3. Winter 2011 Biol/Chem 472 Metabolism Instructor: Gerry Prody Office CB444 Office hrs: TBA gerry@chem.wwu.edu http://lightning.chem.wwu.edu/dept/facstaff/prody/ prody-472.htmhttp://lightning.chem.wwu.edu/dept/facstaff/prody/ prody-472.htm

4. The required textbook for this course is: LEHNINGER Principles of Biochemistry 5/e by David L. Nelson and Michael M. Cox (©2008, W.H. Freeman & Company) Welcome to Biochemistry

5. www.whfreeman.com/lehninger5e This site is chock full of resources to help you succeed in the course. Free Companion Website

6. Student Media Resources www.whfreeman.com/lehninger5e Interactive quizzes help you practice for exams Animated Enzyme Mechanisms and Animated Biochemical Techniques help you understand key mechanisms and techniques at your own pace Molecular Structure Tutorials allow you to explore in more depth the molecular structures included in the text Living Graphs illustrate key equations from the book allowing you to do what if scenarios by changing the parameters Lecture Companion Art allow you to print figures and tables for note-taking and review

7. Additional Saleable Supplement: The Absolute Study Guide & Solutions Manual It combines an innovative study guide with a reliable solutions manual providing extended solutions to the end-of-chapter problems in the textbook. It includes for each chapter: - Major Concepts : A roadmap through the chapter - What to Review : Questions that recap key points from previous chapters - Discussion Questions : Designed for individual review, study groups, or classroom discussion - A Self-Test : “Do you know the terms?”; crossword puzzles; multiple-choice, fact-driven questions; and questions that ask students to apply their knowledge To learn more contact your local bookstore.

8. Need support? 1-800-936-6899 Monday-Friday, 9-5 EST techsupport@bfwpub.com

9. 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”)

10. 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

11. 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

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

13. Map of the major metabolic pathways in a typical cell.

14. 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.

15. Note that figures labeled as Ch 11 come from Voet and Voet. You can find analogous figures in your text.

21. Figure 11-1The stereochemical relationships, shown in Fischer projection, among the D-aldoses with three to six carbon atoms. Page 357

24. Figure 11-2 The stereochemical relationships among the D-ketoses with three to six carbon atoms. Page 358

26. Figure 11-3The reactions of alcohols with (a) aldehydes to form hemiacetals and (b) ketones to form hemiketals. Page 358

28. Figure 11-4Cyclization reactions for hexoses.

29. Figure 11-5The anomeric monosaccharides  -D-glucopyranose and  -D-glucopyranose, drawn as both Haworth projections and ball-and- stick models. Page 359

30. Oxidation of sugars to acids: If the oxidation occurs at C1, it’s an “-onic” acid. If at C6, it’s “-uronic.”

31. Figure 11-8The acid-catalyzed condensation of  -D-glucose with methanol to form an anomeric pair of methyl-D- glucosides. Page 361

32. Some hexose derivatives important in biology

33. Figure 11-11N-Acetylneuraminic acid in its linear and pyranose forms. Page 363 Sialic acid

34. BOX 7-1 FIGURE 1 The glucose oxidase reaction, used in the measurement of blood glucose. A second enzyme, a peroxidase, catalyzes the reaction of the H2O2 with a colorless compound to produce a colored product, which is measured spectrophotometrically. What is the second enzyme? 474 folks…

35. BOX 7-1 FIGURE 2 The nonenzymatic reaction of glucose with a primary amino group in hemoglobin begins with (1) formation of a Schiff base, which (2) undergoes the Amadori rearrangement to generate a stable product; (3) this ketoamine can further cyclize to yield GHB. (4) Subsequent reactions generate advanced glycation end products (AGEs), such as ε-N-carboxymethyllysine and methylglyoxal, compounds that (5) can damage other proteins by cross-linking them, causing pathological changes.

37. Which of these are reducing sugars? Which are non- reducing?

40. Figure 11-13Electron micrograph of the cellulose fibers in the cell wall of the alga Chaetomorpha melagonium. Page 365

41. Figure 11-14The primary structure of cellulose. Page 365

42. Figure 11-15Proposed structural model of cellulose. Page 365

43. Cell wall architecture extensin Pectins

44. Common sugars found in plant polysaccharides

45. Pectin structures

46. Cross-bridging and esterification in pectins

47. A spotted June beetle (Pelidnota punctata), showing its surface armor (exoskeleton) of chitin.

48. Figure 11-16Structure of chitin. Page 366

49. Figure 11-17a  -Amylose. The D-glucose residues of  -amylose are linked by  (1  4) bonds (red). Page 366

50. Figure 11-17b  -Amylose. This regularly repeating polymer forms a left- handed helix. Page 366

51. Figure 11-18aAmylopectin. Its primary structure near one of its  (1  6) branch points (red). Page 367

52. Figure 11-18b Amylopectin. (b) Its bushlike structure with glucose residues at branch points indicated in red. Page 367

53. Figure 11-20The disaccharide repeating units of the common glycosaminoglycans. Page 368

54. Figure 11-23Schematic diagram comparing the cell envelopes of (a) gram- positive bacteria and (b) gram-negative bacteria. Page 373

55. Figure 11-24a Chemical structure of peptidoglycan. (a) The repeating unit of peptidoglycan. Page 373 NAG NAM Both + and - walls

56. Figure 11-24bChemical structure of peptidoglycan. (b) The S. aureus bacterial cell wall peptidoglycan. Page 373

57. Figure 11-25Structure of penicillin. Page 374 From yeast Prevents crosslinking of peptides Alexander Fleming

58. Figure 11-26Enzymatic inactivation of penicillin. Page 374

59. Figure 11-29aN-Linked oligosaccharides. (a) All N-glycosidic protein attachments occur through a  -N-acetylglucosamino–Asn bond to Asn–X–Ser/Thr. Page 376

60. Figure 11-29c N-Linked oligosaccharides. (c) Some examples of N- linked oligosaccharides. Page 376

61. Figure 11-30Some common O-glycosidic attachments of oligosaccharides to glycoproteins (red). Page 376

62. Figure 11-33aThe surfaces of (a) a normal mouse cell as seen in the electron microscope. (b) a cancerous cell as seen in the electron microscope. Page 378 a b Agglutinated with Conconavalin A--specific for glc and man

63. 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

66. Homeostatic conditions

68. Fig 16.2

69. See Figure 16.3 Catabolic pathways Anabolic pathways

70. Figure 16.20

71. Figure 16.25 °

72. Table 16.3 °’

74. 31 P NMR of human muscle: Before exercise 1 min of exercise 19 min of exercise10 min after exercise PiPi phosphocreatine ATP 

77. Oxidized cofactors Reduced cofactors Reduced substratesOxidized substrates + +

78. Fig 17.3

80. Least oxidized Most oxidized

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

82. 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.

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