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University of Houston BCHS 3304: General Biochemistry I, Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101 Instr

University of Houston BCHS 3304: General Biochemistry I, Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101 Instructor: Glen B. Legge, Ph.D., Cambridge UK Phone: 713-743-8380 Fax: 713-743-2636 E-mail: glegge@uh.edu Office hours: Mon. and Wed. (2:30-4:00 PM) or by appointment

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University of Houston BCHS 3304: General Biochemistry I, Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101 Instr

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  1. University of Houston BCHS 3304: General Biochemistry I,Section 07553 Spring 2003 1:00-2:30 PM Mon./Wed. AH 101 Instructor: Glen B. Legge, Ph.D., Cambridge UK Phone: 713-743-8380 Fax: 713-743-2636 E-mail: glegge@uh.edu Office hours: Mon. and Wed. (2:30-4:00 PM) or by appointment 353 SR2  (Science and Research Building 2) Research Interests: Molecular mechanisms of cell adhesion, using primarily multi- dimensional nuclear magnetic resonance (NMR) spectroscopy. 1

  2. Lecture 1 Summary • Life arose from simple organic molecules • Compartmentalization gave rise to cells • All cells are either prokaryotic or eukaryotic • Eukaryotic cells contain membrane-bound oragnelles • Three domains based on phylogeny • Archea, bacteria, and eukarya • Natural selection directs evolution

  3. Thermodynamics and chemical equilibria • Lecture 2 1/15/2003 • Chapter 1 Voet, Voet and Pratt

  4. Thermodynamics: Allows a prediction as to the spontaneous nature of a chemical reaction: Will this reaction proceed in a forward direction as the reaction is written: A + B C Will A react with B to form C or not? Is this reaction going from higher to lower energy? ENERGY not necessarily just heat!!!

  5. Definitions: System: a defined part of the universe a chemical reaction a bacteria a reaction vessel a metabolic pathway Surroundings: the rest of the universe Open system: allows exchange of energy and matter Closed system: no exchange of matter or energy. i.e. A perfect insulated box.

  6. Units

  7. Direction of heat flow by definition is most important. q = heat absorbed by the system from surroundings If q is positive reaction is endothermic system absorbs heat from surroundings If q is negative exothermic system gives off heat. A negative W is work done by the system on the surroundings i.e expansion of a gas

  8. First Law of Thermodynamics: Energy is Conserved Energy is neither created or destroyed. In a chemical reaction, all the energy must be accounted for. Equivalence of work w and energy (heat) q Work (w) is defined as w = F x D (organized motion) Heat (q) is a reflection of random molecular motions (heat)

  9. U = Ufinal - Uinitial = q - w Exothermic system releases heat = -q Endothermic system gains heat = +q U = a state function dependent on the current properties only. U is path independent while q and w are not state functions because they can be converted from one form of energy to the other. (excluding other forms of energy, e.g. electrical, light and nuclear energy, from this discussion.)

  10. Path: is a process by which energy changes in a system I have $100 in my bank account, I withdrew $50, now I have $50. I could have added $100 and withdrew $150. U (money in the account) is same but the path is different.

  11. Enthalpy (H) At constant pressure w = PV + w1 w1 = work from all means other than pressure-volume work. PDV is also a state function. By removing* this type of energy from U, we get enthalpy or ‘to warm in’ *remember the signs and direction H = U + PV H = U + PV = qp -w + PV = qp - w1

  12. Enthalpy (H) When considering only pressure/volume work H = qp - PV + PV = qp DH = qp when other work is 0 qp is heat transferred at constant pressure. In biological systems the differences between U and H are negligible (e.g. volume changes)

  13. The change in enthalpy in any hypothetical reaction pathway can be determined from the enthalpy change in any other reaction pathway between the same products and reactants. This is a calorie (joule) “bean counting” HotCold Which way does heat travel? This directionality, is not mentioned in First Law

  14. Other examples Considering the random thermal motion of molecules, why at any particular time doesn’t all the atoms in the air in this room end up into the upper right corner of the room? or When a driver jumps into the water, energy from that person is dissipated to the water molecules. Have you ever seen the water molecules act in unison and retransfer this energy back to the driver and push him out of the water? In all cases Energy is conserved.

  15. Gas on its own will expand to the available volume. • Disorder increases • Can we put a numerical value on disorder? Yes, most definitely!! • N identical molecules in a bulb, open the stop cock you get 2N equally probable ways that N molecules can be distributed in the bulb.

  16. But gas molecules are indistinguishable. Thus, only N+1 different states exist in the bulb or 0, 1, 2, 3, 4,…., (N-1) molecules in left bulb WL= number of probable ways of placing L of the N molecules in the left bulb is The probability of occurrence of such a state (Is its fraction of the total number of states)

  17. N = 4 particles, 2 orientations or 24 = 16 different arrangements of distinguishable particles 1 { 4 { } N+1 different states 6* { 4 { 1 { * The most probable state is the one with the most arrangements

  18. The state that is the most probable is one with the highest value of WL= N/2 in one bulb and N/2 in the other. The probability that L is equal to N/2 increases when N is large For N=10 the probability that L lies within 20% of N/2 = .66 N=50 probability L lies within 20% of N/2 = .88 N=1023 , L = 1 For a mole of gas in the two bulbs 6.0221 x 1023 The probability of a ratio of 1 in 1010 (one in ten billion) difference or 10,000,000,000 vs. 10,000,000,001 on one side to the other is 10-434 = 0

  19. The reason that direction occurs is not by the laws of motion, but the aggregate probability of all other states is So low!! or insignificant that only the most probable state will occur. Entropy for N = 1023 This number is greater than the number of atoms in the universe!! Possible arrangements

  20. Entropy (S) measure the degree of randomness Each molecule has an inherent amount of energy which drives it to the most probable state or maximum disorder. kb or Boltzman’s constant equates the arrangement probability to calories (joules) per mole. Entropy is a state function and as such its value depends only on parameters that describe a state of matter.

  21. The process of diffusion of a gas from the left bulb initially W2 = 1 and S = 0 to Right (N/2) + Left (N/2) at equilibrium gives a : S that is (+) with a constant energy process such that U = 0 while S>0 This means if no energy flows into the bulbs from the outside expansion will cool the gas! Conservation of Energy says that the increase in Entropy is the same as the decrease in thermal (kinetic) energy of the molecules!!

  22. Entropy is the arrow of time The entropy of the universe is always increasing. What does this mean in a closed system? What does this mean in an open system? What if the universe starts to collapse, does time go backwards?

  23. It is difficult or (impossible) to count the number of arrangements or the most probable state! So how do we measure entropy? It takes 80 kcal/mol of heat to change ice at zero °C to water at zero °C 80,000 = 293 ev’s or entropy units 273 A Reversible process means at equilibrium during the change. This is impossible but makes the calculations easier but for irreversible process

  24. At constant pressure we have changes in qp (Enthalpy) and changes in order - disorder (Entropy) A spontaneous process gives up energy and becomes more disordered. G = H - TS Describes the total usable energy of a system A change from one state to another produces: G = H - TS = qp - TS If DG is negative, the process is spontaneous

  25. S H + - All favorable at all temperature spontaneous - - Enthalpy favored. Spontaneous at temperature below T = H S + + Entropy driven, enthalpy opposed. Spontaneous at Temperatures above T = H S - + Non-spontaneous

  26. STP Standard Temperature and Pressure and at 1M concentration. We calculate DG’s under these conditions. aA + bB cC + dD We can calculate a G for each component (1) (2) combining (1) and (2) (3)

  27. Now if we are at equilibrium or DG = 0 Then OR So what does DGo really mean?

  28. G Go Keq If Keq = 1 then DG = 0 Go equates to how far Keq varies from 1!!

  29. Keq can vary from 106 to 10-6 or more!!! DGo is a method to calculate two reactions whose Keq’s are different However The initial products and reactants maybe far from their equilibrium concentrations so Must be used

  30. Le Chatelier’s principle Any deviation from equilibrium stimulates a process which restores equilibrium. All closed systems must therefore reach equilibrium What does this mean? Keq varies with 1/T If Keq varied with temperature things would be very unstable. Exothermic reactions would heat up causing an increase in Keq generating more heat etc….

  31. Fortunately, this does not happen in nature. R = gas constant for a 1M solution Plot lnKeq vs. 1/T ( remember T is in absolute degrees Kelvin) Van’t Hoff plot = Slope lnKeq = Intercept

  32. The Variation of Keq with DGo at 25 oC KeqDGo (kJ·mole-1 106-34.3 104-22.8 102-11.4 101-5.7 1000.0 10-15.7 10-211.4 10-422.8 10-634.3

  33. The f = for formation. By convention, the free energy of the elements is taken as zero at 25 oC The free energies of any compound can be measured as a sum of components from the free energies of formation.

  34. Standard State for Biochemistry Unit Activity 25 oC pH = 7.0 (not 0, as used in chemistry) [H2O] is taken as 1, however, if water is in the Keq equation then [H2O] = 55.5 The prime indicates Biochemical standard state

  35. Most times However, species with either H2O or H+ requires consideration. For A + B C + D + nH2O This is because water is at unity. Water is 55.5 M and for 1 mol of H2O formed:

  36. For: A + B C + HD H+ + D- K Where a proton is in the equation This is only valid for

  37. Coupled Reactions A + B C + D DG1 (1) D + E F +G DG2 (2) reaction 1 will not occur as written. If is sufficiently exergonic so However, if Then the combined reactions will be favorable through the common intermediate D A + B + E C + F + G DG3

  38. As long as the overall pathway is exergonic, it will operate in a forward manner. Thus, the free energy of ATP hydrolysis, a highly exergonic reaction, is harnessed to drive many otherwise endergonic biological processes to completion!!

  39. Life obeys the Laws of Thermodynamics • Living organisms are open systems • Living things maintain a steady state • Enzymes catalyze biological reactions

  40. Water and elements in life processes • Lecture 3 1/22/2003

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