The atp molecule shown consists of a base,__________, and a chain of three phosphates.

image12.jpg image13.jpg6.4 Enzymes Direct Energy Flow

· What is an enzyme?

· How does an enzyme catalyze a chemical reaction?

· What happens to reactants within the structure of an enzyme?

· How do enzymes control the metabolism of a cell?

6.5 Energy Flow in Reaction Pathways: Metabolism

· What is a metabolic pathway?

· How is the flow of product from a metabolic pathway controlled?

· How can an enzyme's structure contribute to control of a metabolic pathway?

6.6 Energy Pools in the Cell: ATP

· Where does the cell get energy to run its endergonic reactions with?

· What does an ATP molecule look like?

· Where is energy stored within an ATP molecule?

6.7 Energy Flow from Carbohydrates to ATP: Respiration

Why are carbohydrates considered to be "energy-rich"?

What is the purpose of aerobic respiration?

What substances enter glycolysis, and what substances leave it? What is its contribution to respiration?

What substances enter the Krebs cycle, and what substances leave it? What is the cycle's contribution to respiration?

What substances enter the electron transfer system? What substances leave it? What is the system's contribution to respiration?

· What process immediately generates the energy used to make ATP?

· How much ATP is produced from one carbohydrate molecule?

6.8 Energy Flow from Carbohydrates to ATP: Fermentation

· How is fermentation different from respiration? How are they the same?

· How much ATP results from fermentation?

6.9 Energy Flow from Photons to Carbohydrates: Photosynthesis

· How do photons become energy within a cell?

· image14.jpg image15.jpg image16.jpg image17.jpg image18.jpgWhat does chlorophyll actually do in photosynthesis?

· How are the chemical reactions of photosynthesis ordered/organized?

· Where in the plant cell do the stages of photosynthesis take place?

· What carbohydrates are produced by photosynthesis?

6.10 Energy Flow: An Integrated Picture

· How do photosynthesis and respiration work together to support life?

· How did photosynthesis and respiration originate? What came first?

· What is the functional result or value of having photosynthesis limited to just some life-forms?

image19.jpgConcentration

+ +++ + + ++

++++ +++

H+

Q Electrical potential

0 Heat

Figure 6.2 Five major categories of energy change in the cell are shown here. (a) synthetic work

is demonstrated by the making of daughter cells from a parent cell, (b) movement is represented by the streaming movement of the cytoplasm, (c) concentration of a substance within a cell is effected by active transport, (d) electrical potential is generated by ion movement across a membrane,

(e) heat energy is generated by increasing the rate of respiration in the cell.

Standing in the middle of our Elodea cell and glancing around, the first change we would observe is that vast amounts of mem​brane and molecular machinery have been built up from simpler molecules. Biosynthesis of organic monomers, and their subse​quent assembly into polymers and then into supramolecular struc​tures, requires considerable energy.

But were we the size of a carbon dioxide molecule, our observa​tion of synthesized structures would be made "on the run." The cy​toplasm and many organelles within the cell are in constant motion, not the result of slow diffusional forces based on thermal energy of particles. Rather, the cell is investing energy to move its cytoplasm

biosynthesis—the building up of biomolecules about by bulk flow—a streaming process that allows molecules and

or biological structures within a living cell; a pro- materials important to cellular reactions to be quickly circulated to

cess that requires energy. where they need to go. Indeed, as we adjust the fine focus knob

of our microscope to better observe the Elodea cell, muscle cells in our fingers and eyes are also contract​ing, a form of movement that also requires energy.

Another change often required within cells is the movement of materials across membranes both into and within cells. If the molecules of a substance coming into a cell are in higher concentrations out​side the cell, then the thermal energy of random motion will cause the molecules to diffuse into the cell either through the membrane or through spe​cial gates within the membrane (see Figure 6.3). But suppose the substance is a nutrient of great value to the cell. It is to the cell's advantage to bind to and take in that nutrient even if it is already in higher concentration inside the cell. As night approaches and sugar production in Elodea leaf cells subsides, cells in the stem of the plant will take in the last few circulating molecules of sugar even though its concentration is already higher within the cell. This pumping of substances against the diffusional forces that would carry them the other way requires energy: the energy of concentration of substances.

image20.jpg image21.jpg image22.jpg image23.jpg image24.jpg image25.jpg image26.jpg image27.jpg image28.jpg image29.jpg image30.jpg image31.jpg image32.jpg image33.jpg image34.jpg image35.jpg Figure 6.3 Cells are designed to invest chemical energy to move carbohydrate molecules into their cytoplasm even against a concentration difference. Respiration of the carbohydrate will yield far more energy than that expended to acquire it

Sometimes a cell must move ions across a mem​brane. Often it moves them to the side where they are already more concentrated. Later in this chap​ter we will see how concentrating ions on one side of a membrane is a powerful way to generate large amounts of ATP in cell respiration. However, pushing ions to one side of a membrane not only requires energy for concentrating things: These ions are charged. So an electrical potential is building up across our membrane as well. The cell needs energy to push together charged particles that are repelling each other. Indeed, later on, release of this electrical potential across a membrane can be used to make ATP. The cell needs energy to do this electrical work.

Finally, although Elodea cells can live acceptably at a wide variety of temperatures, your cells cannot. Their processes require an internal temperature of 37°C. Sometimes outdoor temperatures are consid​erably below this value. You discover that your mus​cle cells are contracting, not in order to lift a weigh or move food forward in your intestines, but simply to shiver. Shivering uses cellular energy to gener​ate the metabolic heat needed to retain your body temperature close to the 37°C level at which it's de​signed to work. So sometimes cells need energy just to help maintain an optimal operating temperature.

A wide variety of kinds of cells, then, need energy for a variety of changes they are constantly mak​ing. Will there be a correspondingly wide variety of forms in which energy comes to these cells and in which it is handled by these cells? No. An elegantly unified process, governed by a few basic laws, describes energy conversions all across the living world. We'll now explore that unity.

energy of concentration—the work of moving molecules or ions against a concentration gradient, that is, moving them from where they are less concentrated to where they are already more concentrated.

electrical potential a difference in charge across a mem‑

brane based on a difference in the concentration of positive and/ or negative ions across the membrane.

IN OTHER WORDS

1. image36.jpgCathedrals and cells both require energy for their construction.

2. Energy is the ability to make specific changes occur within a cell.

3. Energy is needed within cells for biosynthesis, movement, concentration of substances, generation of elec​trical potentials, and heat.

4. image37.jpgThe generation of cellular energy is a unified process across the living world.

image38.jpg NERGY FLOW IN THE LIVING WORLD

Life Is Energy-Driven. Wonderful structural products are the result. But where does the energy come from to generate those products? Most of it comes from the sun. And as it flows through living systems, two very basic laws gov​ern its behavior. The first law is called the law of conservation of matter and energy. The law is simply diagramed and simply stated: Energy is freely convertible from one form to another, but energy can never be created or destroyed in normal processes. (The fire can't continue when the cardboard of the match is consumed.) Energy from the sun flows through nature obeying this basic law and finds its way into the living cell in the form of C–O–H and C–H bonds within the glucose molecule.

Energy: the ability to make specific changes occur.

Energy (form #1) 4 * Energy (form #2)

The second law that governs the behavior of energy in the living world can be stated as follows: Systems that convert energy from one form to another are not 100% efficient. In each conversion event, the total amount of useful energy decreases because some energy becomes useless, typically in the form of heat (the random motion of individual particles of matter). These relationships are easily seen in the exchanges occurring in an automobile engine (see Figure 6.4). The chemical energy in the gasoline is converted to movement energy within the cylinders in the engine block. Why, then, is a water pump necessary for the engine to continue operating? More than half the energy resulting from the combustion of the octane is lost to the engine block as heat energy. This energy is useless. This same useless heat energy is felt in a crowded

Figure 6.4 Photograph of an automobile engine while running. Taken

with a thermal camera. Yes, the crankshaft is turning, but that represents the minority of the energy given off by the combustion of octane. The combustion of glucose in our bodies has the same effect.

classroom at the end of the lesson period—and for much the same reason. The students burn glucose to maintain cell life and take notes. But the exchange isn't even 50% efficient. The rest of glucose's energy is lost to the room as heat.

Energy, then, flows from the sun through living systems. Eventually it all ends up in the form of heat (see Figure 6.5). It travels through organisms that are energetically classified as producers or consumers (like us). Producers convert solar energy to chemical energy—the energy of C–H and C–O–H bonds. When we ingest producer tissues—broccoli or sugared cereals—that chemical bond energy then gets us

image39.jpg image40.jpg image41.jpgconsumers going in the morning and takes us through our day. Since energy spends most of its time in the living world flowing within and between chemical bonds, we need to examine more closely the chemical reactions that break and form those bonds.

Figure 6.5 Energy flow through the living world is a one-way process. The vast majority of energy enters the living world as sunlight and departs as heat. By contrast, matter does not flow through the living world, it cycles around and back to where it started.

IN OTHER WORDS

1. image42.jpgEnergy is freely convertible from one form to another, but energy can never be created or destroyed in normal processes.

2. In all energy conversions in living systems, some of the energy given off fails to be conserved as useful energy. It is lost as heat.

3. image43.jpgEnergy flows from the sun into the chemical reaction pathways of living things and ends up as heat.

G OWS IN CHEMICAL REACTIONS

image44.jpgEnergy in C—OH and C—H bonds can be removed and then utilized in biosynthesis only through chemical reactions. This means breaking existing bonds between atoms in a molecule called the reac​tant (or substrate) and forming new bonds between different atoms creating a product molecule. For example, some bacteria use the following reaction to gain energy:

Reactants Products

image45.jpg image46.jpg image47.jpg image48.jpg image49.jpg image50.jpg image51.jpg image52.jpg image53.jpg image54.jpg image55.jpg image56.jpg image57.jpg4 hydrogen atoms 4 hydrogen atoms

+ 2 oxygen atoms + 2 oxygen atoms

Notice in the diagram that atoms are simply shuf​fled around. No new atoms or electrons just appear or quietly disappear. Matter is conserved. But in this shuffle, energy is flowing. How does that hap​pen? A chemical reaction has three characteristics we want to notice:

1. Chemical reactions proceed with energy changes. Whenever chemical bonds are broken, energy is required. Whenever chemical bonds are formed, energy is given off. Chemical re​actions can be classified according to which is greater: the requirement for energy to break initial bonds or the energy generated when new bonds form. In the reaction pictured above, less energy is required to break initial bonds than is given off when the new bonds form. We term this sort of reaction exergonic (Gk. ex- = out or away from; Gk. -gonic = energy) because the extra energy given off comes out of the reac​tion and is available to do work for us. In fact, the energy from this single reaction is what the bacterium lives off of!

If greater energy is required to break initial bonds than is generated in forming the new ones, we call the reaction endergonic (Gk. end- = in or into) because outside energy must be

added in to drive the reaction forward. Sup​pose, for example, we wished to hydrolyze water in the reverse reaction to the one shown above.

Products

Reactants

2 H2

+

02

2 H2O

(hydrogen)

(oxygen)

(water)

co co ••

4 hydrogen atoms + 2 oxygen atoms

(Photosynthesis begins with a reaction similar to this one.) Here, more energy is required to break initial bonds in the water molecules than is given off in the formation of new bonds between two hydrogen atoms and two oxygen atoms. Photosynthesis is endergonic: You have to invest solar energy to split those stable water molecules.

2. Chemical reactions are reversible. Suppose we begin our reaction with high levels of reactants A and B and little or no C and D. The reaction will generally proceed in the forward

(1)

direction as written. But reaction rates depend on the relative concentrations of the reactants

chemical reaction -a process in which bonds are broken in one kind of molecule (the reactant) and new bonds are formed to produce a product; energy change accompanies any chemical reaction.

reactant—an initial substance that absorbs energy and enters into a chemical reaction in which it is changed in structure.

product—a substance that is formed during a chemical reaction. exergonic—descriptive of a chemical reaction in which free energy is given off; a spontaneous reaction.

endergonic—descriptive of a chemical reaction in which free energy must be added in order to get the reaction to take place.

and products. As the concentrations of C and D become higher compared with those of A and B, then the reaction will begin to run in the reverse direction.

C + D (2)

Eventually, if no additional amounts of either A, B, C, or D are added to the system, the for​ward reaction will equal the reverse reaction in rate. The system will now be at equilibrium.

C + D (3)

Most cellular reactions run under non-equilib​rium conditions in which products are being removed (used or discarded) such that the reaction continues in the forward direction as in reaction (1) above.

3. Chemical reactions are relatively uncommon and slow in the nonliving world. Consider the dead cellulose in the page you are now star​ing at or the dead cashews in the box on your desk. They could sit there for 100 years and seldom participate in a chemical reaction. For most reactant molecules in nature, the amount of energy required to break their bonds—to start a reaction—is simply not present in their environment. You could strike a match under either the page or the cashew (see Figure 4.14) and supply the initial energy to break a few of those bonds. Then an exergonic reaction would get going and liberated energy would spontaneously keep it going. (It could become a house fire if we don't meddle.) The energy needed to get a chemical reaction going is called its activation energy. In a diagram (see Figure 6.6) that shows the energy state of the

Time

Figure 6.6 In an energy diagram (note the y axis) for a chemical reaction, how shall we represent the fact that energy must be invested to break bonds in the reactants? We use a small"hill"called the activation energy. That hill will prevent this reaction from running at temperatures common in living things.

reactants and their products through time, the activation energy looks like a hill to be got over. And while the size of the activation energy is different for every kind of reaction in nature, most of these energy hills are pro​hibitively high given the energy available at temperatures common on our planet. This is a good thing. It explains the stability of wood in houses and food on shelves. The world's forests would be aflame without these energy hills. No reaction can ever get going unless there's enough energy available to break bonds somewhere in the reactant molecules.

activation energy an amount of energy necessary to break

bonds in a reactant thus getting a chemical reaction started.

IN OTHER WORDS

1. In chemical reactions, energy changes occur when covalent bonds in reactant molecules are broken and

new bonds in product molecules are formed.

2. If more energy is required to break old bonds than is given off when new bonds form, the reaction is endergonic.

3. If less energy is required to break old bonds than is given off when new bonds form, the reaction is exergonic.

4. Chemical reactions are reversible. The direction in which the reaction runs depends on the relative concen​trations of reactants and products already in place.

5. A chemical reaction will never begin unless there is enough energy present to begin breaking bonds in reactant molecules. This amount of energy is termed the activation energy.

ENZYMES DIRECT ENERGY FLOW

Perhaps you are now wondering how our bacterial cells harvest energy from molecular hydrogen (H2) when hydrogen gas floats all around them in the atmosphere "doing nothing." For that matter, you burn glucose for energy. Yet glucose sits around inside of grapes on vines all over the world doing nothing. Like the breakdown of hydrogen or glucose, most important cellular reactions do not proceed spontane​ously at any significant rate when they are apart from the cells they normal occur in. But inside of cells are some very amazing protein molecules called enzymes. Enzymes catalyze chemical reactions. When we say, "George is a catalyst for change," what do we mean? We mean the changes we are seeing were possible before George showed up, but they just didn't occur at any significant rate until he did show up!

Consider the reaction diagram in Figure 6.7a. Of the two lines, focus on the brown one. The reaction—the breakdown of glucose—won't go at any signifi​cant rate at body temperature because its activation

glucose

energy is too great. How does an enzyme help with this? The enzyme is a rather complicated molecule—usually a protein—that has within its structure an active site (see Figure 6.7b). The active site is highly selective for the specific shape of the reactant molecule it is designed to bind to. And it binds the reactant in such a way as to stress just the bond that needs to be broken to get the product that is desired! How in the world is such bond-breaking specificity

enzyme—a type of protein molecule that serves as an organic catalyst in solution. It reproducibly converts one specific sort of molecule into another—a specific reactant into its product.

active site—a precise three-dimensional space within the structure of an enzyme where a specific reactant or reactants selectively bind and are there converted to a product or products.

0

Figure 6.7 Enzymes and activation energy. (a) a chemical reaction diagrammed to show the energy of the reactants and products over the time course of the reaction. The height of the energy hill shown in brown is such that, at cellular temperatures, no bonds in the substrate will be energetically unstable enough

to break. The green (enzyme catalyzed) energy hill is low enough that ordinary thermal energy within the cell will allow bonds in the reactant molecules to break freely. (b) Space-filling models showing how an enzyme combines with the reactant glucose to stress just the bond that needs breaking in order for glucose to begin the energy-yielding process of respiration.

achieved? When the reactant lodges within the ac​tive site, the precise internal shape of the site sets up weak attractions here and there with atoms in the reactant. But which atoms? The ones participating in precisely the bond to be broken! So that bond becomes weaker. But wait! How does stressing a bond in the reactant molecule help us to get over the energy hill in the diagram in Figure 6.7? By putting some stress on just the bond that needs breaking, the energy hill is greatly lowered (see the green line in Figure 6.7a). The thermal energy present in the cell is now sufficient to cause the bond to break. The reaction goes forward! In the case of glucose breakdown, that is how the whole process of cell res​piration begins. In the case of hydrogen breakdown mentioned above, lots of useful energy is given off. The bacterium's metabolism—its life—is driven by this catalyzed breakdown or "burning" of hydrogen.

What elegantly designed pieces of machinery enzymes are! Do you understand their significance for cell metabolism? By their presence, enzymes control which reactions go at significant rates within the cell at normal temperatures. Now think: By controlling which enzymes are produced, the cell controls which reactions will occur. There are 24 covalent bonds in a glucose molecule—all of them breakable. If you burn crystalline glucose with a match, they all do break! And all the useful energy is lost as heat. But only one particular bond must be broken if we want to slowly degrade glucose in an orderly way so as to extract discrete amounts of useful energy from it (see Figure 6.8). So a Genius, familiar with cell chemistry and reactant molecules,

It

H\ /H H H /

\ / '

C—O—H C-0—H

H i H

\,.,1 _ \,_,1 _

H ' ,-,"---u H ,---t-)

/ \c/ H\c/ \c/ H

\C IN*

H-0/ \C—C/ \0—H H-0 \ c_c/ \0—H

/1 I \ /I I \

H H H H

0 0 0 0

I I I I

H H H H

O 0

Figure 6.8 (a) Glucose has 24 different covalent bonds that, with energy input, could be broken. To degrade it in the orderly fashion described in Section 6.7, only the bond indicated by the arrow can be broken. (b) So, "happily"an enzyme exists whose active site holds glucose perfectly, and stresses just the bond that needs to be broken. At cellular temperatures, the available thermal energy will break this bond.

has to design an enzyme that will (1) selectively bind to just glucose and not some other molecule and (2) stress just the bond in glucose needed to produce its first orderly breakdown product. And this glucose degrading enzyme is just one small part of a much larger project in which the Designer surveys the entire set of reactions needed to run a cell. Thousands of enzymes are needed to specifi​cally catalyze them. He then invents the enzymes, the information to code for them, and the system that will access that information at the correct time to generate all the enzymes as needed. It is nothing short of glorious!

IN OTHER WORDS

1. Most chemical reactions in nature do not proceed at any significant rate because the amount of energy present is less than the activation energy for these reactions.

2. An enzyme binds to a specific reactant when the reactant diffuses into the enzyme's active site.

3. Enzymes lower the activation energy hill for specific chemical reactions, enabling them to proceed at sig​nificant rates at low cellular temperatures.

4. Activation energy for a reaction is lowered when the bond in the reactant that initially needs breaking is stressed in some way by the active site of an enzyme.

5. The existence of many kinds of enzymes in a cell allows molecules to be transformed in orderly ways within cells, slowly generating useful free energy and useful structures.

GY FLOW IN REACTION PATHWAYS: METABOLISM

As we implied earlier, it is rare that an energy-containing molecule can be utilized completely (or a cell structure constructed completely!) in a single step. Chemical reactions exist in sequences—metabolic pathways—within cells. Most of the cell's chemical reactions are arranged into this or that series of exergonic (energy yielding) or endergonic (energy requiring) reaction pathways. Consider Figure 6.9, which represents a metabolic pathway that has both linear and cy​clical parts to it. Reactants A and B are converted into product C, which is itself a reactant for another enzyme that converts C to product D, and so on—and on and on I Notice that products D and I are combined by some enzyme to make product E. Product G is split into products H and I, and H is polymerized into product J.

Is all of this controlled? Does the cell ever have too little of A or make too much of J for the cell to use? Do enzymes, glorious as they are, simply rush forward, converting every reactant molecule that comes their way into product? Biochemists have been amazed at both the intricacy and the variety of control mechanisms that govern these pathways. Consider a few ways in which traffic through a pathway like this can be controlled.

First, recall the principle of reversibility. If sub​stance J (see Figure 6.9) at the end of the process is continually used up, making a cell part, for example, it will always be in low concentration. Even though

the reactions in all the pathways are reversible, this low level of J will pull the entire set of reactions in the diagram in the forward direction to make more of J. By this same property of chemical reactions, too much of J will slow the entire pathway down.

But elegance of control rises above the level of simple availability of reactant or use of product. Most metabolic pathways in the cell have an enzyme near the beginning of the pathway that has a second bind​ing site on it—an allosteric site (Gk. allo = other, dif​ferent; Gk. stere = site; see Figure 6.10). This site is

metabolic pathway—a series of chemical reactions in a sequence in which the product of one reaction is the reactant of the next reaction.

allosteric site —a three-dimensional groove, pocket, or surface on or within an enzyme molecule; when a specifically shaped regulatory substance binds the site, the enzyme's active site is altered structurally.

Allosteric inhibition

Enzyme in high-affinity state

Figure 6.9 Metabolic Pathways. Each block represent a reactant for the reaction (arrow) ahead of it while simultaneously being the product from the reaction (arrow) before it. The molecule "J" is a polymer composed of many monomers "H".

Figure 6.10 An Allosteric Enzyme. This enzyme possesses an active site that is alterable in shape as a result of binding an inhibitor molecule at a second site on the enzyme's surface.

physically distinct from the active site where reac​tants bind and products depart. The allosteric site is designed to bind very specifically to regulatory mol​ecules from other strategic points within the cell's metabolic world. Binding of the regulatory molecule to the allosteric site changes the shape of the enzyme so that its active site is now deformed and reactant is no longer converted to product! Thus an entire metabolic pathway can be shut down by a specific kind of regulatory molecule. One obvious approach is to design the allosteric site into the first enzyme of a pathway such that it specifically binds to the product of the last enzyme in the pathway. Neat! Now, too much final product to be used up by normal means causes the product to accumulate. Extra product mol​ecules start binding to the first enzyme's allosteric site, shutting down the whole pathway. We call this pro​cess feedback inhibition (see Figure 6.11). Of course, this causes reactant molecules at the beginning of the pathway to begin to accumulate. However, they may, in turn, be useful in some other pathway.

But the regulatory molecule that precisely fits an enzyme's allosteric site often turns out to be

the product of some other metabolically related pathway or even an intracellular signal molecule arriving from the cell surface. Sometimes a cell needs to respond to a major change in its environment or its role in an organism. One strategy is to design a single regulatory protein that recognizes a carefully chosen set of enzymes, each of which begins a metabolic pathway that needs to be shut down—or started up. The regulatory protein then attaches a phosphate group to each enzyme altering the receptivity of its active site to reactant molecules (see Figure 6.12). Evidently, the control of meta​bolic pathways is elegant and finely tuned. You should be wondering at this point about the genius reflected in the design and linking together of these amazing things called metabolic pathways.

feedback inhibition—a form of rate regulation in metabolic pathways in which the product of some late reaction in the pathway controls the rate of catalysis by an enzyme earlier in the pathway.

Figure 6.11 Feedback Inhibition. This metabolic pathway converts the amino acid threonine into the amino acid isoleucine by five sequential reactions. The end product, isoleucine can be used (removed) in protein sythesis. But if it begins to accumulate, it binds as an allosteric inhibitor to the first enzyme in the pathway, shutting down production of itself.

Initial Enzymes for Four Separate Metabolic Pathways

Inactive

0— = Phosphate group

Figure 6.12 Pathway Inhibition by Enzyme Phosphorylation. Control of cell metabolism on a grand scale is sometimes effected by adding a phosphate group (-P03) to the first enzyme in a wide variety of metabolic pathways. The enzyme's active sites are all altered so as to shut down all of the pathways.

IN OTHER WORDS

1. Single chemical reactions make small changes in reactant molecules. Significant changes require a sequence of chemical reactions: a metabolic pathway.

2. Some metabolic pathways yield free energy as a product; they are exergonic. Others are endergonic.

3. Metabolic pathways can be linear or circular. A circular pathway regenerates one of the original reactants the pathway started with.

4. Removal of the end product of a metabolic pathway causes the entire pathway to be pulled in the direction of generating more of that end product.

5. Often an enzyme at the beginning of a metabolic pathway will have an allosteric site, which, when it binds a small, specific regulatory molecule, causes the enzyme's activity to be altered.

6. Often the regulatory molecule is the end product of the pathway and its binding to the allosteric site results in a deformed active site that is no longer catalytic; this is called feedback inhibition.

7. Sometimes, a single regulatory molecule phosphorylates initial enzymes in a variety of related metabolic pathways, altering their active sites so as to shut them all down or enhance their activity all at once.

OLS IN THE CELL: ATP

We have seen that metabolic pathways are of two fundamental types energetically. Exergonic ones go forward spontaneously and useful energy flows out of them. Endergonic ones (usually the ones that build cell parts) go forward only if energy flows into them and drives them forward. There is an obvious question here. Is there some way that we can har​ness the energy-releasing pathways to drive the bio​synthetic ones? Could we have exergonic pathways depositing their free energy into a pool somewhere from which the endergonic pathways could draw out energy for bringing about all the needed changes outlined at the beginning of this chapter?

Consider Figure 6.13. The cell's metabolism is arranged such that the energy-requiring pathways are nicely driven by the energy-generating pathways (ex​ergonic) shown to the right in the figure. But what is the energetic point of connection between these two types of reactions? Can any biosynthetic enzyme pick up energy from any exergonic reaction? No, that would be horribly complicated, both chemically and

Energy source

spatially within the cell. Instead (this is so brilliant), a few very common exergonic pathways work together to produce a single kind of transient, high-energy bond within an energy-storage molecule called ATP (adenos​ine triphosphate; see Figure 6.13). And the biosynthetic endergonic pathways are all designed to use ATP bond energy to drive their reactions forward! Isn't that neat?

Endergonic pathways, then, are driven forward by energy liberated by breaking the high-energy bond between the last two phosphates on ATP. That bond is easily broken (little energy is required) and lots of energy is given off when the new bonds form. ATP is the ultimate molecular connection between eating and working! You get out of bed at 6:00 a.m. because your cellular ATP pools allow you to.

ATP (adenosine triphosphate)—the major energy-storage compound in most cells; energy is given off following the breaking of a covalent bond between the second and third phosphate groups.

ATP Structure

ribose

cietadenine

(4)46

. ( three phosphate

groups

lL

adenine AMP ADP ATP

ribose P P P

0

1. The exergonic reactions within a cell provide free energy for driving the endergonic reactions in the cell.

2. The medium of exchange between exergonic reactions and endergonic reactions is energy stored in the phosphate bonds of ATP molecules.

GY LOW FROM CARBOHYDRATES TO ATP: RESPIRATION

If they are to generate ATP, all organisms on Earth need stable energy-rich molecules: They must either find them or produce them. These energy sources—molecules that are rich in C–H, N–H, and S–H covalent bonds—are the starting point for the exergonic pathways that generate cellular ATP pools (see Figure 6.13). Higher plants and animals, including humans, use three interrelated exergonic pathways and oxygen to efficiently generate large amounts of ATP from small numbers of energy-rich glucose molecules. We call this process aerobic respiration. Figure 6.14 represents the entire pro​cess: Glucose is degraded all the way to water and carbon dioxide (CO2) with the use of oxygen at the final step. Energy liberated from stable glucose mol​ecules is neatly captured within the last phosphate

glucose bond in ATP molecules. Aerobic respiration is actu​ally about 30 individual, sequential chemical reac​tions, which Figure 6.14 summarizes as just three metabolic pathways. We can further summarize the process into one simple chemical reaction showing only initial reactants and final products (see Fig​ure 6.15). This summary reaction is highly useful for seeing the overall process of respiration. It takes us quickly from the energy of glucose to the energy

aerobic respiration—a metabolic pathway in which energy-rich molecules are degraded chemically with the generation of phosphate bond energy in ATP molecules; electrons from the energy-rich initial reactant end up combining with oxygen to form water.

Aerobic Respiration

Cytoplasm

A The enzymes that carry out glycolysis are found in the cell's cytoplasm. Glucose molecules are degraded to pyruvate molecules. Two ATPs are generated. Two molecules of NAD (electron carriers) receive electrons to be used later in the pathway.

Figure 6.14 Aerobic Respiration within the Cell. The blue parts of this diagram outline the process of respiration itself. The orange sector contains the parts of the process that occur within the mitochondrion.

Aerobic Respiration Summarized

ATP

J

31)C

602

ADP

36

6CO2

6H20

36 ATP

Oxygen

ADP

Carbon

Water

ATP

(energy poor)

(energy poor)

dioxide

(energy poor)

(energy rich)

(energy poor)

Figure 6.15 Aerobic Respiration Summarized

of ATP. But the brilliance of energy manipulation can't be adequately appreciated unless we delve into the process in a bit more detail. Keep referring to Figure 6.14 while we look more closely at the first of the three stages in this process.

Aerobic Respiration: Stage 1 Glycolysis

For most organisms, extracting energy from C–H bonds commences with the sugar molecule glucose, which has seven such bonds. The first stage of the extraction process is an enzyme-catalyzed meta​bolic pathway termed glycolysis (see Figure 6.14). This pathway occurs in the cell cytoplasm and uses no oxygen. It's similar in some respects to a variety of pathways that are used by bacteria and yeast growing under anaerobic conditions (see Sec​tion 6.8). In glycolysis, each six-carbon glucose molecule is degraded and its parts rearranged to form two 3-carbon molecules of pyruvate. What makes this pathway exergonic? It's the tendency of electrons to be attracted out of bonds where they are less stable (like C–H bonds) and into bonds involving oxygen (like C-0 bonds) where they will be more stable. More stability means less kinetic energy—the energy of motion. The kinetic energy lost to the electrons along the pathway is used to create the energy-rich phosphate bonds in ATP molecules. For each molecule of glucose degraded within glycolysis, the cell gains the energy of two ATP molecules while conserving some energy that remains in the bonds within two pyruvate mole​cules (see Figure 6.14). Also, two energetic electrons get transferred from glycolysis pathway reactants into more stable bonds on special diffusible carrier molecules called NADH. These carrier molecules

matter because later in respiration, in a pathway where oxygen is directly involved, they will release these electrons to still more stable molecules, result​ing in additional ATP production.

Aerobic Respiration: Stage 2—The Krebs Cycle

The second stage of aerobic respiration (see Fig​ures 6.14, 6.16) is the Krebs cycle (named for Sir Hans Krebs, a German biochemist who identi​fied it in 1937). The Krebs cycle begins with the products of glycolysis: 2 molecules of pyruvate, both of which have considerable potential energy remaining in their molecular structure. Pyruvate molecules diffuse from the cell cytoplasm into the mitochondrion, where the second and third stages

glycolysis—the initial degradation of glucose molecules to pyruvate molecules with the generation of two molecules of ATP per molecule of glucose processed.

anaerobic—any environment or process in which oxygen is absent.

pyruvate—a three-carbon carbohydrate product of glycolysis whose continued degradation generates two-carbon fragments that serve as reactants in the Krebs cycle.

NADH (nicotinamide adenine dinucleotide)—a biomol​ecule that accepts electrons from reactants in glycolysis and the Krebs cycle and transports them in solution to an electron transfer system. The system accepts the electrons and uses them to generate ATP for the cell.

Krebs cycle—a metabolic pathway in which acetyl groups are stripped of energetic electrons and degraded to carbon dioxide; an integral part of aerobic respiration.

· Pyruvate enters the mitochondrion and loses one of its carbons in the form of 002. The remaining 2-carbon acetyl fragment is carries into the cycle by a coenzyme called CoA. At this point an electron is also conserved on an NADH carrier molecule.

The two carbon fragment adds onto a 4 carbon compound to form the six carbon citrate molecule.

0 Atoms rearranged on the reactant citrate cause another carbon to be lost as CO2 (breathe out right now!) and again an

electron is captured on another NADH.

G Further rearrange​ments on the reactant molecule cause another carbon to be lost as carbon dioxide and another electron to be captured in NADH.

iD In rearrangements at the bottom of the cycle enough energy becomes available to phosphorylate an ADP directly to form an ATP molecule.

· Further electrons are captured and transferred to carrier compounds NADH and FADH2.

· The four carbon product of the cycle at this point is prepared to be the reactant in a second turn of the cycle.

Figure 6.16 The Krebs Cycle Summarized

of aerobic respiration take place. Once inside the mitochondrion, each pyruvate molecule loses one of its carbon atoms, which, along with two oxygen atoms, becomes carbon dioxide (see Figure 6.16). The remaining two-carbon fragment, called an acetyl group, is shown entering the cyclic pathway as part of a complex known as acetyl-CoA (see the top of Figure 6.16). Since glucose degradation in glycolysis gave us two molecules of pyruvate, the Krebs cycle reactions run twice for each glu​cose molecule degraded in glycolysis. Thus four of the carbon atoms that begin glycolysis in glucose end up entering the Krebs cycle.

The Krebs cycle, like glycolysis, is exergonic. What drives all these reactions forward, generat​ing energy, is the tendency of electrons to jump from atoms in molecules like isocitrate. where they are less stable, to atoms in molecules like NADH. where they become more stable. Again, the elec​trons now on the NADH carrier molecules still contain considerable potential energy for generat​ing ATP molecules, as we shall soon see.

The carbon atoms remaining from glucose that go into the Krebs cycle on acetyl-CoA leave the Krebs cycle one after the other in the form of CO2 (see Fig​ure 6.16). Review the summary equation for respira​tion given in Figure 6.15. The Krebs cycle is where

much of the CO2 comes from that you breathe out all day long! "Does that mean I'm breathing out the carbons I ate in my oatmeal this morning?!" Yes, you've got it! The carbon atoms from your break​fast cereal are within the carbon dioxide you exhale each moment. If you see that, you are catching onto a major feature of the carbon cycle in nature.

What then are the products of the Krebs cycle? Two 3-carbon molecules of pyruvate have become six energy-poor, 1-carbon molecules of carbon dioxide. "Energy-poor? Well then, where is the energetic value in the Krebs cycle?" Notice in Fig​ure 6.16 that for each turn of the cycle, enough energy is released in one of the reactions to generate an ATP molecule directly. All the rest of the cycle's energetic value is in the electrons bound to eight carrier molecules of NADH and two of FADH2.

acetyl-CoA—a two-carbon fragment resulting from degradation of pyruvate; the fragment is attached to a large cofactor molecule that transfers the acetyl fragment onto a reactant in the Krebs cycle.

FAN!, (flavin adenine dinucleotide)—a biomolecule that accepts electrons from reactants in the Krebs cycle and transports them in solution to an electron transfer system. The system accepts the electrons and uses them to generate ATP for the cell.

The matter and energy yield of the Krebs cycle is summarized in Figure 6.14.

Aerobic Respiration: Stage 3—Electron Transfer Phosphorylation

Also within the mitochondrion, anchored within its inner membrane, is a series of proteins that receive and transfer electrons (see Figure 6.17b). Electrons are all that connect glycolysis and the Krebs cycle to the electron transfer system—just electrons. The little NADH and FADH, "electron

dump trucks" pull electrons from substrates around the Krebs cycle and travel (are soluble) to the electron transfer system, where they then lose their electrons to membrane-bound proteins that hold them even more tightly! Amazing. The whole system remains wonderfully exergonic as long as each electron "destination" attracts the electron more strongly than the molecule that currently holds it! Some Designer must have had fun see​ing all of this! Aren't you? (Perhaps your brain is fun-fatigued.. .. )

This last stage of aerobic respiration is the most ingenious of all (see Figure 6.17)! As electrons

0 Electron carriers transfer electrons from glycolysis and the Krebs Cycle to the Electron Transfer proteins in the mitochondria! membrane.

As electrons are pulled forward by each successive transfer protein, the energy given off pumps protons across the inner mitochondria! membrane.

A strong positive

charge (potential energy) begins to develop outside the membrane.

CO ATP synthase relieves this electrical potential by allowing protons to flow back into the organelle's interior. The energy of this

flow is used to phosphorylate ADPs creating ATPSs—the desired product of the

entire respiratory process.

Figure 6.17 Aerobic Respiration in relation to Mitochondrial Structure. Details of the electron transfer chain are represented.

transfer from protein to protein, each succeed​ing protein captures and holds the electrons more tightly than the previous protein. So with each step the electrons are held more stably and energy is given off as a result. This energy is used to pump protons (H+ ions) from one side of the inner mitochondrial membrane to the other. Since the outer membrane keeps all of those protons from wandering away, the electrical potential across that inner membrane starts to rise until there's a 200-millivolt (mV) difference in charge across the membrane. There's a net positive charge on the outside—and a net negative charge on the inside (see Figure 6.17c). And the fatty acid interior of the phospholipid bilayer of the inner membrane insulates the inside from the outside; it doesn't allow protons back across. So the charge just builds.

Once it builds to the level of about 200 mV, the protons do cross back over the membrane—but not by escaping through the lipid bilayer. No! There exist these wonderful proteins called ATP synthases (see Figure 6.17d). They sit like gates across that membrane. They allow the protons to respond to their mutual repulsion by racing back into the inner compartment again—but at a price. Every time about three of those protons sail through the gate, enough energy is extracted by that movement to add a phosphate group onto an adenosine diphosphate molecule (ADP), mak​ing it a triphosphate (ATP)! So here is how our mitochondrion powers the cell: It generates about three ATP molecules for each pair of electrons that "ride down" the electron transfer system.

Notice which molecule is waiting at the very end to receive and retain the electrons: It's oxy​gen, the substance you constantly breathe in and transport to this site. Molecular oxygen attracts electrons more forcefully than any molecule from any other point in the entire aerobic respira​tory system. When oxygen picks up these extra electrons, it also picks up extra protons to bal​ance itself electrically. The result is water (see Figure 6.14). Since the oxygen in the water mol​ecule holds the electrons very tightly, we say that water is energy-poor. But the ATP we generated is energy-rich. Metabolically, a fine exchange has just occurred.

Let's summarize the energetics of the whole of respiration (see Figure 6.14). For each molecule of glucose fuel that we "burn," we have a net re​turn of 2 ATP from glycolysis, 2 ATP from the Krebs cycle, and 32 ATP from the transfer of elec​trons supplied by the 12 carrier molecules. That's 36 ATPs harvested from the breakdown of a single glucose molecule.

How much energy is that? Energy can be mea​sured in units called calories. One kilocalorie is equal to 1000 calories' worth of energy. When your body degrades 6.5 ounces of glucose in res​piration, 686 kilocalories of energy are released. Of that amount, 263 kilocalories are retained in ATP bond energy. According to the second law of energetics (see Section 6.2), what happens to the rest of those calories? If we divide 686 into 263, we discover that your body converts glucose energy into ATP energy at an efficiency of about 38%. This may not appear to be very efficient, but remember, on some days, that extra heat energy is quite useful for helping to maintain our body's operating temperature. That 38% efficiency should be compared to another figure as well. Since the early 1800s, designers and engineers have labored to perfect the internal combustion engine. Now, many decades later, the automobile engine converts the energy of octane to the turn​ing of wheels at an efficiency of about 25%. Let's ruminate carefully on these two numbers before we blithely assume that respiration is the prod​uct of an unpredictable sequence of environments operating on a random sequence of mutations.

millivolt—a unit of electrical potential energy equal to 1/1000 of a volt.

ATP synthase—a protein within the mitochondrial membrane; it relieves a proton gradient by allowing protons to flow back across the membrane. It uses the resulting energy production to phos​phorylate ADP making energy-rich ATP molecules.

calorie—the amount of energy required to raise the temperature of 1 gram of water by 1°C.

IN OTHER WORDS

1. Aerobic respiration is a metabolic pathway that degrades carbohydrates capturing their stored energy in the phosphate bonds of ATP.

2. In glycolysis, the first stage of respiration, glucose is degraded to pyruvate and some of its energy is stored in the phosphate bonds of two ATP molecules and in electrons on the carrier molecule NADH.

3. In the Krebs cycle, portions of pyruvate molecules are further degraded to carbon dioxide with energy stored in electrons on the carrier molecules NADH and FADH2.

4. Carrier molecules from glycolysis and the Krebs cycle transport electrons to the electron transfer system, where they release their potential energy during the transfer process.

5. The transfer of electrons from compound to compound in the transfer system causes protons to be pumped from the interior of the mitochondria, creating an electrical potential.

6. The electrical potential is relieved by an inward flow of protons through the ATPase enzyme that phos​phorylates ADP, generating ATP.

7. Respiration generates 36 ATP from the breakdown of a single glucose molecule; in energy conversion, respiration is 38% efficient at conserving glucose bond energy.

OW FROM CARBOHYDRATES TO ATP: FERMENTATION

In exergonic reaction pathways, electrons are always moving. And they always have to end up stored somewhere on some molecule. In nature, the most stable place for electrons to end up is on oxygen molecules (making water). Water is a highly stable, energy-poor molecule. But there are many places on Earth that have little or no oxygen—the bottoms of ponds, or oceans, or wine vats! Living things or their parts die and decay in all of these areas; their bodies contain many energy-rich molecules, such as glucose in grapes (see Figure 6.18). Shall we just give up on using these nutrients because no oxygen is avail​able to respire (burn) them? That would be a major design flaw in a biosphere where most life-forms die. Dead organisms would simply accumulate in these anoxic zones. Eventually, the world's carbon supply would be tied up in those places. But in principle, life is energy-driven not oxygen-driven. Can't energy be derived from C–H bond–containing molecules even if no oxygen is present? The answer is "yes," and the process is called fermentation.