4. Winter Q 2009 Biol/Chem 472 Metabolism Instructor: Gerry Prody Office CB444 Office hrs: TBA gerry@chem.wwu.edu http://lightning.chem.wwu.edu/dept/facstaff/p rody/prody-472.htmhttp://lightning.chem.wwu.edu/dept/facstaff/p rody/prody-472.htm

5. What is Biochemistry? the systematic torture of students with copious incomprehensible jargon, cryptic fomulae, and impossible insoluble problems. “Biochemistry is the study of Life as a process that can be understood.” Primary Objective: understand the molecular mechanisms that constitute the living state (“Molecular Logic”)

6. Lehninger: “Molecular Logic” “A living cell is a self-assembling, self-regulating, self-replicating isothermal open system of organic molecules operating on a principle of maximum economy of parts and processes; it promotes many consecutive, linked organic reactions for the transfer of energy and for the synthesis of its own components by means of organic catalysts that it produces itself.” Biol/Chem 471; Biol/Chem 472 ; Biol/Chem 473

7. Elemental composition of the earth’s surface, including crust, oceans and atmosphere. ElementPercent by mass Oxygen49.1 Silicon26.1 Aluminum7.5 Iron4.7 Calcium3.4 Sodium2.6 Potassium2.4 Magnesium1.9 Hydrogen0.88 Titanium0.58 Chlorine0.19 Carbon0.09 All others0.56

8. Table 1-3Elemental Composition of the Human Body. Page 29

9. Biol/Chem 472 Expected Outcomes draw enzymatic reactions correctly correctly calculate  Gº’ and  G for a given step or a series of steps in a pathway rationalize and/or predict features of pathway regulation and describe regulatory mechanisms recognize how concentrations of metabolites are regulated and the impact that changes in flux and/or concentration will have on other processes.

11. Stryer Fig. 12.30 Fluid Mosaic Model (Nicolson and Singer)

12. Figure 12-20

13. Figure 12-37

14. Figure 12-45 Secretory Pathway

15. Living cells are not at equilibrium! Concentrations of reactants and products are typically far from the equilibrium values (Q  K eq ). We must consider “steady state” concentrations of these species for the determination of  G.  G =  G o' + RTlnQ

18. Homeostatic conditions

20. Fig 16.2

21. See Figure 16.3 Catabolic pathways Anabolic pathways

22. Figure 16.20

23. Figure 16.25 °

24. Table 16.3 °’

26. 31 P NMR of human muscle: Before exercise 1 min of exercise 19 min of exercise10 min after exercise PiPi phosphocreatine ATP 

29. Oxidized cofactors Reduced cofactors Reduced substratesOxidized substrates + +

30. Fig 17.3

32. Least oxidized Most oxidized

33. Page 567 Figure 16-21b Some overall coupled reactions involving ATP. (b) The phosphorylation of ADP by phosphoenolpyruvate to form ATP and pyruvate.

34. “Alfonse, Biochemistry makes my head hurt!!” \