2-Specificity

2-Specificity - Specificity Chemical Basis of Binding(or...

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Specificity – Chemical Basis of Binding (or what makes things stick together in a cell) Eileen Haase Fall 2007 – Lecture #2 1
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What happens at equilibrium? • Association rate = dissociation rate • Kassoc [R][L] = Kd [RL] [RL] = Kassoc = K = Equilibrium Constant [R][L] Kd Just wait for SLIDES 87 & 88! 2 ] [ ] ][ [ 0 ] [ RL Kd L R Kassoc dt d
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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 • Inadequacy of „ Lock & Key • Henderson-Hasselbach equation (pH & ionization) 3
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NO 2 NO 2 NH (CH 2 ) 4 HC CO NH NO 2 NO 2 (CH 2 ) 4 HC CO OH N H 2 NO 2 NO 2 NH (CH 2 ) 3 HC CO OH N H 2 NO 2 NO 2 H 2 N NO 2 NO 2 NO 2 H 2 N 50 nM 125 nM 500 nM 1,250 nM 20,000 nM Protein Backbone Antibody Prepared Against (Immunogen) : Test Molecule (Hapten): K d Based on Fig. 13-6 from General Immunology by HN Eisen R+L n RL Kd = [R][L] conc [RL]
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Antibody Structure & Function 5
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Specificity of An Antibody Cartoon #2 6
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Aside: epitopes can be part of any biopolymer 7 Antigenic Polymer can be protein, sugar, nucleic acid, or any other type of molecule.
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Why vaccination works – similar antigens in cowpox and smallpox 8
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How do molecules attach? • Covalent Bonds – connect atoms within a molecule • Non-Covalent Bonds – stabilizing forces between different molecules and within a molecule – Hydrogen – Ionic – Van der Waals – hydrophobic 9
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Covalent vs Non-Covalent 10 Covalent: share Ionic: transfer
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Hydrogen molecule: simple covalent bond between two H atoms. There is an ideal distance between the 2 H atoms. 11
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Number of Covalent Bonds depends upon number of outer shell electrons 12
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Covalent bonds have a specific geometry – set angles between atoms 13
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Single bonds can rotate, a double bond cannot rotate 14 All atoms lie in the same plane Atoms arranged as a double tetrahedron
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Covalent Bonds are strong g stable 15
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Electrons are shared unequally in polar covalent bonds 16 Oxygen attracts electrons more than hydrogen, causing the molecule to have a positive and negative end, resulting in a dipole moment (charge x distance)
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Asymmetric Carbon Atoms form stereoisomers: L and D 17 Amino Acids: use L isomers Carbohydrates: use D isomers
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Carbon Compounds used to make macromolecules 18
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Sugars (CH 2 O)n, 3<n<8 19
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ISOMERS: Glucose, galactose, and mannose have the same chemical formula: C 6 H 12 O 6 20
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Fatty Acids: Hydrophobic hydrocarbon chain attached to a hydrophilic carboxylic acid group. Different fatty acids have different hydrocarbon tails. Saturated : no double bonds (hard margarine) Unsaturated : one or more double bonds between the C‟s (soft margarine – “kinks” interfere with solid packing) 21
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20 different amino acids 22 Amino acids all have an amino group (H 2 N), and a carboxyl group (COOH).
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This document was uploaded on 10/08/2008.

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2-Specificity - Specificity Chemical Basis of Binding(or...

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