ch05 - 2/14/2011 Protein Function Three non-enzyme examples...

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2/14/2011 1 Protein Function Three non-enzyme examples Myoglobin and Hemoglobin Antibodies Actin/Myosin 5-3 Myoglobin Where are the polar R groups? All except 2 polar R groups of myoglobin chain are on outer surface, and all are hydrated (i.e. bound water molecules) Where are the hydrophobic R groups? Most hydrophobic R groups buried, hidden from water. (leu, val, met, phe) Heme = Prosthetic group
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2/14/2011 2 5-3 Myoglobin There are 4 prolines. Where are they? Each of 4 prolines occurs at a bend at end of -helix. Protein is about 75% -helix Are the peptide bonds cis or trans? all peptide bonds in planar, trans configuration - i.e. carbonyl group is trans to NH group 5-1 Heme porphyrin ferrous state, Fe +2 6
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2/14/2011 3 5-3, 2 His-93 (F8) His-64 (E7) His-93 (F8) 5-5
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2/14/2011 4 His F8 5-11 Why is polypeptide portion of Mb needed for oxygen transport and storage? O 2 is bound directly to heme Fe, not to protein. Look at oxygen binding properties of Mb quantitatively: 1. For any reversible protein-ligand binding interaction: P + L PL What about the dissociation constant, K d ? What is the equation for the association constant, K a ? PL P + L i.e. a d K K 1 ] [ ] ][ [ PL L P K d (M units) (M -1 units) ] ][ [ ] [ L P PL K a
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2/14/2011 5 2. Fraction of ligand-binding sites occupied by ligand, or fractional saturation , = (theta): [ bindingsites occupied ] [ total bindingsites ] [ PL ] [ P ] [ PL ] ] [ ] [ L K L d plot vs [L] hyperbola and substitute into equation for and simplify: rearrange K d equation: d K L P PL ] ][ [ ] [ Don’t forget this fundamental hyperbolic equation! ] [ ] [ L K L d x y y z 5-4a
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2/14/2011 6 Lower K d means sites fill at lower concentration of ligand, i.e. sites bind L with higher affinity. Low K d = high affinity High K d = low affinity Measurements of pressure The weight of air pushing down on earth, at sea level, exerts 14.7 lbs/in 2 (1Kg/cm 2 ), this is equivalent to 1 atmosphere. Torricelli observed he weight of air will counterbalance a
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ch05 - 2/14/2011 Protein Function Three non-enzyme examples...

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