1. Chapter 5
Microbial Metabolism

2. Q&A
All E. coli look alike through a microscope; so how can E. coli O157 be differentiated?

3. Catabolic and Anabolic Reactions
Learning Objectives
5-1 Define metabolism, and describe the fundamental differences between anabolism and catabolism.
5-2 Identify the role of ATP as an intermediate between catabolism and anabolism.

4. Catabolic and Anabolic Reactions
Metabolism: The sum of the chemical reactions in an organism

5. Catabolic and Anabolic Reactions
Catabolism: Provides energy and building blocks for anabolism.
Anabolism: Uses energy and building blocks to build large molecules

6. Role of ATP in Coupling Reactions
Figure 5.1

7. Catabolic and Anabolic Reactions
A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell
Metabolic pathways are determined by enzymes
Enzymes are encoded by genes
ANIMATION Metabolism: Overview

8. Check Your Understanding
Distinguish catabolism from anabolism. 5-1
How is ATP an intermediate between catabolism and anabolism? 5-2

9. Enzyme Learning Objectives 5-3 Identify the components of an enzyme.
5-4 Describe the mechanism of enzymatic action.
5-5 List the factors that influence enzymatic activity.
5-6 Distinguish competitive and noncompetitive inhibition.
5-7 Define ribozyme.

10. Collision Theory
The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide
Activation energy is needed to disrupt electronic configurations
Reaction rate is the frequency of collisions with enough energy to bring about a reaction.
Reaction rate can be increased by enzymes or by increasing temperature or pressure

11. Energy Requirements of a Chemical Reaction
Figure 5.2

12. Enzyme Components Biological catalysts Apoenzyme: Protein
Specific for a chemical reaction; not used up in that reaction
Apoenzyme: Protein
Cofactor: Nonprotein component
Coenzyme: Organic cofactor
Holoenzyme: Apoenzyme plus cofactor

13. Components of a Holoenzyme
Figure 5.3

14. Important Coenzymes
NAD+
NADP+
FAD
Coenzyme A

15. Enzyme Specificity and Efficiency
The turnover number is generally 1 to 10,000 molecules per second
ANIMATION Enzymes: Steps in a Reaction
ANIMATION Enzymes: Overview

16. The Mechanism of Enzymatic Action
Figure 5.4a

17. The Mechanism of Enzymatic Action
Figure 5.4b

18. Enzyme Classification
Oxidoreductase: Oxidation-reduction reactions
Transferase: Transfer functional groups
Hydrolase: Hydrolysis
Lyase: Removal of atoms without hydrolysis
Isomerase: Rearrangement of atoms
Ligase: Joining of molecules, uses ATP

19. Factors Influencing Enzyme Activity
Temperature pH
Substrate concentration
Inhibitors

20. Factors Influencing Enzyme Activity
Temperature and pH denature proteins
Figure 5.6

21. Effect of Temperature on Enzyme Activity
Figure 5.5a

22. Effect of pH on Enzyme Activity
Figure 5.5b

23. Effect of Substrate Concentration on Enzyme Activity
Figure 5.5c

24. Enzyme Inhibitors: Competitive Inhibition
Figure 5.7a–b

25. Enzyme Inhibitors: Competitive Inhibition
ANIMATION Competitive Inhibition

26. Enzyme Inhibitors: Noncompetitive Inhibition
ANIMATION Non-competitive Inhibition
Figure 5.7a, c

27. Enzyme Inhibitors: Feedback Inhibition
Figure 5.8

28. Ribozymes
RNA that cuts and splices RNA

29. Check Your Understanding
What is a coenzyme? 5-3
Why is enzyme specificity important? 5-4
What happens to an enzyme below its optimal temperature?
Above its optimal temperature? 5-5
Why is feedback inhibition noncompetitive inhibition? 5-6
What is a ribozyme? 5-7

30. Energy Production Learning Objectives
5-8 Explain the term oxidation-reduction.
5-9 List and provide examples of three types of phosphorylation reactions that generate ATP.
5-10 Explain the overall function of metabolic pathways.

31. Oxidation-Reduction Reactions
Oxidation: Removal of electrons
Reduction: Gain of electrons
Redox reaction: An oxidation reaction paired with a reduction reaction

32. Oxidation-Reduction
Figure 5.9

33. Oxidation-Reduction Reactions
In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations.
ANIMATION Oxidation-Reduction Reactions

34. Representative Biological Oxidation
Figure 5.10

35. The Generation of ATP
ATP is generated by the phosphorylation of ADP

36. Substrate-Level Phosphorylation
Energy from the transfer of a high-energy PO4– to ADP generates ATP

37. Oxidative Phosphorylation
Energy released from transfer of electrons (oxidation) of one compound to another (reduction) is used to generate ATP in the electron transport chain

38. Photophosphorylation
Light causes chlorophyll to give up electrons. Energy released from transfer of electrons (oxidation) of chlorophyll through a system of carrier molecules is used to generate ATP.

39. Metabolic Pathways of Energy Production

40. Check Your Understanding
Why is glucose such an important molecule for organisms? 5-8
Outline the three ways that ATP is generated. 5-9
What is the purpose of metabolic pathways? 5-10

41. Carbohydrate Catabolism
Learning Objectives
5-11 Describe the chemical reactions of glycolysis.
5-12 Identify the functions of the pentose phosphate and Entner-Doudoroff pathways.
5-13 Explain the products of the Krebs cycle.
5-14 Describe the chemiosmotic model for ATP generation.
5-15 Compare and contrast aerobic and anaerobic respiration.
5-16 Describe the chemical reactions of, and list some products of, fermentation

42. Carbohydrate Catabolism
The breakdown of carbohydrates to release energy
Glycolysis
Krebs cycle
Electron transport chain

43. Glycolysis
The oxidation of glucose to pyruvic acid produces ATP and NADH
Figure 5.11

44. Preparatory Stage of Glycolysis
2 ATP are used
Glucose is split to form 2 glucose-3-phosphate
Figure 5.12, steps 1–5

45. Energy-Conserving Stage of Glycolysis
2 glucose-3-phosphate oxidized to 2 pyruvic acid
4 ATP produced
2 NADH produced
Figure 5.12, steps 6–10

46. Glycolysis
Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+  2 pyruvic acid + 4 ATP + 2 NADH + 2H+
ANIMATION Glycolysis: Steps
ANIMATION Glycolysis: Overview

47. Alternatives to Glycolysis
Pentose phosphate pathway
Uses pentoses and NADPH
Operates with glycolysis
Entner-Doudoroff pathway
Produces NADPH and ATP
Does not involve glycolysis
Pseudomonas, Rhizobium, Agrobacterium

48. Cellular Respiration
Oxidation of molecules liberates electrons for an electron transport chain
ATP is generated by oxidative phosphorylation

49. Intermediate Step
Pyruvic acid (from glycolysis) is oxidized and decarboyxlated
Figure 5.13

50. The Krebs Cycle Oxidation of acetyl CoA produces NADH and FADH2
ANIMATION Krebs Cycle: Steps
ANIMATION Krebs Cycle: Overview

51. The Krebs Cycle
Figure 5.13

52. The Electron Transport Chain
A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain
Energy released can be used to produce ATP by chemiosmosis
ANIMATION Electron Transport Chain: Overview

53. Overview of Respiration and Fermentation
Figure 5.11

54. Chemiosmotic Generation of ATP
Figure 5.16

55. An Overview of Chemiosmosis
ANIMATION Electron Transport Chain: The Process
Figure 5.15

56. A Summary of Respiration
Aerobic respiration: The final electron acceptor in the electron transport chain is molecular oxygen (O2).
Anaerobic respiration: The final electron acceptor in the electron transport chain is not O2. Yields less energy than aerobic respiration because only part of the Krebs cycles operates under anaerobic conditions.

57. Respiration
ANIMATION Electron Transport Chain: Factors Affecting ATP Yield
Figure 5.16

58. Anaerobic Respiration
Electron Acceptor
Products
NO3–
NO2–, N2 + H2O
SO4–
H2S + H2O
CO32 –
CH4 + H2O

59. Carbohydrate Catabolism
Pathway
Eukaryote
Prokaryote
Glycolysis
Cytoplasm
Intermediate step
Krebs cycle
Mitochondrial matrix
ETC
Mitochondrial inner membrane
Plasma membrane

60. Carbohydrate Catabolism
Energy produced from complete oxidation of one glucose using aerobic respiration
Pathway
ATP Produced
NADH Produced
FADH2 Produced
Glycolysis 2
Intermediate step
Krebs cycle 6
Total 4 10

61. Carbohydrate Catabolism
ATP produced from complete oxidation of one glucose using aerobic respiration
Pathway
By Substrate-Level Phosphorylation
By Oxidative Phosphorylation
From NADH
From FADH
Glycolysis 2 6
Intermediate step
Krebs cycle 18 4
Total 30

62. Carbohydrate Catabolism
36 ATPs are produced in eukaryotes
Pathway
By Substrate-Level Phosphorylation
By Oxidative Phosphorylation
From NADH
From FADH
Glycolysis 2 6
Intermediate step
Krebs cycle 18 4
Total 30

63. Fermentation Any spoilage of food by microorganisms (general use)
Any process that produces alcoholic beverages or acidic dairy products (general use)
Any large-scale microbial process occurring with or without air (common definition used in industry)

64. Fermentation Scientific definition:
Releases energy from oxidation of organic molecules
Does not require oxygen
Does not use the Krebs cycle or ETC
Uses an organic molecule as the final electron acceptor

65. An Overview of Fermentation
ANIMATION Fermentation
Figure 5.18a

66. End-Products of Fermentation
Figure 5.18b

67. Fermentation Alcohol fermentation: Produces ethanol + CO2
Lactic acid fermentation: Produces lactic acid
Homolactic fermentation: Produces lactic acid only
Heterolactic fermentation: Produces lactic acid and other compounds

68. Types of Fermentation
Figure 5.19

69. A Fermentation Test
Figure 5.23

70. Types of Fermentation
Table 5.4

71. Types of Fermentation
Table 5.4

72. Check Your Understanding
What happens during the preparatory and energy-conserving stages of glycolysis? 5-11
What is the value of the pentose phosphate and Entner-Doudoroff pathways if they produce only one ATP molecule? 5-12
What are the principal products of the Krebs cycle? 5-13
How do carrier molecules function in the electron transport chain? 5-14
Compare the energy yield (ATP) of aerobic and anaerobic respiration. 5-15
List four compounds that can be made from pyruvic acid by an organism that uses fermentation. 5-16

73. Lipid and Protein Catabolism
Learning Objectives
5-17 Describe how lipids and proteins undergo catabolism.
5-18 Provide two examples of the use of biochemical tests to identify bacteria in the laboratory.

74. Lipid Catabolism
Figure 5.20

75. Catabolism of Organic Food Molecules
Figure 5.21

76. Protein Catabolism Protein Amino acids Organic acid Krebs cycle
Extracellular proteases
Protein
Amino acids
Deamination, decarboxylation, dehydrogenation, desulfurylation
Organic acid
Krebs cycle

77. Protein Catabolism
Decarboxylation
Figure 5.22

78. Protein Catabolism
Desulfurylation
Figure 5.24

79. Protein Catabolism
Urease
Urea
NH3 + CO2
Clinical Focus Figure B

80. Biochemical Tests
Used to identify bacteria.
Clinical Focus Figure A

81. Check Your Understanding
What are the end-products of lipid and protein catabolism? 5-17
On what biochemical basis are Pseudomonas and Escherichia differentiated? 5-18

82. Photosynthesis Learning Objectives
5-19 Compare and contrast cyclic and noncyclic photophosphorylation.
5-20 Compare and contrast the light-dependent and light-independent reactions of photosynthesis.
5-21 Compare and contrast oxidative phosphorylation and photophosphorylation.

83. Photosynthesis
Figure 4.15

84. Photosynthesis
Photo: Conversion of light energy into chemical energy (ATP)
Light-dependent (light) reactions
Synthesis:
Carbon fixation: Fixing carbon into organic molecules
Light-independent (dark) reaction: Calvin-Benson cycle
ANIMATION Photosynthesis: Overview

85. Photosynthesis Oxygenic: Anoxygenic:
ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes

86. Cyclic Photophosphorylation
ANIMATION Photosynthesis: Light Reaction: Cyclic Photophosphorylation
Figure 5.25a

87. Noncyclic Photophosphorylation
ANIMATION Photosynthesis: Light Reaction: Noncyclic Photophosphorylation
Figure 5.25b

88. Calvin-Benson Cycle
ANIMATION Photosynthesis: Light Independent Reactions
Figure 5.26

89. Photosynthesis Compared
Table 5.6

90. Check Your Understanding
How is photosynthesis important to catabolism? 5-19
What is made during the light-dependent reactions? 5-20
How are oxidative phosphorylation and photophosphorylation similar? 5-21

91. A Summary of Energy Production
Learning Objective
5-22 Write a sentence to summarize energy production in cells.

92. Check Your Understanding
Summarize how oxidation enables organisms to get energy from glucose, sulfur, or sunlight. 5-22

93. Metabolic Diversity among Organisms
Learning Objective
5-23 Categorize the various nutritional patterns among organisms according to carbon source and mechanisms of carbohydrate catabolism and ATP generation.

94. Chemotrophs Use energy from chemicals Chemoheterotroph
Energy is used in anabolism
Glucose
NAD+
ETC
Pyruvic acid
NADH
ADP + P
ATP

95. Chemotrophs Use energy from chemicals
Chemoautotroph, Thiobacillus ferrooxidans
Energy used in the Calvin-Benson cycle to fix CO2
2Fe2+
NAD+
ETC
2Fe3+
NADH
ADP + P
ATP
2 H+

96. Phototrophs Use light energy
Photoautotrophs use energy in the Calvin-Benson cycle to fix CO2
Photoheterotrophs use energy
Chlorophyll
Chlorophyll oxidized
ETC
ADP + P
ATP

97. Requirements of ATP Production
Figure 5.27

98. A Nutritional Classification of Organisms
Figure 5.28

99. A Nutritional Classification of Organisms
Figure 5.28

100. A Nutritional Classification of Organisms
Figure 5.28

101. Metabolic Diversity among Organisms
Nutritional Type
Energy Source
Carbon Source
Example
Photoautotroph
Light
CO2
Oxygenic: Cyanobacteria plants
Anoxygenic: Green, purple bacteria
Photoheterotroph
Organic compounds
Green, purple nonsulfur bacteria
Chemoautotroph
Chemical
Iron-oxidizing bacteria
Chemoheterotroph
Fermentative bacteria
Animals, protozoa, fungi, bacteria.

102. Check Your Understanding
Almost all medically important microbes belong to which of the four aforementioned groups? 5-23

103. Metabolic Pathways of Energy Use
Learning Objective
5-24 Describe the major types of anabolism and their relationship to catabolism.
ANIMATION Metabolism: The Big Picture

104. Polysaccharide Biosynthesis
Figure 5.29

105. Lipid Biosynthesis
Figure 5.30

106. Pathways of Amino Acid Biosynthesis
Figure 5.31a

107. Amino Acid Biosynthesis
Figure 5.31b

108. Purine and Pyrimidine Biosynthesis
Figure 5.32

109. Check Your Understanding
Where do amino acids required for protein synthesis come from? 5-24

110. The Integration of Metabolism
Learning Objective
5-25 Define amphibolic pathways.

111. The Integration of Metabolism
Amphibolic pathways: Metabolic pathways that have both catabolic and anabolic functions

112. Amphibolic Pathways
Figure 5.33

113. Amphibolic Pathways
Figure 5.33

114. Check Your Understanding
Summarize the integration of metabolic pathways using peptidoglycan synthesis as an example. 5-25