Storage and Expression of Genetic Information

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1 Storage and Expression of Genetic Information 29. DNA structure, Replication and Repair ->Ch 25. DNA metabolism 30. RNA Structure, Synthesis and Processing ->Ch 26. RNA metabolism 31. Protein Synthesis ->Ch 27. Protein metabolism 32. Regulation of Gene Expression ->Ch 28. Regulation of Gene expression 33. Biotechnology and Human Disease ->Ch 9. DNA based-information technologies

2 DNA replication: genetic information found in DNA is copied and transmitted to daughter cells DNA contained in a fertilized egg -encodes the information that s direct the development of an organism (ie. Production of billions of cells) Each cell is specialized, -expressing only those functions that are required for it to perform its role in maintaining the organism. 1) replicate precisely each time a cell divides 2) have the information that it contains be selectively expressed.

3 CHAPTER 25 DNA Metabolism 25.1 DNA Replication 25.2 DNA Repair 25.3 DNA Recombination

4 Summary 25.1 DNA replication -Replication of DNA occurs with very high fidelity and at a designated time in the cell cycle. Replication is semiconservative, each strand acting as template for a new daughter strand. It is carried out in three identifiable phases: initiation, elongation, and termination. The process starts at a single origin in bacteria and usually proceeds bidirectionally. -DNA is synthesized in the 5 ->3 direction by DNA polymerases. At the replication fork, the leading strand is synthesized continuously in the same direction as replication fork movement; the lagging strand is synthesized discontinuously as Okazaki fragments, which are subsequently ligated. -The fidelity of DNA replication is maintained by (a) base selection by the polymerase, (2) a 3 - >5 profreading exonuclease activity that is part of most DNA polymerase, and (3) specific repir systems for mismatches left behind after replication. -Most cells have several DNA polymerase. In E. Coli DNA polymerase III is the primary replication enzyme. DNA polymerase I is responsible for special function during replication, recombination, and repair. -The separate initiation, elongation, and termination phases of DNA replication involve an array of enzymes and protein factors, many belonging to the AAA+ATPase family. -The replication proteins in bacteria are organized into replication factories, in which template DNA is spooled through two replisomes tethered to the bacterial plasma membrane.

5 The map shows the relative positions of genes encoding many of the proteins important in DNA metabolism. FIGURE 25-1 Map of the E. coli chromosome. The map shows the relative positions of genes encoding many of the proteins important in DNA metabolism. The number of genes known to be involved provides a hint of the complexity of these processes. The numbers 0 to 100 inside the circular chromosome denote a genetic measurement called minutes. Each minute corresponds to ~40,000 bp along the DNA molecule. The three-letter names of genes and other elements generally reflect some aspect of their function. These include mut, mutagenesis; dna, DNA replication; pol, DNA polymerase; rpo, RNA polymerase; uvr, UV resistance; rec, recombination; dam, DNA adenine methylation; lig, DNA ligase; Ter, termination of replication; and ori, origin of replication (oric in E. coli, as shown here).

6 Cell cycle: -The period preceding replication is called the G1 phase (Gap1) -DNA replication occurs during the S(synthesis) phase -G2 phase (Gap2) and M phase (mitosis) -mature neurons (Go phase) - cell cycle check points, cyclins and cyclin-dependent kinases(cdk) FIGURE 25-2 The Meselson-Stahl experiment. Proved the hypothesis of semiconservative replication proposed by Watson and Crick Cells were grown on a medium containing only 15 N isotope (heavy N) until all the DNA became fully 15 N-labeled ONE band when DNA centrifuged in CsCl Cells were then switched to 14 N medium and allowed to divide once ONE band but at a higher position than 15 N DNA but lower than completely 14 N DNA ( hybrid DNA) Cells were allowed to divide once more TWO bands, one with all 14 N DNA, one hybrid Figure (a) Cells were grown for many generations in a medium containing only heavy nitrogen, 15 N, so that all the nitrogen in their DNA was 15 N, as shown by a single band (blue) when centrifuged in a CsCl density gradient. (b) Once the cells had been transferred to a medium containing only light nitrogen, 14 N, cellular DNA isolated after one generation equilibrated at a higher position in the density gradient (purple band). (c) A second cycle of replication yielded a hybrid DNA band (purple) and another band (red), containing only [ 14 N]DNA, confirming semiconservative replication.

7 DNA Replication -The process starts at a single origin in bacteria and usually proceeds bidirectionially -It is carried out in three identifiable phase: initiations, elongation, and termination. ->Separation of the two complementary DNA stands ->Formation of the replication fork ->Direction of DNA replication, RNA primer ->Chain elongation ->Excision of RNA primers and their replacement by DNA ->DNA ligase

8 -DNA is synthesized in the 5->3 direction by DNA polymerases. - At the replication fork, the leading strand is synthesized continuously in the same direction as replication fork movement the lagging strand is synthesized discontinuously as Okazaki fragments, which are subsequently ligated FIGURE 25-4 Defining DNA strands at the replication fork. Initiation!! A. Separation of the two complementary DNA strands: -to be replicated, first, they must separate -> polymerases use only ssdna as a template -> Origin of replication -composed almost exclusively of AT base (Fig.29.9A) *Eukaryotes multiple replication site. (Fig.29.9B)

9 -Double-Helical DNA and RNA can be denatured >Long-term storage of info without alteration is so important to a cells DNA sturucutre pathological alteration ->carcinogenesis, aging Physiological alteration-> DNA replication or transcription >Molecular biology, medicine, forensic science FIGURE 8-26 Reversible denaturation and annealing (renaturation) of DNA. No covalent bonds are broken Heat and extreme ph Transition from double strand to single can be detected by monitoring UV absorption at 260nm-> increase in absorbtion (hyperchromic) <-> hypochromic

10 FIGURE Arrangement of sequences in the E. coli replication origin, oric. Consensus sequences (see p. 102) for key repeated elements are shown. N represents any of the four nucleotides. The horizontal arrows indicate the orientations of the nucleotide sequences (left-to-right arrow denotes sequence in top strand; right-to-left, bottom strand). FIS and IHF are binding sites for proteins described in the text. R sites are bound by DnaA. I sites are additional DnaA-binding sites (with different sequences), bound by DnaA only when the protein is complexed with ATP. -oric consists of 245bp and contains DNA sequence elements that are highly conserved among bacterial replication origins. -DUE: DNA unwinding element and R sites (DnaA protein binding site) *Consensus sequence: A sequence of DNA having similar structure and function in different organisms TABLE 25-3 Proteins Required to Initiate Replication at the E. coli Origin FIGURE Synthesis of Okazaki fragments. (a) At intervals, primase synthesizes an RNA primer for a new Okazaki fragment. Note that if we consider the two template strands as lying side by side, lagging strand synthesis formally proceeds in the opposite direction from fork movement. (b) Each primer is extended by DNA polymerase III. (c) DNA synthesis continues until the fragment extends as far as the primer of the previously added Okazaki fragment. A new primer is synthesized near the replication fork to begin the process again.

11 FIGURE25.5a Elongation of a DNA chain. (a)dna polymerase I activity requires a single unpaired strand to act as template and a primer strand to provide a free hydroxyl group at the 3 end, to which a new nucleotide unit is added. Each incoming nucleotide is selected in part by base pairing to the appropriate nucleotide in the template strand. The reaction product has a new free 3 hydroxyl, allowing the addition of another nucleotide. FIGURE 25-5b Elongation of a DNA chain. (b) The catalytic mechanism likely involves two Mg 2+ ions, coordinated to the phosphate groups of the incoming nucleotide triphosphate and to three Asp residues, two of which are highly conserved in all DNA polymerases. The Mg 2+ ion depicted on the right facilitates attack of the 3 -hydroxyl group of the primer on the α phosphate of the nucleotide triphosphate; the other Mg 2+ ion facilitates displacement of the pyrophosphate. Both ions stabilize the structure of the pentacovalent transition state. RNA polymerases use a similar mechanism (see Figure 26-1b). Direction! 5 ->3

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