Aug 25 - Biochem 423 Robert A. Orlando, Ph.D. SECTION 1:...

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Unformatted text preview: Biochem 423 Robert A. Orlando, Ph.D. SECTION 1: BIOLOGICAL STRUCTURES AND ENZYME FUNCTION WATER – IONIZATION – BUFFERING (REVIEW OF GEN CHEM) WATER = 50‐60% IN ADULTS – 75% IN CHILDREN Biochemistry = chemistry in water (so reactants need to be dissolved in water to function) WATER – ALL FUNCTIONS GEARED TO MAINTAIN HOMEOSTASIS SOLVATION OF SMALL MOLECULES TRANSPORT SMALL MOLECULES THROUGH THE BODY DISSIPATE HEAT CHEMICAL REACTANT – HYDROLYSIS SIDE NOTE: OBESITY HAS LESS WATER ASSOCIATED – DUE TO EXCESS FAT EARLY WEIGHT LOSS DUE TO WATER LOSS 5 | P a g e Biochem 423 Robert A. Orlando, Ph.D. WHY WATER IS A GOOD SOLVENT – WATER IS POLAR DIPOLE NATURE – OXYGEN IS MORE ELECTRONEGATIVE LEADS TO ALTERED CHARGE DISTRIBUTION – PARTIAL CHARGES 6 | P a g e Biochem 423 Robert A. Orlando, Ph.D. ORDERED STRUCTURE OF WATER – ICE ICE IS NOT USEFUL IN BIOCHEMISTRY, BUT SOLVATION IS 7 | P a g e Biochem 423 Robert A. Orlando, Ph.D. IN PROTEINS, WATER HYDRATES PEPTIDE BACKBONE AND AMINO ACID SIDE GROUPS Thermodynamics of water H‐bonds last 10 picoseconds (10 x 10‐12 seconds) Water molecule remains in hydration shell for only 2.4 nanoseconds (2.4 x 10‐9 seconds) Take home message: VERY DYNAMIC FLUIDIC MOVEMENTS 8 | P a g e Biochem 423 Robert A. Orlando, Ph.D. FOUR TYPES OF NON‐COVALENT BONDS ALL NON‐COVALENT BONDS ARE GENERALLY WEAK AND THUS READILY REVERSIBLE. BUT MANY BONDS ARE POSSIBLE, SO CUMULATIVE ENERGY CONTRIBUTIONS PROVIDE SIGNIFICANT STRENGTH. 9 | P a g e Biochem 423 Robert A. Orlando, Ph.D. COMPARISONS OF BOND STRENGTH COVALENT BOND ENERGY = 350‐450 KJ/MOL HYDROGEN BONDS ‐‐ H‐BOND ENERGY = 8‐21 KJ/MOL IONIC BONDS – ELECTROSTATIC INTERACTIONS 40‐90 KJ/MOL 11 Na 17Cl 10 | P a g e Biochem 423 Robert A. Orlando, Ph.D. HYDROPHOBIC INTERACTIONS – BOND ENERGY = 4‐8 KJ/MOLE 11 | P a g e Biochem 423 Robert A. Orlando, Ph.D. VAN DER WAALS INTERACTIONS – BOND ENERGY = 4 KJ/MOLE GECKOS HAVE A MAT OF MILLIONS OF MICROSCOPIC HAIRS, CALLED SETAE, ON THEIR TOES THAT HAVE EVEN TINIER SPLIT ENDS, CALLED SPATULAE. THIS INTRICATE DESIGN ENABLES AN ELECTRIC FORCE THAT ATTRACTS MOLECULES TO EACH OTHER — THE VAN DER WAALS FORCE — TO SUPPLY THE ENERGY TO HOLD A GECKO TO A SMOOTH SURFACE. 12 | P a g e Biochem 423 Robert A. Orlando, Ph.D. PH 13 | P a g e Biochem 423 Robert A. Orlando, Ph.D. IONIZATION OF WATER – PH OF WATER (DEFINES NEUTRALITY) Keq = [H+][OH‐] [H2O] ← (55.5 M = PURE WATER) REARRANGE TO, (55.5 M) Keq = [H+][OH‐] = Kw (ION PRODUCT OF WATER) Keq = 1.8 X 10‐16 M (MEASURED BY ELECTRICAL CONDUCTIVITY) THEN, KW = 1X 10‐14 M2 KW = [H+][OH‐] = [H+]2 (H+ AND OH‐ ARE EQUAL IN PURE WATER) SO, [H+] = SQUARE ROOT OF 1 X 10 ‐14 2 ‐7 M = 1 X 10 M PH = ‐ LOG [H+] = 7 FOR PURE WATER 14 | P a g e Biochem 423 Robert A. Orlando, Ph.D. BUFFERING – ACETIC ACID AS EXAMPLE Ka = EQUILIBRIUM CONSTANT FOR DISSOCIATION OF WEAK ACID Ka = [H+][AC‐] AC‐ = CONJUGATE BASE [HAC] HA = CONJUGATE ACID 15 | P a g e Biochem 423 Robert A. Orlando,Ph.D. RELATIONSHIP BETWEEN PH AND PKa IS DEFINED BY: HENDERSON‐HASSELBALCH EQUATION PH = PKa + LOG [A‐] (PROTON ACCEPTOR) [HA] (PROTON DONOR) PH = PKa at 50% H+ dissociation 16 | P a g e ...
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