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SURVEY OF BIOCHEMISTRY Nucleic Acids

SURVEY OF BIOCHEMISTRY Nucleic Acids. What are nucleic acids?. Building blocks of genetic material that a cell uses to direct cellular functions and heredity 3 Components: Sugar Moiety. Ribose (in RNA). Deoxyribose (in DNA). Ring Numbering in Ribose. 5’. 4’. 1’.

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SURVEY OF BIOCHEMISTRY Nucleic Acids

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  1. SURVEY OF BIOCHEMISTRYNucleic Acids CHEM 3511 - Summer 2008

  2. What are nucleic acids? • Building blocks of genetic material that a cell uses to direct cellular functions and heredity • 3 Components: Sugar Moiety Ribose (in RNA) Deoxyribose (in DNA) CHEM 3511 - Summer 2008

  3. Ring Numbering in Ribose 5’ 4’ 1’ DNA lacks the2’-OH group 3’ 2’ CHEM 3511 - Summer 2008

  4. What are nucleic acids? • Building blocks of genetic material that a cell uses to direct cellular functions and heredity • 3 Components: Phosphate Moiety Phosphate Group Phosphoric Acid CHEM 3511 - Summer 2008

  5. What are nucleic acids? • Building blocks of genetic material that a cell uses to direct cellular functions and heredity • 3 Components: 5 Nitrogenous Bases Guanine G PURINES Adenine A CHEM 3511 - Summer 2008

  6. What are nucleic acids? • Building blocks of genetic material that a cell uses to direct cellular functions and heredity • 3 Components: 5 Nitrogenous Bases Cytosine C Thymine T Uracil U PYRIMIDINES CHEM 3511 - Summer 2008

  7. Ring Numbering in Bases Adenine A 6 7 5 1 8 2 4 9 3 CHEM 3511 - Summer 2008

  8. Ring Numbering in Bases Cytosine C 4 5 3 2 6 1 CHEM 3511 - Summer 2008

  9. Nomenclature Base Nucleoside Nucleotide Adenine Adenosine Adenosine A Monophosphate Guanine Guanosine Guanosine G Monophosphate Etc. Study Table 3-1 for more details… CHEM 3511 - Summer 2008

  10. How do nucleotides link? CHEM 3511 - Summer 2008

  11. Base Pairing Carbon Nitrogen Oxygen Hydrogen CHEM 3511 - Summer 2008

  12. Base Pairing Carbon Nitrogen Oxygen Hydrogen CHEM 3511 - Summer 2008

  13. How Does RNA Differ from DNA? • Ribose vs. Deoxyribose • Bases and Base Pairing • T in DNA vs. U in RNA • A-T in DNA vs. A-U in RNA • 3D Structure • Role CHEM 3511 - Summer 2008

  14. Protein Data Bank http://www.rcsb.org/pdb/home/home.do CHEM 3511 - Summer 2008

  15. Protein Data Bank • Download PDB file to Desktop • Use Freeware to View Contents • RasMol • PyMol • Swiss PDB Viewer • Protein Explorer CHEM 3511 - Summer 2008

  16. Software for Viewing Structures • Rasmol • http://www.rasmol.org • Pymol • http://pymol.sourceforge.net • SwissPDB Viewer • http://www.expasy.ch/spdbv/ • Protein Explorer • http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/frntdoo2.htm CHEM 3511 - Summer 2008

  17. DNA Double Helix CHEM 3511 - Summer 2008

  18. DNA Structural Features • Handedness • Anti-parallel strands • Major and minor grooves CHEM 3511 - Summer 2008

  19. Different Conformations of DNA CHEM 3511 - Summer 2008

  20. DNA has incredible flexibility! Catabolite-ActivatorProtein (CAP) + DNA Yale (1991) CHEM 3511 - Summer 2008

  21. DNA has incredible flexibility! DNA Octahedron Ned SeemanNYU International Society for Nanoscale Science, Computation, and Engineering CHEM 3511 - Summer 2008

  22. More on Friday… • Limitations to DNA Flexibility • Supercoiling and Topoisomerases • RNA Structure • Nucleic Acid Function • Recombinant DNA Technology • Potentially PRS questions… CHEM 3511 - Summer 2008

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