Biology Campbell 12 ed, Introduction to Metabolism PDF

8 An Introduction to Metabolism KEY CONCEPTS 8.1 An organism’s metabolism transforms matter and energy p. 144 8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously p. 147 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic r...

8 An Introduction to Metabolism KEY CONCEPTS 8.1 An organism’s metabolism transforms matter and energy p. 144 8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously p. 147 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions p. 150 8.4 Enzymes speed up metabolic reactions by lowering energy barriers p. 153 8.5 Regulation of enzyme activity helps control metabolism p. 159 Study Tip Make a table: Fill in the following table for each process you read about in this chapter, such as water spilling over a dam or a chemical reaction. Process Water spilling over a dam Starting Materials; Relative Energy Level Ending Materials; Relative Energy Level Water at the top of a dam; higher energy level Water at the bottom of a dam; lower energy level Will this process occur spontaneously (without an input of energy)? Yes Hydrolysis of ATP (Figure 8.9) Figure 8.1 The green glowing spots on the outside of this Brazilian termite mound are larvae of the click beetle, Pyrophorus nyctophanus. These larvae convert the energy stored in organic molecules to light, a process called bioluminescence, which attracts termites that the larvae eat. Bioluminescence and other metabolic activities in a cell are energy transformations that are subject to physical laws. How do the laws of thermodynamics relate to biological processes? The first law of thermodynamics: Energy can be transferred and transformed, but it cannot be created or destroyed. For example: The second law of thermodynamics: Every energy transfer or transformation increases the entropy (disorder) of the universe. For example, during every energy transformation, some energy is converted to thermal energy and released as heat: Light energy from the sun Transformed by plants to Heat Chemical energy in organic molecules in plants Go to Mastering Biology For Students (in eText and Study Area) • Get Ready for Chapter 8 • Animation: Exergonic and Endergonic Reactions • Figure 8.10 Walkthrough: How ATP Drives Chemical Work For Instructors to Assign (in Item Library) • Activity: Energy Transformations • Tutorial: How Enzymes Function Heat Transformed by termites to Chemical energy in organic molecules in termites Plant using light to make organic molecules Heat Termite digesting plant and making new molecules Transformed by click beetle larvae to Light energy produced by bioluminescence Click beetle larva digesting termite and emitting light 143 CONCEPT principles, the concepts demonstrated by these examples also apply to bioenergetics, the study of how energy flows through living organisms. 8.1 An organism’s metabolism transforms matter and energy The totality of an organism’s chemical reactions is called metabolism (from the Greek metabole, change). Metabolism is an emergent property of life that arises from orderly interactions between molecules. Metabolic Pathways We can picture a cell’s metabolism as an elaborate road map of many chemical reactions, arranged as intersecting metabolic pathways. In a metabolic pathway, a specific molecule is altered in a series of defined steps, resulting in a certain product. Each step is catalyzed by a specific enzyme, a macromolecule that speeds up a chemical reaction: Enzyme 1 A Reaction 1 Starting molecule Enzyme 2 B Reaction 2 Enzyme 3 C Reaction 3 D Product The mechanisms that regulate these enzymes balance metabolic supply and demand, just like traffic lights control the flow of traffic. Metabolism as a whole manages the material and energy resources of the cell. Some metabolic pathways release energy by breaking down complex molecules to simpler compounds. These degradative processes are called catabolic pathways, or breakdown pathways. One major catabolic pathway is cellular respiration, which breaks down glucose and other organic fuels in the presence of oxygen to carbon dioxide and water. (Pathways can have more than one starting molecule and/or product.) Energy stored in the organic molecules becomes available to do cellular work, such as ciliary beating or membrane transport. Anabolic pathways, in contrast, consume energy to build complicated molecules from simpler ones; they are sometimes called biosynthetic pathways. Examples of anabolism are synthesis of an amino acid from simpler molecules and synthesis of a protein from amino acids. Catabolic and anabolic pathways are the “downhill” and “uphill” avenues of the metabolic landscape. Energy released from downhill reactions of catabolic pathways can be stored and then used to drive uphill reactions of anabolic pathways. In this chapter, we will focus on mechanisms common to metabolic pathways. Because energy is fundamental to all metabolic processes, a basic knowledge of energy is necessary to understand how the living cell works. Although we’ll look at some nonliving examples here to consider energetic 144 UNIT TWO The Cell Forms of Energy Energy is the capacity to cause change. In everyday life, energy is important because some forms of energy can be used to do work—that is, to move matter against opposing forces, such as gravity and friction. Put another way, energy is the ability to rearrange a collection of matter. For example, you expend energy to turn the pages of this book, and your cells expend energy in transporting certain substances across membranes. Energy exists in various forms, and the work of life depends on the ability of cells to transform energy from one form to another. Energy can be associated with the relative motion of objects; this energy is called kinetic energy. Moving objects can perform work by imparting motion to other matter: A pool player uses the motion of the cue stick to push the cue ball, which in turn moves the other balls; water gushing through a dam turns turbines; and the contraction of leg muscles pushes bicycle pedals. Thermal energy is kinetic energy associated with the random movement of atoms or molecules; thermal energy in transfer from one object to another is called heat. Light is also a type of energy that can be harnessed to perform work, such as powering photosynthesis in green plants. An object not presently moving may still possess energy. Energy that is not kinetic is called potential energy; it is energy that matter possesses because of its location or structure. Water behind a dam, for instance, possesses energy because of its altitude above sea level. Molecules possess energy because of the arrangement of electrons in the bonds between their atoms. Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical reaction. Recall that catabolic pathways release energy by breaking down complex molecules. Biologists say that these complex molecules, such as glucose, are high in chemical energy. During a catabolic reaction, some bonds are broken and others are formed, releasing energy and resulting in lower-energy breakdown products. This transformation also occurs in the engine of a car when the hydrocarbons of gasoline react explosively with oxygen, releasing the energy that pushes the pistons and producing exhaust. Although less explosive, a similar reaction of food molecules with oxygen provides chemical energy in biological systems, producing carbon dioxide and water as waste products. Biochemical pathways, carried out in the context of cellular structures, enable cells to release chemical energy from food molecules and use the energy to power life processes. How is energy converted from one form to another? Consider Figure 8.2. The woman climbing the ladder to the diving platform is releasing chemical energy from the food she ate for lunch and using some of that energy to perform . Figure 8.2 Transformations between potential energy and kinetic energy. derived from light energy absorbed by plants during photosynthesis. Organisms are energy transformers. A diver has more potential energy on the platform than in the water. The Laws of Energy Transformation Climbing up converts the kinetic energy of muscle movement to potential energy. Diving converts potential energy to kinetic energy. A diver has less potential energy in the water than on the platform. Mastering Biology Animation: Energy Transformations the work of climbing. The kinetic energy of muscle movement is thus being transformed into potential energy due to her increasing height above the water. The man diving is converting his potential energy to kinetic energy, which is then transferred to the water as he enters it, resulting in splashing, noise, and increased movement of water molecules. A small amount of energy is lost as heat due to friction. Now let’s consider the original source of the organic food molecules that provided the necessary chemical energy for these divers to climb the steps. This chemical energy was itself The study of the energy transformations that occur in a collection of matter is called thermodynamics. Scientists use the word system to denote the matter under study; they refer to the rest of the universe—everything outside the system—as the surroundings. An isolated system, such as that approximated by liquid in a thermos bottle, is unable to exchange either energy or matter with its surroundings outside the thermos. In an open system, energy and matter can be transferred between the system and its surroundings. Organisms are open systems. They absorb energy—for instance, light energy or chemical energy in the form of organic molecules—and release heat and metabolic waste products, such as carbon dioxide, to the surroundings. Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter. The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. The first law is also known as the principle of conservation of energy. The electric company does not make energy, but merely converts it to a form that is convenient for us to use. By converting sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer. The brown bear in Figure 8.3a will convert the chemical energy of the organic molecules in its food to kinetic and other forms of energy as it carries out biological processes. What happens to this energy after it has performed work? The second law of thermodynamics helps to answer this question. . Figure 8.3 The first two laws of thermodynamics. Heat CO2 + H2O Chemical energy in food (a) First law of thermodynamics: Energy can be transferred or transformed but neither created nor destroyed. For example, chemical reactions in this brown bear will convert the chemical (potential) energy in the fish into the kinetic energy of running. Kinetic energy (b) Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, as the bear runs, disorder is increased around its body by the release of heat and small molecules that are the by-products of metabolism. A brown bear can run at speeds up to 35 miles per hour (56 km/hr) —as fast as a racehorse. Mastering Biology MP3 Tutor: Basic Energy Concepts CHAPTER 8 An Introduction to Metabolism 145 If energy cannot be destroyed, why can’t organisms simply recycle their energy over and over again? It turns out that during every energy transfer or transformation, some energy is converted to thermal energy and released as heat, becoming unavailable to do work. Only a small fraction of the chemical energy from the food in Figure 8.3a is transformed into the motion of the brown bear shown in Figure 8.3b; most is lost as heat, which dissipates rapidly through the surroundings. A system can put thermal energy to work only when there is a temperature difference that results in thermal energy flowing as heat from a warmer location to a cooler one. If temperature is uniform, as it is in a living cell, then the heat generated during a chemical reaction will simply warm a body of matter, such as the organism. (This can make a room crowded with people uncomfortably warm, as each person is carrying out a multitude of chemical reactions!) A consequence of the loss of usable energy as heat to the surroundings is that each energy transfer or transformation makes the universe more disordered. We are all familiar with the word “disorder” in the sense of a messy room or a rundown building. The word “disorder” as used by scientists, however, has a specific molecular definition related to how dispersed the energy is in a system and how many different energy levels are present. For simplicity, we use “disorder” in the following discussion because our common understanding (the messy room) is a good analogy for molecular disorder. Scientists use a quantity called entropy as a measure of molecular disorder, or randomness. The more randomly arranged a collection of matter is, the greater its entropy. We can now state the second law of thermodynamics: Every energy transfer or transformation increases the entropy of the universe. Although order can increase locally, there is an unstoppable trend toward randomization of the universe as a whole. The physical disintegration of a system’s organized structure is a good analogy for an increase in entropy. For example, you can observe increasing entropy in the gradual decay of an unmaintained building over time. Much of the increasing entropy of the universe is more abstract, however, because it takes the form of increasing amounts of heat and less ordered forms of matter. As the bear in Figure 8.3b converts chemical energy to kinetic energy, it is also increasing the disorder of its surroundings by producing heat and small molecules, such as the CO2 it exhales, that are the breakdown products of food. The concept of entropy helps us understand why certain processes are energetically favorable and occur on their own. It turns out that if a given process, by itself, leads to an increase in entropy, that process can proceed without requiring an input of energy. Such a process is called a 146 UNIT TWO The Cell spontaneous process. Note that as we’re using it here, the word spontaneous does not imply that the process would occur quickly; rather, the word signifies that it is energetically favorable. (In fact, it may be helpful for you to think of the phrase “energetically favorable” when you read the formal term spontaneous, the word preferred by chemists.) Some spontaneous processes, such as an explosion, may be virtually instantaneous, while others, such as the rusting of an old car over time, are much slower. A process that, on its own, leads to a decrease in entropy is said to be nonspontaneous: It will happen only if energy is supplied. We know from experience that certain events occur spontaneously and others do not. For instance, we know that water flows downhill spontaneously but moves uphill only with an input of energy, such as when a machine pumps the water against gravity. Some of that energy is inevitably lost as heat, increasing entropy in the surroundings, so usage of energy during a nonspontaneous process also leads to an increase in the entropy of the universe as a whole. Biological Order and Disorder Living systems increase the entropy of their surroundings, as predicted by thermodynamic law. You may wonder, then, how cells create ordered structures from less organized starting materials. For example, simpler molecules are ordered into the more complex structure of an amino acid, and amino acids are ordered into polypeptide chains. At the organismal level as well, complex and beautifully ordered structures result from biological processes that use simpler starting materials (Figure 8.4). How can this happen, if entropy must constantly increase? . Figure 8.4 Order as a characteristic of life. Order is evident in the detailed structures of (a) the Venus flower basket glass sponge, which inspired the Spanish architect Antoni Gaudi in his design of (b) the towers of La Sagrada Família church in Barcelona, Spain. 5 cm The Second Law of Thermodynamics (a) Glass sponge (b) La Sagrada Família towers This increase in order is balanced by an organism’s taking in organized forms of matter and energy from the surroundings and replacing them with less ordered forms. For example, an animal obtains starch, proteins, and other complex molecules from the food it eats. As catabolic pathways break these molecules down, the animal releases CO2 and H2O —small molecules that possess less chemical energy than the food did (see Figure 8.3b). The depletion of chemical energy is accounted for by heat generated during metabolism. On a larger scale, energy flows into most ecosystems in the form of light and exits in the form of heat (see Figure 1.9). During the early history of life, complex organisms evolved from simpler ancestors. For instance, we can trace the ancestry of the plant kingdom from much simpler organisms called green algae to more complex flowering plants. However, this increase in organization over time in no way violates the second law. The entropy of a particular system, such as an organism, may actually decrease as long as the total entropy of the universe—the system plus its surroundings—increases. Thus, organisms are islands of low entropy in an increasingly random universe. The evolution of biological order is perfectly consistent with the laws of thermodynamics. CONCEPT CHECK 8.1 1. MAKE CONNECTIONS How does the second law of thermodynamics help explain the diffusion of a substance across a membrane? (See Figure 7.11.) 2. Describe the forms of energy found in an apple as it grows on a tree, then falls, then is digested by someone who eats it. 3. WHAT IF? If you place a teaspoon of sugar in the bottom of a glass of water, it will dissolve completely over time. Left longer, eventually the water will disappear and the sugar crystals will reappear. Explain these observations in terms of entropy. For suggested answers, see Appendix A. CONCEPT 8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously The laws of thermodynamics that we’ve just explored apply to the universe as a whole. As biologists, we want to understand the chemical reactions of life—for example, which reactions occur spontaneously and which ones require some input of energy from outside. But how can we know this without assessing the energy and entropy changes in the entire universe for each separate reaction? Free-Energy Change, DG Recall that the universe is really equivalent to “the system” plus “the surroundings.” In 1878, J. Willard Gibbs, a professor at Yale, defined a very useful function called the Gibbs free energy of a system (without considering its surroundings), symbolized by the letter G. We’ll refer to the Gibbs free energy simply as free energy. Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. Let’s consider how we determine the free-energy change that occurs when a system changes—for example, during a chemical reaction. The change in free energy, ΔG, can be calculated for a chemical reaction by applying the following equation: ∆G = ∆H - T∆S This equation uses only properties of the system (the reaction) itself: DH symbolizes the change in the system’s enthalpy (in biological systems, equivalent to total energy); DS is the change in the system’s entropy; and T is the absolute temperature in Kelvin (K) units (K = °C + 273; see the back of the book). Using chemical methods, we can measure DG for any reaction. (The value will depend on conditions such as pH, temperature, and concentrations of reactants and products.) Once we know the value of DG for a process, we can use it to predict whether the process will be spontaneous (that is, whether it is energetically favorable and will occur without an input of energy). More than a century of experiments has shown that only processes with a negative DG are spontaneous. For DG to be negative, DH must be negative (the system gives up enthalpy and H decreases) or TDS must be positive (the system gives up order and S increases), or both: When DH and TDS are tallied, DG has a negative value (∆G 6 0) for all spontaneous processes. In other words, every spontaneous process decreases the system’s free energy, and processes that have a positive or zero DG are never spontaneous. This information is immensely interesting to biologists, for it allows us to predict which kinds of change can happen without an input of energy. Such spontaneous changes can be harnessed by the cell to perform work. This principle is very important in the study of metabolism, where a major goal is to determine which reactions can supply energy for cellular work. Free Energy, Stability, and Equilibrium As we saw in the previous section, when a process occurs spontaneously in a system, we can be sure that DG is negative. Another way to think of DG is to realize that it represents the CHAPTER 8 An Introduction to Metabolism 147 difference between the free energy of the final state and the free energy of the initial state: ∆G = Gfinal state - Ginitial state For a reaction to have a negative DG, the system must lose free energy during the change from initial state to final state. Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously. We can think of free energy as a measure of a system’s instability—its tendency to change to a more stable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split (Figure 8.5). Unless something prevents it, each of these systems will move toward greater stability: The diver falls, the solution becomes uniformly colored, and the glucose molecule is broken down into smaller molecules. Another term that describes a state of maximum stability is equilibrium, which you learned about in Concept 2.4 in connection with chemical reactions. At equilibrium, the forward and reverse reactions occur at the same rate, and there is no further net change in the relative concentration of products and reactants. For a system at equilibrium, G is at its lowest possible value in that system. Free energy increases when a reaction is somehow pushed away from equilibrium, perhaps by removing some of the products (and thus changing their concentration relative to that of the reactants). We can think of the equilibrium state as a free-energy valley. Any change from the equilibrium position will have a positive DG and will not be spontaneous. For this reason, systems never spontaneously move away from equilibrium. Because a system at equilibrium cannot spontaneously change, it can do no work. A process is spontaneous and can perform work only when it is moving toward equilibrium. Free Energy and Metabolism We can now apply the free-energy concept more specifically to the chemistry of life’s processes. Exergonic and Endergonic Reactions in Metabolism Based on their free-energy changes, chemical reactions can be classified as either exergonic (“energy outward”) or endergonic (“energy inward”). An exergonic reaction proceeds with a net release of free energy (Figure 8.6a). Because the chemical mixture loses free energy (G decreases), DG is negative for an exergonic reaction. Using DG as a standard for spontaneity, exergonic reactions are those that occur spontaneously. (Remember, the word spontaneous implies that it is energetically favorable, not that it will occur rapidly.) The magnitude of DG for an exergonic reaction . Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change. Unstable systems (top) are rich in free energy, G. They tend to change spontaneously to a more stable state (bottom). This “downhill” change can be harnessed to perform work. • More free energy (higher G) • Less stable • Greater work capacity In a spontaneous change • The free energy of the system decreases (DG < 0). • The system becomes more stable. • The released free energy can be harnessed to do work. • Less free energy (lower G) • More stable • Less work capacity (a) Gravitational motion. Objects move spontaneously from a higher altitude to a lower one. (b) Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed. MAKE CONNECTIONS Compare the redistribution of molecules shown in (b) to the transport of hydrogen ions 1H +2 across a membrane by a proton pump, creating a concentration gradient (see Figure 7.18). Which process(es) result(s) in higher free energy? Which system(s) can do work? 148 UNIT TWO The Cell (c) Chemical reaction. In a cell, a glucose molecule is broken down into simpler molecules. . Figure 8.6 Free energy changes (DG) in exergonic and endergonic reactions. (a) Exergonic reaction: energy released, spontaneous Reactants Free energy Amount of energy released (DG , 0) Energy Products Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous Free energy Products Reactants Energy Amount of energy required (DG . 0) Progress of the reaction Mastering Biology Animation: Exergonic and Endergonic Reactions represents the maximum amount of work the reaction can perform.* The greater the decrease in free energy, the greater the amount of work that can be done. We can use the overall reaction for cellular respiration as an example: C6H12O6 + 6 O2 S 6 CO2 + 6 H2O ∆G = - 686 kcal/mol (- 2,870 kJ/mol) For each mole (180 g) of glucose broken down by respiration under what are called “standard conditions” (1 M of each reactant and product, 25°C, pH 7), 686 kcal (2,870 kJ) of energy is made available for work. Because energy must be conserved, the chemical products of respiration store 686 kcal less free energy per mole than the reactants. The products are, in a sense, the spent exhaust of a process that tapped the free energy stored in the bonds of the sugar molecules. It is important to realize that the breaking of bonds does not release energy; on the contrary, as you will soon see, it requires energy. The phrase “energy stored in bonds” is shorthand for the potential energy that can be released when new bonds are formed after the original bonds break, as long as the products are of lower free energy than the reactants. An endergonic reaction is one that absorbs free energy from its surroundings (Figure 8.6b). Because this kind of reaction essentially stores free energy in molecules (G increases), DG is positive. Such reactions are non-spontaneous, and the magnitude of DG is the quantity of energy required to drive the reaction. If a chemical process is exergonic (downhill), releasing energy in one direction, then the reverse process must be endergonic (uphill), using energy. A reversible process cannot be downhill in both directions. If ∆G = - 686 kcal/mol for respiration, which converts glucose and oxygen to CO2 and H2O, then the reverse process—the conversion of CO2 and H2O to glucose and oxygen (O2)—must be strongly endergonic, with ∆G = + 686 kcal/mol. Such a reaction would never happen by itself. How, then, do plants make sugar? They get the required energy (686 kcal to make a mole of glucose) by capturing light from the sun and converting its energy to chemical energy. Next, in a long series of exergonic steps, they gradually spend that chemical energy to assemble glucose molecules. Equilibrium and Metabolism Reactions in an isolated system eventually reach equilibrium and can then do no work, as illustrated by the isolated hydroelectric system in Figure 8.7. The chemical reactions of metabolism are reversible, and they, too, would reach equilibrium if they occurred in the isolation of a test tube. Because systems at equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead! The fact that metabolism as a whole is never at equilibrium is one of the defining features of life. . Figure 8.7 Equilibrium and work in an isolated hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a lightbulb, but only until the system reaches equilibrium. DG , 0 DG 5 0 * The word maximum qualifies this statement because some of the free energy is released as heat and cannot do work. Therefore, ∆G represents a theoretical upper limit of available energy. CHAPTER 8 An Introduction to Metabolism 149 Like most systems, a living cell is not in equilibrium. Materials flow in and out, keeping metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life. This principle is illustrated by the open (and more realistic) hydroelectric system in Figure 8.8a. However, unlike this simple single-step system, a catabolic pathway in a cell releases free energy in a series of reactions. An example is cellular respiration, illustrated by analogy in Figure 8.8b. Some of the reversible reactions of respiration are constantly “pulled” in one direction—that is, they are kept out of equilibrium. The key to maintaining this lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step; finally, waste products are expelled from the cell. The overall sequence of reactions is kept going by the huge free-energy difference between glucose and O2 at the top of the energy “hill” and CO2 and H2O at the “downhill” end. As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life. Organisms are open systems. Sunlight provides a daily source of free energy for an ecosystem’s plants and other photosynthetic organisms. Animals and other nonphotosynthetic organisms in an ecosystem must have a source of free . Figure 8.8 Equilibrium and work in open systems. (a) An open hydroelectric system. Water flowing through a turbine keeps driving the generator because intake and outflow of water keep the system from reaching equilibrium. DG , 0 DG , 0 DG , 0 DG , 0 energy—the organic products of photosynthesis. Now we are ready to see how a cell actually performs the work of life. CONCEPT CHECK 8.2 1. Cellular respiration uses glucose and O2, which have high levels of free energy, and releases CO2 and H2O, which have low levels of free energy. Is cellular respiration spontaneous or not? Is it exergonic or endergonic? What happens to the energy released from glucose? 2. VISUAL SKILLS How would the processes of catabolism and anabolism relate to Figure 8.5c? 3. WHAT IF? Some partygoers wear glow-in-the-dark necklaces that start glowing once they are “activated” by snapping the necklace. This allows two chemicals to react and emit light in the form of chemiluminescence. Is the reaction exergonic or endergonic? Explain. For suggested answers, see Appendix A. CONCEPT 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: • Chemical work, the pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers (chemical work will be discussed further here; examples are shown in Chapters 9 and 10) • Transport work, the pumping of substances across membranes against the direction of spontaneous movement (see Concept 7.4) • Mechanical work, such as the beating of cilia (see Concept 6.6), the contraction of muscle cells, and the movement of chromosomes during cellular reproduction A key feature in the way cells manage their energy resources to do this work is energy coupling, the use of an exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work. Mastering Biology Animation: Energy Coupling The Structure and Hydrolysis of ATP (b) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucose is broken down in a series of exergonic reactions that power the work of the cell. The product of each reaction is used as the reactant for the next, so no reaction reaches equilibrium. 150 UNIT TWO The Cell ATP (adenosine triphosphate; see Concept 4.3) contains the sugar ribose, with the nitrogenous base adenine and a chain of three phosphate groups (the triphosphate group) bonded to it (Figure 8.9a). In addition to its role in energy coupling, ATP is also one of the nucleoside triphosphates used to make RNA (see Figure 5.23). The bonds between the phosphate groups of ATP can be broken by hydrolysis. When the terminal phosphate bond is broken by addition of a water molecule, a molecule of inorganic phosphate (HOPO32-, abbreviated as P i throughout this book) leaves the ATP, which becomes adenosine diphosphate, or ADP (Figure 8.9b). The reaction is exergonic and releases 7.3 kcal of energy per mole of ATP hydrolyzed: ATP + H2O S ADP + P i ∆G = - 7.3 kcal/mol (- 30.5 kJ/mol) This is the free-energy change measured under standard conditions. In the cell, conditions do not conform to standard conditions, primarily because reactant and product concentrations differ from 1 M. For example, when ATP . Figure 8.9 The structure and hydrolysis of adenosine triphosphate (ATP). Throughout this book, the chemical structure of the triphosphate group seen in (a) will be represented by the three joined yellow circles shown in (b). Adenine N O –O P O O P O– HC O O O P O– C CH2 O– Triphosphate group (3 phosphate groups) C N O H C N N H H H OH NH2 Ribose OH (a) The structure of ATP. In the cell, most hydroxyl groups of phosphates are ionized (—O – ). P P P Adenosine triphosphate (ATP) H2O Pi Inorganic phosphate + P P + Energy Adenosine diphosphate (ADP) (b) The hydrolysis of ATP. The reaction of ATP and water yields inorganic phosphate ( P i ) and ADP and releases energy. Mastering Biology Animation: The Structure of ATP Animation: Space-Filling Model of ATP Animation: Stick Model of ATP hydrolysis occurs under typical cellular conditions, the actual ΔG is about -13 kcal/mol, 78% greater than the energy released by ATP hydrolysis under standard conditions. Because their hydrolysis releases energy, the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, but the term is misleading. The phosphate bonds of ATP are not unusually strong bonds, as “high-energy” may imply; rather, the reactants (ATP and water) themselves have high energy relative to the energy of the products (ADP and P i). The release of energy during the hydrolysis of ATP comes from the chemical change of the system to a state of lower free energy, not from the phosphate bonds themselves. ATP is useful to the cell because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver. But why does this hydrolysis release so much energy? If we reexamine the ATP molecule in Figure 8.9a, we can see that all three phosphate groups are negatively charged. These like charges are crowded together, and their mutual repulsion contributes to the instability of this region of the ATP molecule. The triphosphate tail of ATP is the chemical equivalent of a compressed spring. CH How ATP Provides Energy That Performs Work When ATP is hydrolyzed in a test tube, the release of free energy merely heats the surrounding water. In an organism, this same generation of heat can sometimes be beneficial. For instance, the process of shivering uses ATP hydrolysis during muscle contraction to warm the body. In most cases in the cell, however, the generation of heat alone would be an inefficient (and potentially dangerous) use of a valuable energy resource. Instead, the cell’s proteins harness the energy released during ATP hydrolysis in several ways to perform the three types of cellular work—chemical, transport, and mechanical. For example, with the help of specific enzymes, the cell is able to use the high free energy of ATP to drive chemical reactions that, by themselves, are endergonic. If the DG of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic. This usually involves phosphorylation, the transfer of a phosphate group from ATP to some other molecule, such as the reactant. The recipient molecule with the phosphate group covalently bonded to it is then called a phosphorylated intermediate. The key to coupling exergonic and endergonic reactions is the formation of this phosphorylated intermediate, which is more CHAPTER 8 An Introduction to Metabolism 151 . Figure 8.10 How ATP drives chemical work: energy coupling using ATP hydrolysis. In this example, the exergonic process of ATP hydrolysis drives an endergonic process—synthesis of the amino acid glutamine. (a) Glutamic acid conversion to glutamine. Glutamine synthesis from glutamic acid (Glu) by itself is endergonic (DG is positive), so it is not spontaneous. Glu + NH3 Glu DGGlu = 13.4 kcal/mol Glutamine Glutamic acid Ammonia (b) Conversion reaction coupled with ATP hydrolysis. In the cell, glutamine synthesis occurs in two steps, coupled by a phosphorylated intermediate (Glu- P ). 1 ATP phosphorylates + Glu glutamic acid, making it less stable, with more free energy. 2 Ammonia displaces the Glutamic acid phosphate group, forming glutamine. NH2 NH3 P 1 ATP Glu 2 + ADP Glu Phosphorylated intermediate NH2 + ADP + P i Glutamine DGGlu = 13.4 kcal/mol (c) Free-energy change for coupled reaction. DG for the glutamic acid conversion to glutamine (+3.4 kcal/mol) plus DG for ATP hydrolysis (–7.3 kcal/mol) gives the free-energy change for the overall reaction (–3.9 kcal/mol). Because the overall process is exergonic (net DG is negative), it occurs spontaneously. Glu + NH3 + ATP DGGlu = 13.4 kcal/mol Glu NH2 + ADP + Pi DGATP = –7.3 kcal/mol + DGATP = –7.3 kcal/mol Net DG = –3.9 kcal/mol MAKE CONNECTIONS Referring to Figure 5.14, explain why glutamine (Gln) is drawn in this figure as a glutamic acid (Glu) with an amino group attached. reactive (less stable, with more free energy) than the original unphosphorylated molecule (Figure 8.10). Transport and mechanical work in the cell are also nearly always powered by the hydrolysis of ATP. In these cases, ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind another molecule. Sometimes this occurs via a phosphorylated intermediate, as seen for the transport protein in Figure 8.11a. In most instances of mechanical work involving motor proteins “walking” along cytoskeletal Mastering Biology Figure Walkthrough elements (Figure 8.11b), a cycle occurs in which ATP is first bound noncovalently to the motor protein. Next, ATP is hydrolyzed, releasing ADP and P i. Another ATP molecule can then bind. At each stage, the motor protein changes its shape and ability to bind the cytoskeleton, resulting in movement of the protein along the cytoskeletal track. Phosphorylation and dephosphorylation promote crucial protein shape changes during many other important cellular processes as well. . Figure 8.11 How ATP drives transport and mechanical work. ATP hydrolysis causes changes in the shapes and binding affinities of proteins. This can occur either (a) directly, by phosphorylation, as shown for a membrane protein carrying out active transport of a solute (see also Figure 7.16 and the proton pump in Figure 6.32, upper left), or (b) indirectly, via noncovalent binding of ATP and its hydrolytic products, as is the case for motor proteins that move vesicles (and other organelles) along cytoskeletal “tracks” in the cell (see also Figures 6.21 and 6.32, lower right). Transport protein Solute Cytoskeletal track Vesicle ATP ADP + P i P (a) Transport work: ATP phosphorylates transport proteins, causing a shape change that allows transport of solutes. UNIT TWO The Cell ADP + P i ATP Pi Solute transported 152 ATP Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed, causing a shape change that walks the motor protein forward. . Figure 8.12 The ATP cycle. Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work. ATP synthesis from ADP + P i requires energy. ATP Energy from catabolism (exergonic, energy-releasing processes) ATP hydrolysis to ADP + P i yields energy. + H O 2 Energy for cellular work (endergonic, energy-consuming processes) ADP + P i Mastering Biology Animation: Metabolism Overview The Regeneration of ATP An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP (Figure 8.12). The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell. This shuttling of inorganic phosphate and energy is called the ATP cycle, and it couples the cell’s energy-yielding (exergonic) processes to the energyconsuming (endergonic) ones. The ATP cycle proceeds at an astonishing pace. For example, a working muscle cell recycles its entire pool of ATP in less than a minute. That turnover represents 10 million molecules of ATP consumed and regenerated per second per cell. If ATP could not be regenerated by the phosphorylation of ADP, humans would use up nearly their body weight in ATP each day. Because both directions of a reversible process cannot be downhill, the regeneration of ATP from ADP and P i is necessarily endergonic: ADP + P i S ATP + H2O ∆G = + 7.3 kcal/mol (+30.5 kJ/mol) (standard conditions) Since ATP formation from ADP and P i is not spontaneous, free energy must be spent to make it occur. Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic process of making ATP. Plants also use light energy to produce ATP. Thus, the ATP cycle is a key player in bioenergetics, functioning as a revolving door through which energy passes during its transfer from catabolic to anabolic pathways. CONCEPT CHECK 8.3 1. How does ATP typically transfer energy from an exergonic to an endergonic reaction in the cell? 2. Which combination has more free energy: glutamic acid + ammonia + ATP or glutamine + ADP + P i? Explain. ○ 3. MAKE CONNECTIONS Does Figure 8.11a show passive or active transport? Explain. (See Concepts 7.3 and 7.4.) For suggested answers, see Appendix A. CONCEPT 8.4 Enzymes speed up metabolic reactions by lowering energy barriers The laws of thermodynamics tell us what will and will not happen under given conditions but say nothing about the rate of these processes. A spontaneous chemical reaction occurs without any requirement for outside energy, but it may occur so slowly that it is imperceptible. For example, even though the hydrolysis of sucrose (table sugar) to glucose and fructose is exergonic, occurring spontaneously with a release of free energy (∆G = - 7 kcal/mol), a solution of sucrose dissolved in sterile water will sit for years at room temperature with no appreciable hydrolysis. However, if we add a small amount of the enzyme sucrase to the solution, then all the sucrose may be hydrolyzed within seconds, as shown here: Sucrase + O + H2O Sucrose (C12H22O11) OH Glucose (C6H12O6 ) HO Fructose (C6H12O6 ) How does the enzyme do this? An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction. In this chapter, we focus on enzymes that are proteins. (Some RNA molecules, called ribozymes, can function as enzymes; these will be discussed in Concepts 17.3 and 25.1.) Without regulation by enzymes, chemical traffic through the pathways of metabolism would become terribly congested because many chemical reactions would take such a long time. In the next two sections, we will see why spontaneous reactions can be slow and how an enzyme changes the situation. The Activation Energy Barrier Every chemical reaction between molecules involves both bond breaking and bond forming. For example, the hydrolysis of sucrose involves breaking the bond between glucose and fructose and one of the bonds of a water molecule and then forming two new bonds, as shown above. Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed. This contortion can be compared to the bending of a metal key ring when you pry it open to add a new key. The key ring is highly unstable in its opened form but returns to a stable state once the key is threaded all the way onto the ring. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state. CHAPTER 8 An Introduction to Metabolism 153 The initial investment of energy for starting a reaction— the energy required to contort the reactant molecules so the bonds can break—is known as the free energy of activation, or activation energy, abbreviated E A in this book. We can think of activation energy as the amount of energy needed to push the reactants to the top of an energy barrier, or “uphill,” so that the “downhill” part of the reaction can begin. Activation energy is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings. The absorption of thermal energy accelerates the reactant molecules, so they collide more often and more forcefully. It also agitates the atoms within the molecules, making the breakage of bonds more likely. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state. Figure 8.13 graphs the energy changes for a hypothetical exergonic reaction that swaps portions of two reactant molecules: AB + CD S AC + B Reactants Products The activation of the reactants is represented by the uphill portion of the graph, in which the free-energy content of . Figure 8.13 Energy profile of an exergonic reaction. The “molecules” are hypothetical, with A, B, C, and D representing portions of the molecules. Thermodynamically, this is an exergonic reaction, with a negative DG, and the reaction occurs spontaneously. However, the activation energy (EA) provides a barrier that determines the rate of the reaction. The reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state, where bonds can break. A B C D After bonds have broken, new bonds form, releasing energy to the surroundings. Free energy Transition state A B C D EA Reactants A B C D DG < 0 Products Progress of the reaction DRAW IT Graph the progress of an endergonic reaction in which EF and GH form products EG and FH, assuming that the reactants must pass through a transition state. 154 UNIT TWO The Cell the reactant molecules is increasing. At the summit, when energy equivalent to E A has been absorbed, the reactants are in the transition state: They are activated, and their bonds can be broken. As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings. This corresponds to the downhill part of the curve, which shows the loss of free energy by the molecules. The overall decrease in free energy means that E A is repaid with dividends, as the formation of new bonds releases more energy than was invested in the breaking of old bonds. The reaction shown in Figure 8.13 is exergonic and occurs spontaneously (∆G 6 0). However, the activation energy provides a barrier that determines the rate of the reaction. The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur. For some reactions, E A is modest enough that even at room temperature there is sufficient thermal energy for many of the reactant molecules to reach the transition state in a short time. In most cases, however, E A is so high and the transition state is reached so rarely that the reaction will hardly proceed at all. In these cases, the reaction will occur at a noticeable rate only if energy is provided, usually by heat. For example, the reaction of gasoline and oxygen is exergonic and will occur spontaneously, but energy is required for the molecules to reach the transition state and react. Only when the spark plugs fire in an automobile engine can there be the explosive release of energy that pushes the pistons. Without a spark, a mixture of gasoline hydrocarbons and oxygen will not react because the E A barrier is too high. How Enzymes Speed Up Reactions Proteins, DNA, and other complex cellular molecules are rich in free energy and have the potential to decompose spontaneously; that is, the laws of thermodynamics favor their breakdown. These molecules only persist because at temperatures typical for cells, few molecules can make it over the hump of activation energy. The barriers for selected reactions must occasionally be surmounted, however, for cells to carry out the processes needed for life. Heat can increase the rate of a reaction by allowing reactants to attain the transition state more often, but this would not work well in biological systems. First, high temperature denatures proteins and kills cells. Second, heat would speed up all reactions, not just those that are needed. Instead of heat, organisms carry out catalysis, the process by which a catalyst selectively speeds up a reaction without itself being consumed. (You learned about catalysts earlier in this section.) An enzyme catalyzes a reaction by lowering the E A barrier (Figure 8.14), enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures, as we’ll see shortly. It is crucial to note that an enzyme cannot change the ∆G for a reaction; it cannot make an endergonic reaction exergonic. Enzymes can only . Figure 8.14 The effect of an enzyme on activation energy. Without affecting the free-energy change (ΔG) for a reaction, an enzyme speeds the reaction by reducing its activation energy (EA). Free energy Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Course of reaction with enzyme DG is unaffected by enzyme Products Progress of the reaction the product (or products) of the reaction. The overall process can be summarized as follows: Enzyme + Substrate(s) L Enzyme@ substrate complex L Enzyme + Product(s) Most enzyme names end in -ase. (See if you can find three examples of enzymes in the lower left of Figure 6.32.) For example, the enzyme sucrase catalyzes the hydrolysis of the disaccharide sucrose into its two monosaccharides, glucose and fructose (see the diagram at the beginning of Concept 8.4): Sucrase + Sucrose + H2O L Sucrase@ sucrose@H2O complex L Sucrase + Glucose + Fructose The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds. For instance, sucrase will act only hasten reactions that would eventually occur anyway, but on sucrose and will not bind to other disaccharides, such this enables the cell to have a dynamic metabolism, routas maltose. What accounts for this molecular recognition? ing chemicals smoothly through metabolic pathways. Also, Recall that most enzymes are proteins, and that proteins enzymes are very specific for the reactions they catalyze, so are macromolecules with unique 3-D configurations. The they determine which chemical processes will be going on in specificity of an enzyme results from its shape, which is a the cell at any given time. consequence of its amino acid sequence. Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the active site, is Substrate Specificity of Enzymes typically a pocket or groove on the surface of the enzyme where The reactant an enzyme acts on is referred to as the enzyme’s catalysis occurs (Figure 8.15a; see also Figure 5.16). Usually, the substrate. The enzyme binds to its substrate (or substrates, active site is formed by only a few of the enzyme’s amino acids, when there are two or more reactants), forming an enzymewith the rest of the protein molecule providing a framework substrate complex. While enzyme and substrate are joined, that determines the shape of the active site. The specificity of the catalytic action of the enzyme converts the substrate to an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate. An enzyme is not a stiff structure . Figure 8.15 Induced fit between an enzyme and its substrate. locked into a given shape. In fact, Substrate recent work by biochemists has shown that enzymes (and other proteins) seem to “dance” between subtly different shapes in a dynamic equilibrium, with slight differences in free energy Active site for each “pose.” The shape that best fits the substrate isn’t necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate. The active site itself is also not a rigid receptacle for the subEnzyme Enzyme-substrate strate. As shown in Figure 8.15b, when complex the substrate enters the active site, the (a) In this space-filling model of (b) When the substrate enters the active site, it forms the enzyme hexokinase (blue), the weak bonds with the enzyme, inducing a change in enzyme changes shape slightly due to active site forms a groove on the the shape of the protein. This change allows additional interactions between the substrate’s surface. The enzyme’s substrate is weak bonds to form, causing the active site to enfold chemical groups and chemical groups glucose (red). the substrate and hold it in place. Mastering Biology Animation: How Enzymes Work CHAPTER 8 An Introduction to Metabolism 155 on the side chains of the amino acids that form the active site. This shape change makes the active site fit even more snugly around the substrate. The tightening of the binding after initial contact—called induced fit—is like a clasping handshake. Induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction. Catalysis in the Enzyme’s Active Site In most enzymatic reactions, the substrate is held in the active site by so-called weak interactions, such as hydrogen bonds and ionic bonds. The R groups of a few of the amino acids that make up the active site catalyze the conversion of substrate to product, and the product departs from the active site. The enzyme is then free to take another substrate molecule into its active site. The entire cycle happens so fast that a single enzyme molecule typically acts on about 1,000 substrate molecules per second, and some enzymes are even faster. Enzymes, like other catalysts, emerge from the reaction in their original form. Therefore, very small amounts of enzyme can have a huge metabolic impact by functioning over and over again in catalytic cycles. Figure 8.16 shows a catalytic cycle involving two substrates and two products. Most metabolic reactions are reversible, and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative ∆G. This in turn depends mainly on the relative concentrations of reactants and products. The net effect is always in the direction of equilibrium. Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction (see Figure 8.16, step 3 ): • In reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. • As the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending critical chemical bonds to be broken during the reaction. Because E A is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state. • The active site may also provide a microenvironment that is more conducive to a certain reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids with acidic R groups, it may provide a pocket of low pH in an otherwise neutral cell. Here, an acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction. • Amino acids in the active site may directly participate in the chemical reaction. Sometimes this process involves 156 UNIT TWO The Cell . Figure 8.16 The active site and catalytic cycle of an enzyme. An enzyme can convert one or more reactant molecules to one or more product molecules. The enzyme shown here converts two substrate molecules to two product molecules. 1 Substrates enter the active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). Substrates 6 Active site is available for two new substrate molecules. 2 Substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds. Enzyme-substrate complex 3 The active site lowers EA and speeds up the reaction (see text). Enzyme 45 Products are released. Products 4 Substrates are converted to products. VISUAL SKILLS The enzyme-substrate complex passes through a transition state (see Figure 8.13). Label the part of the cycle where the transition state occurs. Mastering Biology Animation: Enzymes: Steps in a Reaction brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme. Subsequent steps restore the side chains to their original states so that the active site is the same after the reaction as it was before. The rate at which a particular amount of enzyme converts substrate to product is partly a function of the initial concentration of the substrate: The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules. However, there is a limit to how fast the reaction can be pushed by adding more substrate to a fixed concentration of enzyme. At some point, the concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged. As soon as the product exits an active site, another substrate molecule enters. At this substr