Prescott’s Microbiology, 9th Edition

11Catabolism: Energy Release and Conservation

CHAPTER OVERVIEW

This chapter presents an overview of energy release and conservation mechanisms beginning with glucose degradation to pyruvate.Fermentation, aerobic respiration, and anaerobic respiration are then examined.The consideration of chemoorganoheterotrophic metabolism concludes with a discussion of the catabolism of lipids, proteins, and amino acids. Chemolithotrophic metabolism follows and the chapter concludes with a discussion of the trapping of energy by phototrophy.

LEARNINGOUTCOMES

After reading this chapter you should be able to:

•use the terms that describe a microbe’s carbon source, energy source, and electron source

•state the carbon, energy, and electron sources of photolithotrophs, photoorganoheterotrophs, chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs

•describe the products of the fueling reactions

•discuss the metabolic flexibility of microorganisms

•list the three types of chemoorganotrophic metabolisms

•list the pathways of major importance to chemoorganotrophs and explain their importance

•propose an explanation that accounts for the existence of amphibolic pathways

•describe in general terms what happens to a molecule of glucose during aerobic respiration

•list the end products made during aerobic respiration

•identify the process that generates generate the most ATP during aerobic respiration

•list the three major pathways that catabolize glucose to pyruvate

•describe substrate-level phosphorylation

•diagram the major changes made to glucose as it is catabolized by the Embden-Meyerhof, Entner-Doudoroff, and pentose phosphate pathways that consume ATP, produce ATP and NAD(P)H, generate precursor metabolites, or are redox reactions

•calculate the yields of ATP and NAD(P)H by the Embden-Meyerhof, Entner-Doudoroff, and pentose phosphate pathways

•summarize the function of the Embden-Meyerhof, Entner-Doudoroff, and pentose-phosphate pathways

•draw a simple diagram that shows the connection between the Entner-Doudoroff pathway and the Embden-Meyerhof pathway and the connection between the pentose phosphate pathway and the Embden-Meyerhof pathway

•create a table that shows which types of organisms use each of the glycolytic pathways

•state the alternate names for the tricarboxylic acid (TCA) cycle

•diagram the major changes made to pyruvate as it is catalyzed by the TCA cycle

•identify those reactions of the TCA cycle that produce ATP (or GTP) and NAD(P)H, generate precursor metabolites, or are redox reactions

•summarize the function of the TCA cycle

•diagram the connections between the various glycolytic pathways and the TCA cycle

•locate the TCA cycle enzymes in bacterial, archaeal, and eukaryotic cells

•compare and contrast the mitochondrial electron transport chain (ETC) and bacterial ETCs

•describe the chemiosmotic hypothesis

•correlate the length of an ETC and the carriers in it with the strength of the proton motive force (PMF) it generates

•explain how ATP synthase uses PMF (proton motive force) to generate ATP

•draw a simple diagram that shows the connections between the glycolytic pathways, TCA cycle, ETC , and ATP synthesis

•list uses for the PMF generated by bacterial cells in addition to ATP synthesis

•calculate the maximum possible ATP yields when glucose is completely catabolized to six molecules of CO2 during aerobic respiration

•compare and contrast aerobic respiration and anaerobic respiration using glucose as a carbon source

•list examples of terminal electron acceptors used during anaerobic respiration

•defend this statement: “The use of nitrate (NO3-) as a terminal electron acceptor is dissimilatory nitrate reduction.”

•predict the relative amount of energy released for each of the common terminal acceptors used during anaerobic respiration, as compared to energy released during aerobic respiration

•list three examples of the importance of anaerobic respiration

•compare and contrast aerobic respiration, anaerobic respiration, and fermentation of glucose

•list the pathways that may function during fermentation if glucose is the organism’s carbon and energy source

•create a table that lists some of the common fermentation pathways and their products, and gives examples of their importance

•compare the use of ATP synthase during respiration and fermentation

•discuss the role of ATP and UTP in the catabolism of monosaccharides other than glucose

•differentiate the catabolism of disaccharides and polysaccharides by hydrolysis from their catabolism by phosphorolysis

•discuss the fate of the fatty acid and glycerol components of triglycerides when trigylcerides are catabolized

•state the name of the enzymes responsible for hydrolyzing proteins into amino acids

•distinguish deamination from transamination and explain how the two are related

•draw a simple diagram that illustrates how the pathways used to catabolize reduced organic molecules other than glucose connect to the glycolytic pathways and the TCA cycle

•describe in general terms the fueling reactions of chemolithotrophs

•list the molecules commonly used as energy sources and electron donors by chemolithotrophs

•discuss the use of electron transport chains and oxidative phosphorylation by chemolithotrophs

•describe in general terms the fueling reactions of phototrophs

•differentiate phototrophy from photosynthesis

•describe the light and dark reactions that occur during photosynthesis

•summarize the structure and function of the light-absorbing pigments used by oxygenic and anoxygenic phototrophs

•defend this statement: “Oxidative phosphorylation and photophosphorylation by chlorophyll-based phototrophs differ primarily in the energy source driving the process.”

•distinguish cyclic photophosphorylation from noncyclic photophosphorylation

•compare and contrast oxygenic photosynthesis, anoxygenic phototrophy, and rhodopsin-bsaed phototrophy

•list two examples of the importance of chlorophyll-based phototrophy

CHAPTER OUTLINE

  1. Metabolic Diversity and Nutritional Types
  2. Photoorganoheterotrophs
  3. use organic matter as their electron and carbon source
  4. common inhabitants of polluted lakes and streams
  5. chemolithoheterotrophs
  6. used reduced inorganic molecules for energy, derive carbon from organic sources
  7. contribute to biogeochemical cycles
  8. Chemoorganotrophic Fueling Processes
  9. Chemotrophic microorganisms vary in terms of their energy source (light, organic molecules, inorganic molecules), and in terms of their electron acceptors
  10. If the energy source is oxidized and degraded with the use of an exogenous electron acceptor, the process is called respiration; in aerobic respiration the final electron acceptor is oxygen, whereas in anaerobic respiration the final electron acceptor is a molecule other than oxygen
  11. If an organic energy source is oxidized and degraded without the use of an exogenous electron acceptor, the process is called fermentation
  12. For chemoorganoheterotrophic organisms, catabolism is often a three-stage process during which nutrients are fed into common degradative pathways including glycolysis and the tricarboxylic acid (TCA) cycle
  13. Breakdown of polymers and other large molecules into their constituent parts
  14. Initial degradation of the constituents’ parts
  15. Completion of degradation accompanied by the generation of many ATP molecules
  16. Many of the catabolic pathways can also be used for synthesis (anabolic) reactions and are termed amphibolic; reducing power is used to convert precursor metabolites into macromolecules
  17. Aerobic Respiration - completely catabolizes organic energy sources to carbon dioxide using oxygen as the terminal electron acceptor; reducing power derives from the glycolytic and TCA pathways
  18. From Glucose to Pyruvate
  19. The Embden-Meyerhof Pathway
  20. The most common pathway for glucose degradation (glycolysis), it is found in all major groups of microorganisms
  21. Functions in the presence or absence of oxygen and is divided into two parts:
  22. In the 6-carbon stage, glucose is phosphorylated twice to yield fructose 1,6-bisphosphate; this requires the expenditure of two molecules of ATP
  23. The 3-carbon stage cleaves fructose 1,6-bisphosphate into two 3-carbon molecules, which are each oxidized to pyruvate; two molecules of ATP are produced by substrate-level phosphorylation from each of the 3-carbon molecules for a net yield of two molecules of ATP; two molecules of NADH are also produced per glucose molecule
  24. The Entner-Doudoroff pathway is an alternative glycolytic pathway used by some microbes; the 6-carbon stage begins with only one phosphorylation event with phosphogluconate as an intermediate with one pyruvate and one glyceraldehyde 3-phosphate produced; the 3-carbon stage is the same as the Embden-Meyerhof pathway
  25. Pentose Phosphate Pathway: A Major Producer of Reducing Power for Anabolic Reactions
  26. Known as the hexose monophosphate pathway; produces a variety of 3-, 4-, 5-, 6-, and 7-carbon sugar phosphates
  27. Has several catabolic and anabolic functions (amphibolic)
  28. Production of NADPH, which serves as a source of electrons for biosynthetic processes
  29. Production of 4- and 5-carbon skeletons that can be used for the synthesis of amino acids, nucleic acids, and other macromolecules
  30. Complete catabolism of hexoses and pentoses, yielding ATP and NADH (made by converting NADPH to NADH)
  31. Tricarboxylic Acid Cycle
  32. Pyruvate can be oxidized to carbon dioxide by the tricarboxylic acid (TCA) cycle(or Krebs cycle) after first being converted to acetyl-CoA; this preliminary reaction is accompanied by the loss of one carbon atom as carbon dioxide and produces NADH
  33. Acetyl-CoA reacts with oxaloacetate (a 4-carbon molecule) to produce a 6-carbon molecule (citric acid), which is subsequently oxidized to release two molecules of carbon dioxide, regenerating the oxaloacetate; during this process, the following occur:
  34. ATP (as GTP) is produced by substrate-level phosphorylation
  35. Three molecules of NADH and one molecule of FADH2 are produced
  36. Organisms that lack the complete TCA cycle usually have most of the TCA cycle enzymes, because one of the TCA cycle’s major functions is to provide carbon skeletons for use in biosynthesis
  37. Electron Transport and Oxidative Phosphorylation
  38. Electron transport chains
  39. The mitochondrial electron transport chain in eukaryotes uses a series of electron carriers to transfer electrons from NADH and FADH2 to O2
  40. Electron carriers are located within the inner membrane of the mitochondrion
  41. During oxidative phosphorylation, three ATP molecules may be synthesized when a pair of electrons passes from NADH to O2; two ATP molecules may be synthesized when electrons from FADH2 pass to O2
  42. Although they operate according to the same fundamental principles, bacterial electron transport chains usually differ in structure: they may be branched, be composed of different electron carriers, or may be shorter than mitochondrial electron transport chains; bacterial electron transport chains are located in the plasma membrane
  43. Oxidative phosphorylation
  44. The chemiosmotic hypothesis postulates that the energy released during electron transport is used to establish a proton gradient that produces a proton motive force (potential energy due to the difference in proton concentration and charge on either side of the membrane), which can be used to drive ATP synthesis, flagellar rotation, and transport of molecules across the membrane
  45. ATP synthesis is catalyzed by the ATP synthase complex, which is thought to behave like a small rotary motor where the energy released by the movement of protons across the membrane, down the concentration gradient, is used to make high-energy bonds in ATP
  46. ATP yield during aerobic respiration
  47. The net yield from the oxidation of a glucose molecule via glycolysis is 2 ATP
  48. The number of ATP generated by aerobic respiration of a glucose molecule depends on the precise nature of the electron transport system; mitochondrial respiration typically yields 36 ATP (plus 2 from glycolysis)
  49. Anaerobic Respiration
  50. Uses exogenous molecules other than oxygen as terminal electron acceptors; the most commonly used alternative electron acceptors are nitrate, sulfate, and CO2
  51. Dissimilatory nitrate reduction occurs when nitrate is used as the terminal electron acceptor; if the nitrate is reduced to nitrogen gas, the process is called denitrification
  52. Anaerobic respiration is not as efficient in ATP synthesis as aerobic respiration because the alternative electron acceptors do not have as positive a reduction potential as O2; despite this, anaerobic respiration is useful because it is more efficient than fermentation
  53. When several electron acceptors are present in the environment, microorganisms will use these acceptors in succession starting with oxygen, then moving to nitrate, manganese ion, ferric ion, sulfate, and finally carbon dioxide
  54. Fermentation
  55. Fermentation is a process in which an organism oxidizes the NADH produced by one of the glycolytic pathways by using pyruvate or one of its derivatives as an electron and hydrogen acceptor; thus the process involves the use of an endogenous electron acceptor and regenerates NAD+ to act as the oxidant in glycolysis
  56. Fermentation takes place in the absence of oxidative phosphorylation and ATP is only generated through substrate-level phosphorylation
  57. Many different types of fermentations are known
  58. Alcoholic fermentations produce ethanol and CO2
  59. Lactic acid fermentations produce lactic acid (lactate)
  60. Homolactic fermenters reduce almost all pyruvate to lactate
  61. Heterolactic fermenters form substantial amounts of products other than lactate
  62. Formic acid fermentation produces either mixed acids or butanediol
  63. Microorganisms can ferment substances other than sugars (e.g., amino acids); in the Strickland reaction, one amino acid is oxidized while a second acts as the electron acceptor
  64. Catabolism of Organic Molecules other than Glucose
  65. Carbohydrates
  66. Most monosaccharides feed easily into the glycolytic pathway
  67. Disaccharides are cleaved into monosaccharides either by hydrolysis or phosphorolysis
  68. Polysaccharides are cleaved into smaller molecules either by hydrolysis or phosphorolysis; many however, are not easily degraded (e.g., cellulose, agar)
  69. Reserve polymers—when exogenous nutrients are absent, microorganisms catabolize internal carbon and energy stores (e.g., glycogen, starch); this is accomplished either by hydrolysis or phosphorolysis
  70. Lipid Catabolism
  71. Triglycerides are common energy sources; they are hydrolyzed to glycerol and fatty acids
  72. Fatty acids are catalyzed by the β-oxidation pathway, which successively shortens the chain by two carbons producing acetyl-CoA, NADH, and FADH2; NADH and FADH2 can be oxidized by an electron transport chain to produce ATP
  73. Protein and Amino Acid Catabolism
  74. Proteins are degraded by proteases to their component amino acids
  75. Amino acids are first deaminated (often by transamination) and then the remaining carbon skeletons are converted to pyruvate, acetyl-CoA, or a TCA-cycle intermediate
  76. Chemolithotrophy
  77. A metabolic process that uses inorganic molecules as a source of energy; the energy source is oxidized and the electrons are passed to an electron transport chain; the terminal electron acceptor is usually O2, but sulfate and nitrate also are used; the most common electron donors (energy sources) are hydrogen, reduced nitrogen compounds, reduced sulfur compounds, and ferrous iron (Fe2+)
  78. Chemolithotrophs are usually autotrophs; they use the Calvin cycle to fix carbon dioxide; however, the oxidation of most inorganic molecules yields low levels of ATP; therefore, in order to fuel carbon dioxide fixation, chemolithotrophs must oxidize large amounts of inorganic material
  79. Some inorganic energy sources (e.g., ammonia and nitrite) cannot donate electrons directly to NAD+; chemolithotrophs that use such energy sources must use their proton motive force to reverse electron flow in their electron transport chain in order to generate the NADH needed for biosynthetic processes
  80. Phototrophy
  81. During photosynthesis, energy from light is trapped and used to produce ATP and NADPH (light reactions), which are used to reduce carbon dioxide to carbohydrates (dark reactions)
  82. Light reactions in oxygenic photosynthesis
  83. Oxygenic photosynthesis generates molecular oxygen when light energy is converted to chemical energy; this process is found in plants, algae, and cyanobacteria
  84. Chlorophyll molecules and a variety of accessory pigments (carotenoids and bilins) are used to form antennas; the antennas trap photons and transfer their energy to reaction-center chlorophylls; these special chlorophylls are directly involved in photosynthetic electron transport
  85. Eukaryotes and cyanobacteria have two photosystems; in each, electrons from the light-energized reaction-center chlorophylls are transferred to the associated electron transport chain
  86. Photosystem I can carry out cyclic photophosphorylation, producing ATP
  87. Photosystems I and II, working together, can carry out noncyclic photophosphorylation, producing ATP and NADPH; the electrons for noncyclic photophosphorylation are obtained from water, which is oxidized to O2 (oxygenic photosynthesis)
  88. Photosynthetic electron transport takes place in membranes including the thylakoid membranes of chloroplasts and cyanobacteria; ATP can be generated through chemiosmosis
  89. The light reaction in anoxygenic photosynthesis
  90. Green and purple photosynthetic bacteria carry out anoxygenic photosynthesis (they do not use water as a source of electrons, so do not produce O2), and they have modified photosynthetic pigments called bacteriochlorophylls
  91. Many of the differences in the light reactions of the green and purple bacteria are due to the fact that they only have a single photosystem
  92. Green and purple bacteria are usually autotrophs that use NADH or NADPH for carbon dioxide fixation; three methods for making NADH are known:
  93. Reduction of NAD+ directly by hydrogen gas
  94. Reverse electron flow
  95. A simplified form of noncyclic electron flow
  96. Rhodopsin-based phototrophy
  97. Some archaea use light as a source of energy but instead of using chlorophyll, these microbes use bacteriorhodopsin; analogous proteins in bacteria are called proteorhodopsin
  98. A retinal chromophore changes shape when excited by light and acts a proton pump; this creates a proton gradient across a membrane that produces ATP through chemiosmosis

CRITICAL THINKING

1.The authors make the statement, “The use of a few common catabolic pathways, each degrading many nutrients, greatly increases metabolic efficiency by avoiding the need for a large number of less metabolically flexible pathways.”Explain the significance of this statement.

2.The overall yield of ATP in eukaryotes has a theoretical maximum of 38 ATP molecules per molecule of glucose. However, usually only 36 ATP molecules are produced. Explain this apparent discrepancy. Prokaryotes often have lower P/O ratios than eukaryotic systems. Explain the significance of this relative to the aerobic yield of ATP.