Chemical Reactions and Physical Processes That Occur Continuously in Living Cells and Organisms

One property of living things above all makes them seem almost miraculously different from nonliving matter: they create and maintain order, in a universe that is tending always to greater disorder (Figure 2-33). To create this order, the cells in a living organism must perform a never-ending stream of chemical reactions. In some of these reactions, small organic molecules—amino acids, sugars, nucleotides, and lipids—are being taken apart or modified to supply the many other small molecules that the cell requires. In other reactions, these small molecules are being used to construct an enormously diverse range of proteins, nucleic acids, and other macromolecules that endow living systems with all of their most distinctive properties. Each cell can be viewed as a tiny chemical factory, performing many millions of reactions every second.

Figure 2-33

Order in biological structures. Well-defined, ornate, and beautiful spatial patterns can be found at every level of organization in living organisms. In order of increasing size: (A) protein molecules in the coat of a virus; (B) the regular array of microtubules (more...)

Cell Metabolism Is Organized by Enzymes

The chemical reactions that a cell carries out would normally occur only at temperatures that are much higher than those existing inside cells. For this reason, each reaction requires a specific boost in chemical reactivity. This requirement is crucial, because it allows each reaction to be controlled by the cell. The control is exerted through the specialized proteins called enzymes, each of which accelerates, or catalyzes, just one of the many possible kinds of reactions that a particular molecule might undergo. Enzyme-catalyzed reactions are usually connected in series, so that the product of one reaction becomes the starting material, or substrate, for the next (Figure 2-34). These long linear reaction pathways are in turn linked to one another, forming a maze of interconnected reactions that enable the cell to survive, grow, and reproduce (Figure 2-35).

Figure 2-34

How a set of enzyme-catalyzed reactions generates a metabolic pathway. Each enzyme catalyzes a particular chemical reaction, leaving the enzyme unchanged. In this example, a set of enzymes acting in series converts molecule A to molecule F, forming a (more...)

Figure 2-35

Some of the metabolic pathways and their interconnections in a typical cell. About 500 common metabolic reactions are shown diagrammatically, with each molecule in a metabolic pathway represented by a filled circle, as in the yellow box in Figure 2-34. (more...)

Two opposing streams of chemical reactions occur in cells: (1) the catabolic pathways break down foodstuffs into smaller molecules, thereby generating both a useful form of energy for the cell and some of the small molecules that the cell needs as building blocks, and (2) the anabolic, or biosynthetic, pathways use the energy harnessed by catabolism to drive the synthesis of the many other molecules that form the cell. Together these two sets of reactions constitute the metabolism of the cell (Figure 2-36).

Figure 2-36

Schematic representation of the relationship between catabolic and anabolic pathways in metabolism. As suggested here, since a major portion of the energy stored in the chemical bonds of food molecules is dissipated as heat, the mass of food required (more...)

Many of the details of cell metabolism form the traditional subject of biochemistry and need not concern us here. But the general principles by which cells obtain energy from their environment and use it to create order are central to cell biology. We begin with a discussion of why a constant input of energy is needed to sustain living organisms.

Biological Order Is Made Possible by the Release of Heat Energy from Cells

The universal tendency of things to become disordered is expressed in a fundamental law of physics—the second law of thermodynamics—which states that in the universe, or in any isolated system (a collection of matter that is completely isolated from the rest of the universe), the degree of disorder can only increase. This law has such profound implications for all living things that it is worth restating in several ways.

For example, we can present the second law in terms of probability and state that systems will change spontaneously toward those arrangements that have the greatest probability. If we consider, for example, a box of 100 coins all lying heads up, a series of accidents that disturbs the box will tend to move the arrangement toward a mixture of 50 heads and 50 tails. The reason is simple: there is a huge number of possible arrangements of the individual coins in the mixture that can achieve the 50-50 result, but only one possible arrangement that keeps all of the coins oriented heads up. Because the 50-50 mixture is therefore the most probable, we say that it is more "disordered." For the same reason, it is a common experience that one's living space will become increasingly disordered without intentional effort: the movement toward disorder is a spontaneous process, requiring a periodic effort to reverse it (Figure 2-37).

Figure 2-37

An everyday illustration of the spontaneous drive toward disorder. Reversing this tendency toward disorder requires an intentional effort and an input of energy: it is not spontaneous. In fact, from the second law of thermodynamics, we can be certain (more...)

The amount of disorder in a system can be quantified. The quantity that we use to measure this disorder is called the entropy of the system: the greater the disorder, the greater the entropy. Thus, a third way to express the second law of thermodynamics is to say that systems will change spontaneously toward arrangements with greater entropy.

Living cells—by surviving, growing, and forming complex organisms—are generating order and thus might appear to defy the second law of thermodynamics. How is this possible? The answer is that a cell is not an isolated system: it takes in energy from its environment in the form of food, or as photons from the sun (or even, as in some chemosynthetic bacteria, from inorganic molecules alone), and it then uses this energy to generate order within itself. In the course of the chemical reactions that generate order, part of the energy that the cell uses is converted into heat. The heat is discharged into the cell's environment and disorders it, so that the total entropy—that of the cell plus its surroundings—increases, as demanded by the laws of physics.

To understand the principles governing these energy conversions, think of a cell as sitting in a sea of matter representing the rest of the universe. As the cell lives and grows, it creates internal order. But it releases heat energy as it synthesizes molecules and assembles them into cell structures. Heat is energy in its most disordered form—the random jostling of molecules. When the cell releases heat to the sea, it increases the intensity of molecular motions there (thermal motion)—thereby increasing the randomness, or disorder, of the sea. The second law of thermodynamics is satisfied because the increase in the amount of order inside the cell is more than compensated by a greater decrease in order (increase in entropy) in the surrounding sea of matter (Figure 2-38).

Figure 2-38

A simple thermodynamic analysis of a living cell. In the diagram on the left the molecules of both the cell and the rest of the universe (the sea of matter) are depicted in a relatively disordered state. In the diagram on the right the cell has taken (more...)

Where does the heat that the cell releases come from? Here we encounter another important law of thermodynamics. The first law of thermodynamics states that energy can be converted from one form to another, but that it cannot be created or destroyed. Some forms of energy are illustrated in Figure 2-39. The amount of energy in different forms will change as a result of the chemical reactions inside the cell, but the first law tells us that the total amount of energy must always be the same. For example, an animal cell takes in foodstuffs and converts some of the energy present in the chemical bonds between the atoms of these food molecules (chemical bond energy) into the random thermal motion of molecules (heat energy). This conversion of chemical energy into heat energy is essential if the reactions inside the cell are to cause the universe as a whole to become more disordered—as required by the second law.

Figure 2-39

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 the first example, (more...)

The cell cannot derive any benefit from the heat energy it releases unless the heat-generating reactions inside the cell are directly linked to the processes that generate molecular order. It is the tight coupling of heat production to an increase in order that distinguishes the metabolism of a cell from the wasteful burning of fuel in a fire. Later in this chapter, we shall illustrate how this coupling occurs. For the moment, it is sufficient to recognize that a direct linkage of the "burning" of food molecules to the generation of biological order is required if cells are to be able to create and maintain an island of order in a universe tending toward chaos.

Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules

All animals live on energy stored in the chemical bonds of organic molecules made by other organisms, which they take in as food. The molecules in food also provide the atoms that animals need to construct new living matter. Some animals obtain their food by eating other animals. But at the bottom of the animal food chain are animals that eat plants. The plants, in turn, trap energy directly from sunlight. As a result, all of the energy used by animal cells is derived ultimately from the sun.

Solar energy enters the living world through photosynthesis in plants and photosynthetic bacteria. Photosynthesis allows the electromagnetic energy in sunlight to be converted into chemical bond energy in the cell. Plants are able to obtain all the atoms they need from inorganic sources: carbon from atmospheric carbon dioxide, hydrogen and oxygen from water, nitrogen from ammonia and nitrates in the soil, and other elements needed in smaller amounts from inorganic salts in the soil. They use the energy they derive from sunlight to build these atoms into sugars, amino acids, nucleotides, and fatty acids. These small molecules in turn are converted into the proteins, nucleic acids, polysaccharides, and lipids that form the plant. All of these substances serve as food molecules for animals, if the plants are later eaten.

The reactions of photosynthesis take place in two stages (Figure 2-40). In the first stage, energy from sunlight is captured and transiently stored as chemical bond energy in specialized small molecules that act as carriers of energy and reactive chemical groups. (We discuss these activated carrier molecules later.) Molecular oxygen (O₂ gas) derived from the splitting of water by light is released as a waste product of this first stage.

Figure 2-40

Photosynthesis. The two stages of photosynthesis. The energy carriers created in the first stage are two molecules that we discuss shortly—ATP and NADPH.

In the second stage, the molecules that serve as energy carriers are used to help drive a carbon fixation process in which sugars are manufactured from carbon dioxide gas (CO₂) and water (H₂O), thereby providing a useful source of stored chemical bond energy and materials—both for the plant itself and for any animals that eat it. We describe the elegant mechanisms that underlie these two stages of photosynthesis in Chapter 14.

The net result of the entire process of photosynthesis, so far as the green plant is concerned, can be summarized simply in the equation

The sugars produced are then used both as a source of chemical bond energy and as a source of materials to make the many other small and large organic molecules that are essential to the plant cell.

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 these be sugars that a plant has photosynthesized as food for itself or the mixture of large and small molecules that an animal has eaten. In order to use this energy to live, grow, and reproduce, organisms must extract it in a usable form. 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 as CO₂ and that of hydrogen is as 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 respiration.

Photosynthesis and respiration are complementary processes (Figure 2-41). 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 by nearly all organisms. 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 that 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, crossing boundaries between individual organisms (Figure 2-42). Similarly, atoms of nitrogen, phosphorus, and sulfur move between the living and nonliving worlds in cycles that involve plants, animals, fungi, and bacteria.

Figure 2-41

Photosynthesis and respiration as complementary processes in the living world. Photosynthesis uses the energy of sunlight to produce sugars and other organic molecules. These molecules in turn serve as food for other organisms. Many of these organisms (more...)

Figure 2-42

The carbon cycle. Individual carbon atoms are incorporated into organic molecules of the living world by the photosynthetic activity of plants, bacteria, and marine algae. They pass to animals, microorganisms, and organic material in soil and oceans in (more...)

Oxidation and Reduction Involve Electron Transfers

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 the molecules through a large number of reactions that only rarely involve the direct addition of oxygen. Before we consider some of these reactions and the purpose behind them, we need to discuss what is meant by the process of oxidation.

Oxidation, in the sense used above, does not mean only the addition of oxygen atoms; rather, it applies more generally to any reaction in which electrons are transferred from one atom to another. Oxidation in this sense refers to the removal of electrons, and reduction—the converse of oxidation—means the addition of electrons. Thus, Fe²⁺ is oxidized if it loses an electron to become Fe³⁺, and a chlorine atom is reduced if it gains an electron to become Cl^-. Since the number of electrons is conserved (no loss or gain) in a chemical reaction, oxidation and reduction always occur simultaneously: that is, if one molecule gains an electron in a reaction (reduction), a second molecule loses the electron (oxidation). When a sugar molecule is oxidized to CO₂ and H₂O, for example, the O₂ molecules involved in forming H₂O gain electrons and thus are said to have been reduced.

The terms "oxidation" and "reduction" apply even when there is only a partial shift of electrons between atoms linked by a covalent bond (Figure 2-43). When a carbon atom becomes covalently bonded to an atom with a strong affinity for electrons, such as oxygen, chlorine, or sulfur, for example, it gives up more than its equal share of electrons and forms a polar covalent bond: the positive charge of the carbon nucleus is now somewhat greater than the negative charge of its electrons, and the atom therefore acquires a partial positive charge and is said to be oxidized. Conversely, a carbon atom in a C-H linkage has slightly more than its share of electrons, and so it is said to be reduced (see Figure 2-43).

Figure 2-43

Oxidation and reduction. (A) When two atoms form a polar covalent bond (see p. 54), the atom ending up with a greater share of electrons is said to be reduced, while the other atom acquires a lesser share of electrons and is said to be oxidized. The reduced (more...)

When a molecule in a cell picks up an electron (e^-), it often picks up a proton (H⁺) at the same time (protons being freely available in water). The net effect in this case is to add a hydrogen atom to the molecule

Even though a proton plus an electron is involved (instead of just an electron), such hydrogenation reactions are reductions, and the reverse, dehydrogenation reactions, are oxidations. It is especially easy to tell whether an organic molecule is being oxidized or reduced: reduction is occurring if its number of C-H bonds increases, whereas oxidation is occurring if its number of C-H bonds decreases (see Figure 2-43B).

Cells use enzymes to catalyze the oxidation of organic molecules in small steps, through a sequence of reactions that allows useful energy to be harvested. We now need to explain how enzymes work and some of the constraints under which they operate.

Enzymes Lower the Barriers That Block Chemical Reactions

Consider the reaction

The paper burns readily, releasing to the atmosphere both energy as heat and water and carbon dioxide as gases, but 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 loss 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 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." A "downhill" reaction in this sense is often said to be energetically favorable.

Although the most energetically favorable form of carbon under ordinary conditions is as CO₂, and that of hydrogen is as H₂O, a living organism does not disappear in a puff of smoke, and the 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 energy barrier—before it can undergo a chemical reaction that leaves it in a more stable state (Figure 2-44). In the case of a burning book, the activation energy is 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.

Figure 2-44

The important principle of activation energy. Compound X is in a stable state, and energy is required to convert it to compound Y, even though Y is at a lower overall energy level than X. This conversion will not take place, therefore, unless compound (more...)

In a living cell, the kick over the energy barrier is greatly aided by a specialized class of proteins—the enzymes. Each enzyme binds tightly to one or two 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 2-45. Enzymes are among the most effective catalysts known, speeding up reactions by a factor of as much as 10¹⁴, and they thereby allow reactions that would not otherwise occur to proceed rapidly at normal temperatures.

Figure 2-45

Lowering the activation energy greatly increases the probability of reaction. A population of identical substrate molecules will have a range of energies that is distributed as shown on the graph at any one instant. The varying energies come from collisions (more...)

Enzymes are also highly selective. Each enzyme usually catalyzes only one particular reaction: in other words, it selectively lowers the activation energy of only one of the several possible chemical reactions that its bound substrate molecules could undergo. In this way, enzymes direct each of the many different molecules in a cell along specific reaction pathways (Figure 2-46).

Figure 2-46

Floating ball analogies for enzyme catalysis. (A) A barrier dam is lowered to represent enzyme catalysis. The green ball represents a potential enzyme substrate (compound X) that is bouncing up and down in energy level due to constant encounters with (more...)

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 has a unique shape containing an active site, a pocket or groove in the enzyme into which only particular substrates will fit (Figure 2-47). 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, after we have looked in detail at the molecular structure of proteins.

Figure 2-47

How enzymes work. Each enzyme has an active site to which one or two 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 (more...)

How Enzymes Find Their Substrates: The Importance of Rapid Diffusion

A typical enzyme will catalyze the reaction of about a thousand 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 are important in bringing the surfaces of interacting molecules together.

These rates of molecular motions can be measured by a variety of spectroscopic techniques. These indicate that 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 2-48). In such a walk, the average 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.

Figure 2-48

A random walk. Molecules in solution move in a random fashion due to 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 (more...)

The inside of a cell is very crowded (Figure 2-49). 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 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).

Figure 2-49

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 (more...)

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 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 encounter between the surface of an enzyme and the matching surface of its substrate molecule often leads immediately to the formation of an enzyme-substrate complex that is ready to react. 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.

Once an enzyme and substrate have collided and snuggled together properly at the active site, they form multiple weak bonds with each other that persist until random thermal motion causes the molecules to dissociate again. In general, the stronger the binding of the enzyme and substrate, the slower their rate of dissociation. However, when two colliding molecules have poorly matching surfaces, few noncovalent bonds are formed and their total energy is negligible compared with that of thermal motion. In this case the two molecules dissociate as rapidly as they come together. This is what prevents incorrect and unwanted associations from forming between mismatched molecules, such as between an enzyme and the wrong substrate.

The Free-Energy Change for a Reaction Determines Whether It Can Occur

We must now digress briefly to introduce some fundamental chemistry. Cells are chemical systems that must obey all chemical and physical laws. 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.

Before examining how such coupling is achieved, we must consider more carefully the term "energetically favorable." According to the second law of thermodynamics, a chemical reaction can proceed spontaneously only if it results in a net increase in the disorder of the universe (see Figure 2-38). The criterion for an increase in disorder of the universe can be expressed most conveniently in terms of a quantity called the free energy, G , of a system. The value of G is of interest only when a system undergoes a change, and the change in G, denoted Δ G (delta G), is critical. Suppose that the system being considered is a collection of molecules. As explained in Panel 2-7 (pp. 122–123), free energy has been defined such that ΔG directly measures the amount of disorder created in the universe when a reaction takes place that involves these molecules. Energetically favorable reactions, by definition, are those that decrease free energy, or, in other words, have a negative ΔG and disorder the universe (Figure 2-50).

Panel 2-7

Free Energy and Biological Reactions.

Figure 2-50

The distinction between energetically favorable and energetically unfavorable reactions.

A familiar 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 the dissolving of salt in water. Conversely, energetically unfavorable reactions, with a positive ΔG—such as those in which two amino acids are joined together 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 ΔG so large that the ΔG of the entire process is negative (Figure 2-51).

Figure 2-51

How reaction coupling is used to drive energetically unfavorable reactions.

The Concentration of Reactants Influences ΔG

As we have just described, a reaction A ⇌ B will go in the direction A → B when the associated free-energy change, ΔG, 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, ΔG 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 ΔG 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 contains 10 heads and 90 tails. For exactly the same reason, for a reversible reaction A ⇌ B, a large excess of A over B will tend to drive the reaction in the direction A → B; that is, there will be a tendency for there to be more molecules making the transition A → B than there are molecules making the transition B → A. Therefore, the ΔG becomes more negative for the transition A → B (and more positive for the transition B → A) as the ratio of A to B increases.

How much of a concentration difference is needed to compensate for a given decrease in chemical bond energy (and accompanying heat release)? The answer is not intuitively obvious, but it can be determined from a thermodynamic analysis that makes it possible to separate the concentration-dependent and the concentration-independent parts of the free-energy change. The ΔG for a given reaction can thereby be written as the sum of two parts: the first, called the standard free-energy change, Δ G° , depends on the intrinsic characters of the reacting molecules; the second depends on their concentrations. For the simple reaction A → B at 37°C,

where ΔG is in kilocalories per mole, [A] and [B] denote the concentrations of A and B, ln is the natural logarithm, and 0.616 is RT—the product of the gas constant, R, and the abolute temperature, T.

Note that ΔG equals the value of ΔG° when the molar concentrations of A and B are equal (ln 1 = 0). As expected, ΔG becomes more negative as the ratio of B to A decreases (the ln of a number < 1 is negative).

Chemical equilibrium is reached when the concentration effect just balances the push given to the reaction by ΔG°, so that there is no net change of free energy to drive the reaction in either direction (Figure 2-52). Here ΔG = 0, and so the concentrations of A and B are such that

Figure 2-52

Chemical equilibrium. When a reaction reaches equilibrium, the forward and backward flux of reacting molecules are equal and opposite.

which means that there is chemical equilibrium at 37°C when

Table 2-5 shows how the equilibrium ratio of A to B (expressed as an equilibrium constant, K ) depends on the value of ΔG°.

Table 2-5

Relationship Between the Standard Free- Energy Change, ΔG°, and Equilibrium Constant.

It is important to recognize that when an enzyme (or any catalyst) lowers the activation energy for the reaction A → B, it also lowers the activation energy for the reaction B → A by exactly the same amount (see Figure 2-44). The forward and backward reactions will therefore be accelerated by the same factor by an enzyme, and the equilibrium point for the reaction (and ΔG°) remains unchanged (Figure 2-53).

Figure 2-53

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 (more...)

For Sequential Reactions, ΔG° Values Are Additive

The course of most reactions can be predicted quantitatively. A large body of thermodynamic data has been collected that makes it possible to calculate the standard change in free energy, ΔG°, for most of the important metabolic reactions of the cell. The overall free-energy change for a metabolic pathway is then simply the sum of the free-energy changes in each of its component steps. Consider, for example, two sequential reactions

where the ΔG° values are +5 and -13 kcal/mole, respectively. (Recall that a mole is 6 × 10²³ molecules of a substance.) If these two reactions occur sequentially, the ΔG° for the coupled reaction will be -8 kcal/mole. Thus, the unfavorable reaction X → Y, which will not occur spontaneously, can be driven by the favorable reaction Y → Z, provided that the second reaction follows the first.

Cells can therefore cause the energetically unfavorable transition, X → Y, to occur if an enzyme catalyzing the X → Y reaction is supplemented by a second enzyme that catalyzes the energetically favorable reaction, Y → Z. In effect, the reaction Y → Z will then act as a "siphon" to drive the conversion of all of molecule X to molecule Y, and thence to molecule Z (Figure 2-54). For example, several of the reactions in the long pathway that converts sugars into CO₂ and H₂O would be energetically unfavorable if considered on their own. But the pathway nevertheless proceeds rapidly to completion because the total ΔG° for the series of sequential reactions has a large negative value.

Figure 2-54

How an energetically unfavorable reaction can be driven by a second, following reaction. (A) At equilibrium, there are twice as many X molecules as Y molecules, because X is of lower energy than Y. (B) At equilibrium, there are 25 times more Z molecules (more...)

But 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. How these work is the topic we discuss next.

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 other small organic molecules and of the larger and more complex 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 energy is used for biosynthesis and other needed cell activities (Figure 2-55).

Figure 2-55

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 (more...)

The activated carriers store energy in an easily exchangeable form, either as a readily transferable chemical group or as high-energy electrons, 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—as we discuss in detail shortly. We shall see that cells use 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

When a fuel molecule such as glucose is oxidized in a cell, enzyme-catalyzed reactions ensure that a large part of the free energy that is released by oxidation is captured in a chemically useful form, rather than being released wastefully as heat. This is achieved by means of a coupled reaction, in which an energetically favorable reaction is used to drive an energetically unfavorable one that produces an activated carrier molecule or some other useful energy store. Coupling mechanisms require enzymes and are fundamental to all the energy trans-actions of the cell.

The nature of a coupled reaction is illustrated by a mechanical analogy in Figure 2-56, 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 2-39). By careful design, however, part of this energy could be used instead to drive a paddle wheel that lifts a bucket of water (Figure 2-56B). 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 (B), the rocks hit the ground with less velocity than in (A), and correspondingly less energy is wasted as heat.

Figure 2-56

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 (more...)

Exactly analogous processes occur in cells, where enzymes play the role of the paddle wheel in our analogy. By mechanisms that will be discussed later in this chapter, they couple an energetically favorable reaction, such as the oxidation of foodstuffs, to an energetically unfavorable reaction, such as the generation of an activated carrier molecule. As a result, the amount of heat released by the oxidation reaction is reduced by exactly the amount of energy that is stored in the energy-rich covalent bonds of the activated carrier molecule. The activated carrier molecule in turn 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

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 2-56B can be used to drive a wide variety of hydraulic machines, ATP serves as a convenient and versatile store, or currency, of energy 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 2-57). The regenerated ADP is then available to be used for another round of the phosphorylation reaction that forms ATP.

Figure 2-57

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 (more...)

The energetically favorable reaction of ATP hydrolysis is coupled to many otherwise unfavorable reactions through which other molecules are synthesized. We shall encounter several of these reactions later in this chapter. Many of them involve the transfer of the terminal phosphate in ATP to another molecule, as illustrated by the phosphorylation reaction in Figure 2-58.

Figure 2-58

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 (more...)

ATP is the most abundant active carrier in cells. As one example, it is used to supply energy for many of the pumps that transport substances into and out of the cell (discussed in Chapter 11). It also 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

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 (see Figure 2-54). But when the required product is Y and not Z, this mechanism is not useful.

A frequent type of reaction that is needed for biosynthesis 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-OPO₃, in which case the reaction pathway contains only two steps:

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 2-59A).

Figure 2-59

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. (more...)

A biosynthetic reaction of exactly this type is employed to synthesize the amino acid glutamine, as illustrated in Figure 2-59B. We will see shortly that very similar (but more complex) mechanisms are also used to produce nearly all of the large molecules of the cell.

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 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). Later, we examine some of the reactions in which they participate. NAD⁺ and NADP⁺ each pick up a "packet of energy" corresponding to two high-energy electrons plus a proton (H⁺)—being converted to NADH (reduced nicotinamide adenine dinucleotide) and NADPH (reduced nicotinamide adenine dinucleotide phosphate), respectively. These molecules can therefore also be regarded as carriers of hydride ions (the H⁺ plus two electrons, or H^-).

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 2-60A. During a special set of energy-yielding catabolic reactions, a hydrogen atom plus two electrons are removed from the substrate molecule and added to the nicotinamide ring of NADP⁺ to form NADPH. This is a typical oxidation-reduction reaction; the substrate is oxidized and NADP⁺ is reduced. The structures of NADP⁺ and NADPH are shown in Figure 2-60B.

Figure 2-60

NADPH, an important carrier of electrons. (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 (more...)

The hydride ion carried by NADPH is given up readily in a subsequent oxidation-reduction reaction, because the ring can achieve a more stable arrangement of electrons without it. In this subsequent reaction, which regenerates NADP⁺, it is the NADPH that becomes oxidized and the substrate that becomes 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 2-61.

Figure 2-61

The final stage in one of the biosynthetic routes 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 (more...)

The difference of a single phosphate group has no effect on the electron-transfer properties of NADPH compared with NADH, but it is crucial for their distinctive roles. The extra phosphate group on NADPH is far from the region involved in electron transfer (see Figure 2-60B) and is of no importance to the transfer reaction. It does, however, give a molecule of NADPH a slightly different shape from that of NADH, and so NADPH and NADH bind as substrates to different sets of enzymes. Thus the two types of carriers are used to transfer electrons (or hydride ions) between different sets of molecules.

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 that of NADPH from NADP⁺ occur by different pathways and are independently regulated, so that the cell can independently 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—as required for their special roles in catabolism and anabolism, respectively.

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 (Table 2-6). For example, coenzyme A carries an acetyl group in a readily transferable linkage, and in this activated form is known as acetyl CoA (acetyl coenzyme A). The structure of acetyl CoA is illustrated in Figure 2-62; it is used to add two carbon units in the biosynthesis of larger molecules.

Table 2-6

Some Activated Carrier Molecules Widely Used in Metabolism.

Figure 2-62

The structure of the important activated carrier molecule acetyl CoA. A space-filling 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 (more...)

In acetyl CoA and the other carrier molecules in Table 2-6, 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, 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.

Examples of the type of transfer reactions catalyzed by the activated carrier molecules ATP (transfer of phosphate) and NADPH (transfer of electrons and hydrogen) have been presented in Figures 2-58 and 2-61, respectively. The reactions of other activated carrier molecules involve the transfers of methyl, carboxyl, or glucose group, for the purpose of biosynthesis. The activated carriers required are usually generated in reactions that are coupled to ATP hydrolysis, as in the example in Figure 2-63. 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.

Figure 2-63

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 (more...)

The Synthesis of Biological Polymers Requires an Energy Input

As discussed previously, the macromolecules of the cell constitute the vast majority of its dry mass—that is, of the mass not due to water (see Figure 2-29). 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 and are more complex (Figure 2-64).

Figure 2-64

Condensation and hydrolysis as opposite reactions. The macromolecules of the cell are polymers that are formed from subunits (or monomers) by a condensation reaction and are broken down by hydrolysis. The condensation reactions are all energetically unfavorable. (more...)

The nucleic acids (DNA and RNA), proteins, and polysaccharides are all polymers that are produced by the repeated addition of a subunit (also called a monomer) onto one end of a growing chain. The synthesis reactions for these three types of macromolecules are outlined in Figure 2-65. 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?

Figure 2-65

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 (more...)

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 2-59). The principle is exactly the same, in that the OH group that will 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).

There are limits to what each activated carrier can do in driving biosynthesis. The ΔG for the hydrolysis of ATP to ADP and inorganic phosphate (P_i) depends on the concentrations of all of the reactants, but under the usual conditions in a cell it is between -11 and -13 kcal/mole. In principle, this hydrolysis reaction can be used to drive an unfavorable reaction with a ΔG of, perhaps, +10 kcal/mole, provided that a suitable reaction path is available. For some biosynthetic reactions, however, even -13 kcal/mole may not be enough. In these cases the path of ATP hydrolysis can be altered so that it initially produces AMP and pyrophosphate (PP_i), which is itself then hydrolyzed in a subsequent step (Figure 2-66). The whole process makes available a total free-energy change of about -26 kcal/mole. An important biosynthetic reaction that is driven in this way is nucleic acid (polynucleotide) synthesis, as illustrated in Figure 2-67.

Figure 2-66

An alternative route for the hydrolysis of ATP, in which pyrophosphate is first formed and then hydrolyzed. This route releases about twice as much free energy as the reaction shown earlier in Figure 2-57. (A) In the two successive hydrolysis reactions, (more...)

Figure 2-67

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 (more...)

It is interesting to note that the polymerization 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 head polymerization the reactive bond required for the condensation reaction is carried on the end of the 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 2-68).

Figure 2-68

The orientation of the active intermediates in biological polymerization reactions. The head growth of polymers is compared with its alternative tail growth. As indicated, these two mechanisms are used to produce different biological macromolecules.

We shall see in later chapters that both 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.

Summary

Living cells are highly ordered and need to create order within themselves in order 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. The energy 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 these 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.

To make possible the continual generation of order in cells, the energetically favorable hydrolysis of ATP is coupled to energetically unfavorable reactions. In the biosynthesis of macromolecules, this is accomplished by the transfer of phosphate groups to form reactive phosphorylated intermediates. Because the energetically unfavorable reaction 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 active 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.

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Source: https://www.ncbi.nlm.nih.gov/books/NBK26838/

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