2. Figure 5-1

3. Table 5-1

4. Figure 5-4

5. Page 97

6. Figure 5-5

7. Table 5-2

8. Figure 5-6

9. Figure 5-7

10. Figure 5-8

11. VVP Fug, 5-8 Purification of Stapylococcal Nuclease

12. Stryer Fig. 4.7 PAGE

13. Stryer Fig. 4.8

14. Page 106

15. Animation http://bcs.whfreeman.com/biochem5/cat_040/ch04/ch04xd02.htm

16. Stryer Fig. 4.9 Coomassie blue stained SDS gel.

17. Figure 5-9

18. Figure 5-10

19. Figure 5-11

20. Figure 5-12

21. Box 5-1

22. Figure 5-13

23. Page 107

24. Table 5-3

25. Figure 5-14

26. Figure 5-14 part 3

27. Figure 5-15

28. Figure 5-16a

29. Figure 5-16b

30. Figure 5-18

31. Figure 5-19

32. Amino acid Models from Cal LutheranModels

33. See VVP Fig 4-3

35. VVP Fig 6-3 p 126

37. Example of a protein sequence MANSKINKQL DKLPENLRLN GRTPSGKLRS FVCEVCTRAF ARQEHLKRHY RSHTNEKPYP CGLCNRCFTR RDLLIRHAQK IDSGNLGETI SHTKKVSRTI TKARKNSASS VKFQTPTYGT PDNGGSGGTV LSEGEWQLVL HVWAKVEADV AGHGQDILIR LFKSHPETLE KFDRFKHLKT EAEMKASEDL KKHGVTVLTA LGAILKKKGH HEAELKPLAQ SHATKHKIPI KYLEFISEAI IHVLHSRHPG DFGADAQGAM NKALELFRKD IAAKYKELGY G N-terminus C-terminus

38. N-termini C-termini VVP Fig 5-1 p 94

40. 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

41. VVP page 150 “nonpolar” “polar”

42. Figure 6-1 part 4

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

44. Chapter 6 Opener

45. Figure 6-4

46. Figure 6-5

47. Figure 6-6

48. Figure 6-7

49. Figure 6-8

50. Figure 6-9

51. Figure 6-9a

52. Figure 6-9b

53. Figure 6-10

54. VVP Fig 6-16 pdb

55. Table 6-1

56. Figure 6-12

57. Figure 6-15 Keratin: a coiled coil

58. Figure 6-16 Higher order keratin structure

59. 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.

60. Figure 6-20b Protein crystals: flavodoxin

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

62. Figure 6-21

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

65. Figure 6-33 Hemoglobin

66. Table 6-3

67. Figure 6-35 Bovine chymotrypsin

68. Figure 6-38 Molecular dynamics of Mb

69. Page 159

70. Figure 6-39

71. Figure 6-40

72. Figure 6-41

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

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

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

76. 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)

77. Table 6-4

80. Figure 5-3