ATP AND ENZYM
ATP: Transferring Energy in Cells
All living cells rely on adenosine triphosphate, or ATP, for the capture and transfer of the free energy needed to do chemical work and maintain the cells. ATP operates as a kind of energy currency. That is, just as you may earn money from a job and then spend it on a meal, some of the free energy
released by certain exergonic reactions is captured in ATP, which can then release free energy to drive endergonic reactions.
ATP is produced by cells in a number of ways (which we will describe in the next two chapters), and it is used in many ways. ATP is not an unusual molecule. In fact, it has another important use in the cell: it can be converted into a building block for DNA and RNA. But two things about ATP make it especially useful to cells: it releases a relatively large amount of energy when hydrolyzed, and it can phosphorylate (donate a phosphate group to) many different molecules. We will examine these two properties in the discussion
ATP hydrolysis releases energy
An ATP molecule consists of the nitrogenous base adenine bonded to ribose (a sugar), which is attached to a sequence of three phosphate groups. The hydrolysis of ATP yields ADP (adenosine diphosphate) and an inorganic
phosphate ion (abbreviated Pi, short for HPO4 2–), as well as free energy:
ATP + H2O →ADP + Pi + free energy
The important property of this reaction is that it is exergonic, releasing free energy. The change in free energy (ΔG) is about –12 kcal/mol (–50 kJ/mol) at the temperature, pH, and substrate concentrations typical of living cells.*
What characteristics of ATP account for the free energy released by the loss of one of its phosphate groups? First and foremost, the free energy of the P—O bond between phos- phate groups is much higher than the energy of the H—O
bond that forms after hydrolysis. So some usable energy is released upon hydrolysis. Second, because phosphates are negatively charged and so repel each other, it takes energy to get phosphates near enough to each other to make the covalent bond that links them together (e.g., to add a phosphate
to ADP to make ATP).
ATP couples exergonic and endergonic reactions
As we have just seen, the hydrolysis of ATP is exergonic and yields ADP, Pi, and free energy. The reverse reaction, the formation of ATP from ADP and Pi, is endergonic and consumes as much free energy as is released by the breakdown of ATP:
ADP + Pi + free energy →ATP + H2O
Many different exergonic reactions in the cell can provide the energy to convert ADP to ATP. In eukaryotes, the most important of these reactions is cellular respiration, in which some of the energy released from fuel molecules is captured in ATP. The formation and hydrolysis of ATP constitute what
might be called an “energy-coupling cycle,” in which ADP picks up energy from exergonic reactions to become ATP, which donates energy to endergonic reactions. How does this ATP cycle trap and release energy? An exergonic
reaction is coupled to the endergonic reaction that forms ATP from ADP and Pi Coupling of exergonic and endergonic reactions is very common in metabolism.
When it forms, ATP captures free energy and retains it like a compressed spring. ATP then diffuses to another site in the cell, where its hydrolysis releases free energy to drive an endergonic reaction.
The formation of the amino acid glutamine has a positive ΔG (is endergonic) and will not proceed without the input of free energy from ATP hydrolysis, which has a negative ΔG (is exergonic). The total ΔG for the coupled reactions is negative (the two ΔGs are added together). Hence
the reactions proceed exergonically when they are coupled, and glutamine is synthesized. An active cell requires millions of molecules of ATP per
second to drive its biochemical machinery. An ATP molecule is consumed within a second following its formation, on average.
At rest, an average person hydrolyzes and produces about 40 kg of ATP per day—as much as some people weigh! This means that each ATP molecule undergoes about 10,000 cycles of synthesis and hydrolysis every day.
Enzymes: Biological Catalysts
When we know the change in free energy (ΔG) of a reaction, we know where the equilibrium point of the reaction lies: The more negative ΔG is, the further the reaction proceeds toward completion. However, ΔG tells us nothing about the rate of a reaction—the speed at which it moves toward equilibrium.
The reactions that occur in cells are so slow that they could not contribute to life unless the cells did something to speed them up. That is the role of catalysts: substances that speed up a reaction without being permanently altered by
that reaction. Acatalyst does not cause a reaction that would not take place eventually without it, but merely speeds up the rates of both forward and backward reactions, allowing equilibrium to be approached faster. Most biological catalysts are proteins called enzymes. Although we will focus here on proteins, some catalysts—perhaps the earliest ones in the origin of life—are RNA molecules called ribozymes (see Chapter 3). Abiological catalyst,
whether protein or RNA, is a framework or scaffold in which chemical catalysis takes place. It does not matter whether the framework is RNA or protein—indeed, artificial catalysts can be made from DNA. Evolution has selected proteins as catalysts, probably because of their great diversity in three-dimensional structure and variety of chemical functions.
In the discussion that follows, we will identify the energy barrier that controls the rate of reactions. Then we’ll focus on the role of enzymes: how they interact with reactants, how they lower the energy barrier, and how they permit reactions to proceed faster. After exploring the nature and significance
of enzyme specificity, we’ll look at how enzymes contribute to the coupling of reactions.
For a reaction to proceed, an energy barrier must be overcome
An exergonic reaction may release a great deal of free energy, but the reaction may take place very slowly. Some reactions are slow because there is an energy barrier between reactants and products. Think about a gas stove. The burning of the natural gas (methane + O2→CO2 + H2O) is obviously an exergonic reaction—heat and light are released. Once started, the reaction goes to completion: all of the methane reacts with oxygen to form carbon dioxide and water vapor. Because burning methane liberates so much energy, you
might expect this reaction to proceed rapidly whenever methane is exposed to oxygen. But this does not happen. Simply mixing methane with air produces no reaction. Methane will start burning only if a spark—an input of energy—
is provided. (On the stove, this energy is supplied by electricity.) The need for this spark to start the reaction shows that there is an energy barrier between the reactants and the products.
In general, exergonic reactions proceed only after the reactants are pushed over the energy barrier by a small amount of added energy. The energy barrier thus represents the amount of energy needed to start the reaction, known as the activation energy (Ea) Recall the ball rolling down the hill in Figure 6.3. The ball has a lot of potential energy at the top of the hill. However, if the ball is stuck in a small depression, it won’t roll down the hill, even though
that action is exergonic. To start the ball rolling, a small amount of energy (activation energy) is needed to get the ball out of the depression .
In a chemical reaction, the activation energy is the energy needed to change the reactants into unstable molecular forms called transition-state species. Transition-state species have higher free energies than either the reactants or the products. Their bonds may be stretched and hence unstable. Although
the amount of activation energy needed for different reactions varies, it is often small compared with the change in free energy of the reaction. The activation energy that starts a reaction is recovered during the ensuing “downhill” phase
of the reaction, so it is not a part of the net free energy change,
ΔG. Where does the activation energy come from? In any collection
of reactants at room or body temperature, molecules are moving around and could use their kinetic energy of motion to overcome the energy barrier, enter the transition state, and react. However, at normal temperatures, only
a few molecules have enough energy to do this; most have insufficient kinetic energy for activation, so the reaction takes place slowly. If the system were heated, all the reactant molecules would move faster and have more kinetic energy. Since more of them would have energy exceeding the required
activation energy, the reaction would speed up.
However, adding enough heat to increase the average kinetic energy of the molecules won’t work in living systems. Such a nonspecific approach would accelerate all reactions, including destructive ones, such as the denaturation of proteins . A more effective way to speed up a reaction in a living system is to lower the energy barrier. In living cells, enzymes accomplish this task.
Enzymes bind specific reactant molecules
Catalysts increase the rate of chemical reactions. Most nonbiological
catalysts are nonspecific. For example, powdered platinum catalyzes virtually any reaction in which molecular hydrogen (H2) is a reactant. In contrast, most biological catalysts are highly specific. These complex molecules of protein (enzymes) or RNA (ribozymes) catalyze relatively simple chemical
reactions. An enzyme or ribozyme usually recognizes and binds to only one or a few closely related reactants, and it catalyzes only a single chemical reaction. In the discussion that follows, we focus on enzymes, but you should note that
similar rules of chemical behavior apply to ribozymes as well. In an enzyme-catalyzed reaction, the reactants are called substrates. Substrate molecules bind to a particular site on the enzyme, called the active site, where catalysis takes place . The specificity of an enzyme results from the exact three-dimensional shape and structure of its active site, into which only a narrow range of substrates can fit. Other molecules—with different shapes, different functional
groups, and different properties—cannot properly fit and bind to the active site.
The names of enzymes reflect the specificity of their functions and often end with the suffix “-ase.” For example, the enzyme RNA polymerase catalyzes the formation of RNA, but not DNA, and the enzyme hexokinase accelerates the
phosphorylation of hexose sugars, but not pentose sugars.
The binding of a substrate to the active site of an enzyme produces an enzyme–substrate complex (ES) held together by one or more means, such as hydrogen bonding, ionic attraction, or covalent bonding. The enzyme–substrate complex gives rise to product and free enzyme:
E + S → ES → E + P
where E is the enzyme, S is the substrate, P is the product, and ES is the enzyme–substrate complex.
The free enzyme (E) is in the same chemical form at the end of the reaction as
at the beginning. While bound to the substrate, it may change chemically, but by the end of the reaction it has been restored to its initial form.