3 - Kuo, 580.221 9 Sept 2004 Concepts/Vocabulary Molecules...

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Kuo, 580.221 9 Sept 2004 1 BME 580.221 Intro to Thermodynamics Lecture #03, 9 Sep 2004 Scot C. Kuo 9 Sept 2004 Kuo, 580.221 Concepts/Vocabulary • Three laws of Thermodynamics (Energetics) • Energetics are additive: unfavorable reactions can be coupled to favorable reactions • Energy and Entropy are statistical; Boltzmann distribution (why logarithms in expressions) • Thermodynamics of water (entropy of water drives hydrophobic interactions) 9 Sept 2004 Kuo, 580.221 Specificity of An Antibody Cartoon #2 9 Sept 2004 Kuo, 580.221 Motivational Issue • The 4 molecular forces: – H-bonds – Ionic –van de rWa a l s – Hydrophobic/hydrophilic • Polarity/Directionality of some bonds • How to predict which bonds important ( specificity ) and which affect the final affinity ? NOT a ‘real’ force • Attraction depends on water Add the forces? • Known F vs. r relationships F is pair-wise (like affinity) 9 Sept 2004 Kuo, 580.221 Strengths of Non-covalent Bonds <3 kcal/mole each, but thousands keep a protein in the ‘right’ shape Typ # protein: ~1000 ~100 ~500 ~5000 9 Sept 2004 Kuo, 580.221 Instead of Force, consider Energy Energy ‘Landscape’ – want the minimum Energy = x Fds U Advantages of considering energy: • can have energy of a whole system • multiple configurations have the same energy • energies are additive • unfavored bonds can be overwhelmed by other bonds Board Example: electrostatic U ~ -r -1
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Kuo, 580.221 9 Sept 2004 2 9 Sept 2004 Kuo, 580.221 Strengths of Non-covalent Bonds <3 kcal/mole each, but thousands keep a protein in the ‘right’ shape Typ # protein: ~1000 ~100 ~500 ~5000 This approach should be familiar as H f (heat of formation). Hydrophobic/hydrophilic is MISSING! ??How to include hydrophobic/hydrophilic attraction?? 9 Sept 2004 Kuo, 580.221 What is Thermodynamics? • Thermodynamics = Energetics Is there enough energy to do something useful? • In general, atomic/molecular understanding is not necessary to apply thermodynamics – Heat (steam) engines (Nicolas Leonard Sadi Carnot, 1824) – Information theory (Claude Shannon, 1950’s) • Thermodynamics does not address: When does something happen? (Kinetics) How to do something? (Technology) 9 Sept 2004 Kuo, 580.221 Three Laws of Thermodynamics 1. Energy can neither be created nor destroyed ( conservation of energy ), but can be converted into different forms. 2. For any process, entropy of the entire system (including surroundings) must increase until equilibrium is attained. 3. A pure, perfect crystal has no entropy at absolute 0 ° Kelvin (-273.15 ° C). Reversible
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3 - Kuo, 580.221 9 Sept 2004 Concepts/Vocabulary Molecules...

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