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Chapter 3

Chapter 3. Thermodynamic Principles: A Review. Basic Concepts. The system: the portion of the universe with which we are concerned The surroundings: everything else Isolated system cannot exchange matter or energy Closed system can exchange energy Open system can exchange either or both.

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Chapter 3

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  1. Chapter 3 Thermodynamic Principles: A Review

  2. Basic Concepts • The system: the portion of the universe with which we are concerned • The surroundings: everything else • Isolated system cannot exchange matter or energy • Closed system can exchange energy • Open system can exchange either or both

  3. The First LawEnergy (U) of an isolated system is conserved. It can be neither created or destroyed. • U = Ufinal - Uinitial = q - w • U is the energy (a function that keeps track of heat transfer and work expenditure in the system) q is heat absorbed by the system w is work done by the system q is negative (-), exothermic (system releases heat) q is positive (+), endothermic (system takes up heat)

  4. Enthalpy (H) For conditions of constant pressure, enthalpy, H, is usually a more useful function than energy, U, because the amount of heat absorbed or generated is relatively easy to measure. H = U + PV If P is constant, then H = U + PV= qp - w + PV Divide work into that done by an expanding volume, PV, and other work, w’, in other words, w =PV + w' H = U + PV = qp - w + PV = qp - w' For chemical reactions, all the work is usually PV work so w' = 0. For biochemical reactions in solution, V is usually zero or very small. Therefore H is approximately equal to U, and H is the heat absorbed at constant P.

  5. The Second LawSpontaneous processes occur in directions that increase the overall disorder of the universe. • Systems tend to proceed from ordered to disordered states • The entropy change for (system + surroundings) is unchanged in reversible processes and positive for irreversible processes • All spontaneous processes proceed toward equilibrium, not away from it.

  6. Entropy • A measure of disorder • An ordered state is low entropy • A disordered state is high entropy • dSreversible = dq/T

  7. 2 bulbs of equal volumes connected by a stopcock Page 53

  8. Improbability of even a small amount of order Page 54

  9. Relationship of entropy and temperature The structure of water becomes more disordered as its temperature rises, that is, its entropy increases with temperature Page 55

  10. Amphipathic compounds in aqueous solution Polar head group Hydrophillic Non-polar Hydrophobic tail From Lehninger Principles of Biochemistry

  11. Free Energy • Hypothetical quantity - allows chemists to asses whether reactions will occur • The Gibbs free energy: G = H - TS • For any process at constant P and T: G = H - TS If G = 0, reaction is at equilibrium If G < 0, reaction proceeds as written Exergonic: Spontaneous processes with negative (-) G Endergonic: Processes that are not spontaneous with positive (+) G

  12. Variation of Reaction Spontaneity (Sign of DG) with the signs of DH and DS Page 56

  13. Consider a reaction: A + B C Then: G = Go + RT ln ([C]/[A][B]) Go =free energy change of the reaction under standard conditions Go used in physical chemistry Go'used in biochemistry In "Chemistry": The standard state convention defines the standard state of solute as that with unit activity at 25oC and 1 atm. (So if H+ is a reactant or product, pH = 0.) In "Biochemistry": The standard state convention is modified because most reactions occur in dilute solutions near pH 7 with activities of water and proton at unity Remember that G = G'

  14. Table 3-4 Free Energies of Formation of Some Compounds of Biochemical Interest Page 58

  15. Page 58

  16. Page 58

  17. Consider a reaction: A + B C Go = free energy change of the reaction under standard conditions • G = Go + RT ln Keq • G = Go + RT ln([C]/[A][B]) At equilibrium,G = 0 Therefore, Go = - RT ln Keq = - RT ln ([C]/[A][B]) Thus the equilibrium constant can be calculated from standard free energy data and vice versa.

  18. Variation of Keq with DG° at 25°C - - - - Page 57

  19. Many biological reactions lead to an increase in order (decrease in entropy) Linking of individual amino acids Protein Cells cope this situation by coupling this reaction to a highly negative DG reaction

  20. An unfavorable reaction can proceed spontaneously if it is coupled to an energetically favorable reaction A B + X DG = + 50 kJ/mol X Y + Z DG = -100 kJ/mol Overall reaction: A B + Y + Z DG = - 50 kJ/mol

  21. Values from human erythrocytes PEP + H2O Pyruvate + PiDG = -78 kJ/mol ADP + Pi ATP + H2O DG = 55 kJ/mol PEP + ADP Pyruvate + ATP Total DG = -23 kJ/mol

  22. Phosphocreatine + H2O Creatine + PiDGo' at 37oC = - 43.1 kJ/molPhysiological concentrations of phosphocreatine, creatine and Pi are between 1 and 10 mM.Assuming 1 mM concentration and using equation G = Go' + RT ln ([C][D]/[A][B])G = - 43.1 kJ/mol + (8.314 J/mol. K) (310 K) ln ([0.001][0.001]/[0.001])G = - 60.9 kJ/molDifference between standard state and 1 mM concentration for the above reaction is -17.8 kJ/mol Free energy change can be very different from standard state if concentration of reactant and product are different from unit activity (1 M)

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