1. Chapter 8 Microbial Metabolism
Topics
Metabolism
Energy
Pathways
Biosynthesis

2. Metabolism
Catabolism
Anabolism
Enzymes

3. Metabolism
Collection of controlled biochemical reactions that take place within a microbe
Ultimate function of metabolism is to reproduce the organism
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4. Catabolism and Anabolism
Two major classes of metabolic reactions
Catabolic pathways
Break larger molecules into smaller products
Exergonic
Anabolic pathways
Synthesize large molecules from the products of catabolism
Endergonic
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5. Catabolism
Enzymes are involved in the breakdown of complex organic molecules in order to extract energy and form simpler end products

6. Anabolism
Enzymes are involved in the use of energy from catabolism in order to synthesize macromolecules and cell structures from precursors (simpler products)

7. The relationship between catabolism and anabolism.
Fig. 8.1 Simplified model of metabolism

8. Enzymes Function Structure Enzyme-substrate interaction Cofactors
Regulation

9. Function Catalysts for chemical reactions
Lower the energy of activation

10. Structure Simple enzyme Conjugated enzyme Three-dimensional features
protein alone
Conjugated enzyme
protein and nonprotein
Three-dimensional features
Enable specificity
Active site or catalytic site

11. Conjugated enzymes contain a metallic cofactor, coenzyme, or both in order for it to function as a catalyst.
Fig. 8.2 Conjugated enzyme structure

13. Specific active sites (amino acids) arise due to the folding of the protein (enzyme).
Fig. 8.3 How the active site and specificity of the apoenzyme arise.

14. Enzyme-substrate interactions
Substrates specifically bind to the active sites on the enzyme
“lock-and-key”
Induced fit
Once the reaction is complete, the product is released and the enzyme reused

15. An example of the “lock-and-key” model, and the induced fit model.
Fig. 8.4 Enzyme-substrate reactions

16. Cofactors Bind to and activate the enzyme Ex. Metallic cofactors
Iron, copper, magnesium
Coenzymes

17. Coenzyme
Transient carrier - alter a substrate by removing a chemical group from one substrate and adding it to another substrate
Ex. vitamins

18. An example of how a coenzyme transfers chemical groups from one substrate to another.
Fig. 8.5 The carrier functions of coenzymes

19. Action Exoenzymes Endoenzymes Constitutive Induction or repression
Types of reactions

20. Exoenzymes are inactive while inside the cell, but upon release from the cell they become active. In contrast, endoenzymes remain in the cell and are active.
Fig. 8.6 Types of enzymes, as described by their location of action.

21. Constitutive enzymes are present in constant amounts, while regulated enzymes are either induced or repressed.
Fig. 8.7 Constitutive and regulated enzymes

22. Types of Reaction
Condensation
Hydrolysis
Transfer reactions

23. Condensation reactions are associated with anabolic reactions, and hydrolysis reactions are associated with catabolic reactions.
Fig. 8.8 Examples of enzyme-catalyzed synthesis
and hydrolysis reactions

24. Transfer reactions Transfer of electrons from one substrate to another
Oxidation and reduction
Oxidoreductase
Transfer of functional groups from one molecule to another
Transferases
Aminotransferases

25. Examples of oxidoreductase, transferase, and hydrolytic enzymes.
Table 8.A A sampling of enzymes, their substrates, and their reactions

26. Regulation
Metabolic pathways
Direct control
Genetic control

27. The different metabolic pathways are regulated by the enzymes that catalyze the reactions.
Fig.8.9 Patterns of
metabolism

28. Competitive inhibition and noncompetitive inhibition are examples of direct control (regulation) of the action of the enzymes.
Fig Examples of two common control mechanisms
for enzymes.

29. Genetic control
Repression
Induction

30. Repression is when end products can stop the expression of genes that encode for proteins (enzymes) which are responsible for metabolic reactions.
Fig One type of genetic control of enzyme synthesis

31. Summary of major enzyme characteristics.
Table 8.1 Checklist of enzyme characteristics

32. Energy Cell energetics Redox reaction Electron carrier
Exergonic
Endergonic
Redox reaction
Electron carrier
Adenosine Triphosphate (ATP)

33. The general scheme associated with metabolism of organic molecules, the redox reaction, and the capture of energy in the form of ATP.
Fig A simplified model that summarizes the cell’s
energy machine.

34. Redox reaction Reduction and oxidation reaction
Electron carriers transfer electrons and hydrogens
Electron donor
Electron acceptor
Energy is also transferred and captured by the phosphate in form of ATP

35. Figure 5.2 Oxidation-reduction, or redox, reactions
Electron donor
Oxidized donor
Electron acceptor
Reduced acceptor
Oxidation

36. Electron carriers Coenzymes Respiratory chain carriers
Nicotinamide adenine dinucleotide (NAD)
Respiratory chain carriers
Cytochromes (protein)

37. Electron carriers, such as NAD, accept electrons and hydrogens from the substrate (organic molecule).
Fig Details of NAD reduction

38. Adenosine Triphosphate (ATP)
Temporary energy repository
Breaking of phosphates bonds will release free energy
Three part molecule
Nitrogen base
5-carbon sugar (ribose)
Chain of phosphates

39. The phosphates capture the energy and becomes part of the ATP molecule.
Fig The structure of adenosine triphosphate and its
partner compounds, ADP and AMP.

40. ATP can be used to phosphorylate an organic molecule such as glucose during catabolism.
Fig An example of phosphorylation of glucose by ATP

41. ATP can be synthesized by substrate-level phosphorylation.
Fig ATP formation by substrate-level phosphorylation

42. Carbohydrate Catabolism
Many organisms oxidize carbohydrates as primary energy source for anabolic reactions
Glucose most common carbohydrate used
Glucose catabolized by two processes: cellular respiration and fermentation
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43. Pathways Catabolism Embden-Meyerhof-Parnas (EMP) pathway or glycolysis
Tricarboxylic acid cycle (TCA)
Respiratory chain
Aerobic
Anaerobic
Alternate pathways
Fermentation

45. A summary of the metabolism of glucose and the synthesis of energy.
Fig Overview of the flow, location, and products of
Pathways in aerobic respiration.

46. Aerobic respiration Glycolysis Tricarboxylic acid (TCA)
Electron transport

47. Glycolysis Oxidation of glucose
Phosphorylation of some intermediates (Uses two ATPs)
Splits a 6 carbon sugar into two 3 carbon molecules
Coenzyme NAD is reduced to NADH
Substrate-level-phosphorylation (Four ATPs are synthesized)

48. Glycolysis continued Water is generated Net yield of 2 ATPs
Final intermediates are two Pyruvic acid molecules

49. The glycolytic steps associated with the metabolism of glucose to pyruvic acid (pyruvate).
Fig Summary of glycolysis

50. TCA cycle
Each pyruvic acid is processed to enter the TCA cycle (two complete cycles)
CO2 is generated
Coenzymes NAD and FAD are reduced to NADH and FADH2
Net yield of two ATPs
Critical intermediates are synthesized

51. The steps associated with TCA cycle.
Fig The reaction of a single turn of the TCA cycle

52. Electron transport
NADH and FADH2 donate electrons to the electron carriers
Membrane bound carriers transfer electrons (redox reactions)
The final electron acceptor completes the terminal step (ex. Oxygen)

53. Electron transport continued
Chemiosmosis
Proton motive force (PMF)

54. Chemiosmosis entails the electron transport and formation of a proton gradient (proton motive force).
Fig The electron transport system and oxidative
phosphorylation

55. Figure 5.17 An electron transport chain
Respiration
Fermentation
Path of electrons
Reduced
FMN
Oxidized
Oxidized
FeS
Reduced
Reduced
CoQ
Oxidized 2
Oxidized
Cyt
Reduced
Reduced
Cyt
Oxidized 2
Oxidized
Cyt
Reduced 2 2
Final electron acceptor

57. Figure 5.18 One possible arrangement of an electron transport chain
Bacterium
Mitochondrion
Intermembrane space
Matrix
Exterior
Cytoplasmic membrane
Cytoplasm
Exterior of prokaryote or intermembrane space of mitochondrion
FMN
Ubiquinone
Cyt b
Phospholipid membrane
Cyt a3
Cyt c
Cyt a
NADH from glycolysis, Krebs cycle, pentose phosphate pathway, and Entner-Doudoroff pathway
Cyt c2
FADH2 from Krebs cycle
ATP synthase
Cytoplasm of prokaryote or matrix of mitochondrion

58. Electron transport chain
Mitochondria
eucaryotes
Cytoplasmic membrane
procaryotes

59. Total yield of ATP for one glucose molecule from aerobic respiration.
Table 8.4 Summary of aerobic respiration for
one glucose molecule

60. Anaerobic respiration
Similar to aerobic respiration, except nitrate or nitrite is the final electron acceptor

61. Fermentation
Sometimes cells cannot completely oxidize glucose by cellular respiration
Cells require constant source of NAD+
Cannot be obtained simply using glycolysis and Krebs cycle
Fermentation pathways provide cells with source of NAD+
Partial oxidation of sugar or other metabolites to release energy
Uses organic molecule within cell as final electron acceptor
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62. Fermentation Glycolysis only
NADH from glycolysis is used to reduce the organic products
Organic compounds as the final electron acceptors
ATP yields are small (per glucose molecule), compared to respiration
Must metabolize large amounts of glucose to produce equivalent respiratory ATPs

63. The fermentation of ethyl alcohol and lactic acid.
Fig The chemistry of fermentation systems

64. Types of fermenters Facultative anaerobes Strict fermenters
Fermentation in the absence of oxygen
Respiration in the presence of oxygen
Ex. Escherichia coli
Strict fermenters
No respiration
Ex. yeast

65. Products of fermentation
Alcoholic fermentation
Acidic fermentation
Mixed acid fermentation

66. An example of mixed acid fermentation and the diverse products synthesized.
Fig Miscellaneous products of pyruvate

67. Figure 5.22 Representative fermentation products and the organisms that produce them
Glucose
Pyruvic acid
Aspergillus Lactobacillus Streptococcus
Organisms
Propionibacterium
Saccharomyces
Clostridium
Fermentation
CO2, propionic acid
Lactic acid
CO2, ethanol
Acetone, isopropanol
Fermentation products
Swiss cheese
Cheddar cheese, yogurt, soy sauce
Wine, beer
Nail polis remover, rubbing alcohol

68. Biosynthesis Anabolism Amphibolic Gluconeogenesis Beta oxidation
Amination
Transamination
Deamination
Macromolecules

69. Amphibolic Integration of the catabolic and anabolic pathways
Intermediates serve multiple purposes

70. Intermediates can serve to synthesize amino acids, carbohydrates and lipids.
Fig An amphibolic view of metabolism

71. Gluconeogenesis Pyruvate (intermediate) is converted to glucose
Occurs when the glucose supply is low

72. Beta oxidation
Metabolism of fats into acetyl, which can then enter the TCA cycle as acetyl CoA.

73. Examples of amination, transamination, and deamination.
Fig Reactions that produce and convert amino acids

74. Macromolecules Cellular building blocks Monosaccharides Amino acids
Fatty acids
Nitrogen bases
Vitamins