DNA - Replication and Repair

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DNA - Replication and Repair

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Cell Cycle Regulators Replication Commitment Cell Growth & Completion of Replication Cell Division Cell Division and DNA Replication Replication Initiation

Replication:

Replication Replication is the process by which each strand of the DNA duplex is copied precisely, by base pairing with complementary nucleotides. Replication – Semi conservative, bidirectional, discontinuous, antiparallel copying of each strand of a DNA duplex, directed by base pairing, to form two identical duplexes.

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DNA Replication DNA replication is semi-conservative , one strand serves as the template for the second strand. Furthermore, DNA replication only occurs at a specific step in the cell cycle. The following table describes the cell cycle for a hypothetical cell with a 24 hr cycle. Stage Activity Duration G1 Growth and increase in cell size 10 hr S DNA synthesis 8 hr G2 Post-DNA synthesis 5 hr M Mitosis 1 hr DNA replication has two requirements that must be met: 1. DNA template 2. Free 3' -OH group

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The mammalian cell cycle G1 S G2 M G0 DNA synthesis and histone synthesis Growth and preparation for cell division Rapid growth and preparation for DNA synthesis Quiescent cells phase phase phase phase Mitosis

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DNA replication is semi-conservative Parental DNA strands Daughter DNA strands Each of the parental strands serves as a template for a daughter strand

Replication of DNA:

Prentice Hall © 2007 Chapter Twenty Six 6 Replication of DNA DNA replication begins in the nucleus with partial unwinding of the double helix; this process involves enzymes known as helicases . The unwinding occurs simultaneously in many specific locations known as origins of replication . The DNA strands separate, exposing the bases. These branch points, called replication forks , provide a “bubble” into which the replication process can begin.

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A General Model for DNA Replication 1. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. 2. A free 3'OH group is required for replication, but when the two chains separate no group of that nature exists. RNA primers are synthesized, and the free 3'OH of the primer is used to begin replication. 3. The replication fork moves in one direction, but DNA replication only goes in the 5' to 3' direction. This paradox is resolved by the use of Okazaki fragments. These are short, discontinuous replication products that are produced off the lagging strand . This is in comparison to the continuous strand that is made off the leading strand . 4. The final product does not have RNA stretches in it. These are removed by the 5' to 3' exonuclease action of Polymerase I. 5. The final product does not have any gaps in the DNA that result from the removal of the RNA primer. These are filled in by the 5’ to 3’ polymerase action of DNA Polymerase I. 6. DNA polymerase does not have the ability to form the final bond. This is done by the enzyme DNA ligase .

Features of Replication :

Features of Replication Replication is bidirectional The double helix must be unwound - by helicases Supercoiling must be compensated - by DNA gyrase Replication is semidiscontinuous Leading strand is formed continuously Lagging strand is formed from Okazaki fragments - discovered DNA Pol III uses an RNA primer A special primase forms the required primer DNA Pol I excises the primer DNA ligase seals the "nicks" between Okazaki fragments.

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Proteins of DNA Replication To prepare DNA for replication, a series of proteins aid in the unwinding and separation of the double-stranded DNA molecule. 1. DNA Helicases - These proteins bind to the double stranded DNA and stimulate the separation of the two strands. 2. DNA single-stranded binding proteins - These proteins bind to the DNA as a tetramer and stabilize the single-stranded structure that is generated by the action of the helicases. Replication is 100 times faster when these proteins are attached to the single- stranded DNA. 3. DNA Topoisomerase - This enzyme catalyzes the formation of negative supercoils that is thought to aid with the unwinding process.

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4. DNA Polymerase - DNA Polymerase I (Pol I) was the first enzyme discovered with polymerase activity. That enzyme is DNA Polymerase III (Pol III). Three activities are associated with DNA polymerase I; * 5' to 3' elongation (polymerase activity) * 3' to 5' exonuclease (proof-reading activity) * 5' to 3' exonuclease (repair activity) The second two activities of DNA Pol I are important for replication, but DNA Polymerase III (Pol III) is the enzyme that performs the 5'-3' polymerase function. 5. Primase - The requirement for a free 3' hydroxyl group is fulfilled by the RNA primers that are synthesized at the initiation sites by these enzymes. 6. DNA Ligase - Nicks occur in the developing molecule because the RNA primer is removed and synthesis proceeds in a discontinuous manner on the lagging strand. The final replication product does not have any nicks because DNA ligase forms a covalent phosphodiester linkage between 3'-hydroxyl and 5'-phosphate groups.

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BACTERIAL DNA Polymerase Enzyme Primary function DNA Pol I (PolA) Major DNA repair enzyme DNA Pol II DNA repair DNA Pol III De novo synthesis of new DNA _______________________________________________ MAMMALIAN Enzyme Primary function Location DNA Pol I ( ) Strand synthesis initiation Nucleus DNA Pol II () DNA repair Nucleus DNA Pol III () Strand extension Nucleus DNA Pol  DNA repair Nucleus DNA Pol  De novo synthesis of new DNA Mitochon.

DNA Repair :

DNA Repair Mismatch repair systems scan DNA duplexes for mismatched bases, excise the mispaired region and replace it Pyrimidine dimers can be repaired by photolyase Excision repair : DNA glycosylase removes damaged base, creating an "AP site" . AP endonuclease cleaves backbone, exonuclease removes several residues and gap is repaired by DNA polymerase and DNA ligase