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, by Campbell and Reece)
An Introduction to Metabolism (Chapter Six)
METABOLISM, ENERGY, AND LIFE Metabolism is the sum total of all chemical reactions in an organism. The Chemistry of Life is Organized Into Metabolic Pathways The thousands of chemical reactions in the cell are arranged in intricate metabolic pathways that alter molecules in a step-by-step fashion. Metabolism manages the material and energy resources of the cell. Catabolic pathways release energy by breaking down complex molecules to simpler compounds. An example of such pathway is cellular respiration, in which glucose and other fuels are broken down into carbon dioxide and water. Anabolic pathways consume energy to build complicated molecules from simpler ones. An example is the building of a protein from amino acids. Catabolic and anabolic pathways transfer energy – the energy produced by catabolism is used to power anabolism. This transfer is called energy coupling. The concepts in this chapter are central to bioenergetics the study bioenergetics, of how organisms manage their energy resources. Organisms Transform Energy Energy is the capacity to do work. Cells must be able to transform energy from one type into another. Anything that moves has kinetic energy the energy of motion. Moving objects perform work through energy, imparting motion to other matter. Light is also a type of kinetic energy – light can power photosynthesis. Heat is kinetic energy that results from the random movement of molecules. Resting objects have stored energy, or potential energy the energy matter energy, possesses because of its location or structure. Chemical energy is a form of potential energy stored in molecules because of the arrangement of atoms in those molecules. An example of potential energy being transformed into kinetic energy can be seen by a ball being thrown into the air – when the ball is highest, there is the most potential energy. This becomes kinetic energy as the ball moves toward the ground. When chemical reactions rearrange the atoms of molecules in such a way that potential energy in the molecules is converted into kinetic, chemical energy
2 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) can be used. Cellular respiration and other catabolic pathways can release stored energy in molecules and make it available to the cell. The Energy Transformations of Life Are Subject To Two Laws of Thermodynamics Thermodynamics is the study of the energy transformations that occur in a collection of matter. The term system is used to refer to matter being studied, while everything outside the system is referred to as surroundings. A closed system is isolated from its surroundings. In an open system, energy and matter can be transferred between the system and its surroundings. Organisms are considered open systems, since they can absorb energy (light or chemical) and release waste products to the surroundings. Two laws of thermodynamics are central in energy transformations in organisms as well as all matter.
The First Law of Thermodynamics
The first law of thermodynamics states that the energy of the universe is constant: energy can be transferred and transformed, but it cannot be created or destroyed. This law is also known as the principle of conservation of energy.
The Second Law of Thermodynamics
The main idea behind the second law of thermodynamics is that every energy transfer or transformation makes the universe more disordered. Entropy is a measure of disorder and randomness. The greater entropy a collection of matter has, the more disorganized it is. Thus, the second law can also be written as: every energy transfer increases the entropy of the universe. Increasing entropy can be easy to observe in cases of physical disintegration – think of an old building crumbling to the ground. Increasing heat is also increasing entropy, since heat is the energy of random molecular motion. In most energy transformations, ordered forms of energy are at least partly converted into heat. Although forms of energy have been converted to heat, the first law of thermodynamics is still upheld, since heat is a form of energy. While the quantity of energy in the universe is constant, the quality of the energy is not. Heat can be put to work only when there is a temperature difference that results in heat moving from a warmer location to a cooler one – as a result, it can be seen as the “lowest grade” of energy. While cells created ordered structures from less organized starting materials, organisms also take in organized forms of matter and break them down into less ordered forms. For example, animals take in starch, proteins, and complex molecules, then break them down, releasing carbon dioxide and water.
3 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) Energy flows into an ecosystem as light, and then leaves as heat. Living systems ultimately increase entropy of their surroundings. Additionally, while the entropy of a particular system can decrease, the total entropy of the entire decrease, universe increases. Organisms Live at the Expense of Free Energy A spontaneous process is a change that can occur without outside assistance. Such changes can be harnessed to perform work. For example, the downhill flow of water can be used to turn a windmill to downhill generate power. Nonspontaneous processes will only occur if energy is added to the system. For example, cells must expend energy to create a protein about amino acids. The stability of a system increases when a spontaneous process occurs. Unstable systems tend to change in a way that they become stable. For example, a body of water in a reservoir is less stable than the same water at sea level. The water will fall in order move toward greater stability (once the reservoir wall is removed). A standard for spontaneous process is free energy.
Free Energy: A Criterion for Spontaneous Change Free energy is the portion of a system’s energy that can perform work when temperature is uniform throughout the system. It is termed “free” because it is available for work.
Unstable Systems • More free energy • Less stable • Greater work capacity
•The free energy decreases (∆G<0) •The system becomes more stable •The released free energy can be harnessed to do work
Stable Systems • Less free energy • More stable • Less work capacity
4 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) A system’s quantity of free energy is symbolized by G. The two components of G are the system’s total energy (H) and its entropy (S). G = H – TS, where T is absolute temperature in Kelvin. Since temperature measures the intensity of heat (random molecular motion), it is important to the equation. Not all energy stored in a system (H) is available for work. The entropy factor (disorder) is subtracted from the total energy to determine the maximum capacity of useful work the system can perform. Free energy is then less than the system’s total energy. Free energy G is a measure of how unstable a system is. Systems rich in energy or highly organized systems are unstable and want to change to a more stable state. In other words, these systems have high energy, low entropy, or both – they are more likely to change spontaneously into a more stable state. In any spontaneous process, the free energy of a system decreases. ∆G = ∆H – T∆S For a process to occur spontaneously, the system must either give up energy (decrease H), give up order (an increase in S), or both. Once these changes occur, ∆G must have a negative value (∆G < 0). The greater the decrease in free energy, the greater the maximum amount of work the spontaneous process can perform.
Free Energy and Equilibrium
Maximum stability is equilibrium, where ∆G = 0. As a reaction proceeds toward equilibrium, the free energy of the mixture of reactants and products decreases. Free energy increases when a reaction is pushed away from equilibrium. When ∆G = 0, there is no net change in the system and equilibrium has been reached. A chemical reaction at equilibrium performs no work. A process is spontaneous and can perform work when sliding toward equilibrium. Movement away from equilibrium is nonspontaneous and can only occur with the help of an outside energy source. Equilibrium is an energy valley: Spontaneous Process: Does not require input of energy Example: water flowing downhill Exergonic Reaction -∆G Equilibrium (∆G = 0) Nonspontaneous Process: Requires an outside energy source Example: machine pumps water up against gravity Endergonic Reaction +∆G
5 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece)
Free Energy and Metabolism
Endergonic Exergonic and Endergonic Reactions in Metabolism Chemical reactions can be classified as either exergonic (“energy outward”) or endergonic (“energy inward”). An exergonic reaction proceeds with a net release of free energy. Since the mixture loses free energy, ∆G is negative. (Remember – free energy (G) moves out from the reactants, so G is negative). Exergonic reactions are those that occur spontaneously. The magnitude of ∆G is the maximum amount of work the reaction can perform. An endergonic reaction is one that absorbs free energy from its surroundings. This takes free energy from the surroundings and stores it in molecules, which makes ∆G positive. (Free energy (G) is moving into the products, so there is a positive G). These reactions are nonspontaneous, and the magnitude of ∆G is the quantity of energy required to power the reaction. Metabolic Disequilibrium In a closed system, reactions will reach equilibrium and be unable to do work. A cell that reaches metabolic disequilibrium is dead – no work is being performed. Thus, metabolic disequilibrium is extremely important for life. Since a cell is an open system, it can maintain disequilibrium. The constant transfer of materials in and out of the cell prevents the metabolic pathways from reaching equilibrium. A catabolic pathway in a cell releases free energy in a serious of reactions. The product of one reaction never continually accumulates: instead, it becomes the reactant in the next step. The overall sequence of reactions is powered by the large free-energy difference between glucose and the carbon dioxide and water (waste products) at the end. Free energy is transmitted to an ecosystem through sunlight – animals and nonphotosynthetic organisms depend on free-energy transfusions in the form of the products of photosynthesis. Remember that energy coupling is the use of an exergonic process to drive an endergonic one.
6 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions A cell does: 1. Mechanical work, such as the contraction of muscle cells or the beating of cilia contraction 2. Transport work, pumping substances across membranes against the direction of spontaneous movement 3. Chemical work, the pushing of endergonic reactions that would not occur spontaneously, such as synthesizing polymers from monomers lymers ATP is usually the source of energy powering cellular work.
The Structure and Hydrolysis of ATP
ATP (adenosine triphosphate) is closely related to one type of nucleotide found in nucleic acids. ATP has the nitrogenous base adenine bonded to b ribose. It is very similar to an adenine nucleotide in RNA. The bonds between the phosphate groups in ATP can be broken by hydrolysis. When the end phosphate bond is broken, a molecule of inorganic phosphate leaves the ATP, which now becomes ADP (adenosine disphosphate). This is an exergonic reaction that releases 7.3 kcal of energy per mole of ATP hydrolyzed. However, that was the free-energy change measured in laboratory conditions. In the cell, the actual energy ∆G is about -13 kcal/mole, which is 78% greater than the energy released in the standard laboratory 13 conditions. Since the hydrolysis of the phosphate bonds release energy, the bonds are sometimes referred to as high-energy phosphate bonds. Be careful to not see “high-energy” and think that the energy energy” bonds are unusually strong – “high energy” in this case means that the hydrolysis yields energy. In “high-energy” fact, the bonds are relatively weak and unstable, which allows for the energy released when they are broken. The ADP and phosphate are more stable than the ATP. Thus, the change is exergonic – free energy is being released to create stability. Since the phosphate groups are all negatively charged, being bonded together so closely results in instability of the bonds. This is comparable to a loaded spring. s.
7 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece)
How ATP Performs Work
A cell can couple the energy of ATP hydrolysis directly to endergonic processes by transferring a phosphate group from ATP to some other molecule. The molecule that receives the phosphate group is said to have been phosphorylated. phosphorylated Once a molecule is phosphorylated, it becomes more reactive than the original, which helps create a spontaneous reaction. The diagram at right illustrates how phosphorylation can induce spontaneous reactions. (a) Normally, the formation of glutamine is nonspontaneous and requires 3.4 kcal/mol. (b) With ATP present, glutamic acid becomes phosphorylated, making it more reactive. Thus, it will spontaneously join with ammonia. (c) The originally endergonic process became exergonic with the help of ATP.
The Regeneration of ATP
An organism at work constantly uses ATP, but ATP is a renewable resource. When a phosphate group is added to ADP, ATP can be created. The free energy required to phosphorylate ADP comes from catabolism in the cell. The ATP cycle is a coupling of the cell’s energy-yielding processes to the energy-producing ones. This cycle moves extremely quickly: a working muscle cell can recycle its entire supply of ATP about once each minute. The regeneration of ATP from ADP is endergonic – it is an example of anabolism in the cell. Catabolic pathways, especially cellular respiration, provide energy for the endergonic process of making ATP. ENZYMES Enzymes Speed up Metabolic Reactions by Lowering Energy Barriers A catalyst is a chemical agent that changes the rate of a reaction without being consumed by the reaction; an enzyme is a catalytic protein (ribozymes, made up of RNA, are also enzymes).
The Activation Energy Barrier
Every chemical reaction between molecules involves both bond breaking and bond forming. For example, hydrolyzing a sucrose molecule involves breaking the bonds between glucose and fructose, then bonding the hydrogen and hydroxyl group to make water. Whenever a reaction rearranges the
8 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) atoms of molecules, existing bonds must be broken and new bonds of the product must be formed. The reactant molecules absorb energy from their surroundings (free energy) to break, and then release the energy when the new bonds of the product molecules are formed. The energy required to start a reaction (break the bonds) is the free energy of activation also known activation, as activation energy (EA). It is usually provided through heat the molecules absorb. When the molecules absorb enough energy to become unstable, the bonds will break. Remember, systems rich in free energy become unstable, and seek to become stable (breaking bonds). The speed of the reactant molecules is increased as they absorb more heat, which makes the molecules collide more often and more forcefully. When the molecules settle into a new, more stable bonding arrangement, energy is released into the surroundings. If the reaction was exergonic, EA will be repaid, since the formation of the new bonds will give off more energy than was invested in the activation energy. In the graph of a reaction, the free energy of activation is represented as the energy needed to push the reactants over a hill, where the “downhill” portion is where the reaction actually takes place. The graph at right shows hypothetical molecules being rearranged in a chemical reaction. This is an exergonic reaction, since the products have less free energy than the reactants.
Enzymes and Activation Energy
Proteins, DNA, and other complex molecules are rich in free energy and have the potential to break down spontaneously. They exist only because only a few molecules have sufficient activation energy at a cell’s temperature to break them apart. Occasionally, the barrier for certain reactions must be lowered, or else metabolism could not take place. While heat speeds a reaction, too much heat will kill cells. Thus, organisms use catalysts. Through lowering the AE barrier, the transition stage is accessible even at moderate temperatures. An enzyme does not change the ∆G for a reaction. It only speeds up reactions that would eventually occur. Since enzymes are so selective about which reactions they catalyze, they determine which chemical processes will be occurring in the cell.
9 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) Enzymes are Substrate Specific The reactant an enzyme acts on is referred to as its substrate The enzyme binds to its substrate (or substrate. substrates). When the two are joined, the catalytic action of the enzyme changes the substrate to the product of the reaction. An enzyme can distinguish its substrate from even closely related compounds, such as isomers, so that each type of enzyme catalyzes a particular reaction. For instance, sucrose will only accept sucrose. Enzymes, as proteins, have a unique three-dimensional shape that allows them to recognize their substrates. A restricted region of the enzyme molecule binds to the substrate – this region is the active site and site, is typically a pocket or groove on the surface of the protein. While the active site is formed by only a few of the enzyme’s amino acids, the R groups play a large part in reinforcing the shape of the active site. When the substrate enters the active site, it induces the enzyme to change in its shape slightly so the active site fits even more snugly around the substrate. This induced fit brings chemical groups of the active site into positions that help the enzyme catalyze the chemical reaction.
The Active Site is the Enzyme’s Catalytic Center In an enzymatic reaction, the substrate binds to the active site to form an enzyme-substrate complex. The substrate is usually held in the active site with weak bonds, such as hydrogen or ionic bonds. Side chains of a few of the amino acids in the active site catalyze the conversion of substrate to product, and the product departs from the active site. The enzyme can then take another substrate molecule into its active site. The entire cycle happens quickly, and a single enzyme molecule can act on a thousand substrate molecules per second.
10 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) An enzyme can catalyze both the forward and reverse reactions of reversible metabolic reactions. Enzymes catalyze in the direction of equilibrium: if there is more A than B, enzymes will transform B to A and vice versa. There are different ways enzymes can lower activation energy and speed up a reaction. In reactions involving two or more reactants, the active site provides a template for the substrates to come together in the proper position for a reaction to occur. As the active site folds around the substrates, the enzyme may stress the substrate molecules in order to stretch and bend critical chemical bonds that need to broken. EA involves the energy needed to break bonds, thus, distorting the substrate reduces the amount of heat energy needed to reach the transition state. The active site could also provide a small environment that is conducive to a particular type of reaction. For example, if the active site has amino acids with acidic side chains, the active site could be a pocket of low pH in an otherwise neutral cell. The active site could move H+ into the substrate as a key step in catalyzing the reaction. Another mechanism involves brief covalent bonding between the substrate and a side chain of an amino acid of the enzyme. Of course, the reaction will always restore the side chains to their original state in order to keep the active site the same as before. The rate at which a certain amount of enzyme converts substrate to product is partly a function of the initial concentration of the substrate. The more substrate molecules there are, the more frequently they can access the active sites of enzyme molecules. However, at a certain point, all enzymes will be busy converting substrates and adding more substrate will not speed up the reaction. The enzyme is said to be saturated at the point when enzymes are constantly converting substrates. The rate of the reaction can then be determined by the speed at which the active site can convert substrate to product. When an enzyme population is saturated, the only way to increase productivity is to add more enzymes. A Cell’s Physical and Chemical Environment Affects Enzyme Activity
Optimal Temperature for Enzyme
Effects of Temperature and pH
As a protein, an enzyme has conditions in which it works optimally, because that environment favors the most active conformation for the enzyme molecule. Up to a point, the velocity of an enzymatic reaction will increase with increasing temperature, partly because substrates will collide with active sites more frequently when moving quickly. Beyond a certain point, the speed will drop sharply, since too much heat will denature the enzyme, which after all, is a protein.
Rate of Reaction
11 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) The temperature to the left of the optimal temperature-mark (dotted line) is perfectly fine for the enzyme. Although it may be too cold to catalyze a reaction, the enzyme will still be in its original form. After the optimal temperature, right of the dotted line, the enzyme will be denatured. Just as an enzyme has an optimal temperature, it also has a pH at which it is most active. Most enzymes work best from pH 68, but there are exceptions. Unlike temperature, enzymes cannot fall too far down either side, or they will denature. If they become either too acidic or too basic, they denature. In the diagram to the right, the area within the dotted line denotes the acceptable range for the hypothetical enzyme.
Optimal pH for Enzyme
Rate of Reaction
Many enzymes require nonprotein helpers for catalytic activity. These adjuncts, called cofactors may cofactors, be bound tightly to the active site as permanent residents, or they could bind loosely and reversibly along with the substrate. Some cofactors are inorganic, such as zinc, iron, and copper ions. If the cofactor is an organic molecule, it is called a coenzyme Most vitamins are coenzymes or raw coenzyme. materials from which coenzymes are made.
Certain chemicals selectively prevent the action of specific enzymes. If the inhibitor attaches to the enzyme with covalent bonds, inhibition is usually permanent. However, reversible inhibition occurs when the inhibitor binds with weak bonds. Some reversible inhibitors are competitive inhibitors inhibitors, resembling the normal substrate and competing for entrance into the active site. They can reduce the productivity of enzymes by physically blocking the substrate from entering the active site. This kind of inhibition can be overcome by increasing substrate content where more substrate molecules than inhibitor molecules are available to enter the sites. Noncompetitive inhibitors do not directly compete with the substrate. Instead, they bind to another part of the enzyme, which causes the active site to change shape and either become unreceptive to substrate or less effective at catalyzing conversion of substrate to product.
12 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece) THE CONTROL OF METABOLISM All a cell’s metabolic pathways are not open at the same time. A cell carefully regulates when and where various enzymes are active by either switching on and off the genes that encode specific enzymes or regulating the activity of enzymes. Metabolic Control Often Depends on Allosteric Regulation In many cases, molecules that naturally regulate enzyme activity in the cell behave like reversible noncompetitive inhibitors. They change an enzyme’s shape and function by binding weakly to an site, Allosteric site a specific receptor site on some part of the enzyme molecule away from the active site. It can either inhibit or stimulate the enzyme’s activity through binding to it.
Most allosterically regulated enzymes are constructed from two or more polypeptide subunits. Each subunit has its own active site, and allosteric sites are often located where two subunits are joined. The entire complex switches between the two conformational states, of which one is active and one is inactive. The binding of an activator to an allosteric site stabilizes the shape with a functional active site, while the binding of an inhibitor stabilizes the inactive form of the enzyme. The areas of contact between the subunits of an allosteric enzyme fit in such a way that a conformation change in one subunit is transmitted to all others. Thus, a single activator or inhibitor molecule binding to one allosteric site will affect the active sites of all subunits. Sometimes, an inhibitor and an activator are similar enough in shape to compete for the same allosteric site. For example, some enzymes of catabolic pathways may have an allosteric site fitting both AMP (adenosine monophosphate) and ATP, being activated by AMP and inhibited by ATP. This makes sense because a purpose of catabolism is to make ATP: if there are too many AMP, it will stimulate key enzymes to speed up catabolism and make more ATP. If there is a large supply of ATP, the ATP will compete for allosteric sites and slow down the catabolism.
13 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Chapter Six: An Introduction To Metabolism (Text from Biology, 6th Edition, by Campbell and Reece)
Feedback inhibition is the switching off of a metabolic pathway by its end product, which acts as an inhibitor of an enzyme within the pathway. Once the end product accumulates in enough numbers, it will allosterically inhibit the enzyme for the first step of the pathway. This prevents the cell from wasting chemical resources to synthesize more of a product than necessary.
Similar to allosteric activation, substrate molecules may stimulate the catalytic powers of an enzyme. Recall that the binding of a substrate to an enzyme can induce a favorable change in the shape of the enzyme’s active site. If an enzyme has two or more subunits, an interaction with one substrate molecule can trigger the same conformational change in all other subunits. Called cooperativity this cooperativity vity, mechanism amplifies the response of enzymes to substrates: one substrate molecule primes an enzyme to accept additional substrate molecules more readily. The Localization of Enzymes Within a Cell Helps Order Metabolism Structures within the cell help bring order to metabolic pathways. In some cases, enzymes for several steps of a metabolic pathway are arranged together as a multienzyme complex. The arrangement helps control the sequence of reactions. Some enzymes and enzyme complexes have fixed locations in the cell as structural components. Others are in solution with specific membrane-enclosed eukaryotic organelles, each with its own internal chemical environment. For example, enzymes used in cellular respiration are kept within mitochondria.