1. Chapter 3 The Chemistry of Organic Molecules

2. Figure 4.3 Valences for the major elements of organic molecules

3. Why Carbon? Most versatile building blocks of molecules –Tetravalence –Can link together –Covalent compatibility with variety of elements Variation in carbon skeletons contributes to the diversity of organic molecules –Hydrocarbons –Isomers – shape can dramatically alter activity

4. Figure 4.4 Variations in carbon skeletons

5. Figure 4.2 The shapes of three simple organic molecules

6. Figure 4.6 Three types of isomers

7. Figure 4.6ax Structural isomers

8. Figure 4.7 The pharmacological importance of enantiomers

9. Functional Groups A specific configuration of atoms commonly attached to C-skeletons, usually involved in chemical reactions Behave consistently from one organic molecule to the next Contribute to distinctive properties of organic molecules Most molecules have two or more

10. Table 4.1 Functional Groups of Organic Compounds

11. Functional Groups cont. Hydroxyl –Alcohols –Polar –Increase solubility Carbonyl

12. Functional Groups cont. Carboxyl –Carboxylic acids –Very polar Amino –Amines –Basic

13. Functional Groups Cont. Sulfhydryl –Thiols –Can interact to help stabilize structures Phosphate –One fxn includes energy transfer

14. Recap Emergent properties of organic compounds due to: –Arrangement of carbon skeleton –Functional groups added to skeleton Variation at molecular level underlies biological diversity

15. Macromolecules Large biological molecules formed from small organic molecules Polymers…made up of monomers Synthesized by cells…how?

16. Figure 5.2 The synthesis and breakdown of polymers

17. Carbohydrates Sugars End in -ose CH 2 O Carbonyl group and multiple hydroxyl groups Monosaccharides and disaccharides = fuel and carbon sources

18. Figure 5.3 The structure and classification of some monosaccharides

19. Figure 5.3x Hexose sugars Glucose Galactose

20. Figure 5.4 Linear and ring forms of glucose

21. Figure 5.5 Examples of disaccharide synthesis

22. Figure 5.5x Glucose monomer and disaccharides Glucose monomer Sucrose Maltose

23. Polysaccharides thousands of monosaccharides Storage and structural roles Glycogen, starch, cellulose, peptidoglycan (sugars + amino acids), and chitin (contains nitrogen)

24. Figure 5.7a Starch and cellulose structures

25. Figure 5.7b,c Starch and cellulose structures

26. Figure 5.7x Starch and cellulose molecular models  Glucose  Glucose Starch Cellulose

27. Figure 5.6 Storage polysaccharides

28. Figure 5.8 The arrangement of cellulose in plant cell walls

29. Figure 5.x1 Cellulose digestion: termite and Trichonympha

30. Figure 5.x2 Cellulose digestion: cow

31. Chitin

32. Figure 5.9 Chitin, a structural polysaccharide: exoskeleton and surgical thread

33. Peptidoglycan

34. Lipids Diverse group of nonpolymers Share one trait: hydrophobic Consist mainly of hydrocarbons Fats, phospholipids, waxes, steroids

35. Fats Glycerol + fatty acids Fatty acids: carbon chain with carboxyl group at end Triglycerols Saturated vs unsaturated

36. Figure 5.11 Examples of saturated and unsaturated fats and fatty acids

37. Fats cont. Functions: –Energy (2x a polysaccharide) –Storage – adipose tissue – swells and shrinks –Cushions –Warmth

38. Artherosclerosis

39. Phospholipids Glycerol + 2 fatty acids + phosphate group Amphipathic Major components of cell membranes

40. Figure 5.12 The structure of a phospholipid

41. Figure 5.13 Two structures formed by self-assembly of phospholipids in aqueous environments

42. Steroids Carbon skeletons consisting of four fused rings Hormones (many produced from cholesterol) Vary in their functional groups

43. Figure 4.8 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

44. Waxes Protectant Water-proofing Corrosion prevention

45. Proteins Greek: “first place” 50% + of dry weight of most cells Instrumental in activities Structural support, storage, transport, signaling within organism, movement of organism, defense against foreign substances, enzymes (help regulate metabolism)

46. Proteins cont. Vary extensively in structure Unique 3d shape Polymers of amino acids: polypeptides

47. Figure 5.15 The 20 amino acids of proteins: nonpolar

48. Figure 5.15 The 20 amino acids of proteins: polar and electrically charged

49. Peptide Bonds

50. Proteins cont. A functional protein consists of 1+ polypeptides precisely twisted, folded, and coiled into a precise 3d conformation Globular vs fibrous Function depends on ability to recognize and bind to some other molecule Determined by amino acid sequence

51. Figure 5.18 The primary structure of a protein

52. Figure 5.20 The secondary structure of a protein

53. Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein

54. Figure 5.23 The quaternary structure of proteins

55. Figure 5.24 Review: the four levels of protein structure

56. Figure 5.17 Conformation of a protein, the enzyme lysozyme

57. Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease

58. Fibrous vs globular

59. Figure 5.21 Spider silk: a structural protein

60. What determines protein conformation? Amino acid sequence pH Salt concentration Temperature Chaperonins – protein molecules that assist the proper folding other proteins; keep it away from “bad influences” If environment is changed or altered from “native” conditions = denatured

61. Figure 5.25 Denaturation and renaturation of a protein

62. Figure 5.27 X-ray crystallography

63. Table 5.1 An Overview of Protein Functions

64. Nucleic Acids DNA and RNA Genetic material DNA directs the synthesis of RNA, which then directs the ribosomes to make proteins Polymers of nucleotides

65. Figure 5.29 The components of nucleic acids

66. Figure 5.x3 James Watson and Francis Crick

67. Figure 5.x4 Rosalind Franklin

68. Erwin Chargaff

71. 3’ and 5’ ends

72. Genetic Material

73. Figure 5.30 The DNA double helix and its replication

74. DNA and proteins as tape measures of evolution Two species that are more closely related share a greater proportion of their DNA and protein sequences than do distantly related species

75. ATP RNA nucleotide + 2 more P groups Energy transfer!