JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 559 Introduction to Metabolism CHAPTER 16 1 Metabolic Pathways obtained from other organisms, ultimately phototrophs. 2 Organic Reaction Mechanisms This free energy is most often coupled to endergonic reac- A. Chemical Logic tions through the intermediate synthesis of “high-energy” B. Group-Transfer Reactions phosphate compounds such as adenosine triphosphate C. Oxidations and Reductions (ATP; Section 16-4). In addition to being completely oxi- D. Eliminations, Isomerizations, and Rearrangements dized, nutrients are broken down in a series of metabolic E. Reactions That Make and Break Carbon–Carbon Bonds reactions to common intermediates that are used as precur- 3 Experimental Approaches to the Study of Metabolism sors in the synthesis of other biological molecules. A. Metabolic Inhibitors, Growth Studies, A remarkable property of living systems is that, despite and Biochemical Genetics the complexity of their internal processes, they maintain a B. Isotopes in Biochemistry steady state. This is strikingly demonstrated by the observa- C. Isolated Organs, Cells, and Subcellular Organelles tion that, over a 40-year time span, a normal human adult D. Systems Biology consumes literally tons of nutrients and imbibes over 20,000 L 4 Thermodynamics of Phosphate Compounds of water, but does so without significant weight change. This A. Phosphoryl-Transfer Reactions steady state is maintained by a sophisticated set of metabolic B. Rationalizing the “Energy” in “High-Energy” Compounds regulatory systems. In this introductory chapter to metabo- C. The Role of ATP lism, we outline the general characteristics of metabolic 5 Oxidation–Reduction Reactions pathways, study the main types of chemical reactions that A. The Nernst Equation comprise these pathways, and consider the experimental B. Measurements of Redox Potentials techniques that have been most useful in their elucidation. C. Concentration Cells We then discuss the free energy changes associated with re- 6 Thermodynamics of Life actions of phosphate compounds and oxidation–reduction A. Living Systems Cannot Be at Equilibrium reactions. Finally we consider the thermodynamic nature B. Nonequilibrium Thermodynamics and the Steady State of biological processes, that is, what properties of life are C. Thermodynamics of Metabolic Control responsible for its self-sustaining character. 1 METABOLIC PATHWAYS Living organisms are not at equilibrium. Rather, they require a continuous influx of free energy to maintain order in a uni- Metabolic pathways are series of consecutive enzymatic re- verse bent on maximizing disorder. Metabolism is the over- actions that produce specific products. Their reactants, inter- all process through which living systems acquire and utilize mediates, and products are referred to as metabolites. Since the free energy they need to carry out their various func- an organism utilizes many metabolites, it has many meta- tions. They do so by coupling the exergonic reactions of nutri- bolic pathways. Figure 16-1 shows a metabolic map for a ent oxidation to the endergonic processes required to main- typical cell with many of its interconnected pathways. Each tain the living state such as the performance of mechanical reaction on the map is catalyzed by a distinct enzyme, of work, the active transport of molecules against concentra- which there are ϳ4000 known. At first glance, this network tion gradients, and the biosynthesis of complex molecules. seems hopelessly complex. Yet, by focusing on its major How do living things acquire this necessary free energy? areas in the following chapters, for example, the main And what is the nature of the energy coupling process? pathways of glucose oxidation (the shaded areas of Fig. Phototrophs (plants and certain bacteria; Section 1-1A) 16-1), we shall become familiar with its most important av- acquire free energy from the sun through photosynthesis, a enues and their interrelationships. Maps of metabolic path- process in which light energy powers the endergonic reac- ways in a more readable form can be found on the Web tion of CO2 and H2O to form carbohydrates and O2 at http://www.expasy.org/cgi-bin/search-biochem-index, (Chapter 24). Chemotrophs obtain their free energy by ox- http://www.iubmb-nicholson.org/, and http://www.genome. idizing organic compounds (carbohydrates, lipids, proteins) ad.jp/kegg/metabolism.html. 559 JWCL281_c16_557-592.qxd 2/26/10 11:10 AM Page 560 560 Chapter 16. Introduction to Metabolism Figure 16-1 Map of the major metabolic pathways in a typical cell. The main pathways of glucose metabolism are shaded. [Designed by Donald Nicholson. Published by BDH Ltd., Poole 2, Dorset, England.] JWCL281_c16_557-592.qxd 6/10/10 11:51 AM Page 561 Section 16-1. Metabolic Pathways 561 The reaction pathways that comprise metabolism are from the first to the second must differ from the pathway often divided into two categories: from the second back to the first: 1. Catabolism, or degradation, in which nutrients and A cell constituents are broken down exergonically to salvage 1 2 their components and/or to generate free energy. YX 2. Anabolism, or biosynthesis, in which biomolecules are synthesized from simpler components. This is because if metabolite 1 is converted to metabolite 2 by an exergonic process, the conversion of metabolite 2 to The free energy released by catabolic processes is con- metabolite 1 requires that free energy be supplied in order served through the synthesis of ATP from ADP and phos- to bring this otherwise endergonic process “back up the phate or through the reduction of the coenzyme NADPϩ to hill.” Consequently, the two pathways must differ in at least NADPH (Fig. 13-2). ATP and NADPH are the major free energy sources for anabolic pathways (Fig. 16-2). A striking characteristic of degradative metabolism is that it converts large numbers of diverse substances (carbohy- drates, lipids, and proteins) to common intermediates. These Proteins Carbohydrates Lipids intermediates are then further metabolized in a central ox- idative pathway that terminates in a few end products. Figure Amino acids Glucose Fatty acids & Glycerol 16-3 outlines the breakdown of various foodstuffs, first to their monomeric units, and then to the common intermedi- ate, acetyl-coenzyme A (acetyl-CoA) (Fig. 21-2). ADP ATP Biosynthesis carries out the opposite process. Relatively NAD+ Glycolysis NADH few metabolites, mainly pyruvate, acetyl-CoA, and the citric acid cycle intermediates, serve as starting materials for a host of varied biosynthetic products. In the next several chapters Pyruvate we discuss many degradative and biosynthetic pathways in detail. For now, let us consider some general characteristics CO2 of these processes. Five principal characteristics of metabolic pathways Acetyl-CoA stem from their function of generating products for use by the cell: NH3 1. Metabolic pathways are irreversible. A highly exer- Citric NAD+ NADH gonic reaction (having a large negative free energy change) Acid FAD FADH is irreversible; that is, it goes to completion. If such a reaction Cycle 2 is part of a multistep pathway,it confers directionality on the pathway; that is, it makes the entire pathway irreversible. 2. Catabolic and anabolic pathways must differ. If two CO2 metabolites are metabolically interconvertible, the pathway NAD+ Oxidative NADH FAD phosphorylation FADH Complex metabolites 2 2– ADP ADP + HPO 4 NADP + O2 H O ATP 2 Degradation Biosynthesis Figure 16-3 Overview of catabolism. Complex metabolites ATP such as carbohydrates, proteins, and lipids are degraded first to NADPH their monomeric units, chiefly glucose, amino acids, fatty acids, and glycerol, and then to the common intermediate, Simple products acetyl-coenzyme A (acetyl-CoA). The acetyl group is then oxidized to CO2 via the citric acid cycle with the concomitant Figure 16-2 ATP and NADPH are the sources of free energy reduction of NADϩ and FAD. Reoxidation of these latter for biosynthetic reactions. They are generated through the coenzymes by O2 via the electron-transport chain and oxidative degradation of complex metabolites. phosphorylation yields H2O and ATP. JWCL281_c16_557-592.qxd 6/10/10 11:51 AM Page 562 562 Chapter 16. Introduction to Metabolism one of their reaction steps. The existence of independent in- the presence in membranes of specific transport proteins. terconversion routes, as we shall see, is an important property The transport protein that facilitates the passage of ATP of metabolic pathways because it allows independent control through the mitochondrial membrane is discussed in of the two processes. If metabolite 2 is required by the cell, it Section 20-4C, along with the characteristics of membrane is necessary to “turn off” the pathway from 2 to 1 while transport processes in general.The synthesis and utilization “turning on” the pathway from 1 to 2. Such independent of acetyl-CoA are also compartmentalized. This metabolic control would be impossible without different pathways. intermediate is utilized in the cytosolic synthesis of fatty 3. Every metabolic pathway has a first committed step. acids but is synthesized in mitochondria. Yet there is no Although metabolic pathways are irreversible, most of transport protein for acetyl-CoA in the mitochondrial their component reactions function close to equilibrium. membrane. How cells solve this fundamental problem is Early in each pathway, however, there is an irreversible discussed in Section 25-4D. In multicellular organisms, com- (exergonic)