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Catabolism of Organic Compounds

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Catabolism of Organic Compounds 14 Catabolism of Organic Compounds Methanogens produce natural I Fermentations 373 14.10 Methanogenesis 390 gas (methane, CH4) and are 14.1 Energetic and Redox 14.11 Proton Reduction 394 able to do so because they Considerations 373 14.12 Other Electron Acceptors 395 contain a series of unusual 14.2 Lactic and Mixed-Acid 14.13 Anoxic Hydrocarbon Oxidation coenzymes, such as the Fermentations 374 Linked to Anaerobic 14.3 Clostridial and Propionic Acid Respiration 397 green-fluorescing F420, that participate in biochemical Fermentations 377 III Aerobic Chemoorganotrophic reactions unique to these 14.4 Fermentations Lacking Substrate- Processes 400 Level Phosphorylation 379 organisms. 14.14 Molecular Oxygen as a Reactant 14.5 Syntrophy 381 and Aerobic Hydrocarbon II Anaerobic Respiration 383 Oxidation 400 14.6 Anaerobic Respiration: 14.15 Methylotrophy and General Principles 383 Methanotrophy 401 14.7 Nitrate Reduction and 14.16 Sugar and Polysaccharide Denitrification 384 Metabolism 403 14.8 Sulfate and Sulfur Reduction 386 14.17 Organic Acid Metabolism 406 14.9 Acetogenesis 388 14.18 Lipid Metabolism 406 CHAPTER 14 • Catabolism of Organic Compounds 373 n Chapter 13 we considered phototrophy and chemolithotro- Uptake Excretion Iphy, strategies for energy conservation that do not use organic compounds as electron donors. In this chapter we focus on organic compounds as electron donors and the many ways in which chemoorganotrophic microorganisms conserve energy. A Organic Fermentation major focus will be on anaerobic forms of metabolism, because compound product novel strategies for anaerobic growth are a hallmark of prokary- otic diversity. We end the chapter with a consideration of the aer- NAD+ obic catabolism of key organic compounds, primarily monomers NADH released from the degradation of macromolecules. Substrate-level Energy-rich phosphorylation Oxidized I Fermentations compound compound wo broad metabolic processes for the catabolism of organic ADP ATP Tcompounds are fermentation and respiration. These processes differ fundamentally in terms of oxidation–reduction (redox) considerations and mechanism of ATP synthesis. In respiration, Figure 14.1 The essentials of fermentation. The fermentation product whether aerobic or anaerobic, exogenous electron acceptors are is excreted from the cell, and only a relatively small amount of the original required to accept electrons generated from the oxidation of elec- organic compound is used for biosynthesis. tron donors. In fermentation, this is not the case. Thus in respira- tion but not fermentation we will see a common theme of electron transport and the generation of a proton motive force. energy-rich compounds. These are organic compounds that con- We begin our exploration of organic catabolism with fermen- tain an energy-rich phosphate bond or a molecule of coenzyme tations. Compared with respirations, fermentations are typically A; the hydrolysis of either of these is highly exergonic ( Figure UNIT 5 energetically marginal. However, we will see that a little free 4.12). Table 14.1 lists some energy-rich intermediates formed energy can go a long way and that bacterial fermentative diversity during biochemical processes. The hydrolysis of most of the D 09 = is both extensive and innovative. compounds listed can be coupled to ATP synthesis ( G -31.8 kJ/mol). In other words, if an organism can form one of 14.1 Energetic and Redox Considerations Many microbial habitats are anoxic (oxygen-free). In such envi- Energy-rich compounds involved in substrate-level ronments, decomposition of organic material occurs anaerobi- Table 14.1 phosphorylationa cally. If adequate supplies of electron acceptors such as sulfate 2- - 3+ (SO4 ), nitrate (NO3 ), ferric iron (Fe ), and others to be con- Free energy of 0 sidered later are unavailable in anoxic habitats, organic com- hydrolysis, ⌬G 9 Compound (kJ/mol)b pounds are catabolized by fermentation (Figure 14.1). In Chapter 4 we discussed some key fermentations that yield alcohol or lactic Acetyl-CoA -35.7 acid as products by way of the glycolytic pathway. There we Propionyl-CoA -35.6 emphasized how fermentations are internally balanced redox Butyryl-CoA -35.6 processes in which the fermentable substrate becomes both oxi- - dized and reduced. Caproyl-CoA 35.6 An organism faces two major problems when it catabolizes Succinyl-CoA -35.1 organic compounds for the purpose of energy conservation: (1) Acetyl phosphate -44.8 ATP synthesis, and (2) redox balance. In fermentations, with rare Butyryl phosphate -44.8 exception ATP is synthesized by substrate-level phosphorylation. - This is the mechanism in which energy-rich phosphate bonds 1,3-Bisphosphoglycerate 51.9 from phosphorylated organic compounds are transferred directly Carbamyl phosphate -39.3 to ADP to form ATP ( Section 4.7). The second problem, Phosphoenolpyruvate -51.6 redox balance, is solved by the production and subsequent excre- Adenosine phosphosulfate (APS) -88 tion of fermentation products generated from the original sub- N10 - strate (Figure 14.1). -Formyltetrahydrofolate 23.4 Energy of hydrolysis of ATP (ATP S ADP + Pi ) -31.8 Energy-Rich Compounds and aData from Thauer, R. K., K. Jungermann, and K. Decker, 1977. Energy conservation in Substrate-Level Phosphorylation chemotrophic anaerobic bacteria. Bacteriol. Rev. 41: 100–180. bThe DG09 values shown here are for “standard conditions,” which are not necessarily Energy can be conserved by substrate-level phosphorylation those of cells. Including heat loss, the energy costs of making an ATP are more like from many different compounds. However, central to an under- 60 kJ than 32 kJ, and the energy of hydrolysis of the energy-rich compounds shown here is thus likely higher. But for simplicity and comparative purposes, the values in this standing of substrate-level phosphorylation is the concept of table will be taken as the actual energy released per reaction. 374 UNIT 5 • Metabolic Diversity and Commercial Biocatalyses Pyruvate (C3) Many anaerobic bacteria produce acetate as a major or minor CoA CoA fermentation product. The production of acetate and certain other fatty acids (Table 14.1) is energy conserving because it allows the organism to make ATP by substrate-level phosphory- 2 e– lation. The key intermediate generated in acetate production is Acetyl-CoA + Formate Acetyl-CoA + CO2 P acetyl-CoA (Table 14.1), an energy-rich compound. Acetyl-CoA i can be converted to acetyl phosphate (Table 14.1) and the phos- Formate Ferredoxin Acetyl~P phate group of acetyl phosphate subsequently transferred to hydrogenlyase Hydrogenase ADP ADP, yielding ATP. One of the precursors of acetyl-CoA is pyru- 2 H+ vate, a major product of glycolysis. The conversion of pyruvate to Acetate Acetate + ATP acetyl-CoA is a key oxidation reaction, and the electrons gener- CO (C2) 2 (C2) ated are used to form fermentation products or are released as + H (Figure 14.2). ATP H2 2 Figure 14.2 Production of H2 and acetate from pyruvate. At least MiniQuiz two mechanisms are known, one that produces H directly and the other 2 • What is substrate-level phosphorylation? that makes formate as an intermediate. When acetate is produced, ATP synthesis is possible (Table 14.1). • Why is acetate formation in fermentation energetically beneficial? these compounds during fermentative metabolism, it can make ATP by substrate-level phosphorylation. 14.2 Lactic and Mixed-Acid Fermentations Redox Balance, H2, and Acetate Production In any fermentation there must be atomic and redox balance; the Many fermentations are classified by either the substrate fer- total number of each type of atom and electrons in the products mented or the products formed. Table 14.2 lists some of the of the reaction must balance those in the substrates. This is major fermentations classified on the basis of products formed. obtained by the production and excretion from the cell of fer- Note some of the broad categories, such as alcohol, lactic acid, mentation products (Figure 14.1). In several fermentations, propionic acid, mixed acid, butyric acid, and acetogenic. Some redox balance is maintained by the production of molecular fermentations are described by the substrate fermented rather than the fermentation product. For instance, some endospore- hydrogen, H2. The production of H2 is associated with the activ- ity of the iron–sulfur protein ferredoxin, a very low-potential forming anaerobic bacteria (genus Clostridium) ferment amino electron carrier, and is catalyzed by the enzyme hydrogenase, as acids, whereas others ferment purines and pyrimidines. Other anaerobes ferment aromatic compounds (Table 14.3). Clearly, a illustrated in Figure 14.2. H2 can also be produced from the C1 wide variety of organic compounds can be fermented. Certain fatty acid formate. Either way, the H2 is then made available for use by other organisms. fermentations are carried out by only a very restricted group of anaerobes; in some cases this may be only a single known Table 14.2 Common bacterial fermentations and some of the organisms carrying them out Type Reaction Organisms Alcoholic Hexose S 2 ethanol + 2 CO2 Yeast, Zymomonas Homolactic Hexose S 2 lactate- + 2 H+ Streptococcus, some Lactobacillus - + Heterolactic Hexose S lactate + ethanol + CO2 + H Leuconostoc, some Lactobacillus - - - Propionic acid 3 Lactate S 2 propionate + acetate + CO2 + H2O Propionibacterium, Clostridium propionicum Mixed acida,b Hexose S ethanol + 2,3-butanediol + succinate2- + lactate- + Enteric bacteria including Escherichia, Salmonella, - -
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