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Introduction to Chemical Bonds and Interactions in Biology

Introduction to Chemical Bonds and Interactions in Biology. Chemistry and Chemical Biology Rutgers University. Overview. Atoms and Bonds Properties of single bonds (covalent) Chirality Configuration Conformation Interactions in Biology Non-covalent Hydrogen bonding

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Introduction to Chemical Bonds and Interactions in Biology

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  1. Introduction to Chemical Bonds and Interactions in Biology Chemistry and Chemical Biology Rutgers University

  2. Overview • Atoms and Bonds • Properties of single bonds (covalent) • Chirality • Configuration • Conformation • Interactions in Biology • Non-covalent • Hydrogen bonding • Hydrophobic interactions • Electrostatic interactions • Covalent • Disulfide bridges • Coordinate bonds

  3. Atoms

  4. Bonds • The atoms of the elements form characteristic number of bonds. • The grey atoms represent atoms of elements that can form one, two or three bonds.

  5. More on Bonds

  6. Even more on Bonds

  7. Representing Bonds

  8. Properties of Single Bonds (Covalent) • Chirality • Configuration • Conformation

  9. Chirality

  10. Molecular Chirality

  11. Configuration • To go from a-D-glucose to b-D-glucose a bond has to be broken

  12. L- and D- configurations of amino acids

  13. Conformation • Described in terms of torsion angles • Rotation around bond • No bonds broken • Minimize non bonded interactions

  14. Nomenclature Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, p. 16.

  15. Cyclohexanes Pyranose sugars Conformation Examples Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, pp. 249-250.

  16. Non-covalent Interactions in Biology • Non-covalent: • Hydrogen bonds • Hydrophobic interactions • Electrostatic interactions • Covalent: • Disulfide bonds • Coordinate bonds

  17. Hydrogen bonding

  18. Examples of Hydrogen Bonding Water Hydrogen Bonding Ice structure Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, p. 30.

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

  20. Electrostatic interactions Example of electrostatic interaction in PDB entry 1HSA (MHC complex)

  21. Disulfide Bridges Example of a disulfide bond in PDB entry 1HSA (MHC complex)

  22. Coordinate Bonding N-ter Example of a Zinc Finger domain From PDB entry 1ZAA (ZIF268 protein) C-ter

  23. References Creighton, Thomas. Proteins: Structures and Molecular Principles. W. H. Freeman and Company, 1984, p. 160. Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, pp. 15-16. Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, pp. 30-33, 68-69, 179, 248-250.

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