1. 09/01/2009Biology 401: Thermodynamics II1 Thermodynamics, concluded Andy Howard Biochemistry, Fall 2009 IIT

2. 09/01/2009Biology 401: Thermodynamics IIp. 2 of 27 Thermodynamics matters! Thermodynamics tells us which reactions will go forward and which ones won’t.

3. 09/01/2009Biology 401: Thermodynamics IIp. 3 of 27 Thermodynamics Special topics in Thermodynamics –Free energy –Equilibrium –Work –Coupled reactions –ATP: energy currency –Other high-energy compounds –Dependence on concentration

4. 09/01/2009Biology 401: Thermodynamics IIp. 4 of 27 Entropy matters a lot! Most biochemical reactions involve very small ( < 10 kJ/mol) changes in enthalpy Driving force is often entropic Increases in solute entropy often is at war with decreases in solvent entropy. The winner tends to take the prize.

5. 09/01/2009Biology 401: Thermodynamics IIp. 5 of 27 Apolar molecules in water Water molecules tend to form ordered structure surrounding apolar molecule Entropy decreases because they’re so ordered

6. 09/01/2009Biology 401: Thermodynamics IIp. 6 of 27 Binding to surfaces Happens a lot in biology, e.g. binding of small molecules to relatively immobile protein surfaces Bound molecules suffer a decrease in entropy because they’re trapped Solvent molecules are displaced and liberated from the protein surface

7. 09/01/2009Biology 401: Thermodynamics IIp. 7 of 27 Free Energy Gibbs: Free Energy Equation G = H - TS So if isothermal,  G =  H - T  S Gibbs showed that a reaction will be spontaneous (proceed to right) if and only if  G < 0

8. 09/01/2009Biology 401: Thermodynamics IIp. 8 of 27 Standard free energy of formation,  G o f Difference between compound’s free energy & sum of free energy of the elements from which it is composed Substance  G o f, kJ/mol Substance  G o f, kJ/mol Lactate -516 Pyruvate -474 Succinate -690 Glycerol -488 Acetate -369 Oxaloacetate -797 HCO 3 - -394

9. 09/01/2009Biology 401: Thermodynamics IIp. 9 of 27 Free energy and equilibrium Gibbs:  G o = -RT ln K eq Rewrite: K eq = exp(-  G o /RT) K eq is equilibrium constant; formula depends on reaction type For aA + bB  cC + dD, K eq = ([C] c [D] d )/([A] a [B] b )

10. 09/01/2009Biology 401: Thermodynamics IIp. 10 of 27 Spontaneity and free energy Thus if reaction is just spontaneous, i.e.  G o = 0, then K eq = 1 If  G o 1: Exergonic If  G o > 0, then K eq < 1: Endergonic You may catch me saying “exoergic” and “endoergic” from time to time: these mean the same things.

11. 09/01/2009Biology 401: Thermodynamics IIp. 11 of 27 Free energy as a source of work Change in free energy indicates that the reaction could be used to perform useful work If  G o < 0, we can do work If  G o > 0, we need to do work to make the reaction occur

12. 09/01/2009Biology 401: Thermodynamics IIp. 12 of 27 What kind of work? Movement (flagella, muscles) Chemical work: –Transport molecules against concentration gradients –Transport ions against potential gradients To drive otherwise endergonic reactions –by direct coupling of reactions –by depletion of products

13. 09/01/2009Biology 401: Thermodynamics IIp. 13 of 27 Coupled reactions Often a single enzyme catalyzes 2 reactions, shoving them together: reaction 1, A  B:  G o 1 0 Coupled reaction: A + C  B + D:  G o C =  G o 1 +  G o 2 If  G o C < 0, then reaction 1 is driving reaction 2!

14. 09/01/2009Biology 401: Thermodynamics IIp. 14 of 27 How else can we win? Concentration of product may play a role As we’ll discuss in a moment, the actual free energy depends on  G o and on concentration of products and reactants So if the first reaction withdraws product of reaction B away, that drives the equilibrium of reaction 2 to the right

15. 09/01/2009Biology 401: Thermodynamics IIp. 15 of 27 Adenosine Triphosphate ATP readily available in cells Derived from catabolic reactions Contains two high-energy phosphate bonds that can be hydrolyzed to release energy: O O - || | (AMP)-O~P-O~P-O - | || O - O

16. 09/01/2009Biology 401: Thermodynamics IIp. 16 of 27 Hydrolysis of ATP Hydrolysis at the rightmost high-energy bond: ATP + H 2 O  ADP + P i  G o = -33kJ/mol Hydrolysis of middle bond: ATP + H 2 O  AMP + PP i  G o = -33kJ/mol BUT PP i + H 2 O  2 P i,  G o = -33 kJ/mol So, appropriately coupled, we get roughly twice as much!

17. 09/01/2009Biology 401: Thermodynamics IIp. 17 of 27 ATP as energy currency Any time we wish to drive a reaction that has  G o < +30 kJ/mol, we can couple it to ATP hydrolysis and come out ahead If the reaction we want has  G o < +60 kJ/mol, we can couple it to ATP  AMP and come out ahead So ATP is a convenient source of energy — an energy currency for the cell

18. 09/01/2009Biology 401: Thermodynamics IIp. 18 of 27 Coin analogy Think of store of ATP as a roll of quarters Vendors don’t give change Use one quarter for some reactions, two for others Inefficient for buying $0.35 items

19. 09/01/2009Biology 401: Thermodynamics IIp. 19 of 27 Other high-energy compounds Creatine phosphate: ~ $0.40 Phosphoenolpyruvate: ~ $0.35 So for some reactions, they’re more efficient than ATP

20. 09/01/2009Biology 401: Thermodynamics IIp. 20 of 27 Why not use those always? There’s no such thing as a free lunch! In order to store a compound, you have to create it in the first place So an intermediate-energy currency is the most appropriate

21. 09/01/2009Biology 401: Thermodynamics IIp. 21 of 27 Dependence on Concentration Actual  G of a reaction is related to the concentrations / activities of products and reactants:  G =  G o + RT ln [products]/[reactants] If all products and reactants are at 1M, then the second term drops away; that’s why we describe  G o as the standard free energy

22. 09/01/2009Biology 401: Thermodynamics IIp. 22 of 27 Is [A] = [B] = 1M… realistic? No, but it doesn’t matter; as long as we can define the concentrations, we can correct for them Often we can rig it so [products]/[reactants] = 1 even if all the concentrations are small Typically [ATP]/[ADP] > 1 so ATP coupling helps even more than 33 kJ/mol!

23. 09/01/2009Biology 401: Thermodynamics IIp. 23 of 27 How does this matter? Often coupled reactions involve withdrawal of a product from availability If that happens, [product] / [reactant] shrinks, the second term becomes negative, and  G 0

24. 09/01/2009Biology 401: Thermodynamics IIp. 24 of 27 How to solve energy problems involving coupled equations General principles: –If two equations are added, their energetics add –An item that appears on the left and right side of the combined equation can be cancelled –Reversing a reaction reverses the sign of  G.

25. 09/01/2009Biology 401: Thermodynamics IIp. 25 of 27 A bit more detail Suppose we couple two equations: A + B  C + D,  G o ’ = x C + F  B + G,  G o ’ = y The result is: A + B + C + F  B + C + D + G or A + F  D + G,  G o ’ = x + y … since B and C appear on both sides

26. 09/01/2009Biology 401: Thermodynamics IIp. 26 of 27 Slightly more complex… Suppose we couple two equations: A + B  C + D,  G o ’ = x H + A  J + C,  G o ’ = z Reverse the second equation: J + C  A + H,  G o ’ = -z Add this to 1st eqn. & simplify: B + J  D + H,  G o ’ = x - z … since A and C appear on both sides

27. 09/01/2009Biology 401: Thermodynamics IIp. 27 of 27 What do we mean by hydrolysis? It simply means a reaction with water Typically involves cleaving a bond: U + H 2 O  V + W is described as hydrolysis of U to yield V and W