Biochemistry 2024-2025 4th Stage Introduction to Metabolism PDF

Biochemistry 2024-2025 4th Stage Introduction to Metabolism Living organisms are not at equilibrium. Rather, they require a continuous influx of free energy to maintain order in a universe bent on maximizing disorder. Metabolism is the o...

Biochemistry 2024-2025 4th Stage Introduction to Metabolism Living organisms are not at equilibrium. Rather, they require a continuous influx of free energy to maintain order in a universe bent on maximizing disorder. Metabolism is the overall process through which living systems acquire and utilize the free energy they need to carry out their various functions. They do so by coupling the exergonic reactions of nutrient oxidation to the endergonic processes required to maintain the living state such as the performance of mechanical work, the active transport of molecules against concentration gradients, and the biosynthesis of complex molecules. How do living things acquire this necessary free energy? And what is the nature of the energy coupling process? Phototrophs (plants and certain bacteria) acquire free energy from the sun through photosynthesis, a process in which light energy powers the endergonic reaction of CO2 and H2O to form carbohydrates and O2. Chemotrophs obtain their free energy by oxidizing organic compounds (carbohydrates, lipids, proteins) obtained from other organisms, ultimately phototrophs. This free energy is most often coupled to endergonic reactions through the intermediate synthesis of “high- energy” phosphate compounds such as adenosine triphosphate (ATP). In addition to being completely oxidized, nutrients are broken down in a series of metabolic reactions to common intermediates that are used as precursors in the synthesis of other biological molecules. 1  Biochemistry 2024-2025 4th Stage A remarkable property of living systems is that, despite the complexity of their internal processes, they maintain a steady state. This is strikingly demonstrated by the observation that, over a 40-year time span, a normal human adult consumes literally tons of nutrients and imbibes over 20,000 L of water but does so without significant weight change. This steady state is maintained by a sophisticated set of metabolic regulatory systems. In this introductory chapter to metabolism, we outline the general characteristics of metabolic pathways, study the main types of chemical reactions that comprise these pathways, and consider the experimental techniques that have been most useful in their elucidation. We then discuss the free energy changes associated with reactions of phosphate compounds and oxidation–reduction reactions. Finally, we consider the thermodynamic nature of biological processes, that is, what properties of life are responsible for its self-sustaining character. 1.1 Metabolic Pathways Metabolic pathways are series of consecutive enzymatic reactions that produce specific products. Their reactants, intermediates, and products are referred to as metabolites. Since an organism utilizes many metabolites, it has many metabolic pathways. Figure 1-1 shows a metabolic map for a typical cell with many of its interconnected pathways. Each reaction on the map is catalyzed by a distinct enzyme, of which there are ,4000 known. At first glance, this network seems hopelessly complex. Yet, by focusing on its major areas in the following 2  Biochemistry 2024-2025 4th Stage chapters, for example, the main pathways of glucose oxidation (the shaded areas of Fig. 1-1), we shall become familiar with its most important avenues and their interrelationships. Figure 1.1. Map of the major metabolic pathways in a typical cell. 3  Biochemistry 2024-2025 4th Stage The reaction pathways that comprise metabolism are often divided into two categories: 1. Catabolism, or degradation, in which nutrients and cell constituents are broken down exergonically to salvage their components and/or to generate free energy. 2. Anabolism, or biosynthesis, in which biomolecules are synthesized from simpler components. The free energy released by catabolic processes is conserved through the synthesis of ATP from ADP and phosphate or through the reduction of the coenzyme NADP+ to NADPH. ATP and NADPH are the major free energy sources for anabolic pathways (Fig. 1-2). Figure 1.2. ATP and NADPH are the sources of free energy for biosynthetic reactions. 4  Biochemistry 2024-2025 4th Stage A striking characteristic of degradative metabolism is that it converts large numbers of diverse substances (carbohydrates, lipids, and proteins) to common intermediates. These intermediates are then further metabolized in a central oxidative pathway that terminates in a few end products. Figure 1-3 outlines the breakdown of various foodstuffs, first to their monomeric units, and then to the common intermediate, acetyl-coenzyme A (acetyl-CoA). Figure 1.3. Overview of catabolism. 5  Biochemistry 2024-2025 4th Stage Biosynthesis carries out the opposite process. Relatively 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 we will discuss many degradative and biosynthetic pathways in detail. For now, let us consider some general characteristics of these processes. Five principal characteristics of metabolic pathways stem from their function of generating products for use by the cell: 1. Metabolic pathways are irreversible. A highly exergonic reaction (having a large negative free energy change) is irreversible; that is, it goes to completion. If such a reaction 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 metabolites are metabolically interconvertible, the pathway from the first to the second must differ from the pathway from the second back to the first: This is because if metabolite 1 is converted to metabolite 2 by an exergonic process, the conversion of metabolite 2 to metabolite 1 requires that free energy be supplied in order to bring this otherwise endergonic process “back up the hill.” Consequently, the two pathways 6  Biochemistry 2024-2025 4th Stage must differ in at least one of their reaction steps. The existence of independent interconversion routes, as we shall see, is an important property of metabolic pathways because it allows independent control of the two processes. If metabolite 2 is required by the cell, it is necessary to “turn off” the pathway from 2 to 1 while “turning on” the pathway from 1 to 2. Such independent control would be impossible without different pathways. 3. Every metabolic pathway has a first committed step. Although metabolic pathways are irreversible, most of their component reactions function close to equilibrium. Early in each pathway, however, there is an irreversible (exergonic) reaction that “commits” the intermediate it produces to continue down the pathway. 4. All metabolic pathways are regulated. Metabolic pathways are regulated by laws of supply and demand. In order to exert control on the flux of metabolites through a metabolic pathway, it is necessary to regulate its rate-limiting step. The first committed step, being irreversible, functions too slowly to permit its substrates and products to equilibrate (if the reaction were at equilibrium, it would not be irreversible). Since most of the other reactions in a pathway function close to equilibrium, the first committed step is often one of its rate-limiting steps. Most metabolic pathways are therefore controlled by regulating the enzymes that catalyze their first committed step(s). This is an efficient way to exert control because it 7  Biochemistry 2024-2025 4th Stage prevents the unnecessary synthesis of metabolites further along the pathway when they are not required. 5. Metabolic pathways in eukaryotic cells occur in specific cellular locations. The compartmentation of the eukaryotic cell allows different metabolic pathways to operate in different locations, as is listed in Table 1-1. Table 1-1: Metabolic Functions of Eukaryotic Organelles. For example, ATP is mainly generated in the mitochondrion but much of it is utilized in the cytoplasm. The synthesis of metabolites in specific membrane-bounded subcellular compartments makes their transport between these compartments a vital component of eukaryotic metabolism. Biological membranes are selectively permeable to metabolites because of the presence in membranes of specific transport proteins. The transport protein that facilitates the passage of ATP through the mitochondrial membrane, along with the characteristics of membrane transport processes in general. The synthesis and utilization 8  Biochemistry 2024-2025 4th Stage of acetyl-CoA are also compartmentalized. This metabolic intermediate is utilized in the cytosolic synthesis of fatty acids but is synthesized in mitochondria. Yet there is no transport protein for acetyl-CoA in the mitochondrial membrane. In multicellular organisms, compartmentation is carried a step further to the level of tissues and organs. The mammalian liver, for example, is largely responsible for the synthesis of glucose from noncarbohydrate precursors (gluconeogenesis) so as to maintain a relatively constant level of glucose in the circulation, whereas adipose tissue is specialized for the storage and mobilization of triacylglycerols. 1.2 Organic Reaction Mechanisms Almost all the reactions that occur in metabolic pathways are enzymatically catalyzed organic reactions. The various mechanisms enzymes have at their disposal for catalyzing reactions: acid–base catalysis, covalent catalysis, metal ion catalysis, electrostatic catalysis, proximity and orientation effects, and transition state binding. Few enzymes alter the chemical mechanisms of these reactions, so much can be learned about enzymatic mechanisms from the study of nonenzymatic model reactions. We therefore begin our study of metabolic reactions by outlining the types of reactions we shall encounter and the mechanisms by which they have been observed to proceed in nonenzymatic systems. 9