3-Thermodynamics

3-Thermodynamics - Thermodynamics How much energy does a...

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Thermodynamics How much energy does a cell need for a reaction to take place? Eileen Haase Fall 2006 – Lecture #3
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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
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Effects of K Temperature on The Four Molecular Weak Forces Hydrogen Bonds – increased kinetic energy and molecule movement would destroy an H-bond Hydrophobic ‘Forces’ – increased water movement would make it more hydrophobic Electrostatic Attraction – no direct effect Van der Waals forces – no direct effect except by other forces
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Effects of decreased pH on The Four Molecular Weak Forces Hydrogen Bonds – ionization would destroy an H-bond Hydrophobic ‘Forces’ – ionization would make it more hydrophilic Electrostatic Attraction – ionization is required for electrostatic attraction Van der Waals forces – no direct effect except by other forces
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Are Forces Strong or Weak? • What are strong forces? -- makes molecules (covalent bonds) • What are weak forces? -- between molecules (H, ionic, Van der Waals, and hyrdophobic) • How to quantify?
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Specificity versus Affinity • Affinity : Between Receptor and 1 Ligand – Does the receptor “like” the ligand? – How much time does it want to spend with this ligand? • Specificity : Between Receptor and > 2 different Ligands – Which does the receptor like better, Ligand A or Ligand B?
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Many weak bonds result in a tight bond between two molecules
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Importance of Weak Forces Receptor A can bind to molecules B, C, or D. Binds with different affinity depending upon number and strength of non-covalent bonds
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How do you quantify affinity? •A + B Q C + D; K = products = [C][D] reactants [A][B] • (Binding) Association R + L Q RL Kassoc = [RL] conc -1 [R][L] • (Binding) Dissociation RL Q R + L Kd = [R][L]
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Quantifying Affinity Smallest Kd – tightest bond Largest Kd – weakest bond
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What happens at equilibrium? • R + L Q RL • Association rate = dissociation rate • Kassoc [R][L] = Kd [RL] [RL] = Kassoc = Keq = Equilibrium Constant [R][L] Kd As Keq L , more substrate than products
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What does the equilibrium constant tell you about affinity? [A] = [B] = 1000 molecules initially (10 -9 M) At equilibrium; K = 10 10 = [AB] D [AB]=10 -8 M [10 -9 M][10 -9 M] If K = 10 8 D [AB] = 10 -10 M As Keq K , get more product, [AB] K
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] [ ] ][ [ RL L R d = Kd L R RL ] ][ [ ] [ = Derivation of Fractional Occupancy, θ R total = total amount of receptor R total = [R] + [RL] [R] = concentration of free receptor [L] = concentration of free ligand [RL] concentration of receptor bound to ligand RL Q R + L
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Fractional Occupancy, θ [] [] [ ][ ] [] [] [] [] [] L K L K L R R K L R R RL d d d total + = + = θ NOTE : θ has no dependence on R or Rtotal • when Kd=[L], θ
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[] L K L d + = θ NOTE : • Since has no dependence on R or Rtotal – the amount of receptor doesn’t matter! important
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3-Thermodynamics - Thermodynamics How much energy does a...

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