let us turn now to the details of the processes that take place during DNA replication. Like virtually all metabolic processes, DNA replication is under the control of enzymes. The evidence for the details we describe comes from physical, chemical, and biochemical studies of enzymes and nucleic acids and from the analysis of mutations that in uence the replication processes. More recent techniques of recombinant DNA technology and nucleotide sequencing have allowed us to determine the nucleotide sequences of many of these key regions in DNA and RNA. We will look rst at E. coli. There are three major enzymes that will polymerize nucleotides into a growing strand of DNA in E. coli. These enzymes are DNA polymerase I, II, and III. DNA polymerase I, discovered by Arthur Kornberg, who subsequently won the Nobel Prize for his work, is primarily utilized in lling in small DNA segments during replication and repair processes. DNA polymerase II can serve as an alternative repair polymerase; it can also replicate DNA if the template is damaged. DNA polymerase III is the primary polymerase during normal DNA replication.
refer to the numbering of carbon atoms across the sugar. In gure 9.25, going from the bottom of the gure to the top, the left-hand strand is a 3 5 strand, and the right-hand strand is a 5 3 strand. Since DNA replication involves the formation of two new antiparallel strands with the old single strands as templates, one new strand would have to be replicated in the 5 3 direction and the other in the 3 5 direction. However, all the known polymerase enzymes add nucleotides in only the 5 3 direction. That is, the polymerase catalyzes a bond between the rst 5 -PO4 group of a new nucleotide and the 3 -OH carbon of the last nucleotide in the newly synthesized strand ( g. 9.25). The polymerases cannot create the same bond with the 5 phosphate of a nucleotide already in the DNA and the 3 end of a new nucleotide. Thus, the simple model needs some revision.
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