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ch05.1 - Which of the following binding constants...

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Which of the following binding constants represents the highest affinity? A. K dn = 1.0 x 10 7 M B. K dn = 1.0 x 10 -9 M C. K dn = 1.5 x 10 -8 M D. K dn = 2.0 x 10 8 M
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Protein Function Myoglobin and Hemoglobin Chapter 5
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5-3 Most hydrophobic R groups buried in the interior, hidden from water. (leu, val, met, phe) Myoglobin 1. 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) 2. Where are the hydrophobic R groups?
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5-3 Myoglobin 3. There are 4 prolines. Where are they? Each of 4 prolines occurs at a bend at end of α -helix. Protein is about 75% α -helix
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5-1 Heme porphyrin ferrous state, Fe +2 How many coordination bonds does Fe have? 6 Heme group uses Fe to reversibly bind oxygen
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5-3, 2 His-93 (F8) His-64 (E7) His-93 (F8) Structural properties of heme binding in Mb
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5-5 What kind of interaction is indicated here? H-bond
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His F8 5-11 O 2 is bound directly to heme Fe, not to protein. Why is polypeptide portion of Mb needed for oxygen transport and storage? Prevent oxidation of Fe 2+ in heme…
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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 dn ? What is the equation for the association constant, K an ? PL P + L i.e. K dn = 1 K an K an = [ PL ] [ P ][ L ] (M -1 units) K dn = [ P ][ L ] [ PL ] (M units)
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2. Define fraction of ligand-binding sites occupied by ligand, or fractional saturation , = θ (theta): " = [ bindingsitesoccupied ] [ totalbindingsites ] = [ PL ] [ P ] + [ PL ] = [ L ] K dn + [ L ] plot θ vs [L] hyperbola and substitute into equation for θ and simplify: rearrange K an equation: [PL] = K an [L][P] 1/K an θ = [ L ] + [ L ]
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" = [ L ] K dn + [ L ] x = y y + z 5-4a What is it called when curve approaches a limit, it never quite reaches? asymptotic 50% saturation
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Lower value of K dn means ligand binding sites fill at lower concentration of ligand, i.e. sites bind L with higher affinity… Low K dn = high affinity High K dn = low affinity
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WORKED EXAMPLE 5-1 Two proteins, X and Y, bind to the same ligand, A, with the binding curves shown below.
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