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Torsion Angles Dihedral Angles

Torsion Angles Dihedral Angles. Saenger, Wolfram. Principles of Nucleic Acid Structure . Springer-Verlag New York Inc., 1984, p. 15. Water hydrogen bonding. Voet, Donald and Judith G. Biochemistry . John Wiley & Sons, 1990, p. 30. Ice structure.

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Torsion Angles Dihedral Angles

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  1. Torsion Angles Dihedral Angles Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p. 15.

  2. Water hydrogen bonding Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 30.

  3. Ice structure Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 31.

  4. Clathrate hydrates Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 179.

  5. Torsion Angles Dihedral Angles Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p. 15.

  6. Components: Sugar, Base, Phosphate • 5’ to 3’ direction • RNA - ribose • DNA- deoxyribose • Numbering Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 792.

  7. Names Numbering Bonding character Position of hydrogen Tautomers Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 18.

  8. Geometry of Watson Crick base pairs A:T and G:C are similar Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 797.

  9. Backbone conformation Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 807.

  10. B DNA View down helix axis Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 799.

  11. Space filling B DNA Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 796.

  12. A DNA Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 800.

  13. Z DNA Left handed Very deep minor groove Major groove on outside Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 802.

  14. A form conformation Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, p. 141.

  15. Conserved and semi conserved bases Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 905.

  16. Ribosome

  17. Four Levels of Protein Structure • Primary, 1o • the amino acid sequence • Secondary, 2o • Local conformation of main-chain atoms (FandYangles) • Tertiary, 3o • 3-D arrangement of all the atoms in space (main-chain and side-chain) • Quaternary, 4o • 3-D arrangement of subunit chains

  18. Primary, alent bonds. Secondary, Tertiary, Quaternary - determined by weak forces (H-bonds, etc.)

  19. Amino Acids • It is the amino acid sequence that “exclusively” determines the 3D structure of a protein • 20 amino acids – modifications do occur post protein synthesis

  20. Amino Acids “corn crib” Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 68.

  21. Peptide Bond Formation • Individual amino acids form a polypeptide chain • Such a chain is a component of a hierarchy for describing macromolecular structure • The chain has its own set of attributes

  22. A dihedral angle is the angle between two planes defined by 4 atoms – 123 make one plane 234 the other • Omega is the rotation around the peptide bond Cn – Nn+1 – it is planar and is 180 under ideal conditions • Phi is the angle around N – Calpha • Psi is the angle around Calpha C’ • The values of phi and psi are constrained to certain values based on steric clashes of the R group. Thus these values show characteristic patterns as defined by the Ramachandran plot Geometry of the Chain From Brandon and Tooze

  23. Shows allowed and disallowed regions Gly and Pro are acceptions: Gly has no limitation; Pro is constrained by the fact its side chain binds back to the main chain Gray = allowed conformations. bA, antiparallel b sheet; bP, parallel b sheet; bT, twisted b sheet (parallel or anti-parallel); a, right-handed a helix; L, left-handed helix; 3, 310 helix; p, p helix. Ramachandran Plot

  24. aHelix

  25. If N-terminus is at bottom, then all peptide N-H bonds point “down” and all peptide C=O bonds point “up”. N-H of residue n is H-bonded to C=O of residue n+4. a-Helixhas: 3.6 residues per turn Rise/residue = 1.5 Å Rise/turn = 5.4Å aHelix

  26. Polar Hydrophobic Amphipathic R-groups extend radially from the a-helix core, shown in helical wheel diagram. a-helicescan be:

  27. Stabilized by interchain H-bonds between N-H & C=O Peptide chains are fully extended; pleated shape because adjacent peptides groups can’t be coplanar. b Sheet

  28. bSheet - 2 Orientations Parallel Not optimum H-bonds; less stable Anti-parallel Optimum H-bonds; more stable

  29. The Beta Turn – 2 Conformations Only Difference

  30. Quaternary Structure: Ferritin The Body’s Iron Storage Protein

  31. Super-secondary Structure b-turnsin a protein chain allow helices and sheets to align side-by-side bab aa bmeander

  32. Super-secondary Structure

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