1. CARBON AND THE MOLECULAR DIVERSITY OF LIFE
CHAPTER 4

2. ISOMERS FUNCTIONAL GROUPS
Compounds with the same chemical formula but different structures
FUNCTIONAL GROUPS
See diagram of functional groups

3. Figure 4.6 Three types of isomers

4. Figure 4.6ax Structural isomers

5. Table 4.1 Functional Groups of Organic Compounds

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

7. Figure 4.8x1 Estrone and testosterone

9. THE STRUCTURE AND FUNCTION OF MACROMOLECULES
CHAPTER 5

10. SYNTHESIS AND BREAKDOWN
Dehydration synthesis (condensation reaction) – removal of water to join 2 compounds
Hydrolysis – addition of water to break a bond between 2 compounds

11. Figure 5.2 The synthesis and breakdown of polymers

12. CARBOHYDRATES Monosaccharides
Examples: glucose, fructose, and galactose
One sugar
Disaccharides
Examples: Lactose, sucrose and maltose
Two sugars
Joined by glycosidic linkage via dehydration synthesis
Polysaccharides
Examples: starch, glycogen, and cellulose
Many sugars

13. Figure 5.3 The structure and classification of some monosaccharides

14. Figure 5.4 Linear and ring forms of glucose

15. Figure 5.5 Examples of disaccharide synthesis

16. Figure 5.6 Storage polysaccharides

17. Figure 5.7a Starch and cellulose structures

18. Figure 5.7b,c Starch and cellulose structures

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

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

21. Figure 5.x2 Cellulose digestion: cow

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

23. LIPIDS Little or no affinity for water (hydrophobic)
Examples: Fat, phospholipids, and steroids
Fats – composed of glycerol (an alcohol) and fatty acids
Saturated – no double bonds in carbon chain
Unsaturated – at least one double bond in carbon chain

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

25. Figure 5.11x Saturated and unsaturated fats and fatty acids: butter and oil

26. Figure 5.12 The structure of a phospholipid

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

28. Figure 5.10 The synthesis and structure of a fat, or triacylglycerol

29. Figure 5.14 Cholesterol, a steroid

30. Figure 5.14x Cholesterol    

31. Table 5.1 An Overview of Protein Functions

32. PROTEIN Polypeptide – polymer of amino acids
There are 20 different amino acids differing only by the R group

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

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

36. Figure 5.16 Making a polypeptide chain

37. FOUR LEVELS OF PROTEIN STRUCTURE
Primary – sequences of amino acids
Secondary – hydrogen bonds cause coils and folds
Pleated sheet and alpha helix
Tertiary – irregular contortions due to various weak bonds:
Hydrophobic interactions
Disulfide bridges
Ionic bonds
Van der Waals interactions
Quaternary – two or more polypeptide chains aggregated into one functional macromolecule
Examples: collagen and hemoglobin

38. Figure 5.18 The primary structure of a protein

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

40. Figure 5.19x Sickled cells

41. Figure 5.20 The secondary structure of a protein

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

43. Figure 5.23 The quaternary structure of proteins

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

45. Figure 5.25 Denaturation and renaturation of a protein

46. Figure 5.21 Spider silk: a structural protein

47. Figure 5.21x Silk drawn from the spinnerets at the rear of a spider

48. NUCLEIC ACIDS Examples: DNA and RNA
We will discuss these in great detail later in the semester! 

49. Figure 5.29 The components of nucleic acids

50. Figure 5.30 The DNA double helix and its replication

51. AN INTRODUCTION TO METABOLISM
CHAPTER 8

52. Figure 6.2 Transformations between kinetic and potential energy

53. Figure 6.2x1 Kinetic and potential energy: dam

54. Figure 6.2x2 Kinetic and potential energy: cheetah at rest and running

55. THERMODYNAMICS
First Law of Thermodynamics – energy can be transferred and transformed, but not created nor destroyed
Second Law of Thermodynamics – every energy transfer or transformation makes the universe more disordered (have more entropy)

56. Entropy – measure of disorder or randomness
Most energy transformations involve at least some energy be changed to heat
Heat is the lowest form of energy
Biological order has increased over time
Second law requires only that processes increase the entropy of the universe
Organisms may decrease entropy but entire universe must increase entropy

57. Figure 6.4 Order as a characteristic of life

58. Free energy (G) – energy available to do work when temperature is uniform throughout system
G = H – TS
H = system’s total energy (enthalpy)
T = temp in Kelvin (° C + 273)
S = entropy

59. ∆ G = G final state – G starting state
∆ G = ∆ H - T∆ S
For a spontaneous reaction:
∆ G = negative
So must: give up energy (decrease H) and/or give up order (increase S)
∆ G = 0 at equilibrium
Free energy increases if move away from equilibrium and decreases if move toward equilibrium

60. Figure 6.5 The relationship of free energy to stability, work capacity, and spontaneous change

61. Exergonic
∆ G = negative
Spontaneous
Net release of energy
Endergonic
∆ G = positive
NOT spontaneous
Stores free energy in molecules

62. Figure 6.6 Energy changes in exergonic and endergonic reactions

63. Cells at equilibrium are dead!
Cells can keep disequilibrium by having products of one reaction not accumulate but instead become reactants of another reaction
Energy coupling – an exergoinc reaction drives an endergoinc reaction

64. Figure 6.7 Disequilibrium and work in closed and open systems

65. ATP = ADENOSINE TRIPHOSPHATE
ATP + H2O ADP + Pi
∆ G = -7.3kcal/mol
ADP = adenosine diphosphate
Normally the phosphate is bonded to an intermediate compound which is then considered phosphorylated
The reverse reaction is endergonic and requires +7.3 kcal/mol to make ATP from ADP

66. Figure 6.8 The structure and hydrolysis of ATP

67. Figure 6.9 Energy coupling by phosphate transfer

68. Figure The ATP cycle

69. ENZYMES
Catalytic proteins or enzymes – change the rate of reaction without being consumed by the reaction
Activation energy (EA) – energy needed to start a reaction
Energy needed to contort the reactants so the bonds can change
Enzymes lower activation energy by enabling reactants to absorb enough energy to reach transition state at moderate temps

70. Enzymes are substrate specific
Substrate – the reactant on which an enzyme works
Active site – area on enzyme where substrate fits
Induced fit – model of enzyme activity

71. Figure 6.12 Energy profile of an exergonic reaction

72. Figure 6.14 The induced fit between an enzyme and its substrate

73. Figure 6.15 The catalytic cycle of an enzyme

74. Effects of pH and Temp
Optimal temperatures and pH ranges exist for enzymes

75. Figure 6.16 Environmental factors affecting enzyme activity

76. Cofactors – non-protein helpers that bind to active site or substrate (zinc, iron)
Coenzymes – cofactors that are organic (vitamins)
Enzyme Inhibitors – reduce enzyme activity
Competitive inhibitors – block substrate from entering active site
Reversible
Overcome by adding more substrate
Noncompetitive inhibitors – bind to another part of enzyme thereby changing the enzyme’s shape making it inactive
Irreversible
Examples: DDT, sarin gas, and penicillin

77. Figure 6.17 Inhibition of enzyme activity

78. Allosteric regulation
Allosteric sites – receptors on enzymes (not the active site) that may either inhibit or stimulate enzyme activity
Feedback inhibition
End product of a pathway acts as a inhibitor of an enzyme within the pathway
Cooperativity – an enzyme with multiple subunits where binding to one active site causes shape changes to rest of subunits which in turn activates those subunits

79. Figure 6.18 Allosteric regulation of enzyme activity

80. Figure 6.19 Feedback inhibition

81. Figure Cooperativity