2. There are three scholarships for pre-medical students that are available for the 2010- 2011 academic year. These are: Whatcom County Medical Society Scholarship: one $500 award Dr. Ralph & Mrs. Eleanor Rinne Pre-Medical Scholarship: two $1500 awards If you would like to apply, please visit http://www.careers.wwu.edu/prehealth_financialaid.shtml for a statement of eligibility and for application details. Or, you may stop by Old Main 380 or Old Main 280 to pick up an application. Completed applications are due in Old Main 380 (Academic Advising Center) by Monday, May 3, 2010.

3. Figure 6-1 part 4

4. Protein Data Bank Workshop pdb Rasmol Do the protein explorer tour!!!!! http://www.umass.edu/microbio/chime/pe_ beta/pe/protexpl/qtour.htm

5. Chapter 6 Opener

6. Figure 6-4

7. Figure 6-5

8. Figure 6-6

9. Figure 6-7

10. Figure 6-8

11. Figure 6-9

12. Figure 6-9a

13. Figure 6-9b

14. Figure 6-10

15. VVP Fig 6-16 pdb

16. Other Properties of Amino Acids Stereochemistry (all biosynthetic proteins made up of L-isomer) Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) (see Table 6-2 in VVP p 150) these two properties are major determinants of peptide conformation

17. Table 6-1

18. Figure 6-12

19. Figure 6-15 Keratin: a coiled coil

20. Figure 6-16 Higher order keratin structure

21. Globular Protein 3 o Structure 2 o structural elements (helices, sheets, turns…) pack together to give a folded protein or subunit. This so-called “tertiary” structure is stabilized by non- covalent interactions, the hydrophobic effect and disulfides. Within the 3 o structure are “motifs” and “domains”. The 3 o structure can be derived from one or more domains.

22. Figure 6-20b Protein crystals: flavodoxin

23. Figure 6-20e Protein crystals: lamprey hemoglobin

24. Figure 6-21

25. Figure 6-27 cytochrome c: hydrophillic residues and hydrophobic residues

27. Figure 6-33 Hemoglobin

28. Table 6-3

29. Figure 6-35 Bovine chymotrypsin

30. Figure 6-38 Molecular dynamics of Mb

31. Page 159

32. Figure 6-39

33. Figure 6-40

34. Figure 6-41

35. Many conformational states Fewer conformational states A “single” conformational state Low energy High energy (Fig 6-38)

36. Many conformational states Fewer conformational states A “single” conformational state See VVP Fig 6-37 p153

37. “Ideal” “Real” ? See VVP Fig 6-38 p154

38. H-bond Fun Fact 1984 survey of protein crystal data shows that “almost all groups capable of forming H-bonds do so.” (mainchain amides, polar sidechains)

39. Table 6-4

42. Figure 5-3

43. Fundamentals of Biochemistry Third Edition Fundamentals of Biochemistry Third Edition Chapter 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies Chapter 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies Copyright © 2008 by John Wiley & Sons, Inc. Donald Voet Judith G. Voet Charlotte W. Pratt

44. Oxygen is transported to cells which are remote from air O 2 is required in cells, in the mitochondria for ATP production aerobic metabolism Glucose + O 2 ----------------------------> ATP + CO 2 oxidative phosphorylation

45. Normal Red Blood Cells have a flattened discoid shape rather than a spherical shape vs. O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2 O2O2

47. Table 6-4

48. Chapter 7 Opener

49. Figure 7-1

50. Figure 7-2

51. Figure 7-3

52. Figure 7-4

53. Box 7-1

54. Figure 7-5