Cell_Biology_Alberts

Cell_Biology_Alberts. heat is released to pull of the foor 1 potential energy due to position kinetic energy heat energy two hydrogen oxygen gas rapid vibrations and heat dispersed to gas molecules molecule rotations of two newly surroundings formed water molecules in order that distinguishes the metabolism of a cell from the wasteful burning of fuel in a fire. Later, we illustrate how this coupling occurs. For now, it is sufficient to recognize that a direct linkage of the “controlled burning” of food molecules to the generation of biological order is required for cells to create and maintain an island of order in a universe tending toward chaos. Cells obtain energy by the oxidation of organic molecules


Cell_Biology_Alberts

Cell_Biology_Alberts. Cells obtain energy by the oxidation of organic molecules All animal and plant cells are powered by energy stored in the chemical bonds of organic molecules, whether they are sugars that a plant has photosynthesized as food for itself or the mixture of large and small molecules that an animal has eaten. Organisms must extract this energy in usable form to live, grow, and reproduce. In both plants and animals, energy is extracted from food molecules by a process of gradual oxidation, or controlled burning. The Earth’s atmosphere contains a great deal of oxygen, and in the presence of oxygen the most energetically stable form of carbon is CO2 and that of hydrogen Figure 2–17 Some interconversions between different forms of energy.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–17 Some interconversions between different forms of energy. all energy forms are, in principle, interconvertible. in all these processes the total amount of energy is conserved. Thus, for example, from the height and weight of the brick in (1), we can predict exactly how much heat will be released when it hits the floor. in (2), note that the large amount of chemical-bond energy released when water is formed is initially converted to very rapid thermal motions in the two new water molecules; but collisions with other molecules almost instantaneously spread this kinetic energy evenly throughout the surroundings (heat transfer), making the new molecules indistinguishable from all the rest. is H2O. A cell is therefore able to obtain energy from sugars or other organic molecules by allowing their carbon and hydrogen atoms to combine with oxygen to produce CO2 and H2O, respectively—a process called aerobic respiration.


Cell_Biology_Alberts

Cell_Biology_Alberts. Photosynthesis (discussed in detail in Chapter 14) and respiration are complementary processes (Figure 2–18). This means that the transactions between plants and animals are not all one way. Plants, animals, and microorganisms have existed together on this planet for so long that many of them have become an essential part of the others’ environments. The oxygen released by photosynthesis is consumed in the combustion of organic molecules during aerobic respiration. And some of the CO2 molecules that are fixed today into organic molecules by photosynthesis in a green leaf were yesterday released into the atmosphere by the respiration of an animal—or by the respiration of a fungus or bacterium decomposing dead organic matter. We therefore see that carbon utilization forms a huge cycle that involves the biosphere (all of the living organisms on Earth) as a whole (Figure 2–19). Similarly, atoms of nitrogen, phosphorus, and sulfur move between the living and nonliving worlds in cycles that


Cell_Biology_Alberts

Cell_Biology_Alberts. the biosphere (all of the living organisms on Earth) as a whole (Figure 2–19). Similarly, atoms of nitrogen, phosphorus, and sulfur move between the living and nonliving worlds in cycles that involve plants, animals, fungi, and bacteria.


Cell_Biology_Alberts

Cell_Biology_Alberts. The cell does not oxidize organic molecules in one step, as occurs when organic material is burned in a fire. Through the use of enzyme catalysts, metabolism takes these molecules through a large number of reactions that only rarely involve the direct addition of oxygen. Before we consider some of these reactions and their purpose, we discuss what is meant by the process of oxidation.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–18 Photosynthesis and respiration as complementary processes in the living world. photosynthesis converts the electromagnetic energy in sunlight into chemical-bond energy in sugars and other organic molecules. plants, algae, and cyanobacteria obtain the carbon atoms that they need for this purpose from atmospheric Co2 and the hydrogen from water, releasing o2 gas as a by-product. The organic molecules produced by photosynthesis in turn serve as food for other organisms. many of these organisms carry out aerobic respiration, a process that uses o2 to form Co2 from the same carbon atoms that had been taken up as Co2 and converted into sugars by photosynthesis. in the process, the organisms that respire obtain the chemical-bond energy that they need to survive.


Cell_Biology_Alberts

Cell_Biology_Alberts. The first cells on the earth are thought to have been capable of neither photosynthesis nor respiration (discussed in Chapter 14). however, photosynthesis must have preceded respiration on the earth, since there is strong evidence that billions of years of photosynthesis were required before o2 had been released in sufficient quantity to create an atmosphere rich in this gas. (The earth’s atmosphere currently contains 20% o2.) HUMUS AND DISSOLVED ORGANIC MATTER SEDIMENTS AND FOSSIL FUELS RESPIRATION PHOTOSYNTHESIS FOOD CHAIN CO2 IN ATMOSPHERE AND WATER PLANTS, ALGAE, BACTERIA ANIMALS Figure 2–19 The carbon cycle. individual carbon atoms are incorporated into organic molecules of the living world by the photosynthetic activity of bacteria, algae, and plants. They pass to animals, microorganisms, and organic material in soil and oceans in cyclic paths. Co2 is restored to the atmosphere when organic molecules are oxidized by cells or burned by humans as fuels.


Cell_Biology_Alberts

Cell_Biology_Alberts. Chapter 2: Cell Chemistry and Bioenergetics enzymes lower the activation-energy Barriers That Block Chemical Reactions


Cell_Biology_Alberts

Cell_Biology_Alberts. Consider the reaction paper + O2→ smoke + ashes + heat + CO2 + H2O Once ignited, the paper burns readily, releasing to the atmosphere both energy as heat and water and carbon dioxide as gases. The reaction is irreversible, since the smoke and ashes never spontaneously retrieve these entities from the heated atmosphere and reconstitute themselves into paper. When the paper burns, its chemical energy is dissipated as heat—not lost from the universe, since energy can never be created or destroyed, but irretrievably dispersed in the chaotic random thermal motions of molecules. At the same time, the atoms and molecules of the paper become dispersed and disordered. In the language of thermodynamics, there has been a loss of free energy; that is, of energy that can be harnessed to do work or drive chemical reactions. This loss reflects a reduction of orderliness in the way the energy and molecules were stored in the paper. We shall discuss free energy in more detail shortly, but the general


Cell_Biology_Alberts

Cell_Biology_Alberts. chemical reactions. This loss reflects a reduction of orderliness in the way the energy and molecules were stored in the paper. We shall discuss free energy in more detail shortly, but the general principle is clear enough intuitively: chemical reactions proceed spontaneously only in the direction that leads to a loss of free energy. In other words, the spontaneous direction for any reaction is the direction that goes “downhill,” where a “downhill” reaction is one that is energetically favorable. Although the most energetically favorable form of carbon under ordinary conditions is CO2, and that of hydrogen is H2O, a living organism does not disappear in a puff of smoke, and the paper book in your hands does not burst into flames. This is because the molecules both in the living organism and in the book are in a relatively stable state, and they cannot be changed to a state of lower energy without an input of energy: in other words, a molecule requires activation energy—a kick over an


Cell_Biology_Alberts

Cell_Biology_Alberts. in the book are in a relatively stable state, and they cannot be changed to a state of lower energy without an input of energy: in other words, a molecule requires activation energy—a kick over an energy barrier—before it can undergo a chemical reaction that leaves it in a more stable state (Figure 2–21). In the case of a burning book, the activation energy can be provided by the heat of a lighted match. For the molecules in the watery solution inside a cell, the kick is delivered by an unusually energetic random collision with surrounding molecules—collisions that become more violent as the temperature is raised. The chemistry in a living cell is tightly controlled, because the kick over energy barriers is greatly aided by a specialized class of proteins—the enzymes. Each enzyme binds tightly to one or more molecules, called substrates, and holds them in a way that greatly reduces the activation energy of a particular chemical reaction that the bound substrates can undergo. A


Cell_Biology_Alberts

Cell_Biology_Alberts. tightly to one or more molecules, called substrates, and holds them in a way that greatly reduces the activation energy of a particular chemical reaction that the bound substrates can undergo. A substance that can lower the activation energy of a reaction is termed a catalyst; catalysts increase the rate of chemical reactions because they allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates over the energy barrier, as illustrated in Figure 2–22. Enzymes are among the most effective catalysts


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–21 The important principle of activation energy. (a) Compound Y (a reactant) is in a relatively stable state, and energy is required to convert it to compound X (a product), even though X is at a lower overall energy level than Y. This conversion will not take place, therefore, unless compound Y can acquire enough activation energy (energy a minus energy b) from its surroundings to undergo the reaction that converts it into compound X. This energy may be provided by means of an unusually energetic collision with other molecules. for the reverse reaction, X → Y, the activation energy will be d more rarely. activation energies are always positive; note, however, that the total energy change for the energetically known: some are capable of speeding up reactions by factors of 1014 or more. Enzymes thereby allow reactions that would not otherwise occur to proceed rapidly at normal temperatures.


Cell_Biology_Alberts

Cell_Biology_Alberts. An enzyme cannot change the equilibrium point for a reaction. The reason is simple: when an enzyme (or any catalyst) lowers the activation energy for the reaction Y → X, of necessity it also lowers the activation energy for the reaction X → Y by exactly the same amount (see Figure 2–21). The forward and backward reactions will therefore be accelerated by the same factor by an enzyme, and the equilibrium point for the reaction will be unchanged (Figure 2–23). Thus no matter how much an enzyme speeds up a reaction, it cannot change its direction.


Cell_Biology_Alberts

Cell_Biology_Alberts. Despite the above limitation, enzymes steer all of the reactions in cells through specific reaction paths. This is because enzymes are both highly selective and very precise, usually catalyzing only one particular reaction. In other words, each enzyme selectively lowers the activation energy of only one of the several possible chemical reactions that its bound substrate molecules could undergo. In this way, sets of enzymes can direct each of the many different molecules in a cell along a particular reaction pathway (Figure 2–24). The success of living organisms is attributable to a cell’s ability to make enzymes of many types, each with precisely specified properties. Each enzyme


Cell_Biology_Alberts

Cell_Biology_Alberts. The success of living organisms is attributable to a cell’s ability to make enzymes of many types, each with precisely specified properties. Each enzyme Figure 2–23 enzymes cannot change the equilibrium point for reactions. enzymes, like all catalysts, speed up the forward and backward rates of a reaction by the same factor. Therefore, for both the catalyzed and the uncatalyzed reactions shown here, the number of molecules undergoing the transition X → Y is equal to the number of molecules undergoing the transition Y → X when the ratio of Y molecules to X molecules is 3 to 1. in other words, the two reactions reach equilibrium at exactly the same point.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–22 lowering the activation energy greatly increases the probability of a reaction. at any given instant, a population of identical substrate molecules will have a range of energies, distributed as shown on the graph. The varying energies come from collisions with surrounding molecules, which make the substrate molecules jiggle, vibrate, and spin. for a molecule to undergo a chemical reaction, the energy of the molecule must exceed the activation-energy barrier for that reaction (dashed lines). for most biological reactions, this almost never happens without enzyme catalysis. even with enzyme catalysis, the substrate molecules must experience a particularly energetic collision to react (red shaded area). Raising the temperature will also increase the number of molecules with sufficient energy to overcome the activation energy needed for a reaction; but in marked contrast to enzyme catalysis, this effect is nonselective, speeding up all reactions (Movie 2.2).


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–24 Directing substrate molecules through a specific reaction pathway by enzyme catalysis. a substrate molecule in a cell (green ball) is converted into a different molecule (blue ball) by means of a series of enzyme-catalyzed reactions. as indicated (yellow box), several reactions are energetically favorable at each step, but only one is catalyzed by each enzyme. sets of enzymes thereby determine the exact reaction pathway that is followed by each molecule inside the cell. has a unique shape containing an active site, a pocket or groove in the enzyme into which only particular substrates will fit (Figure 2–25). Like all other catalysts, enzyme molecules themselves remain unchanged after participating in a reaction and therefore can function over and over again. In Chapter 3, we discuss further how enzymes work. how enzymes find Their substrates: The enormous Rapidity of molecular motions


Cell_Biology_Alberts

Cell_Biology_Alberts. how enzymes find Their substrates: The enormous Rapidity of molecular motions An enzyme will often catalyze the reaction of thousands of substrate molecules every second. This means that it must be able to bind a new substrate molecule in a fraction of a millisecond. But both enzymes and their substrates are present in relatively small numbers in a cell. How do they find each other so fast? Rapid binding is possible because the motions caused by heat energy are enormously fast at the molecular level. These molecular motions can be classified broadly into three kinds: (1) the movement of a molecule from one place to another (translational motion), (2) the rapid back-and-forth movement of covalently linked atoms with respect to one another (vibrations), and (3) rotations. All of these motions help to bring the surfaces of interacting molecules together.


Cell_Biology_Alberts

Cell_Biology_Alberts. The rates of molecular motions can be measured by a variety of spectroscopic techniques. A large globular protein is constantly tumbling, rotating about its axis about a million times per second. Molecules are also in constant translational motion, which causes them to explore the space inside the cell very efficiently by wandering through it—a process called diffusion. In this way, every molecule in a cell collides with a huge number of other molecules each second. As the molecules in a liquid collide and bounce off one another, an individual molecule moves first one way and then another, its path constituting a random walk (Figure 2–26). In such a walk, the average net distance that each molecule travels (as the “crow flies”) from its starting point is proportional to the square root of the time involved: that is, if it takes a molecule 1 second on average to travel 1 μm, it takes 4 seconds to travel 2 μm, 100 seconds to travel 10 μm, and so on.


Cell_Biology_Alberts

Cell_Biology_Alberts. The inside of a cell is very crowded (Figure 2–27). Nevertheless, experiments in which fluorescent dyes and other labeled molecules are injected into cells show that small organic molecules diffuse through the watery gel of the cytosol nearly Figure 2–25 How enzymes work. each enzyme has an active site to which one or more substrate molecules bind, forming an enzyme–substrate complex. a reaction occurs at the active site, producing an enzyme–product complex. The product is then released, allowing the enzyme to bind further substrate molecules. as rapidly as they do through water. A small organic molecule, for example, takes only about one-fifth of a second on average to diffuse a distance of 10 μm. Diffusion is therefore an efficient way for small molecules to move the limited distances in the cell (a typical animal cell is 15 μm in diameter).


Cell_Biology_Alberts

Cell_Biology_Alberts. Since enzymes move more slowly than substrates in cells, we can think of them as sitting still. The rate of encounter of each enzyme molecule with its substrate will depend on the concentration of the substrate molecule. For example, some abundant substrates are present at a concentration of 0.5 mM. Since pure water is 55.5 M, there is only about one such substrate molecule in the cell for every 105 water molecules. Nevertheless, the active site on an enzyme molecule that binds this substrate will be bombarded by about 500,000 random collisions with the substrate molecule per second. (For a substrate concentration tenfold lower, the number of collisions drops to 50,000 per second, and so on.) A random collision between the active site of an enzyme and the matching surface of its substrate molecule often leads immediately to the formation of an enzyme–substrate complex. A reaction in which a covalent bond is broken or formed can now occur extremely rapidly. When one appreciates how


Cell_Biology_Alberts

Cell_Biology_Alberts. molecule often leads immediately to the formation of an enzyme–substrate complex. A reaction in which a covalent bond is broken or formed can now occur extremely rapidly. When one appreciates how quickly molecules move and react, the observed rates of enzymatic catalysis do not seem so amazing.


Cell_Biology_Alberts

Cell_Biology_Alberts. Two molecules that are held together by noncovalent bonds can also dissociate. The multiple weak noncovalent bonds that they form with each other will persist until random thermal motion causes the two molecules to separate. In general, the stronger the binding of the enzyme and substrate, the slower their rate of dissociation. In contrast, whenever two colliding molecules have poorly matching surfaces, they form few noncovalent bonds and the total energy of association will be negligible compared with that of thermal motion. In this case, the two molecules dissociate as rapidly as they come together, preventing incorrect and unwanted associations between mismatched molecules, such as between an enzyme and the wrong substrate. The free-energy Change for a Reaction, ∆G, Determines Whether it Can occur spontaneously


Cell_Biology_Alberts

Cell_Biology_Alberts. The free-energy Change for a Reaction, ∆G, Determines Whether it Can occur spontaneously Although enzymes speed up reactions, they cannot by themselves force energetically unfavorable reactions to occur. In terms of a water analogy, enzymes by themselves cannot make water run uphill. Cells, however, must do just that in order to grow and divide: they must build highly ordered and energy-rich molecules from small and simple ones. We shall see that this is done through enzymes that directly couple energetically favorable reactions, which release energy and produce heat, to energetically unfavorable reactions, which produce biological order.


Cell_Biology_Alberts

Cell_Biology_Alberts. What do cell biologists mean by the term “energetically favorable,” and how can this be quantified? According to the second law of thermodynamics the universe tends toward maximum disorder (largest entropy or greatest probability). Thus, a chemical reaction can proceed spontaneously only if it results in a net increase in the disorder of the universe (see Figure 2–16). This disorder of the universe can be expressed most conveniently in terms of the free energy of a system, a concept we touched on earlier. Free energy, G, is an expression of the energy available to do work—for example, the work of driving chemical reactions. The value of G is of interest only when a system undergoes a change, denoted ∆G (delta G). The change in G is critical because, as explained in Panel 2–7 (pp. 102–103), ∆G is a direct measure of the


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–27 The structure of the cytoplasm. The drawing is approximately to scale and emphasizes the crowding in the cytoplasm. only the macromolecules are shown: Rnas are shown in blue, ribosomes in green, and proteins in red. enzymes and other macromolecules diffuse relatively slowly in the cytoplasm, in part because they interact with many other macromolecules; small molecules, by contrast, diffuse nearly as rapidly as they do in water (Movie 2.4). (adapted from D.s. Goodsell, Trends Biochem. Sci. 16:203–206, 1991. With permission from elsevier.) Figure 2–26 a random walk. molecules in solution move in a random fashion as a result of the continual buffeting they receive in collisions with other molecules. This movement allows small molecules to diffuse rapidly from one part of the cell to another, as described in the text (Movie 2.3).


Cell_Biology_Alberts

Cell_Biology_Alberts. amount of disorder created in the universe when a reaction takes place. Energetically favorable reactions, by definition, are those that decrease free energy; in other words, they have a negative ∆G and disorder the universe (Figure 2–28). An example of an energetically favorable reaction on a macroscopic scale is the “reaction” by which a compressed spring relaxes to an expanded state, releasing its stored elastic energy as heat to its surroundings; an example on a microscopic scale is salt dissolving in water. Conversely, energetically unfavorable reactions with a positive ∆G—such as the joining of two amino acids to form a peptide bond—by themselves create order in the universe. Therefore, these reactions can take place only if they are coupled to a second reaction with a negative ∆G so large that the ∆G of the overall process is negative (Figure 2–29). The Concentration of Reactants influences the free-energy Change and a Reaction’s Direction


Cell_Biology_Alberts

Cell_Biology_Alberts. The Concentration of Reactants influences the free-energy Change and a Reaction’s Direction As we have just described, a reaction Y ↔ X will go in the direction Y →X when the associated free-energy change, ∆G, is negative, just as a tensed spring left to itself will relax and lose its stored energy to its surroundings as heat. For a chemical reaction, however, ∆G depends not only on the energy stored in each individual molecule, but also on the concentrations of the molecules in the reaction mixture. Remember that ∆G reflects the degree to which a reaction creates a more disordered—in other words, a more probable—state of the universe. Recalling our coin analogy, it is very likely that a coin will flip from a head to a tail orientation if a jiggling box contains 90 heads and 10 tails, but this is a less probable event if the box has 10 heads and 90 tails.


Cell_Biology_Alberts

Cell_Biology_Alberts. The same is true for a chemical reaction. For a reversible reaction Y ↔ X, a large excess of Y over X will tend to drive the reaction in the direction Y → X. Therefore, as the ratio of Y to X increases, the ∆G becomes more negative for the transition Y → X (and more positive for the transition X → Y). The amount of concentration difference that is needed to compensate for a given decrease in chemical-bond energy (and accompanying heat release) is not intuitively obvious. In the late nineteenth century, the relationship was determined through a thermodynamic analysis that makes it possible to separate the concentration-dependent and the concentration-independent parts of the free-energy change, as we describe next. The standard free-energy Change, ∆G°, makes it possible to Compare the energetics of Different Reactions


Cell_Biology_Alberts

Cell_Biology_Alberts. The standard free-energy Change, ∆G°, makes it possible to Compare the energetics of Different Reactions Because ∆G depends on the concentrations of the molecules in the reaction mixture at any given time, it is not a particularly useful value for comparing the relative energies of different types of reactions. To place reactions on a comparable basis, we need to turn to the standard free-energy change of a reaction, ∆G°. The ∆G° is the change in free energy under a standard condition, defined as that where the concentrations of all the reactants are set to the same fixed value of 1 mole/liter. Defined in this way, ∆G° depends only on the intrinsic characters of the reacting molecules.


Cell_Biology_Alberts

Cell_Biology_Alberts. For the simple reaction Y → X at 37°C, ∆G° is related to ∆G as follows: where ∆G is in kilojoules per mole, [Y] and [X] denote the concentrations of Y and X in moles/liter, ln is the natural logarithm, and RT is the product of the gas constant, R, and the absolute temperature, T. At 37°C, RT = 2.58 J mole–1. (A mole is 6 × 1023 molecules of a substance.) A large body of thermodynamic data has been collected that has made it possible to determine the standard free-energy change, ∆G°, for the important metabolic reactions of a cell. Given these ∆G° values, combined with additional information about metabolite concentrations and reaction pathways, it is possible to quantitatively predict the course of most biological reactions. The free energy of Y is greater than the free energy of X. Therefore ˜G < 0, and the disorderENERGETICALLY of the universe increasesFAVORABLE during the reactionREACTION Y X. If the reaction X Y occurred, ˜G would be > 0, and theENERGETICALLY universe would


Cell_Biology_Alberts

Cell_Biology_Alberts. X. If the reaction X Y occurred, ˜G would be > 0, and theENERGETICALLY universe would REACTION ordered. this reaction can occur only if it is coupled to a second, energetically favorable reaction Figure 2–28 The distinction between energetically favorable and energetically unfavorable reactions. the energetically unfavorable reaction X Y is driven by the energetically favorable reaction C D, because the net free-energy change for the pair of coupled reactions is less than zero Figure 2–29 How reaction coupling is used to drive energetically unfavorable reactions. FOR THE ENERGETICALLY FAVORABLE REACTION Y °X, Figure 2–30 Chemical equilibrium. When a reaction reaches equilibrium, the forward and backward fluxes of reacting molecules are equal and opposite.


Cell_Biology_Alberts

Cell_Biology_Alberts. FOR THE ENERGETICALLY FAVORABLE REACTION Y °X, Figure 2–30 Chemical equilibrium. When a reaction reaches equilibrium, the forward and backward fluxes of reacting molecules are equal and opposite. when X and Y are at equal concentrations, [Y] = [X], the formation of X is energetically favored. In other words, the ˜G of Y °X is negative and the ˜G of X °Y is positive. But because of thermal bombardments, there will always be some X converting to Y. THUS, FOR EACH INDIVIDUAL MOLECULE, conversion of Y to X will occur often. Conversion of X to Y will occur less often than the transition Y °X, because it requires a more energetic collision. Therefore the ratio of X to Y molecules will increase with time


Cell_Biology_Alberts

Cell_Biology_Alberts. Conversion of X to Y will occur less often than the transition Y °X, because it requires a more energetic collision. Therefore the ratio of X to Y molecules will increase with time EVENTUALLY, there will be a large enough excess of X over Y to just compensate for the slow rate of X °Y, such that the number of Y molecules being converted to X molecules each second is exactly equal to the number of X molecules being converted to Y molecules each second. At this point, the reaction will be at equilibrium. AT EQUILIBRIUM, there is no net change in the ratio of Y to X, and the ˜G for both forward and backward reactions is zero. The equilibrium Constant and ∆G° are Readily Derived from each other


Cell_Biology_Alberts

Cell_Biology_Alberts. The equilibrium Constant and ∆G° are Readily Derived from each other Inspection of the above equation reveals that the ∆G equals the value of ∆G° when the concentrations of Y and X are equal. But as any favorable reaction proceeds, the concentrations of the products will increase as the concentration of the substrates decreases. This change in relative concentrations will cause [X]/[Y] to become increasingly large, making the initially favorable ∆G less and less negative (the logarithm of a number x is positive for x > 1, negative for x < 1, and zero for x =1). Eventually, when ∆G = 0, a chemical equilibrium will be attained; here there is no net change in free energy to drive the reaction in either direction, inasmuch as the concentration effect just balances the push given to the reaction by ∆G°. As a result, the ratio of product to substrate reaches a constant value at chemical equilibrium (Figure 2–30).


Cell_Biology_Alberts

Cell_Biology_Alberts. We can define the equilibrium constant, K, for the reaction Y →X as where [X] is the concentration of the product and [Y] is the concentration of the reactant at equilibrium. Remembering that ∆G = ∆G° + RT ln [X]/[Y], and that ∆G = 0 at equilibrium, we see that At 37°C, where RT = 2.58, the equilibrium equation is therefore: ∆G° = –2.58 ln K


Cell_Biology_Alberts

Cell_Biology_Alberts. At 37°C, where RT = 2.58, the equilibrium equation is therefore: ∆G° = –2.58 ln K Converting this equation from the natural logarithm (ln) to the more commonly used base 10 logarithm (log), we get ∆G° = –5.94 log K The above equation reveals how the equilibrium ratio of X to Y (expressed as the equilibrium constant, K) depends on the intrinsic character of the molecules, (as expressed in the value of ∆G° in kilojoules per mole). Note that for every 5.94 kJ/mole difference in free energy at 37°C, the equilibrium constant changes by a factor of 10 (Table 2–2). Thus, the more energetically favorable a reaction, the more product will accumulate if the reaction proceeds to equilibrium. More generally, for a reaction that has multiple reactants and products, such as A + B → C + D,


Cell_Biology_Alberts

Cell_Biology_Alberts. The concentrations of the two reactants and the two products are multiplied because the rate of the forward reaction depends on the collision of A and B and the rate of the backward reaction depends on the collision of C and D. Thus, at 37°C, ∆G° = –5.94 log where ∆G° is in kilojoules per mole, and [A], [B], [C], and [D] denote the concentrations of the reactants and products in moles/liter. The free-energy Changes of Coupled Reactions are additive We have pointed out that unfavorable reactions can be coupled to favorable ones to drive the unfavorable ones forward (see Figure 2–29). In thermodynamic terms, this is possible because the overall free-energy change for a set of coupled reactions is the sum of the free-energy changes in each of its component steps. Consider, as a simple example, two sequential reactions


Cell_Biology_Alberts

Cell_Biology_Alberts. X →Y and Y →Z whose ∆G° values are +5 and –13 kJ/mole, respectively. If these two reactions occur sequentially, the ∆G° for the coupled reaction will be –8 kJ/mole. This means that, with appropriate conditions, the unfavorable reaction X → Y can be driven by the favorable reaction Y → Z, provided that this second reaction follows the first. For example, several of the reactions in the long pathway that converts sugars into CO2 and H2O have positive ∆G° values. But the pathway nevertheless proceeds because the total ∆G° for the series of sequential reactions has a large negative value. Forming a sequential pathway is not adequate for many purposes. Often the desired pathway is simply X → Y, without further conversion of Y to some other product. Fortunately, there are other more general ways of using enzymes to couple reactions together. These often involve the activated carrier molecules that we discuss next. activated Carrier molecules are essential for Biosynthesis


Cell_Biology_Alberts

Cell_Biology_Alberts. activated Carrier molecules are essential for Biosynthesis The energy released by the oxidation of food molecules must be stored temporarily before it can be channeled into the construction of the many other molecules needed by the cell. In most cases, the energy is stored as chemical-bond energy in a small set of activated “carrier molecules,” which contain one or more energy-rich covalent bonds. These molecules diffuse rapidly throughout the cell and thereby carry their bond energy from sites of energy generation to the sites where the energy will be used for biosynthesis and other cell activities (Figure 2–31).


Cell_Biology_Alberts

Cell_Biology_Alberts. The activated carriers store energy in an easily exchangeable form, either as a readily transferable chemical group or as electrons held at a high energy level, and they can serve a dual role as a source of both energy and chemical groups in biosynthetic reactions. For historical reasons, these molecules are also sometimes referred to as coenzymes. The most important of the activated carrier molecules are ATP and two molecules that are closely related to each other, NADH and NADPH. Cells use such activated carrier molecules like money to pay for reactions that otherwise could not take place. The formation of an activated Carrier is Coupled to an energetically favorable Reaction


Cell_Biology_Alberts

Cell_Biology_Alberts. Coupling mechanisms require enzymes and are fundamental to all the energy transactions of the cell. The nature of a coupled reaction is illustrated by a mechanical analogy in Figure 2–32, in which an energetically favorable chemical reaction is represented by rocks falling from a cliff. The energy of falling rocks would normally be entirely wasted in the form of heat generated by friction when the rocks hit the ground (see the falling-brick diagram in Figure 2–17). By careful design, however, part of this energy could be used instead to drive a paddle wheel that lifts a bucket of water (Figure 2–32B). Because the rocks can now reach the ground only after moving the paddle wheel, we say that the energetically favorable reaction of rock falling has been directly coupled to the energetically unfavorable reaction of lifting the bucket of water. Note that because part of the energy is used to do work in Figure 2–32B, the rocks hit the ground with less velocity than in Figure 2–32A, and


Cell_Biology_Alberts

Cell_Biology_Alberts. unfavorable reaction of lifting the bucket of water. Note that because part of the energy is used to do work in Figure 2–32B, the rocks hit the ground with less velocity than in Figure 2–32A, and correspondingly less energy is dissipated as heat.


Cell_Biology_Alberts

Cell_Biology_Alberts. Similar processes occur in cells, where enzymes play the role of the paddle wheel. By mechanisms that we discuss later in this chapter, enzymes couple an Figure 2–31 energy transfer and the role of activated carriers in metabolism. By serving as energy shuttles, activated carrier molecules perform their function as go-betweens that link the breakdown of food molecules and the release of energy (catabolism) to the energy-requiring biosynthesis of small and large organic molecules (anabolism).


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–32 a mechanical model illustrating the principle of coupled chemical reactions. The spontaneous reaction shown in (a) could serve as an analogy for the direct oxidation of glucose to Co2 and h2o, which produces heat only. in (B), the same reaction is coupled to a second reaction; this second reaction is analogous to the synthesis of activated carrier molecules. The energy produced in (B) is in a more useful form than in (a) and can be used to drive a variety of otherwise energetically unfavorable reactions (C).


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Cell_Biology_Alberts. energetically favorable reaction, such as the oxidation of foodstuffs, to an energetically unfavorable reaction, such as the generation of an activated carrier molecule. In this example, the amount of heat released by the oxidation reaction is reduced by exactly the amount of energy stored in the energy-rich covalent bonds of the activated carrier molecule. And the activated carrier molecule picks up a packet of energy of a size sufficient to power a chemical reaction elsewhere in the cell. aTp is the most Widely Used activated Carrier molecule


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Cell_Biology_Alberts. aTp is the most Widely Used activated Carrier molecule The most important and versatile of the activated carriers in cells is ATP (adenosine triphosphate). Just as the energy stored in the raised bucket of water in Figure 2–32B can drive a wide variety of hydraulic machines, ATP is a convenient and versatile store, or currency, of energy used to drive a variety of chemical reactions in cells. ATP is synthesized in an energetically unfavorable phosphorylation reaction in which a phosphate group is added to ADP (adenosine diphosphate). When required, ATP gives up its energy packet through its energetically favorable hydrolysis to ADP and inorganic phosphate (Figure 2–33). The regenerated ADP is then available to be used for another round of the phosphorylation reaction that forms ATP.


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Cell_Biology_Alberts. The energetically favorable reaction of ATP hydrolysis is coupled to many otherwise unfavorable reactions through which other molecules are synthesized. Many of these coupled reactions involve the transfer of the terminal phosphate in ATP to another molecule, as illustrated by the phosphorylation reaction in Figure 2–34. As the most abundant activated carrier in cells, ATP is the principle energy currency. To give just two examples, it supplies energy for many of the pumps that transport substances into and out of the cell (discussed in Chapter 11), and it powers the molecular motors that enable muscle cells to contract and nerve cells to transport materials from one end of their long axons to another (discussed in Chapter 16). energy stored in aTp is often harnessed to Join Two molecules Together


Cell_Biology_Alberts

Cell_Biology_Alberts. energy stored in aTp is often harnessed to Join Two molecules Together We have previously discussed one way in which an energetically favorable reaction can be coupled to an energetically unfavorable reaction, X → Y, so as to enable it to occur. In that scheme, a second enzyme catalyzes the energetically favorable reaction Y → Z, pulling all of the X to Y in the process. But when the required product is Y and not Z, this mechanism is not useful.


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Cell_Biology_Alberts. Figure 2–33 The hydrolysis of aTP to aDP and inorganic phosphate. The two outermost phosphates in aTp are held to the rest of the molecule by high-energy phosphoanhydride bonds and are readily transferred. as indicated, water can be added to aTp to form aDp and inorganic phosphate (pi). hydrolysis of the terminal phosphate of aTp yields between 46 and 54 kJ/mole of usable energy, depending on the intracellular conditions. The large negative ΔG of this reaction arises from several factors: release of the terminal phosphate group removes an unfavorable repulsion between adjacent negative charges, and the inorganic phosphate ion (pi) released is stabilized by resonance and by favorable hydrogen-bond formation with water.


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Cell_Biology_Alberts. Figure 2–34 an example of a phosphate transfer reaction. Because an energy-rich phosphoanhydride bond in aTp is converted to a phosphoester bond, this reaction is energetically favorable, having a large negative ΔG. Reactions of this type are involved in the synthesis of phospholipids and in the initial steps of reactions that catabolize sugars. A typical biosynthetic reaction is one in which two molecules, A and B, are joined together to produce A–B in the energetically unfavorable condensation reaction There is an indirect pathway that allows A–H and B–OH to form A–B, in which a coupling to ATP hydrolysis makes the reaction go. Here, energy from ATP hydrolysis is first used to convert B–OH to a higher-energy intermediate compound, which then reacts directly with A–H to give A–B. The simplest possible mechanism involves the transfer of a phosphate from ATP to B–OH to make B–O–PO3, in which case the reaction pathway contains only two steps: 1. 2.


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Cell_Biology_Alberts. 2. A–H + B–O–PO3 →A–B + Pi Net result: B–OH + ATP + A–H →A–B + ADP + Pi The condensation reaction, which by itself is energetically unfavorable, is forced to occur by being directly coupled to ATP hydrolysis in an enzyme-catalyzed reaction pathway (Figure 2–35A). A biosynthetic reaction of exactly this type synthesizes the amino acid glutamine (Figure 2–35B). We will see shortly that similar (but more complex) mechanisms are also used to produce nearly all of the large molecules of the cell.


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Cell_Biology_Alberts. Figure 2–35 an example of an energetically unfavorable biosynthetic reaction driven by aTP hydrolysis. (a) schematic illustration of the formation of a–B in the condensation reaction described in the text. (B) The biosynthesis of the common amino acid glutamine from glutamic acid and ammonia. Glutamic acid is first converted to a high-energy phosphorylated intermediate (corresponding to the compound B–o–po3 described in the text), which then reacts with ammonia (corresponding to a–h) to form glutamine. in this example, both steps occur on the surface of the same enzyme, glutamine synthetase. The high-energy bonds are shaded red; here, as elsewhere throughout the book, the symbol pi = hpo42–, and a yellow “circled p” = po3 . naDh and naDph are important electron Carriers


Cell_Biology_Alberts

Cell_Biology_Alberts. naDh and naDph are important electron Carriers Other important activated carrier molecules participate in oxidation–reduction reactions and are commonly part of coupled reactions in cells. These activated carriers are specialized to carry electrons held at a high energy level (sometimes called “high-energy” electrons) and hydrogen atoms. The most important of these electron carriers are NAD+ (nicotinamide adenine dinucleotide) and the closely related molecule NADP+ (nicotinamide adenine dinucleotide phosphate). Each picks up a “packet of energy” corresponding to two electrons plus a proton (H+), and they are thereby converted to NADH (reduced nicotinamide adenine dinucleotide) and NADPH (reduced nicotinamide adenine dinucleotide phosphate), respectively (Figure 2–36). These molecules can therefore be regarded as carriers of hydride ions (the H+ plus two electrons, or H–).


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Cell_Biology_Alberts. Like ATP, NADPH is an activated carrier that participates in many important biosynthetic reactions that would otherwise be energetically unfavorable. The NADPH is produced according to the general scheme shown in Figure 2–36A. During a special set of energy-yielding catabolic reactions, two hydrogen atoms are removed from a substrate molecule. Both electrons but just one proton (that is, a hydride ion, H–) are added to the nicotinamide ring of NADP+ to form NADPH; the second proton (H+) is released into solution. This is a typical oxidation–reduction reaction, in which the substrate is oxidized and NADP+ is reduced. NADPH readily gives up the hydride ion it carries in a subsequent oxidation–reduction reaction, because the nicotinamide ring can achieve a more stable arrangement of electrons without it. In this subsequent reaction, which Figure 2–36 NaDPH, an important carrier of electrons.


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Cell_Biology_Alberts. Figure 2–36 NaDPH, an important carrier of electrons. HC (a) naDph is produced in reactions of the general type shown on the left, in which two hydrogen atoms are removed from a substrate. The oxidized form of the carrier molecule, naDp+, receives one hydrogen atom plus an electron (a hydride ion); the proton (h+) from the other h atom is released into solution. Because naDph holds its hydride ion in a high-energy linkage, the hydride ion can easily be transferred to other molecules, as shown on the right. (B) and (C) The structures of naDp+ and naDph. The part of the naDp+ molecule known as the nicotinamide ring accepts the hydride ion, h–, forming naDph. The molecules naD+ and naDh are identical in structure to naDp+ and naDph, respectively, except that they lack the indicated phosphate group.


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Cell_Biology_Alberts. this phosphate group is missing in NAD+ and NADH regenerates NADP+, it is the NADPH that is oxidized and the substrate that is reduced. The NADPH is an effective donor of its hydride ion to other molecules for the same reason that ATP readily transfers a phosphate: in both cases the transfer is accompanied by a large negative free-energy change. One example of the use of NADPH in biosynthesis is shown in Figure 2–37. The extra phosphate group on NADPH has no effect on the electron-transfer properties of NADPH compared with NADH, being far away from the region involved in electron transfer (see Figure 2–36C). It does, however, give a molecule of NADPH a slightly different shape from that of NADH, making it possible for NADPH and NADH to bind as substrates to completely different sets of enzymes. Thus, the two types of carriers are used to transfer electrons (or hydride ions) between two different sets of molecules.


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Cell_Biology_Alberts. Why should there be this division of labor? The answer lies in the need to regulate two sets of electron-transfer reactions independently. NADPH operates chiefly with enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological molecules. NADH, by contrast, has a special role as an intermediate in the catabolic system of reactions that generate ATP through the oxidation of food molecules, as we will discuss shortly. The genesis of NADH from NAD+, and of NADPH from NADP+, occur by different pathways and are independently regulated, so that the cell can adjust the supply of electrons for these two contrasting purposes. Inside the cell the ratio of NAD+ to NADH is kept high, whereas the ratio of NADP+ to NADPH is kept low. This provides plenty of NAD+ to act as an oxidizing agent and plenty of NADPH to act as a reducing agent (Figure 2–37B)—as required for their special roles in catabolism and anabolism, respectively.


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Cell_Biology_Alberts. There are many other activated Carrier molecules in Cells Other activated carriers also pick up and carry a chemical group in an easily transferred, high-energy linkage. For example, coenzyme A carries a readily transferable Figure 2–37 NaDPH as a reducing agent. (a) The final stage in the biosynthetic route leading to cholesterol. as in many other biosynthetic reactions, the reduction of the C=C bond is achieved by the transfer of a hydride ion from the carrier molecule naDph, plus a proton (h+) from the solution. (B) Keeping naDph levels high and naDh levels low alters their affinities for electrons (see panel 14–1, p. 765). This causes naDph to be a much stronger electron donor (reducing agent) than naDh, and naD+ therefore to be a much better electron acceptor (oxidizing agent) than naDp+, as indicated.


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Cell_Biology_Alberts. acetyl group in a thioester linkage, and in this activated form is known as acetyl CoA (acetyl coenzyme A). Acetyl CoA (Figure 2–38) is used to add two carbon units in the biosynthesis of larger molecules.


Cell_Biology_Alberts

Cell_Biology_Alberts. In acetyl CoA, as in other carrier molecules, the transferable group makes up only a small part of the molecule. The rest consists of a large organic portion that serves as a convenient “handle,” facilitating the recognition of the carrier molecule by specific enzymes. As with acetyl CoA, this handle portion very often contains a nucleotide (usually adenosine), a curious fact that may be a relic from an early stage of evolution. It is currently thought that the main catalysts for early life-forms—before DNA or proteins—were RNA molecules (or their close relatives), as described in Chapter 6. It is tempting to speculate that many of the carrier molecules that we find today originated in this earlier RNA world, where their nucleotide portions could have been useful for binding them to RNA enzymes (ribozymes).


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Cell_Biology_Alberts. Thus, ATP transfers phosphate, NADPH transfers electrons and hydrogen, and acetyl CoA transfers two-carbon acetyl groups. FADH2 (reduced flavin adenine dinucleotide) is used like NADH in electron and proton transfers (Figure 2–39). The reactions of other activated carrier molecules involve the transfer of a methyl, carboxyl, or glucose group for biosyntheses (Table 2–3). These activated carriers Figure 2–38 The structure of the important activated carrier molecule acetyl Coa. a ball-and-stick model is shown above the structure. The sulfur atom (yellow) forms a thioester bond to acetate. Because this is a high-energy linkage, releasing a large amount of free energy when it is hydrolyzed, the acetate molecule can be readily transferred to other molecules. Figure 2–39 FaDH2 is a carrier of hydrogens and high-energy electrons, like NaDH and NaDPH. (a) structure of faDh2, with its hydrogen-carrying atoms highlighted in yellow. (B) The formation of faDh2 from faD.


Cell_Biology_Alberts

Cell_Biology_Alberts. are generated in reactions that are coupled to ATP hydrolysis, as in the example in Figure 2–40. Therefore, the energy that enables their groups to be used for biosynthesis ultimately comes from the catabolic reactions that generate ATP. Similar processes occur in the synthesis of the very large molecules of the cell—the nucleic acids, proteins, and polysaccharides—that we discuss next. The synthesis of Biological polymers is Driven by aTp hydrolysis


Cell_Biology_Alberts

Cell_Biology_Alberts. The synthesis of Biological polymers is Driven by aTp hydrolysis As discussed previously, the macromolecules of the cell constitute most of its dry mass (see Figure 2–7). These molecules are made from subunits (or monomers) that are linked together in a condensation reaction, in which the constituents of a water molecule (OH plus H) are removed from the two reactants. Consequently, the reverse reaction—the breakdown of all three types of polymers—occurs by the enzyme-catalyzed addition of water (hydrolysis). This hydrolysis reaction is energetically favorable, whereas the biosynthetic reactions require an energy input (see Figure 2–9).


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Cell_Biology_Alberts. The nucleic acids (DNA and RNA), proteins, and polysaccharides are all polymers that are produced by the repeated addition of a monomer onto one end of a growing chain. The synthesis reactions for these three types of macromolecules are outlined in Figure 2–41. As indicated, the condensation step in each case depends on energy from nucleoside triphosphate hydrolysis. And yet, except for the nucleic acids, there are no phosphate groups left in the final product molecules. How are the reactions that release the energy of ATP hydrolysis coupled to polymer synthesis? For each type of macromolecule, an enzyme-catalyzed pathway exists which resembles that discussed previously for the synthesis of the amino acid glutamine (see Figure 2–35). The principle is exactly the same, in that the –OH group that will


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–40 a carboxyl group-transfer reaction using an activated carrier molecule. Carboxylated biotin is used by the enzyme pyruvate carboxylase to transfer a carboxyl group in the production of oxaloacetate, a molecule needed for the citric acid cycle. The acceptor molecule for this group-transfer reaction is pyruvate. other enzymes use biotin, a B-complex vitamin, to transfer carboxyl groups to other acceptor molecules. note that synthesis of carboxylated biotin requires energy that is derived from aTp—a general feature of many activated carriers.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 2–41 The synthesis of polysaccharides, proteins, and nucleic acids. synthesis of each kind of biological polymer involves the loss of water in a condensation reaction. not shown is the consumption of high-energy nucleoside triphosphates that is required to activate each monomer before its addition. in contrast, the reverse reaction—the breakdown CH2OHOHOOHOHCH2OHOHOOHOHCH2OHOOHOHOOCH2OHOOHOHCH2OHOOHOHOOCH2OHOOHOHOHOOH(A)POLYSACCHARIDESglucoseglycogenglycogenH2O energy from nucleoside triphosphate hydrolysis HCROCNHHCRCOOHHHRHCCNOOHHCROCNHHCRCRHCCNOOHHOprotein amino acid (C) PROTEINS A OCH2OHOOOO_POC OCH2OHOHOHOPOG OOHOHCH2O_A OCH2OHOOOO_POC OCH2OHOOPOG OOHOHCH2O_H2O (B) NUCLEIC ACIDS RNA nucleotide H2O energy from nucleoside triphosphate hydrolysis energy from nucleoside triphosphate hydrolysis RNA protein of all three types of polymers—occurs by the simple addition of water (hydrolysis).


Cell_Biology_Alberts

Cell_Biology_Alberts. be removed in the condensation reaction is first activated by becoming involved in a high-energy linkage to a second molecule. However, the actual mechanisms used to link ATP hydrolysis to the synthesis of proteins and polysaccharides are more complex than that used for glutamine synthesis, since a series of high-energy intermediates is required to generate the final high-energy bond that is broken during the condensation step (discussed in Chapter 6 for protein synthesis).


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Cell_Biology_Alberts. Each activated carrier has limits in its ability to drive a biosynthetic reaction. The ∆G for the hydrolysis of ATP to ADP and inorganic phosphate (Pi) depends on the concentrations of all of the reactants, but under the usual conditions in a cell it is between –46 and –54 kJ/mole. In principle, this hydrolysis reaction could drive an unfavorable reaction with a ∆G of, perhaps, +40 kJ/mole, provided that a suitable reaction path is available. For some biosynthetic reactions, however, even –50 kJ/mole does not provide enough of a driving force. In these cases, the path of ATP hydrolysis can be altered so that it initially produces AMP and pyrophosphate (PPi), which is itself then hydrolyzed in a subsequent step (Figure 2–42). The whole process makes available a total free-energy change of about –100 kJ/ mole. An important type of biosynthetic reaction that is driven in this way is the synthesis of nucleic acids (polynucleotides) from nucleoside triphosphates, as illustrated on the


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Cell_Biology_Alberts. of about –100 kJ/ mole. An important type of biosynthetic reaction that is driven in this way is the synthesis of nucleic acids (polynucleotides) from nucleoside triphosphates, as illustrated on the right side of Figure 2–43.


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Cell_Biology_Alberts. Note that the repetitive condensation reactions that produce macromolecules can be oriented in one of two ways, giving rise to either the head polymerization or the tail polymerization of monomers. In so-called head polymerization, the reactive bond required for the condensation reaction is carried on the end of the Figure 2–43 Synthesis of a polynucleotide, RNa or DNa, is a multistep process driven by aTP hydrolysis. in the first step, a nucleoside monophosphate is activated by the sequential transfer of the terminal phosphate groups from two aTp molecules. The high-energy intermediate formed—a nucleoside triphosphate—exists free in solution until it reacts with the growing end of an Rna or a Dna chain with release of pyrophosphate. hydrolysis of the latter to inorganic phosphate is highly favorable and helps to drive the overall reaction in the direction of polynucleotide synthesis. for details, see Chapter 5.


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Cell_Biology_Alberts. Figure 2–42 an alternative pathway of aTP hydrolysis, in which pyrophosphate is first formed and then hydrolyzed. This route releases about twice as much free energy (approximately –100 kJ/mole) as the reaction shown earlier in figure 2–33, and it forms amp instead of aDp. (a) in the two successive hydrolysis reactions, oxygen atoms from the participating water molecules are retained in the products, as indicated, whereas the hydrogen atoms dissociate to form free hydrogen ions (h+, not shown). (B) summary of overall reaction. HEAD POLYMERIZATION (e.g., PROTEINS, FATTY ACIDS) TAIL POLYMERIZATION (e.g., DNA, RNA, POLYSACCHARIDES) growing polymer, and it must therefore be regenerated each time that a monomer is added. In this case, each monomer brings with it the reactive bond that will be used in adding the next monomer in the series. In tail polymerization, the reactive bond carried by each monomer is instead used immediately for its own addition (Figure 2–44).


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Cell_Biology_Alberts. We shall see in later chapters that both of these types of polymerization are used. The synthesis of polynucleotides and some simple polysaccharides occurs by tail polymerization, for example, whereas the synthesis of proteins occurs by a head polymerization process.


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Cell_Biology_Alberts. Living cells need to create and maintain order within themselves to survive and grow. This is thermodynamically possible only because of a continual input of energy, part of which must be released from the cells to their environment as heat that disorders the surroundings. The only chemical reactions possible are those that increase the total amount of disorder in the universe. The free-energy change for a reaction, ∆G, measures this disorder, and it must be less than zero for a reaction to proceed spontaneously. This ∆G depends both on the intrinsic properties of the reacting molecules and their concentrations, and it can be calculated from these concentrations if either the equilibrium constant (K) for the reaction or its standard free-energy change, ∆G°, is known.


Cell_Biology_Alberts

Cell_Biology_Alberts. The energy needed for life comes ultimately from the electromagnetic radiation of the sun, which drives the formation of organic molecules in photosynthetic organisms such as green plants. Animals obtain their energy by eating organic molecules and oxidizing them in a series of enzyme-catalyzed reactions that are coupled to the formation of ATP—a common currency of energy in all cells.


Cell_Biology_Alberts

Cell_Biology_Alberts. To make possible the continual generation of order in cells, energetically favorable reactions, such as the hydrolysis of ATP, are coupled to energetically unfavorable reactions. In the biosynthesis of macromolecules, ATP is used to form reactive phosphorylated intermediates. Because the energetically unfavorable reaction of biosynthesis now becomes energetically favorable, ATP hydrolysis is said to drive the reaction. Polymeric molecules such as proteins, nucleic acids, and polysaccharides are assembled from small activated precursor molecules by repetitive condensation reactions that are driven in this way. Other reactive molecules, called either activated carriers or coenzymes, transfer other chemical groups in the course of biosynthesis: NADPH transfers hydrogen as a proton plus two electrons (a hydride ion), for example, whereas acetyl CoA transfers an acetyl group.


Cell_Biology_Alberts

Cell_Biology_Alberts. The constant supply of energy that cells need to generate and maintain the biological order that keeps them alive comes from the chemical-bond energy in food molecules. The proteins, lipids, and polysaccharides that make up most of the food we eat must be broken down into smaller molecules before our cells can use them—either Figure 2–44 The orientation of the active intermediates in the repetitive condensation reactions that form biological polymers. The head growth of polymers is compared with its alternative, tail growth. as indicated, these two mechanisms are used to produce different types of biological macromolecules.


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Cell_Biology_Alberts. as a source of energy or as building blocks for other molecules. Enzymatic digestion breaks down the large polymeric molecules in food into their monomer subunits—proteins into amino acids, polysaccharides into sugars, and fats into fatty acids and glycerol. After digestion, the small organic molecules derived from food enter the cytosol of cells, where their gradual oxidation begins. Sugars are particularly important fuel molecules, and they are oxidized in small controlled steps to carbon dioxide (CO2) and water (Figure 2–45). In this section, we trace the major steps in the breakdown, or catabolism, of sugars and show how they produce ATP, NADH, and other activated carrier molecules in animal cells. A very similar pathway also operates in plants, fungi, and many bacteria. As we shall see, the oxidation of fatty acids is equally important for cells. Other molecules, such as proteins, can also serve as energy sources when they are funneled through appropriate enzymatic pathways.


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Cell_Biology_Alberts. Glycolysis is a Central aTp-producing pathway The major process for oxidizing sugars is the sequence of reactions known as glycolysis—from the Greek glukus, “sweet,” and lusis, “rupture.” Glycolysis produces ATP without the involvement of molecular oxygen (O2 gas). It occurs in the cytosol of most cells, including many anaerobic microorganisms. Glycolysis probably evolved early in the history of life, before photosynthetic organisms introduced oxygen into the atmosphere. During glycolysis, a glucose molecule with six carbon atoms is converted into two molecules of pyruvate, each of which contains three carbon atoms. For each glucose molecule, two molecules of ATP are hydrolyzed to provide energy to drive the early steps, but four molecules of ATP are produced in the later steps. At the end of glycolysis, there is consequently a net gain of two molecules of ATP for each glucose molecule broken down. Two molecules of the activated carrier NADH are also produced.


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Cell_Biology_Alberts. The glycolytic pathway is outlined in Figure 2–46 and shown in more detail in Panel 2–8 (pp. 104–105) and Movie 2.5. Glycolysis involves a sequence of 10 separate reactions, each producing a different sugar intermediate and each catalyzed by a different enzyme. Like most enzymes, these have names ending in ase—such as isomerase and dehydrogenase—to indicate the type of reaction they catalyze. Although no molecular oxygen is used in glycolysis, oxidation occurs, in that electrons are removed by NAD+ (producing NADH) from some of the carbons derived from the glucose molecule. The stepwise nature of the process releases the energy of oxidation in small packets, so that much of it can be stored in activated carrier molecules rather than all of it being released as heat (see Figure 2–45). Thus, some of the energy released by oxidation drives the direct synthesis of ATP molecules from ADP and Pi, and some remains with the electrons in the electron carrier NADH.


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Cell_Biology_Alberts. Figure 2–45 Schematic representation of the controlled stepwise oxidation of sugar in a cell, compared with ordinary burning. (a) if the sugar were oxidized to Co2 and h2o in a single step, it would release an amount of energy much larger than could be captured for useful purposes. (B) in the cell, enzymes catalyze oxidation via a series of small steps in which free energy is transferred in conveniently sized packets to carrier molecules—most often aTp and naDh. at each step, an enzyme controls the reaction by reducing the activation-energy barrier that has to be surmounted before the specific reaction can occur. The total free energy released is exactly the same in (a) and (B). large activation energy overcome by the heat from a fre all free energy is released as heat; none is stored


Cell_Biology_Alberts

Cell_Biology_Alberts. large activation energy overcome by the heat from a fre all free energy is released as heat; none is stored Two molecules of NADH are formed per molecule of glucose in the course of glycolysis. In aerobic organisms, these NADH molecules donate their electrons to the electron-transport chain described in Chapter 14, and the NAD+ formed from the NADH is used again for glycolysis (see step 6 in Panel 2–8, pp. 104–105). fermentations produce aTp in the absence of oxygen For most animal and plant cells, glycolysis is only a prelude to the final stage of the breakdown of food molecules. In these cells, the pyruvate formed by glycolysis is rapidly transported into the mitochondria, where it is converted into CO2 plus acetyl CoA, whose acetyl group is then completely oxidized to CO2 and H2O.


Cell_Biology_Alberts

Cell_Biology_Alberts. In contrast, for many anaerobic organisms—which do not utilize molecular oxygen and can grow and divide without it—glycolysis is the principal source of the cell’s ATP. Certain animal tissues, such as skeletal muscle, can also continue to function when molecular oxygen is limited. In these anaerobic conditions, the pyruvate and the NADH electrons stay in the cytosol. The pyruvate is converted into products excreted from the cell—for example, into ethanol and CO2 in the yeasts used in brewing and breadmaking, or into lactate in muscle. In this process, the NADH gives up its electrons and is converted back into NAD+. This regeneration of NAD+ is required to maintain the reactions of glycolysis (Figure 2–47). Energy-yielding pathways like these, in which organic molecules both donate and accept electrons (and which are often, as in these cases, anaerobic), are called one molecule of glucose


Cell_Biology_Alberts

Cell_Biology_Alberts. Energy-yielding pathways like these, in which organic molecules both donate and accept electrons (and which are often, as in these cases, anaerobic), are called one molecule of glucose OH to be fructose 1,6 six-carbon sugar to two three-carbon sugarsSTEP 5 two molecules of glyceraldehyde Figure 2–46 an outline of glycolysis. each of the 10 steps shown is catalyzed by a different enzyme. note that step 4 cleaves a six-carbon sugar into two three-carbon sugars, so that the number of molecules at every stage after this doubles. as indicated, step 6 begins the energy-generation phase of glycolysis. Because two molecules of aTp are hydrolyzed in the early, energy-investment phase, glycolysis results in the net synthesis of 2 aTp and 2 naDh molecules per molecule of glucose (see also panel 2–8). Figure 2–47 Two pathways for the anaerobic breakdown of pyruvate.


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Cell_Biology_Alberts. Figure 2–47 Two pathways for the anaerobic breakdown of pyruvate. (a) When there is inadequate oxygen, for example, in a muscle cell undergoing vigorous contraction, the pyruvate produced by glycolysis is converted to lactate as shown. This reaction regenerates the naD+ consumed in step 6 of glycolysis, but the whole pathway yields much less energy overall than complete oxidation. (B) in some organisms that can grow anaerobically, such as yeasts, pyruvate is C regeneration C converted via acetaldehyde into carbon dioxide and ethanol. again, this pathway CO HCOH regenerates naD+ from naDh, as required to enable glycolysis to continue. Both (a) and (B) are examples of fermentations.


Cell_Biology_Alberts

Cell_Biology_Alberts. fermentations. Studies of the commercially important fermentations carried out by yeasts inspired much of early biochemistry. Work in the nineteenth century led in 1896 to the then startling recognition that these processes could be studied outside living organisms, in cell extracts. This revolutionary discovery eventually made it possible to dissect out and study each of the individual reactions in the fermentation process. The piecing together of the complete glycolytic pathway in the 1930s was a major triumph of biochemistry, and it was quickly followed by the recognition of the central role of ATP in cell processes. Glycolysis illustrates how enzymes Couple oxidation to energy storage


Cell_Biology_Alberts

Cell_Biology_Alberts. Glycolysis illustrates how enzymes Couple oxidation to energy storage The formation of ATP during glycolysis provides a particularly clear demonstration of how enzymes couple energetically unfavorable reactions with favorable ones, thereby driving the many chemical reactions that make life possible. Two central reactions in glycolysis (steps 6 and 7) convert the three-carbon sugar intermediate glyceraldehyde 3-phosphate (an aldehyde) into 3-phosphoglycerate (a carboxylic acid; see Panel 2–8, pp. 104–105), thus oxidizing an aldehyde group to a carboxylic acid group. The overall reaction releases enough free energy to convert a molecule of ADP to ATP and to transfer two electrons (and a proton) from the aldehyde to NAD+ to form NADH, while still liberating enough heat to the environment to make the overall reaction energetically favorable (∆G° for the overall reaction is –12.5 kJ/mole).


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Cell_Biology_Alberts. Figure 2–48 outlines this remarkable feat of energy harvesting. The chemical reactions are precisely guided by two enzymes to which the sugar intermediates A short-lived covalent bond is formed between glyceraldehyde 3-phosphate and the –SH group of a cysteine side chain of the enzyme glyceraldehyde 3-phosphate dehydrogenase. The enzyme also binds noncovalently to NAD+. Glyceraldehyde 3-phosphate is oxidized as the enzyme removes a hydrogen atom (yellow) and transfers it, along with an electron, to NAD+, forming NADH (see Figure 2–37). Part of the energy + H+ released by the oxidation of the aldehyde is thus stored in NADH, and part is stored in the high- glyceraldehyde 3-phosphate to the CO enzyme. A molecule of inorganic phosphatehigh-energy inorganic displaces the high-energy thioesterphosphate phosphate bond to create 1,3-bisphospho-glycerate, which contains a high-energy phosphate bond. 1,3-bisphosphoglycerate


Cell_Biology_Alberts

Cell_Biology_Alberts. 1,3-bisphosphoglycerate The high-energy phosphate group is transferred to ADP to form ATP. The oxidation of an aldehyde to a carboxylic acid releases energy, much of which is captured in the activated carriers ATP and NADH.


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Cell_Biology_Alberts. The oxidation of an aldehyde to a carboxylic acid releases energy, much of which is captured in the activated carriers ATP and NADH. Figure 2–48 energy storage in steps 6 and 7 of glycolysis. (a) in step 6, the enzyme glyceraldehyde 3-phosphate dehydrogenase couples the energetically favorable oxidation of an aldehyde to the energetically unfavorable formation of a high-energy phosphate bond. at the same time, it enables energy to be stored in naDh. The formation of the high-energy phosphate bond is driven by the oxidation reaction, and the enzyme thereby acts like the “paddle wheel” coupler in figure 2–32B. in step 7, the newly formed high-energy phosphate bond in 1,3-bisphosphoglycerate is transferred to aDp, forming a molecule of aTp and leaving a free carboxylic acid group on the oxidized sugar. The part of the molecule that undergoes a change is shaded in blue; the rest of the molecule remains unchanged throughout all these reactions.


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Cell_Biology_Alberts. (B) summary of the overall chemical change produced by reactions 6 and 7. are tightly bound. As detailed in Figure 2–48, the first enzyme (glyceraldehyde 3-phosphate dehydrogenase) forms a short-lived covalent bond to the aldehyde through a reactive –SH group on the enzyme, and catalyzes its oxidation by NAD+ in this attached state. The reactive enzyme–substrate bond is then displaced by an inorganic phosphate ion to produce a high-energy phosphate intermediate, which is released from the enzyme. This intermediate binds to the second enzyme (phosphoglycerate kinase), which catalyzes the energetically favorable transfer of the high-energy phosphate just created to ADP, forming ATP and completing the process of oxidizing an aldehyde to a carboxylic acid. Note that the C–H bond oxidation energy in step 6 drives the formation of both NADH and a high-energy phosphate bond. The breakage of the high-energy bond then drives ATP formation.


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Cell_Biology_Alberts. We have shown this particular oxidation process in some detail because it provides a clear example of enzyme-mediated energy storage through coupled reactions (Figure 2–49). Steps 6 and 7 are the only reactions in glycolysis that create a high-energy phosphate linkage directly from inorganic phosphate. As such, they account for the net yield of two ATP molecules and two NADH molecules per molecule of glucose (see Panel 2–8, pp. 104–105). As we have just seen, ATP can be formed readily from ADP when a reaction intermediate is formed with a phosphate bond of higher energy than the terminal phosphate bond in ATP. Phosphate bonds can be ordered in energy by comparing the standard free-energy change (∆G°) for the breakage of each bond by hydrolysis. Figure 2–50 compares the high-energy phosphoanhydride bonds in ATP with the energy of some other phosphate bonds, several of which are generated during glycolysis.


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Cell_Biology_Alberts. All organisms need to maintain a high ATP/ADP ratio to maintain biological order in their cells. Yet animals have only periodic access to food, and plants need to survive overnight without sunlight, when they are unable to produce sugar from photosynthesis. For this reason, both plants and animals convert sugars and fats to special forms for storage (Figure 2–51). To compensate for long periods of fasting, animals store fatty acids as fat droplets composed of water-insoluble triacylglycerols (also called triglycerides). The triacylglycerols in animals are mostly stored in the cytoplasm of specialized fat cells called adipocytes. For shorter-term storage, sugar is stored as glucose 1,3-bisphosphoglycerate formation of hydrolysis of high-energy bond high-energy bond TOTAL ENERGY CHANGE for step 6 followed by step 7 is a favorable –12.5 kJ/mole


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Cell_Biology_Alberts. TOTAL ENERGY CHANGE for step 6 followed by step 7 is a favorable –12.5 kJ/mole Figure 2–49 Schematic view of the coupled reactions that form NaDH and aTP in steps 6 and 7 of glycolysis. The C–h bond oxidation energy drives the formation of both naDh and a high-energy phosphate bond. The breakage of the high-energy bond then drives aTp formation. bond to carbon anhydride bond to phosphate type of phosphate bond –61.9 kJ (see Panel 2–8, pp. 104–105) for example, 1,3-bisphosphoglycerate –49.0 kJ (see Panel 2–8) –40 creatine phosphate (activated carrier that –43.0 kJ stores energy in muscle) for example, ATP when hydrolyzed –30.6 kJ to ADP –20 for example, glucose 6-phosphate –17.5 kJ (see Panel 2–8) specifc examples showing the standard free-energy change (˜G°) for hydrolysis of phosphate bond


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Cell_Biology_Alberts. Figure 2–50 Phosphate bonds have different energies. examples of different types of phosphate bonds with their sites of hydrolysis are shown in the molecules depicted on the left. Those starting with a gray carbon atom show only part of a molecule. examples of molecules containing such bonds are given on the right, with the standard free-energy change for hydrolysis in kilojoules. The transfer of a phosphate group from one molecule to another is energetically favorable if the free-energy change (ΔG) for hydrolysis of the phosphate bond of the first molecule is more negative than that for hydrolysis of the phosphate bond in the second. Thus, under standard conditions, a phosphate group is readily transferred from 1,3-bisphosphoglycerate to aDp to form aTp. (standard conditions often do not pertain to living cells, where the relative concentrations of reactants and products will influence the actual change in free energy.) The hydrolysis reaction can be viewed as the transfer of the


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Cell_Biology_Alberts. not pertain to living cells, where the relative concentrations of reactants and products will influence the actual change in free energy.) The hydrolysis reaction can be viewed as the transfer of the phosphate group to water.


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Cell_Biology_Alberts. subunits in the large branched polysaccharide glycogen, which is present as small granules in the cytoplasm of many cells, including liver and muscle. The synthesis and degradation of glycogen are rapidly regulated according to need. When cells need more ATP than they can generate from the food molecules taken in from the bloodstream, they break down glycogen in a reaction that produces glucose 1-phosphate, which is rapidly converted to glucose 6-phosphate for glycolysis (Figure 2–52). Quantitatively, fat is far more important than glycogen as an energy store for animals, presumably because it provides for more efficient storage. The oxidation of a gram of fat releases about twice as much energy as the oxidation of a gram of glycogen. Moreover, glycogen differs from fat in binding a great deal of water, producing a sixfold difference in the actual mass of glycogen required to store the same amount of energy as fat. An average adult human stores enough glycogen


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Cell_Biology_Alberts. Figure 2–51 The storage of sugars and fats in animal and plant cells. (a) The structures of starch and glycogen, the storage form of sugars in plants and animals, respectively. Both are storage polymers of the sugar glucose and differ only in the frequency of branch points. There are many more branches in glycogen than in starch. (B) an electron micrograph of glycogen granules in the cytoplasm of a liver cell. (C) a thin section of a chloroplast from a plant cell, showing the starch granules and lipid (fat droplets) that have accumulated as a result of the biosyntheses occurring there. (D) fat droplets (stained red) beginning to accumulate in developing fat cells of an animal. (B, courtesy of Robert fletterick and Daniel s. friend; C, courtesy of K. plaskitt; D, courtesy of Ronald m. evans and peter Totonoz.) for only about a day of normal activities, but enough fat to last for nearly a month. If our main fuel reservoir had to be carried as glycogen instead of fat, body weight would


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Cell_Biology_Alberts. and peter Totonoz.) for only about a day of normal activities, but enough fat to last for nearly a month. If our main fuel reservoir had to be carried as glycogen instead of fat, body weight would increase by an average of about 60 pounds.


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Cell_Biology_Alberts. The sugar and ATP needed by plant cells are largely produced in separate organelles: sugars in chloroplasts (the organelles specialized for photosynthesis), 2 Figure 2–52 How sugars are produced from glycogen. Glucose subunits are released from glycogen by the enzyme glycogen phosphorylase. This produces glucose 1-phosphate, which is rapidly converted to glucose 6-phosphate for OH glycolysis. Figure 2–53 Some plant seeds that serve as important foods for humans.


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Cell_Biology_Alberts. Corn, nuts, and peas all contain rich stores of starch and fat that provide the young plant embryo in the seed with energy and building blocks for biosynthesis. (Courtesy of the John innes foundation.) and ATP in mitochondria. Although plants produce abundant amounts of both ATP and NADPH in their chloroplasts, this organelle is isolated from the rest of its plant cell by a membrane that is impermeable to both types of activated carrier molecules. Moreover, the plant contains many cells—such as those in the roots— that lack chloroplasts and therefore cannot produce their own sugars. Thus, sugars are exported from chloroplasts to the mitochondria present in all cells of the plant. Most of the ATP needed for general plant cell metabolism is synthesized in these mitochondria, using exactly the same pathways for the oxidative breakdown of sugars as in nonphotosynthetic organisms; this ATP is then passed to the rest of the cell (see Figure 14–42).


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Cell_Biology_Alberts. During periods of excess photosynthetic capacity during the day, chloroplasts convert some of the sugars that they make into fats and into starch, a polymer of glucose analogous to the glycogen of animals. The fats in plants are triacyl-glycerols (triglycerides), just like the fats in animals, and differ only in the types of fatty acids that predominate. Fat and starch are both stored inside the chloroplast until needed for energy-yielding oxidation during periods of darkness (see Figure 2–51C). The embryos inside plant seeds must live on stored sources of energy for a prolonged period, until they germinate and produce leaves that can harvest the energy in sunlight. For this reason plant seeds often contain especially large amounts of fats and starch—which makes them a major food source for animals, including ourselves (Figure 2–53).


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Cell_Biology_Alberts. After a meal, most of the energy that an animal needs is derived from sugars obtained from food. Excess sugars, if any, are used to replenish depleted glycogen stores, or to synthesize fats as a food store. But soon the fat stored in adipose tissue is called into play, and by the morning after an overnight fast, fatty acid oxidation generates most of the ATP we need. Low glucose levels in the blood trigger the breakdown of fats for energy production. As illustrated in Figure 2–54, the triacylglycerols stored in fat droplets in adipocytes are hydrolyzed to produce fatty acids and glycerol, and the fatty acids released are transferred to cells in the body through the bloodstream. While animals readily convert sugars to fats, they cannot convert fatty acids to sugars. Instead, the fatty acids are oxidized directly. sugars and fats are Both Degraded to acetyl Coa in mitochondria


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Cell_Biology_Alberts. sugars and fats are Both Degraded to acetyl Coa in mitochondria In aerobic metabolism, the pyruvate that was produced by glycolysis from sugars in the cytosol is transported into the mitochondria of eukaryotic cells. There, it is rapidly decarboxylated by a giant complex of three enzymes, called the pyruvate dehydrogenase complex. The products of pyruvate decarboxylation are a molecule of CO2 (a waste product), a molecule of NADH, and acetyl CoA (see Panel 2–9). The fatty acids imported from the bloodstream are moved into mitochondria, where all of their oxidation takes place (Figure 2–55). Each molecule of fatty acid (as the activated molecule fatty acyl CoA) is broken down completely by a cycle of reactions that trims two carbons at a time from its carboxyl end, generating one molecule of acetyl CoA for each turn of the cycle. A molecule of NADH and a molecule of FADH2 are also produced in this process (Figure 2–56).


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Cell_Biology_Alberts. Sugars and fats are the major energy sources for most nonphotosynthetic organisms, including humans. However, most of the useful energy that can be extracted from the oxidation of both types of foodstuffs remains stored in the acetyl CoA molecules that are produced by the two types of reactions just described. The citric acid cycle of reactions, in which the acetyl group (–COCH3) in acetyl CoA is oxidized to CO2 and H2O, is therefore central to the energy metabolism of aerobic organisms. In eukaryotes, these reactions all take place in mitochondria. We should therefore not be surprised to discover that the mitochondrion is the place where most of the ATP is produced in animal cells. In contrast, aerobic bacteria carry out all of their reactions, including the citric acid cycle, in a single compartment, the cytosol. The Citric acid Cycle Generates naDh by oxidizing acetyl Groups to Co2


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Cell_Biology_Alberts. The Citric acid Cycle Generates naDh by oxidizing acetyl Groups to Co2 In the nineteenth century, biologists noticed that in the absence of air cells produce lactic acid (for example, in muscle) or ethanol (for example, in yeast), while in its presence they consume O2 and produce CO2 and H2O. Efforts to define the pathways of aerobic metabolism eventually focused on the oxidation of pyruvate and led in 1937 to the discovery of the citric acid cycle, also known as the


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Cell_Biology_Alberts. Figure 2–54 How stored fats are mobilized for energy production in animals. low glucose levels in the blood trigger the hydrolysis of the triacylglycerol molecules in fat droplets to free fatty acids and glycerol. These fatty acids enter the bloodstream, where they bind to the abundant blood protein, serum albumin. special fatty acid transporters in the plasma membrane of cells that oxidize fatty acids, such as muscle cells, then pass these fatty acids into the cytosol, from which they are moved into mitochondria for energy production.


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Cell_Biology_Alberts. Figure 2–55 Pathways for the production of acetyl Coa from sugars and fats. The mitochondrion in eukaryotic cells is where acetyl Coa is produced from both types of major food molecules. it is therefore the place where most of the cell’s oxidation reactions occur and where most of its aTp is made. amino acids (not shown) can also enter the mitochondria, to be converted there into acetyl Coa or another intermediate of the citric acid cycle. The structure and function of mitochondria are discussed in detail in Chapter 14.


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Cell_Biology_Alberts. tricarboxylic acid cycle or the Krebs cycle. The citric acid cycle accounts for about two-thirds of the total oxidation of carbon compounds in most cells, and its major end products are CO2 and high-energy electrons in the form of NADH. The CO2 is released as a waste product, while the high-energy electrons from NADH are passed to a membrane-bound electron-transport chain (discussed in Chapter 14), eventually combining with O2 to produce H2O. The citric acid cycle itself does not use gaseous O2 (it uses oxygen atoms from H2O). But the cycle does require O2 in subsequent reactions to keep it going. This is because there is no other efficient way for the NADH to get rid of its electrons and thus regenerate the NAD+ that is needed.


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Cell_Biology_Alberts. The citric acid cycle takes place inside mitochondria in eukaryotic cells. It results in the complete oxidation of the carbon atoms of the acetyl groups in acetyl CoA, converting them into CO2. But the acetyl group is not oxidized directly. Instead, this group is transferred from acetyl CoA to a larger, four-carbon molecule, oxaloacetate, to form the six-carbon tricarboxylic acid, citric acid, for which the subsequent cycle of reactions is named. The citric acid molecule is then gradually oxidized, allowing the energy of this oxidation to be harnessed to produce energy-rich activated carrier molecules. The chain of eight reactions forms a cycle because at the end the oxaloacetate is regenerated and enters a new turn of the cycle, as shown in outline in Figure 2–57.


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Cell_Biology_Alberts. We have thus far discussed only one of the three types of activated carrier molecules that are produced by the citric acid cycle; NADH, the reduced form of the NAD+/NADH electron carrier system (see Figure 2–36). In addition to three molecules of NADH, each turn of the cycle also produces one molecule of FADH2 (reduced flavin adenine dinucleotide) from FAD (see Figure 2–39), and one molecule of the ribonucleoside triphosphate GTP from GDP. The structure of GTP is illustrated in Figure 2–58. GTP is a close relative of ATP, and the transfer of its terminal phosphate group to ADP produces one ATP molecule in each cycle. As we discuss shortly, the energy that is stored in the readily transferred electrons of NADH and FADH2 will be utilized subsequently for ATP production through the rest of hydrocarbon tail fatty acyl CoA shortened by two carbons


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Cell_Biology_Alberts. Figure 2–56 The oxidation of fatty acids to acetyl Coa. (a) electron micrograph of a lipid droplet in the cytoplasm. (B) The structure of fats. fats are triacylglycerols. The glycerol portion, to which three fatty acids are linked through ester bonds, is shown in blue. fats are insoluble in water and form large lipid droplets in the specialized fat cells (adipocytes) in which they are stored. (C) The fatty acid oxidation cycle. The cycle is catalyzed by a series of four enzymes in mitochondria. each turn of the cycle shortens the fatty acid chain by two carbons (shown in red) and generates one molecule of acetyl Coa and one molecule each of naDh and faDh2. (a, courtesy of Daniel s. friend.)


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Cell_Biology_Alberts. NET RESULT: ONE TURN OF THE CYCLE PRODUCES THREE NADH, ONE GTP, AND ONE FADH2 MOLECULE, AND RELEASES TWO MOLECULES OF CO2 process of oxidative phosphorylation, the only step in the oxidative catabolism of foodstuffs that directly requires gaseous oxygen (O2) from the atmosphere. Panel 2–9 (pp. 106–107) and Movie 2.6 present the complete citric acid cycle. Water, rather than molecular oxygen, supplies the extra oxygen atoms required to make CO2 from the acetyl groups entering the citric acid cycle. As illustrated in the panel, three molecules of water are split in each cycle, and the oxygen atoms of some of them are ultimately used to make CO2.


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Cell_Biology_Alberts. In addition to pyruvate and fatty acids, some amino acids pass from the cytosol into mitochondria, where they are also converted into acetyl CoA or one of the other intermediates of the citric acid cycle. Thus, in the eukaryotic cell, the mitochondrion is the center toward which all energy-yielding processes lead, whether they begin with sugars, fats, or proteins. Both the citric acid cycle and glycolysis also function as starting points for important biosynthetic reactions by producing vital carbon-containing intermediates, such as oxaloacetate and α-ketoglutarate. Some of these substances produced by catabolism are transferred back from the mitochondria to the cytosol, where they serve in anabolic reactions as precursors for the synthesis of many essential molecules, such as amino acids (Figure 2–59). electron Transport Drives the synthesis of the majority of the aTp in most Cells


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Cell_Biology_Alberts. Most chemical energy is released in the last stage in the degradation of a food molecule. In this final process, NADH and FADH2 transfer the electrons that they gained when oxidizing food-derived organic molecules to the electron-transport chain, which is embedded in the inner membrane of the mitochondrion (see Figure 14–10). As the electrons pass along this long chain of specialized electron acceptor and donor molecules, they fall to successively lower energy states. The energy that the electrons release in this process pumps H+ ions (protons) across the membrane—from the innermost mitochondrial compartment (the matrix) to the intermembrane space (and then to the cytosol)—generating a gradient of H+ ions (Figure 2–60). This gradient serves as a major source of energy for cells, being tapped like a battery to drive a variety of energy-requiring reactions. The most prominent of these reactions is the generation of ATP by the phosphorylation of ADP.


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Cell_Biology_Alberts. Figure 2–57 Simple overview of the citric acid cycle. The reaction of acetyl Coa with oxaloacetate starts the cycle by producing citrate (citric acid). in each turn of the cycle, two molecules of Co2 are produced as waste products, plus three molecules of naDh, one molecule of GTp, and one molecule of faDh2. The number of carbon atoms in each intermediate is shown in a yellow box. for details, see panel 2–9 (pp. 106–107). O Figure 2–58 The structure of GTP. GTp and GDp are close relatives of aTp and aDp, respectively.


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Cell_Biology_Alberts. O Figure 2–58 The structure of GTP. GTp and GDp are close relatives of aTp and aDp, respectively. At the end of this series of electron transfers, the electrons are passed to molecules of oxygen gas (O2) that have diffused into the mitochondrion, which simultaneously combine with protons (H+) from the surrounding solution to produce water. The electrons have now reached a low energy level, and all the available energy has been extracted from the oxidized food molecule. This process, termed oxidative phosphorylation (Figure 2–61), also occurs in the plasma membrane of bacteria. As one of the most remarkable achievements of cell evolution, it is a central topic of Chapter 14. In total, the complete oxidation of a molecule of glucose to H2O and CO2 is used by the cell to produce about 30 molecules of ATP. In contrast, only 2 molecules of ATP are produced per molecule of glucose by glycolysis alone. amino acids and nucleotides are part of the nitrogen Cycle


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Cell_Biology_Alberts. amino acids and nucleotides are part of the nitrogen Cycle So far we have concentrated mainly on carbohydrate metabolism and have not yet considered the metabolism of nitrogen or sulfur. These two elements are important constituents of biological macromolecules. Nitrogen and sulfur atoms pass Figure 2–59 Glycolysis and the citric acid cycle provide the precursors needed to synthesize many important biological molecules. The amino acids, nucleotides, lipids, sugars, and other molecules—shown here as products—in turn serve as the precursors for the many macromolecules of the cell. each black arrow in this diagram denotes a single enzyme-catalyzed reaction; the red arrows generally represent pathways with many steps that are required to produce the indicated products. from compound to compound and between organisms and their environment in a series of reversible cycles.


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Cell_Biology_Alberts. from compound to compound and between organisms and their environment in a series of reversible cycles. Although molecular nitrogen is abundant in the Earth’s atmosphere, nitrogen is chemically unreactive as a gas. Only a few living species are able to incorporate it into organic molecules, a process called nitrogen fixation. Nitrogen fixation occurs in certain microorganisms and by some geophysical processes, such as lightning discharge. It is essential to the biosphere as a whole, for without it life could not exist on this planet. Only a small fraction of the nitrogenous compounds in today’s organisms, however, is due to fresh products of nitrogen fixation from the atmosphere. Most organic nitrogen has been in circulation for some time, passing from one living organism to another. Thus, present-day nitrogen-fixing reactions can be said to perform a “topping-up” function for the total nitrogen supply.


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Cell_Biology_Alberts. Vertebrates receive virtually all of their nitrogen from their dietary intake of proteins and nucleic acids. In the body, these macromolecules are broken down to amino acids and the components of nucleotides, and the nitrogen they contain is used to produce new proteins and nucleic acids—or other molecules. About half of the 20 amino acids found in proteins are essential amino acids for vertebrates (Figure 2–62), which means that they cannot be synthesized from other ingredients of the diet. The other amino acids can be so synthesized, using a variety of raw materials, including intermediates of the citric acid cycle. The essential amino acids are made by plants and other organisms, usually by long and energetically expensive pathways that have been lost in the course of vertebrate evolution.


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Cell_Biology_Alberts. The nucleotides needed to make RNA and DNA can be synthesized using specialized biosynthetic pathways. All of the nitrogens in the purine and pyrimidine bases (as well as some of the carbons) are derived from the plentiful amino acids glutamine, aspartic acid, and glycine, whereas the ribose and deoxyribose sugars are derived from glucose. There are no “essential nucleotides” that must be provided in the diet. Amino acids not used in biosynthesis can be oxidized to generate metabolic energy. Most of their carbon and hydrogen atoms eventually form CO2 or H2O, whereas their nitrogen atoms are shuttled through various forms and eventually appear as urea, which is excreted. Each amino acid is processed differently, and a whole constellation of enzymatic reactions exists for their catabolism.


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Cell_Biology_Alberts. Sulfur is abundant on Earth in its most oxidized form, sulfate (SO42–). To be useful for life, sulfate must be reduced to sulfide (S2–), the oxidation state of sulfur required for the synthesis of essential biological molecules, including the amino acids methionine and cysteine, coenzyme A (see Figure 2–39), and the iron-sulfur centers essential for electron transport (see Figure 14–16). The sulfur-reduction process begins in bacteria, fungi, and plants, where a special group of enzymes use ATP and reducing power to create a sulfate assimilation pathway. Humans and other animals cannot reduce sulfate and must therefore acquire the sulfur they need for their metabolism in the food that they eat.


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Cell_Biology_Alberts. Figure 2–60 The generation of an H+ gradient across a membrane by electron-transport reactions. an electron held in a high-energy state (derived, for example, from the oxidation of a metabolite) is passed sequentially by carriers a, B, and C to a lower energy state. in this diagram, carrier B is arranged in the membrane in such a way that it takes up h+ from one side and releases it to the other as the electron passes. The result is an h+ gradient. as discussed in Chapter 14, this gradient is an important form of energy that is harnessed by other membrane proteins to drive the formation of aTp (for an actual example, see figure 14–21).