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Biochem synthesis of dna

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  • Enzymes more than a dozen enzymes & other proteins participate in DNA replication
  • The energy rules the process.
  • In 1953, Kornberg was appointed head of the Department of Microbiology in the Washington University School of Medicine in St. Louis. It was here that he isolated DNA polymerase I and showed that life (DNA) can be made in a test tube. In 1959, Kornberg shared the Nobel Prize for Physiology or Medicine with Severo Ochoa — Kornberg for the enzymatic synthesis of DNA, Ochoa for the enzymatic synthesis of RNA.
  • The energy rules the process.
  • Transcript

    • 1. 2007-2008 Synthesis of DNA June.21.2010
    • 2. DNA synthesis occurs by the process of replication. During replication, each of the two parental strands of DNA serves as a template for the synthesis of a Complementary strand.
    • 3. Each molecule generated by the replication process contains one intact parental strand and one newly synthesized strand .
    • 4. In eukaryotes, DNA replication occurs during the S phase of the cell cycle The cell divides during the next phase ( M ), and each daughter cell receives an exact copy of the DNA of the parent cells.
    • 5. Cultured MDCK cells Day 1 Day 3
    • 6. Watson and Crick 1953 article in Nature
    • 7. Double helix structure of DNA “ It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” Watson & Crick
    • 8. Directionality of DNA
      • You need to number the carbons!
        • it matters!
      OH CH 2 O 4  5  3  2  1  PO 4 N base ribose nucleotide This will be IMPORTANT !!
    • 9. The DNA backbone
      • Putting the DNA backbone together
        • refer to the 3  and 5  ends of the DNA
          • the last trailing carbon
      OH O 3  PO 4 base CH 2 O base O P O C O – O CH 2 1  2  4  5  1  2  3  3  4  5  5  Sounds trivial, but … this will be IMPORTANT !!
    • 10. Anti-parallel strands
      • Nucleotides in DNA backbone are bonded from phosphate to sugar between 3  & 5  carbons
        • DNA molecule has “direction”
        • complementary strand runs in opposite direction
      3  5  5  3 
    • 11. Bonding in DNA … . strong or weak bonds? How do the bonds fit the mechanism for copying DNA? 3  5  3  5  covalent phosphodiester bonds hydrogen bonds
    • 12. Base pairing in DNA
      • Purines
        • adenine (A)
        • guanine (G)
      • Pyrimidines
        • thymine (T)
        • cytosine (C)
      • Pairing
        • A : T
          • 2 bonds
        • C : G
          • 3 bonds
    • 13. Copying DNA
      • Replication of DNA
        • base pairing allows each strand to serve as a template for a new strand
        • new strand is 1/2 parent template & 1/2 new DNA
    • 14. DNA Replication
      • Large team of enzymes coordinates replication
      Let ’ s meet the team …
    • 15. Replication: 1st step
      • Unwind DNA
        • helicase enzyme
          • unwinds part of DNA helix
          • stabilized by single-stranded binding proteins
      single-stranded binding proteins replication fork helicase
    • 16. Replication: 2nd step DNA Polymerase III But … We ’ re missing something ! What? Where ’ s the ENERGY for the bonding !
      • Build daughter DNA strand
        • add new complementary bases
        • DNA polymerase III
    • 17. Energy of Replication
      • Where does energy for bonding usually come from?
      energy ATP GTP TTP CTP ADP AMP GMP TMP CMP modified nucleotide energy We come with our own energy ! And we leave behind a nucleotide ! You remember ATP ! Are there other ways to get energy out of it? Are there other energy nucleotides? You bet !
    • 18. Energy of Replication
      • The nucleotides arrive as nucleosides
        • DNA bases with P – P – P
          • P-P-P = energy for bonding
        • DNA bases arrive with their own energy source for bonding
        • bonded by enzyme: DNA polymerase III
      ATP GTP TTP CTP
    • 19.
      • Adding bases
        • can only add nucleotides to 3  end of a growing DNA strand
          • need a “starter” nucleotide to bond to
        • strand only grows 5  3 
      Replication DNA Polymerase III DNA Polymerase III DNA Polymerase III DNA Polymerase III energy energy energy energy 3  3  5  B.Y.O. ENERGY ! The energy rules the process 5 
    • 20. energy 3  5  5  5  3  need “primer” bases to add on to energy energy energy 3  no energy to bond energy energy energy 3  5   ligase
    • 21. Leading & Lagging strands
      • Limits of DNA polymerase III
        • can only build onto 3  end of an existing DNA strand
      Leading strand Lagging strand Okazaki fragments
      • Leading strand
        • continuous synthesis
      • Lagging strand
        • Okazaki fragments
        • joined by ligase
          • “ spot welder” enzyme
      DNA polymerase III   growing replication fork 5  5  5  5  3  3  3  5  3  5  3  3  ligase Okazaki 3  5 
    • 22. Replication fork / Replication bubble leading strand lagging strand leading strand lagging strand leading strand lagging strand DNA polymerase III 5  3  5  3  5  3  3  5  5  3  5  3  5  3  5  3  growing replication fork growing replication fork 5  5  5  5  5  3  3  5  5  5  3 
    • 23. Starting DNA synthesis: RNA primers
      • RNA primer
        • built by primase
        • serves as starter sequence for DNA polymerase III
      • Limits of DNA polymerase III
        • can only build onto 3  end of an existing DNA strand
      growing replication fork primase RNA DNA polymerase III 5  5  5  3  3  3  5  3  5  3  5  3 
    • 24. Replacing RNA primers with DNA
      • DNA polymerase I
        • removes sections of RNA primer and replaces with DNA nucleotides
      But DNA polymerase I still can only build onto 3  end of an existing DNA strand growing replication fork DNA polymerase I RNA 5  5  5  5  3  3  3  3  ligase
    • 25. Chromosome erosion
      • Loss of bases at 5  ends in every replication
        • chromosomes get shorter with each replication
        • limit to number of cell divisions?
      DNA polymerase III All DNA polymerases can only add to 3  end of an existing DNA strand growing replication fork DNA polymerase I RNA Houston, we have a problem ! 5  5  5  5  3  3  3  3 
    • 26. Telomeres
      • Repeating, non-coding sequences at the end of chromosomes = protective cap
        • limit to ~50 cell divisions
      • Telomerase
        • enzyme extends telomeres
        • can add DNA bases at 5  end
        • different level of activity in different cells
          • high in stem cells & cancers -- Why?
      telomerase growing replication fork TTAAGGG TTAAGGG TTAAGGG 5  5  5  5  3  3  3  3 
    • 27. Replication fork 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ helicase SSB = single-stranded binding proteins primase DNA polymerase III DNA polymerase III DNA polymerase I ligase Okazaki fragments leading strand lagging strand SSB direction of replication
    • 28. DNA polymerases
      • DNA polymerase III
        • 1000 bases/second !
        • main DNA builder
      • DNA polymerase I
        • 20 bases/second
        • editing, repair & primer removal
      DNA polymerase III enzyme Arthur Kornberg 1959 Roger Kornberg 2006
    • 29. Editing & proofreading DNA
      • 1000 bases/second = lots of typos!
      • DNA polymerase I
        • proofreads & corrects typos
        • repairs mismatched bases
        • removes abnormal bases
          • repairs damage throughout life
        • reduces error rate from 1 in 10,000 to 1 in 100 million bases
    • 30. Fast & accurate!
      • It takes E . coli <1 hour to copy 5 million base pairs in its single chromosome
        • divide to form 2 identical daughter cells
      • Human cell copies its 6 billion bases & divide into daughter cells in only few hours
        • remarkably accurate
        • only ~1 error per 100 million bases
        • ~30 errors per cell cycle
    • 31. What does it really look like? 1 2 3 4
    • 32. 2007-2008 Any Questions??
    • 33. Energy of Replication
      • Where does energy for bonding usually come from?
      energy ATP GTP TTP ATP ADP AMP GMP TMP AMP modified nucleotide We come with our own energy ! And we leave behind a nucleotide ! You remember ATP ! Are there other ways to get energy out of it?
    • 34.
      • Adding bases
        • can only add nucleotides to 3  end of the growing DNA strand
          • need a primer nucleotide to bond to
        • strand grows 5  3 
      Replication DNA Polymerase III energy 3  3  5  B.Y.O. ENERGY ! The energy rules the process 5 
    • 35. 5  3  3  5  3  5  3  5  no energy to bond 
    • 36. energy 5  3  3  5  3  5  3  5  ligase
    • 37. Chromosome erosion
      • Loss of bases at 5  ends in every replication
        • chromosomes get shorter with each replication
        • limit to number of cell divisions?
      DNA polymerase III DNA polymerases can only add to 3  end of an existing DNA strand growing replication fork DNA polymerase I Houston, we have a problem ! 5  5  5  5  3  3  3  3 
    • 38. Replication fork 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ direction of replication
    • 39. DNA synthesis in prokaryotes
      • Replication is bidirectional.
      • Replication is semi-conservative.
    • 40. Bidirectional replication of a circular chromosome Replication begins at the point of origin ( oriC ) and proceeds in both directions at the same time.
    • 41. Unwinding of Parental Strands Topoisomerases: can break phosphodiester bonds and rejoin them relieve the supercoiling of the parental duplex caused by unwinding . DNA gyrase is a major topoisomerase in bacterial cells.
    • 42. 以上です。