1. Cell Chemistry and Biosynthesis

2. Chemical Components of A Cell Major Atoms Covalent bonds, Ionic bonds Four major families of small molecules Sugar, fatty acids, amino acids, nucleotides Three macromolecule families: polysaccharide, protein, nucleic acid Non covalent bonds determine molecular shape and interactions

3. Carbon and Hydrogen

4. Chemical Elements for Live Organisms

5. Covalent Bond and Ionic Bond

6. Sodium Chloride: ionic bond formation

7. The geometry of covalent bonds

8. Important Energy Levels

9. The Van der Waals forces

10. Acid Donate a proton Base Absorb a proton or donate OH - NH3+H2O->NH4 + +OH - NaOH->Na + +OH -

11. Ionic bonds in Water

12. Hydrogen bond Polar interaction: a elecgtropositive hydrogen is shared by two neighboring electornegative atoms

13. Molecular Interaction in solution 1. H-bond (hydrogen bond), 2. Ionic bond, 3. Van der Waals 4. Hydrophobic “force”

14. Four Major Small Organic Molecules

15. Sugar [(CH2O)n, carbohydrates] Glucose

16. Disaccharide Condensation and hydrolysis

17. Fatty Acids

18. Phospholipid (amphipathic)

19. Amino Acid

20. Amino Acid and pH values

21. Peptides and proteins

22. ATP (ribonucleotide adenosine triphosphate) Nucleotides

23. Nucleotides and DNA, RNA DNA: deoxyribonucleic acids A(adenine) G(guanine) T(thymine) C (cytosine) RNA: ribonucleic acids A G U(Uracil) C

24. Macromolecules

25. Three families of macromolecules

26. The assembly of macromolecules

27. Proteins Protein Structures and Shapes Protein Functions

28. Protein Structures and Shapes Amino acids Peptide bonds  helix and  sheet Domains and Modules Classification of Families Protein Assembly

29. Amino Acids form polypeptide through peptide bond

30. Structural Components of a protein

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

34. Limitations on the bond angles Ramachandran plot

35. Three major noncovalent bonds that help protein folding 1. Ionic bond 2. van der Waals 3. Hydrogen bond

36. Hydrophobic “forces”

37. The importance of hydrogen bond

38. Folding and Refolding

39. Secondary structures  helix and  sheet

41. Coiled-coil structure  -keratin

42. Two types of  sheet structures

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

44. Green Fluorescence Protein

45. Classification of protein families Two serine proteases

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

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

48. Module Examples

50. The combination of Modules

51. 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

52. The Src reporter with CFP and YFP monomers 0.5 0.35

53. Protein Subunits Hydrophobic forces

55. Hemoglobin

56. Protein assemblies

57. Actin Filaments

58. Disulfide bonds

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

61. Hexagonally packed globular protein subunits can form flat sheets

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

63. The formation of Virus shell

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

65. Three mechanisms of length determination for self-assembly

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

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

68. Protein binding

69. Protein binding sites

70. Protein binding site Cyclic AMP

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

72. Sequence Comparison to find conserved binding sites

73. Three ways for two proteins to bind

74. Antibody

75. Noncovalent bonds and protein interactions

76. Binding Energy and Equilibrium constant

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