The document discusses microbial metabolism and the basic chemical reactions that underlie metabolism. It covers the two major classes of metabolic reactions - catabolism which breaks down molecules and releases energy, and anabolism which uses that energy to build larger molecules. Key metabolic processes like glycolysis, the Krebs cycle, and the electron transport chain are described, which ultimately generate ATP through oxidative phosphorylation or substrate-level phosphorylation. These metabolic pathways allow microbes to acquire nutrients, store energy, build macromolecules, grow and reproduce.

1. Chapter 5 Microbial Metabolism

2. Basic Chemical Reactions Underlying Metabolism Metabolism Collection of controlled biochemical reactions that take place within cells of an organism Ultimate function of metabolism is to reproduce the organism

3. Basic Chemical Reactions Underlying Metabolism Metabolic Processes Guided by Eight Elementary Statements Every cell acquires nutrients Metabolism requires energy from light or from catabolism of nutrients Energy is stored in adenosine triphosphate (ATP) Cells catabolize nutrients to form precursor metabolites Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions Enzymes plus ATP form macromolecules Cells grow by assembling macromolecules Cells reproduce once they have doubled in size

4. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Metabolism: Overview

5. Basic Chemical Reactions Underlying Metabolism Catabolism and Anabolism Two major classes of metabolic reactions Catabolic pathways break larger molecules into smaller products; they are exergonic (release energy) Anabolic pathways synthesize large molecules from the smaller products of catabolism; they are endergonic (require more energy than they release)

6. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.1]

7. Basic Chemical Reactions Underlying Metabolism Oxidation and Reduction Reactions Transfer of electrons from molecule that donates an electron to a molecule that accepts an electron Reactions always occur simultaneously Cells use electron carrier molecules to carry electrons (often in H atoms) Three important electron carriers Nicotinamide adenine dinucleotide (NAD + ) Nicotinamide adenine dinucleotide phosphate (NADP + ) Flavine adenine dinucleotide (FAD) -> FADH2

8. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.2]

9. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Oxidation-Reduction Reactions

10. Basic Chemical Reactions Underlying Metabolism ATP Production and Energy Storage Organisms release energy from nutrients; can be concentrated and stored in high-energy phosphate bonds of ATP Phosphorylation – organic phosphate is added to substrate Cells phosphorylate ADP to ATP in three ways Substrate-level phosphorylation Oxidative phosphorylation Photophosphorylation Anabolic pathways use some energy of ATP by breaking a phosphate bond

11. Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Naming and classifying enzymes Enzymes are organic catalysts – increase the likelihood of a reaction but are not permanently changed Six categories of enzymes based on mode of action Hydrolases Isomerases Ligases or polymerases Lyases Oxidoreductases Transferases

12. Basic Chemical Reactions Underlying Metabolism [INSERT TABLE 5.1]

13. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Enzymes: Overview

14. Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Makeup of enzymes Many protein enzymes are complete in themselves Others are composed of protein portions (apoenzymes) that are inactive if not bound to non-protein cofactors (inorganic ions or coenzymes) Binding of apoenzyme and its cofactor(s) yields holoenzyme Some are RNA molecules called ribozymes

15. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.3]

16. Basic Chemical Reactions Underlying Metabolism [INSERT TABLE 5.2]

17. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.4]

18. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.5]

19. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.6]

20. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Enzymes: Steps in a Reaction

21. Basic Chemical Reactions Underlying Metabolism The Roles of Enzymes in Metabolism Enzyme activity Many factors influence the rate of enzymatic reactions Temperature pH Enzyme and substrate concentrations Presence of inhibitors Inhibitors Substances that block an enzyme’s active site Do not denature enzymes Three types

22. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.7]

23. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.8]

24. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.9]

25. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Enzymes: Competitive Inhibition

26. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.10]

27. Basic Chemical Reactions Underlying Metabolism Animation: Microbial Metabolism: Enzymes: Noncompetitive Inhibition

28. Basic Chemical Reactions Underlying Metabolism [INSERT FIGURE 5.11]

29. Carbohydrate Catabolism Many organisms oxidize carbohydrates as the primary energy source for anabolic reactions Glucose most common carbohydrates used Glucose catabolized by Cellular respiration Fermentation

30. Carbohydrate Catabolism [INSERT FIGURE 5.12]

31. Carbohydrate Catabolism Glycolysis Occurs in cytoplasm of most cells Involves splitting of a six-carbon glucose into two three-carbon sugar molecules Direct transfer of phosphate between two substrates occurs four times – substrate = level phosphorylation Net gain of two ATP molecules, two molecules of NADH, and precursor metabolite pyruvic acid

32. Carbohydrate Catabolism Animation: Microbial Metabolism: Glycolysis: Overview

33. Carbohydrate Catabolism Glycolysis Divided into three stages involving ten total steps Energy-investment stage Lysis stage Energy-conserving stage

34. Carbohydrate Catabolism [INSERT FIGURE 5.13]

35. Carbohydrate Catabolism Animation: Microbial Metabolism: Glycolysis: Steps

36. Carbohydrate Catabolism [INSERT FIGURE 5.14]

37. Carbohydrate Catabolism Alternatives to Glycolysis Yield fewer molecules of ATP than glycolysis Reduce coenzymes and yield different metabolites needed in anabolic pathways Two pathways Pentose phosphate pathway – net gain of two molecules of NADPH, one molecule of ATP, and five-carbon precursor metabolites Entner-Doudoroff pathway – net gain of two molecules of NADPH, one molecule of ATP, and precursor metabolites

38. Carbohydrate Catabolism [INSERT FIGURE 5.15]

39. Carbohydrate Catabolism

40. Carbohydrate Catabolism Continuation of Cellular Respiration Resultant pyruvic acid completely oxidized to produce ATP by a series of redox reactions Three stages of cellular respiration 1. Synthesis of acetyl-CoA 2. Krebs cycle 3. Final series of redox reactions (electron transport chain)

41. Carbohydrate Catabolism [INSERT FIGURE 5.17]

42. Carbohydrate Catabolism Continuation of Cellular Respiration Synthesis of acetyl-CoA Results in Two molecules of acetyl-CoA Two molecules of CO 2 Two molecules of NADH

43. Carbohydrate Catabolism Continuation of Cellular Respiration The Krebs cycle Great amount of energy remains in bonds of acetyl-CoA The Krebs cycle transfers much of this energy to coenzymes NAD + and FAD Occurs in cytoplasm of prokaryotes and in matrix of mitochondria in eukaryotes

44. Carbohydrate Catabolism Continuation of Cellular Respiration The Krebs cycle Six types of reactions in Krebs cycle Anabolism of citric acid Isomerization reactions Hydration reaction Redox reactions Decarboxylations Substrate-level phosphorylation

45. Carbohydrate Catabolism [INSERT FIGURE 5.18]

46. Carbohydrate Catabolism Animation: Microbial Metabolism: Krebs Cycle—Overview

47. Carbohydrate Catabolism Animation: Microbial Metabolism: Krebs Cycle— Steps

48. Carbohydrate Catabolism Continuation of Cellular Respiration The Krebs cycle Results in Two molecules of ATP Two molecules of FADH 2 Six molecules of NADH Four molecules of CO 2

49. Carbohydrate Catabolism Continuation of Cellular Respiration Electron transport Most significant production of ATP occurs through stepwise release of energy from series of redox reactions known as an electron transport chain (ETC) Consists of series of membrane-bound carrier molecules that pass electrons from one to another and ultimately to final electron acceptor Energy from electrons used to pump protons (H + ) across the membrane, establishing a proton gradient Located in cristae of eukaryotes and in cytoplasmic membrane of prokaryotes

50. Carbohydrate Catabolism [INSERT FIGURE 5.19]

51. Carbohydrate Catabolism Animation: Microbial Metabolism: Electron Transport Chain: Overview

52. Carbohydrate Catabolism Continuation of Cellular Respiration Electron transport Four categories of carrier molecules Flavoproteins Ubiquinones Metal-containing proteins Cytochromes Some organisms can vary their carrier molecules under different environmental conditions In aerobic respiration oxygen serves as final electron acceptor to yield water In anaerobic respiration molecules other than oxygen serve as final electron acceptor

53. Carbohydrate Catabolism [INSERT FIGURE 5.20]

54. Carbohydrate Catabolism Animation: Microbial Metabolism: Electron Transport Chain: The Process

55. Carbohydrate Catabolism Animation: Microbial Metabolism: Electron Transport Chain: Factors Affecting ATP Yield

56. Carbohydrate Catabolism Continuation of Cellular Respiration Chemiosmosis Membrane maintains electrochemical gradient by keeping one or more chemicals in higher concentration on one side Cells use energy released in redox reactions of ETC to create proton gradient, which has potential energy known as proton motive force Protons, propelled by proton motive force, flow down electrochemical gradient through ATP synthases (protein channels) that phosphorylate ADP to ATP Called oxidative phosphorylation because proton gradient created by oxidation of components of ETC Total of ~34 ATP molecules formed from one molecule of glucose

57. Carbohydrate Catabolism [INSERT TABLE 5.3]

58. Carbohydrate Catabolism Fermentation Sometimes cells cannot completely oxidize glucose by cellular respiration Cells require constant source of NAD + that cannot be obtained by simply using glycolysis and the Krebs cycle In respiration, electron transport regenerates NAD + from NADH Fermentation pathways provide cells with alternate source of NAD + Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as an electron acceptor

59. Carbohydrate Catabolism [INSERT FIGURE 5.21]

60. Carbohydrate Catabolism [INSERT TABLE 5.4]

61. Carbohydrate Catabolism [INSERT FIGURE 5.22]

62. Carbohydrate Catabolism Animation: Microbial Metabolism: Fermentation

63. Other Catabolic Pathways Lipid Catabolism Protein Catabolism

64. Other Catabolic Pathways [INSERT FIGURE 5.23]

65. Other Catabolic Pathways [INSERT FIGURE 5.24]

66. Photosynthesis Every food chain begins with anabolic pathways in organisms that synthesize their own organic molecules from inorganic carbon dioxide Most of these organisms capture light energy from the sun and use it to drive the synthesis of carbohydrates from CO 2 and H 2 O by a process called photosynthesis

67. Photosynthesis Animation: Microbial Metabolism: Photosynthesis: Overview

68. Photosynthesis Chemicals and Structures Chlorophylls Most important of organisms that capture light energy with pigment molecules Composed of hydrocarbon tail attached to light-absorbing active site centered around magnesium ion Active sites structurally similar to cytochrome molecules in ETC Vary slightly in lengths and structures of hydrocarbon tails and in atoms that extend from active site They subsequently absorb light of different wavelengths

69. Photosynthesis Chemicals and Structures Cells arrange molecules of chlorophyll and other pigments in protein matrix to form light-harvesting matrices called photosystems Embedded in cellular membranes called thylakoids In prokaryotes – invagination of cytoplasmic membrane In eukaryotes – formed from infoldings of inner membrane of chloroplasts Arranged in stacks called grana Stroma is space between outer membrane of grana and thylakoid membrane

70. Photosynthesis [INSERT FIGURE 5.25]

71. Photosynthesis Chemicals and Structures Two types of photosystems Photosystem I (PS I) Photosystem II (PS II) Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPH Classified as light-dependent reactions because they depend on light energy Light-independent reactions synthesize glucose from carbon dioxide and water

72. Photosynthesis Light-Dependent Reactions As electrons move down the chain, their energy is used to pump protons across the membrane Photophosphorylation uses proton motive force to generate ATP Photophosphorylation can be cyclic or noncyclic

73. Photosynthesis [INSERT FIGURE 5.26]

74. Photosynthesis [INSERT FIGURE 5.27]

75. Photosynthesis Animation: Microbial Metabolism: Photosynthesis: Cyclic Photophosphorylation

76. Photosynthesis Animation: Microbial Metabolism: Photosynthesis: Noncyclic Photophosphorylation

77. Photosynthesis [INSERT TABLE 5.5]

78. Photosynthesis Light-Independent Reactions Do not require light directly, but use ATP and NADPH generated by light-dependent reactions Key reaction is carbon fixation by Calvin-Benson cycle For every three molecules of CO 2 that enter the cycle, one molecule of glyceraldehyde 3-phosphate leaves For every two molecules of glyceraldehyde 3-phosphate, one molecule of glucose 6-phosphate is anabolically synthesized by glycolysis

79. Photosynthesis [INSERT FIGURE 5.28]

80. Photosynthesis Animation: Microbial Metabolism: Photosynthesis: Light-Independent Reactions

81. Other Anabolic Pathways Anabolic reactions are synthesis reactions requiring energy and a source of metabolites Energy derived from ATP from catabolic reactions Glycolysis, the Krebs cycle, and the pentose phosphate pathway provide twelve basic precursor metabolites from which all macromolecules and cellular structures are made Many anabolic pathways are the reversal of the catabolic pathways Reactions that can proceed in either direction are amphibolic

82. Other Anabolic Pathways [INSERT TABLE 5.6]

83. Other Anabolic Pathways [INSERT FIGURE 5.29]

84. Other Anabolic Pathways [INSERT FIGURE 5.30]

85. Other Anabolic Pathways [INSERT FIGURE 5.31]

86. Other Anabolic Pathways [INSERT FIGURE 5.32]

87. Integration and Regulation of Metabolic Function Cells synthesize or degrade channel and transport proteins Cells often synthesize enzymes needed to catabolize a particular substrate only when that substrate is available If two energy sources are available, cells catabolize the more energy efficient of the two first. Cells synthesize the metabolites they need, but typically cease synthesis if metabolite is available

88. Integration and Regulation of Metabolic Function Eukaryotic cells keep metabolic processes from interfering with each other by isolating particular enzyme within membrane-bounded organelles Cells use allosteric sites on enzymes to control the activity of enzymes Feedback inhibition slows or stops anabolic pathways when product is in abundance Cells regulate amphibolic pathways that use the same substrate by requiring different coenzymes for each pathway

89. Integration and Regulation of Metabolic Function Two types of regulatory mechanisms Control of gene expression Cells control amount and timing of protein (enzyme) production Control of metabolic expression Cells control activity of proteins (enzymes) once produced

90. Integration and Regulation of Metabolic Function [INSERT FIGURE 5.33]

91. Integration and Regulation of Metabolic Function Animation: Microbial Metabolism: Metabolism: The Big Picture