1. Proteins Protein Structures and Shapes Protein Functions

2. Protein Structures and Shapes Amino acids Peptide bonds alpha helix and beta sheet Domains and Modules Classification of Families Protein Assembly

3. Amino Acids form polypeptide through peptide bond

4. Structural Components of a protein

7. The 20 Amino Acids 2 negative, 3 positive, 5 non-charged polar, 10 nonpolar Read Page 132-133, panel 3-1

10. Limitations on the bond angles Ramachandran plot

11. Four major noncovalent bonds that help protein folding 1. Ionic bond 2. van der Waals 3. Hydrogen bond, 4. Hydrophobic force

12. Hydrophobic “forces”

13. The importance of hydrogen bond

14. Folding and Refolding

16. Secondary structures  helix and  sheet

17. Coiled-coil structure  -keratin

19. Two types of  sheet structures

20. Src Kinase The combination of  - helix and  -sheets

21. Classification of protein families Two serine proteases

22. Two homeodomains from different species (yeast  2, green; drosophila engrailed protein, red)

23. Domains and Modules Domain shuffling Calcium binding domain Kringle domain

24. Module Examples

26. The combination of Modules

27. Design Strategy Weak FRET Phosphatase Strong FRET 433 nm 527 nm 433 nm 490 nm ECFP (1-227) SH2 (from c-Src) SubstrateEYFP Linker Src Activation

28. Protein Subunits Hydrophobic forces

30. Hemoglobin

31. Protein assemblies

32. Actin Filaments

33. Disulfide bonds

34. Extracellular matrix protein are covalently cross-linked by Disulfide bonds

36. Hexagonally packed globular protein subunits can form flat sheets

37. Self-Assembly Tobacco mosaic virus (TMV) Electron Micrograph Model Structure

38. The formation of Virus shell

39. X-Ray Crystallography of different virus (A) Tomato bushy stunt virus (B) poliovirus (C) simian virus 40 (SV40) (D) satellite tobacco necrosis virus

40. Three mechanisms of length determination for self-assembly

41. Protein assembly aided by assembly factors (insulin assembly)

42. Protein Functions Protein Binding Protein conformation Antibody Enzyme and substrate Catalytic Reaction Kinase and phosphatase GTPase, GEF, GAP Motor protein Membrane-bound protein

43. Protein binding

44. Protein binding sites

45. Protein binding site Cyclic AMP

46. Protein binding sites 1.Restriction of water entrance 2.Alteration of reactivity

47. Sequence Comparison to find conserved binding sites Sh2 domain

48. Three ways for two proteins to bind

49. Antibody

50. Noncovalent bonds and protein interactions

51. Binding Energy and Equilibrium constant

54. Enzyme Kinetics Read Panel 3-3, page 165

55. Enzymes lower the activation energy to accelerate chemical reactions

56. Lysozyme actions Bending of the polysaccharide bond

57. Steps of lysozyme actions

60. Strategies of enzyme catalysis

61. Feedback inhibitions

62. Coupled regulation: Positive Regulations

63. Coupled regulation: negative Regulations

64. Coupled regulation on multiple subunits

65. Aspartate transcarbamoylase

67. Kinase and phosphatase

68. Kinase Domain

69. Kinase families

70. Cyclin-dependent Kinase (CdK): Signal integrator threonine tyrosine

71. Src Kinase

73. Multiple Inputs for Src Kinase activation

74. GTPases

75. Ras Structure: One kind of GTPases

76. Phosphorylation and GTP binding regulations

77. EF-Tu and its regulation of tRNA

78. Motor Protein Regulation Myosin on Actin and Kinesin on Microtubules

79. Membrane Protein Calcium Pump on Sarcoplasmic reticulum