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Chapter 2: DNA Synthesis (Replication)

Chapter 2: DNA Synthesis (Replication). Required reading: Stryer’s Biochemistry 5 th edition p. 127-128, 750-754, 759-766, 768-773 (or Stryer’s Biochemistry 4 th edition p. 88-93, 799-809, 982-986, 809-814). DNA Replication is semi-conservative. Meselson, Stahl 1958.

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Chapter 2: DNA Synthesis (Replication)

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  1. Chapter 2: DNA Synthesis (Replication) Required reading: Stryer’s Biochemistry 5th edition p. 127-128, 750-754, 759-766, 768-773 (or Stryer’s Biochemistry 4th edition p. 88-93, 799-809, 982-986, 809-814)

  2. DNA Replication is semi-conservative Meselson, Stahl 1958 • Both strands serve as templates for DNA synthesis • Each DNA molecule contains one • strand from original DNA and one • new strand

  3. DNA Polymerization Reaction Requirements for DNA polymerization • Template DNA (single stranded or double-stranded with a “nick”) • A primer strand with a free 3'- hydroxyl group (usually RNA) • Deoxynucleoside 5'-triphosphates (dATP, dGTP, dTTP and dCTP) • Mg2+ to activate the dNTPs • Polymerase and other accessory enzymes General reaction: 2Pi

  4. DNA Polymerization Reaction

  5. DNA Synthesis: addition of new dNTPsfollows Watson-Crick rules O H N N 2 NH N N N N NH 2 O G•C N NH 2 O N N HN N N O A•T Template base Incoming base G C C G T A A T

  6. 3’ 5’ Exonuclease

  7. 5’  3’ -exonuclease

  8. E. coli DNA Polymerase I Klenow Fragment 5' 3' Nucl. Polymerase N 3' 5‘ Nucl. C

  9. Typical Polymerase Structure: E. Coli Pol I fingers thumb palm polymerase exonuclease

  10. Polymerase with bound DNA

  11. Mechanism of phosphoryl transfer

  12. Polymerase fidelity mechanisms • Watson-Crick base pairing between the incoming dNTP • and the corresponding base in the template strand. • 2. H-bond formation between the minor groove of the new base pair • and the amino acids in the polymerase active site. • 3. Proofreading mechanism via 3' exonuclease that excises • incorrectly added nucleotides.

  13. 1. Correct Watson-Crick base pairing between the incoming dNTP and the corresponding base in the template strand induces conformational change required for polymerization reaction: Thumb Fingers

  14. 2. H-bond formation between the minor groove of the new base pair and amino acids in the polymerase active site:

  15. All Watson-Crick base pairs contain two H-bond acceptors at the same sites of the minor groove O N H N NH2 2 2 NH N N N N NH NH 2 2 O N NH 2 O N N HN N N HN 2 N O O N A•T N HN N N O G•C O N N NH N N O N T:A C:G

  16. 3. 3’-Exonuclease Proofreading function of DNA polymerases excises incorrectly added nucleotides.

  17. Fidelity of DNA Polymerization: Absolutely Essential!! Error Probability = Polymerization error (10-4) X 3' 5' Nuclease error (10-3) = 10-7 (1 in 10,000,000 nt)

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