2 - Kuo, 580.221 7 Sept 2004 Concepts/Vocabulary Molecules...

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Kuo, 580.221 7 Sept 2004 1 BME 580.221 Chemical Basis of Binding Lecture #02, 7 Sep 2004 Scot C. Kuo 7 Sept 2004 Kuo, 580.221 Concepts/Vocabulary • Molecular specificity (role of concentration and affinity, K d ) • Covalent vs. Non-covalent bonds • 4 Weak Forces: H-bonds , Ionic ( pH ), Hydrophobic/hydrophilic , van der Waals polarity/directionality of some weak bonds 7 Sept 2004 Kuo, 580.221 Osmotic pressure (movement of water) Note: Water also moves through the membrane … 7 Sept 2004 Kuo, 580.221 Specificity vs. Affinity Affinity : Between Receptor and 1 Ligand Specificity : Between Receptor and 2 different Ligands (RA) R + A or (RB) R + B or hence: Remember, smaller K d means tighter binding. Numerical example onto board. ] [ ] ][ [ RA A R K A = A K A R RA ] [ ] [ ] [ = ] [ ] ][ [ RB B R K B = B K B R RB ] [ ] [ ] [ = A B K A B K RB RA ] [ ] [ ] [ ] [ × = 7 Sept 2004 Kuo, 580.221 Explaining Specificity of An Antibody Approximation: (complementary shapes) 7 Sept 2004 Kuo, 580.221 • Empiricism (historical experiments, e.g. dialysis) • Theory/Principles – What forces do you know? Physics : • Gravitational (F=Gm 1 m 2 /r 2 ) • Electrostatic (F=Kq 1 q 2 /r 2 ; K=1/4 πε 0 ) • Electromagnetic {F=q(E + v × B)} Chemistry : • Kinetic Theory of Gases (heat) {PV=nRT} • Covalent Bonds (sharing electrons)
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7 Sept 2004 2 7 Sept 2004 Kuo, 580.221 Covalent vs Ionic (non-covalent) 7 Sept 2004 Kuo, 580.221 Geometry of Covalent Bonds 7 Sept 2004 Kuo, 580.221 Freedom of Bond Rotation: H 3 C-CH 3 vs H 2 C=CH 2 bonds 7 Sept 2004 Kuo, 580.221 BioPolymers Assembled from Subunits Condensation’ Reactions 7 Sept 2004 Kuo, 580.221 Covalent Molecules – Polymers of Amino Acids ( proteins ) 7 Sept 2004 Kuo, 580.221
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2 - Kuo, 580.221 7 Sept 2004 Concepts/Vocabulary Molecules...

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