Energy rich molecule that powers all cellular activities

· 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.

A variety of microbes inhabit places in the world's environments where there is no oxygen. These bacteria and yeasts use large numbers of energy-rich molecules in short exergonic pathways to generate modest amounts of ATP that they can survive on (see Figure 6.19). Fermentation path​ways vary depending on the energy-rich molecules

Glucose

Stable energy source

Figure 6.19 Alcoholic Fermentation. This process requires no oxygen. In the initial decay process, complex carbohydrates are degraded to the glucose shown here. Glucose is

them degraded through glycolysis as in aerobic respiration with a net production of 2 ATP Electrons are pulled off of reactants along the glycolytic pathway and are finally dumped onto the small organic molecule acetaldehyde to generate ethyl alcoholic. The entire baking and brewing industry rest upon this reaction. The bakers run it to get the

carbon dioxide which raises the bread. The brewers run it to get the alcohol.

available for use. Some of these pathways are very much like glycolysis—especially when glucose is available. But what do such pathways end with? If oxygen's not the final electron acceptor (as in aerobic respiration), then where are the electrons "dumped"? One very common molecule that acts as a terminal electron holder in anaerobic energy generation is ethanol (ethyl alcohol, grain alcohol, "juice"!). Yeast cells, of species Saccharomyces cerevisiae, do fermentation at the bottom of wine vats all over Europe and upstate New York (see Figure 6.19).

Ethanol, then, is a major ingredient in a fungal (yeast) waste product that our society concentrates and drinks! If you took a yeast cell and dropped

it into a bottle of bourbon whiskey, it would die marinating in a concentrated form (70% ethanol) of its own metabolic waste. Suppose we were to concentrate urine—human metabolic waste—to that same degree. Many of us, who wouldn't consider drinking such a product, are quite casual about drinking a yeast cell's metabolic waste. Think about that one a bit. (There are bacteria in nature that neatly degrade ethanol to simpler compounds: Our services were never needed for this task.)

ethanol—a two-carbon alcohol formed when electrons on NADH are transferred to a molecule of acetaldehyde; beverage alcohol.

IN OTHER WORDS

1. The Earth has many anoxic (oxygen deficient) environments where respiration cannot take place.

2. Fermentation derives ATP energy from energy-rich carbohydrates in the absence of any oxygen.

3. The final electron acceptor in fermentation is usually a small organic molecule like ethanol or acetic acid (vinegar).

R OW FROM PHOTONS TO

• RATES: PHOTOSYNTHESIS

The flow of energy we have traced out thus far prepares us to take in an even bigger picture: The way in which the sun drives all of life! Many microbes and higher plants are called autotrophs (GK. auto = self; Gk. troph = feed on). Autotrophs need energy-rich molecules containing C–H bonds just as we do and for all the same reasons. But oak trees don't eat the squirrels inside of them, and yet, their ATP supplies are just fine. What is the source of energy-rich molecules for autotrophs? They build their own using solar energy. Then, to meet their own energy needs, they turn round and degrade these molecules, using the same respiration pathway we use. (see Figure 6.5). Autotrophs possess an amazing collection of molecules called chlorophylls, which channel solar energy into the production of high energy carbohydrates in a process called photosynthesis. Like respiration, this process has separate stages and represents something like 30 separate sequential reactions. Once again, the process can be summarized by the single expression in Figure 6.20. The glucose product of this pathway is then degraded by respiratory pathways in the same cell to generate all the ATP needed for biosynthesis, movement, and transport of materials. Just imagine over 300,000 widely differing species of plants—everything from roses to redwood trees—all carrying out photosynthesis and respiration in essentially the

same way using the same enzymes and organellar compartments! A glorious Designer envisioned it all first! Then . . . then . . . we made sense of it!

We slowly discovered that photosynthesis is really two somewhat separate processes. In the first process, called the light-dependent pathway, solar energy is used to split water molecules, gener​ate free oxygen and the temporary energy storage molecules ATP and NADPH (see Figure 6.21a). In the second process, the light-independent pathway (see Figure 6.21b), the ATP energy and the electrons

autotroph—any organism capable of taking in carbon dioxide gas from nature and using it to generate energy-rich carbohydrates.

chlorophyll—a green pigment biomolecule capable of absorb​ing solar photons and using the resultant energy to break and form covalent bonds.

photosynthesis—a metabolic pathway in which light energy is used to generate carbohydrates from carbon dioxide gas and water.

light-dependent pathway—a sequence of reactions within photosynthesis that utilize light energy to generate ATP molecules and to transfer electrons to NADP generating NADPH.

light-independent pathway—a cyclical sequence of reac​tions within photosynthesis that utilize ATP bond energy and electrons from NADPH to generate energy-rich carbohydrates.

Photosynthesis Summarized

zoc

6CO2 6H20

Carbon dioxide (energy poor)

Water (energy poor)

Chloroplasts (chlorophyll)

Glucose Oxygen

(energy rich) (energy poor)

Figure 6.20 Photosynthesis Summarized.

Suq H2O ri4

image1.jpg

Figure 6.21 Photosynthesis Dissected. (a) Light-Dependent Reactions. To the left a chloroplast is shown in a cut-away view that reveals the thylakoids

within. The reactions shown in color take place within the thylakoid and across the thylakoid membrane. (b) Light-Independent Reactions. To the right, a chloroplast is shown in a cut-away view that reveals the stromal fluid and space around the thylakoids. The reactions shown in color take place within the stromal fluid of the chloroplast.

Figure 6.22 Light Energy. (a) The sun emits energy from a broad range of the electromagnetic spectrum, including all the visible wavelengths of light. (b) Visible light is only a small portion of the total electromagnetic spectrum of wavelengths of energy that exist. It is most convenient to measure visible wavelenths of light in nanometers (10—s meters). Radio waves can be as long as 20 kilometers in length.

on NADPH are used to attach carbon dioxide to a small, existing sugar molecule making it larger and generating the additional C—H bonds that make it more "energetic." So the light-dependent pathway converts solar energy into chemical energy. The light-independent pathway uses this chemical en​ergy to "grow" sugar molecules one carbon at a time. Let's dissect these two processes a bit starting with the first.

Photosynthesis: Stage 1​Light-Dependent Reactions

Generating energy-rich carbohydrates begins with light. Visible light from the sun can be described either as energetic particles or as waves. If you bend light with a glass prism, it breaks up into its constituent wavelengths, which appear to our eyes in all the colors of the rainbow (see Figure 6.22a). Each wavelength of light has its own energy level. The shortest visible wavelength of light (violet)

consists of particles with almost twice the energy of red light, which has the longest wavelength in the visible spectrum of light.

Life was designed with visible light in mind. Visible light is only a tiny portion of an exceed​ingly broad electromagnetic spectrum of radiation that extends from ultrashort and highly powerful gamma rays to much longer and lower-powered radio waves that surround us constantly (see Fig​ure 6.22b). What is surprising is that wavelengths of radiation from most parts of this spectrum are minimally felt on the Earth's surface. The chem​istry of space and our atmosphere absorb almost all electromagnetic radiation shorter or longer in wavelength than visible light. Yet visible light waves are just the ones that are most useful for transferring energy from light to electrons in or​ganic molecules. Higher-energy wavelengths in​discriminately disrupt the structure and function of organic molecules—degrading the photosyn​thetic machinery itself. Lower-energy wavelengths increase overall molecular motion in fluids but aren't strong enough to encourage the breaking of specific covalent bonds. How wonderful! Precisely the wavelengths of energy we need for life are the ones that survive space and our atmosphere, ar​riving safely on the surface . . . of leaves.

Visible light enters the biological world when it is absorbed by pigment molecules (see Fig​ure 6.23). A variety of pigment molecules called chlorophylls are found in plants, many protistans, and many bacteria. They absorb principally vio​let, blue, and red wavelengths of light. Since they don't absorb green light very effectively, this is reflected to our eyes, causing chlorophylls—and thus plants—to appear green. Much of the light that powers photosynthesis is absorbed by these chlorophylls. Some wavelengths of light are ab​sorbed by other accessory pigment molecules, but their absorbed energy is then channeled toward the chlorophyll molecules, where the actual en​ergy conversion takes place. The result of light ab​sorption by chlorophyll is that an electron within one of its atoms suddenly gains energy and orbits its nucleus at a much higher level. This electron could, after a brief period of time, simply drop back to a more stable orbit, losing its energy in the form of heat or reradiated light (see Figure 6.24). But in photosynthesis that does not happen! In​stead, the electron leaves the chlorophyll molecule and is transferred to a nearby electron transfer compound called a quinone. Covalent bonds are

broken and formed. What was previously solar energy has now become chemical bond energy.

How does the chlorophyll molecule always have a quinone adjacent to it to pass electrons to? The glorious photosynthetic chemistry is housed in a meticulously arranged set of compartments within the green cells of the lettuce leaves you ate for din​ner tonight. Inside each cell (were!) many chloro​plasts whose insides were packed with a stacked, convoluted system of (green) membranes called thylakoids. The membranes are green because the chlorophyll we've described is situated within them (see Figure 6.25). Within the thylakoid membranes hundreds of chlorophylls and accessory pigments are held together in clusters called photosystems (see Figure 6.26). The pigment molecules harvest light and channel it to two special chlorophyll mol​ecules within each photosystem. These two mole​cules actually transfer their excited electrons along to electron-accepting quinones. There are two dif​ferent kinds of photosystems in the membrane that possess chlorophylls differing in the wavelength of light that excites them. These two kinds of photo-systems cooperate to generate a continuous flow of electrons between them. That flow results in the ATP production needed to drive the growth of sugar molecules.

electromagnetic spectrum—the entire range of radiation extending in frequency from approximately 10-" centimeters to infinity and including cosmic-ray photons, gamma rays, X-rays, ultraviolet radiation, visible light, infrared radiation, microwaves, and radio waves.

pigment molecules—organic compounds that absorb and reflect wavelengths of light selectively such that they appear to the human eye to have a particular color.

accessory pigments—organic compounds such as carot​enoids that absorb wavelengths of light not readily absorbed by chlorophyll; they transfer the energy of that absorption to nearby chlorophyll molecules, enhancing their excitation of electrons.

quinone—a class of yellow compounds found in thylakoid membranes; they accept electrons from chlorophyll molecules.

thylakoid—a membrane-enclosed sac within a chloroplast inside of which are the enzymes, pigments, and electron transfer compounds of the light-dependent reactions of photosynthesis.

photosystem—a membrane-bound collection of chlorophylls and accessory pigments that harvest light energy and make it available to the light-dependent pathway of photosynthesis.

CH2

11

CHCH3 /C /F% /% H3C—C\ /

C C C CH2CH3

I I

C—N N =C

/ \Mgr\ % \ HC, ,CH

C—N N—C

II I \

H3C—C/ C C C —CH3

/ \ / \ % \ % H /CI C C

1 1

H CH2 HC C=0

1 1

CH2 C =0

1 1 C=0 0

1 1

0 CH3

CH2 1

CH

11

C — CH3

CH2 1

CH2 1

CH2 1

HC — CH,

CH2 CH2 1

CH2

HC — CH3

1

CH2 1

CH2

CH2

CH / \ H3C CH3

Figure 6.23 Plant Pigments. (a) The molecular structure of chlorophyll a exhibits a long hydrophobic"tail"that anchors it in a thylakoid membrane. The"green" portion of the diagrammed molecule is where solar energy becomes the chemical energy of excited electrons. (b) Because chlorophyll's structure renders it particularly poor at absorbing green light wavelengths, these are reflected and leaves appear a cool green color to our eyes.

(c) Chlorophyll is constantly made and degraded all summer long. In the fall it's production stops and its degradation reveals the presence of other accessory pigments in the leaf that help to absorb some wavelengths of light that chlorophylls don't absorb as well. They also bring to our eyes the glory of fall colors.

O

Positioned right next to one of the photosystems, within the membrane, are the quinone molecules that quickly trap the excited electrons from a chlo​rophyll molecule. The electrons then enter an elec​tron transfer system similar to the one described for aerobic respiration (see Figure 6.17, right-hand side of the diagram). As the electrons move from one transfer component to the next, they release energy used to pump protons (F1+ ions) from the exterior to the interior of the thylakoid membrane. A charge begins to build up across the membrane. But again that charge is relieved by a membrane-bound ATPase enzyme (see Figure 6.26) that uses the energy to generate ATP.

The first law—the conservation of matter—states that electrons cannot simply come from

The electron may return to 0 The electron may be

its former level giving off accepted by an adjacent

light or heat. receptor molecule.

Figure 6.24 Photon Absorption by an Atom within Chlorphyll. The absorbed light energy promotes an electron to a higher energy level. (a) The electron could simply return to its more stable configuration with the energy given off either as re-emitted light or as heat. (b) If an appropriate acceptor molecule is nearby, the energized electron may jump to the acceptor molecule, resulting in a new energy-rich covalent bond. Light energy has become chemical energy.

nowhere. Once chlorophyll loses its electron to the nearby electron transport system, how does it acquire another electron for the next solar excitation event? An enzyme activity that is closely associated with the photosystem of chlorophyll molecules uses solar energy to drive an otherwise very unfavorable reaction—the splitting of (very stable) water molecules. There are plenty of water molecules around—the roots of the plant are al​ways supplying more of them. The enzyme splits away protons (H+ ions) from two water molecules and captures the now available electrons on behalf of the "wanting" chlorophyll molecule. The en​zyme then goes on to combine the two remaining oxygens to form a molecule of oxygen gas (which makes your breathing worthwhile). But what a breath-takingly facile enzyme is this amazing ma​chine that our lives are so entirely dependent upon!

Consider the electrons stolen from water. They take a long but very fast ride, chemically. They get excited by chlorophyll and travel down an electron transfer chain only to be picked up by a second, some​what different, chlorophyll in the second of the two photosystems mentioned above. In this photosys​tem they are again excited by solar energy—but to a still higher energy level (see Figure 6.26). With this additional energy they are capable of being transferred to the soluble electron carrier NADPH

Figure 6.25 Finding Photosynthesis in a Leaf. Cells within leaves (a) are arranged in discrete layers or"tissues': Toward the leaf's upper surface is a high density of

cells (b) filled with chloroplasts. In (c) the interior of a chloroplast is diagrammed. The compartments within a chloroplast remind us that Life is Complex.

Figure 6.26 The Light-Dependent Part of Photosynthesis. Two differently designed photosystems convert the energy of light into the energy of electron acceleration. The solid yellow lines represent how that added energy is relieved. The electrons are transferred from compound to compound, all the while their energy is used to pump protons (H± ions) into the thylakoid. The electrons, initially stolen from water molecules (energy poor) finally end up on a molecule of NADPH (energy rich). The ATPase enzyme (shown to the right in the thylakoid membrane) allows the protons back to the exterior. The energy given off in that flow is used to phosphorylate ADP to generate energy rich ATP

which has a role similar to the NADH used in res​piration. NADPH carries high-energy electrons to the second stage of photosynthesis where they are used to create energy-rich C-H bonds.

So then, fundamentally, the light dependent reac​tion of photosynthesis is simply a long flow of elec​trons. First they are pushed up an energy hill by the "power of the photon!." As they then flow down the energy hill, they pump protons. The displaced protons return across the membrane making ATP. Finally the electrons themselves generate NADPH once their transfer is complete.

You may be thinking, "Wait! Why not just have the light-dependent part of photosynthesis make lots of ATP and be done with it? The plant can get all its ATP from that source (instead of doing respiration), and then I'll get that ATP when I eat the plant tissue" (see Figure 6.27). But there is a design problem here. Many changes required by the cell involve substantial amounts of energy input at specific endergonic reactions. That energy can be made available to those reactions, concentrated into one single bond—if that bond is somewhat un​stable. That's what we have with ATP. It delivers, in a single bond, ample free energy to the many endergonic processes that require it. But the price is instability. ATP breaks down almost as soon as it's formed if you don't use it right away. Since it's needed within your individual cells, that's really where you need to produce it. Sugars like glucose are much more stable, absorbable, and trans​portable energy sources. So a brilliant Designer made photosynthesis complete enough to generate stable sugar molecules that we can then absorb and use at leisure to make unstable but highly useful ATP molecules.

Photosynthesis: Stage 2​Light-Independent Reactions

We must therefore invest our ATP and NADPH almost immediately into making stable sugar mol​ecules. This requires the second stage of photosyn​thesis, the light-independent stage. We call it that because it needs only the products of the light-dependent stage to operate. If we were to supply the second stage of photosynthesis with a continuous

Light-Dependent Reactions Imagined

Changes needed in Plants cells

6H20 602 12H+ 12e + ATP

411110

Chloroplasts (chlorophyll)

Oxygen (energy poor)

ingestion

of plants by animals

Figure 6.27 "If Only". ATP's available energy is highly concentrated in the covalent bond between the last two phosphates. The bond takes very little energy to break and much energy is given off when new bonds form. If only ATP were a more stable molecule, respiration and the light-independent part of photosynthesis would be entirely unnecessary—so much less to learn! It is the diffusely energetic but stable glucose and the highly energetic but unstable ATP molecule that require all the additional chemistry of respiration and photosynthesis. But an infinite Designer saw all of that and chose to use two molecular versions of energy storage—ATP and glucose.

supply of ATP and NADPH, it would generate sugar for us all day long with no input of solar energy whatever.

The light-independent reaction is simply a way of using ATP energy and NADPH's electrons to first add carbon dioxide to the structure of an existing sugar molecule and then to replace some of the en​ergy-poor C-0 bonds with energy-rich C–H bonds on that sugar molecule (see Figure 6.28a). How does this pathway begin? Land plants allow carbon diox​ide into their leaves by stomata on the undersurface of the leaf. Algae use carbon dioxide dissolved in the surrounding water.

Carbon dioxide diffuses into the cytoplasm of photosynthetic cells and then into the chloroplast. There in the semifluid matrix of the chloroplast​called the stroma—the light-independent pathway takes place. The reactions in the pathway take the form of a cycle somewhat like the Krebs cycle, only here, as you might have expected, CO, is added to the substrate molecules rather than being taken off as in the Krebs cycle! The CO, gets added to the five-carbon sugar ribulose 1,5-bisphosphate (RuBP), which is then regenerated by the end of the cycle. The enzyme that catalyzes this reaction, RuBP carboxylase, is believed to be the most abun​dant protein on the face of the Earth! Why might this be true?

Adding one carbon to a five-carbon sugar cre​ates a six-carbon hexose (sugar) that immediately is split into two 3-carbon sugars within the cycle. These small carbohydrates then receive electrons from NADPH to enrich their structures chemically with C–H bonds. Next, a series of cutting and past​ing reactions then occur among three-, four-, five-, and seven-carbon sugars within the cycle in order to regenerate RuBP. The cycle must turn six times, capturing six carbon atoms as CO2, in order to form the equivalent of one 6-carbon glucose mol​ecule. The whole process can be represented with the summary statement shown in Figure 6.28b. Ac​tually, glucose is not present in high concentrations within the cytoplasm of the plant cell. It is quickly combined with fructose to form sucrose, the major transported form of sugar in the plant, or it is po​lymerized into long molecules of starch, the major storage form of carbohydrate in the plant. Starch can be stored in the chloroplast itself until nighttime

stomata—regulated openings on the undersurfaces of leaves that control the influx of carbon dioxide and efflux of water from internal leaf tissues.

stroma—a syrupy fluid within chloroplasts that surrounds the stacks of thylakoids; the enzymes of the light-independent reaction are found in the stroma.

ribulose 1,5-bisphosphate—a twice-phosphorylated five-carbon sugar that combines with carbon dioxide in the light-independent reaction of photosynthesis to form two 3-carbon sugars.

sucrose—a disaccharide sugar composed of the monomers glu​cose and fructose; the sugar used for transporting energy through​out the tissues of a plant.

starch—a polymer of glucose molecules; used as a storage form of energy in plant tissues.

Figure 6.28 The Light-Independent Reactions of Photosynthesis. (a) The brown spheres represent carbon atoms. Note that the 6CO2 molecules entering the reaction pathway require six"turns"of the cycle in order to generate one 6-carbon glucose molecule. (b) A summary of the reactants and products of the light-independent metabolic pathway.

0

when it's converted to sucrose and distributed as needed for energy throughout the plant.

Finally, as the preceding summary reaction sug​gests, more ATP than NADPH is needed to generate our glucose molecule. Continuous operation of the light-dependent pathway as we've described it here would thus lead to a surplus of NADPH. This prob​lem is avoided, however, because a simpler version

Cyclic Electron Flow

of the light-dependent reaction exists that uses only the first photosystem. It is cyclic. Excited electrons leave chlorophyll from the first photosystem, travel an electron transfer sequence, and then return to the same photosystem, their energy spent (see Fig​ure 6.29). The spent energy pumps protons and yields ATP. But because the second photosystem is not involved, no NADPH is generated. The chloro​plast can shift freely between the simpler or more prolonged systems keeping the pools of ATP and NADPH is precise balance. Such elegant control!

Figure 6.29 Cyclic Electron Flow. If NADPH supplies in the chloroplast are adequate, solar energy is sometimes used to simply excite electrons in chlorophyll. Their carefully crafted flow back through electron transfer compounds pumps protons into the thylakoid and results in extra ATP production. Only one photosystem is involved and no NADPH is generated.

IN OTHER WORDS

1. Autotrophs are cells or organisms that generate their own energy-rich molecules using energy-poor car​bon dioxide from the environment.

2. Many autotrophs generate energy-rich molecules by capturing solar energy using chlorophyll in an energy conversion process called photosynthesis.

3. Essentially similar over hundreds of thousands of plant species, photosynthesis consists of two component parts, a light-dependent pathway, and a subsequent light-independent pathway.

4. The light-dependent pathway uses solar energy to split water molecules, release free oxygen, generate ATP, and shuttle electrons to the carrier compound NADPH.

5. The light energy used in photosynthesis derives from a very narrow portion of wavelengths of energy in the electromagnetic spectrum.

6. Excited electrons quickly lose their energy either as heat or as reradiated light unless they can be passed to an acceptor molecule that enables them to retain their added energy.

7. Electrons passed to an acceptor molecule flow rapidly through an electron transfer system formally similar to one in respiration with a similar result: ATP production.

8. The electrons leave the electron transfer system, get reexcited in a second photosystem and are finally accepted by a carrier molecule of NADP making NADPH.

9. The chloroplast can use just one photosystem or two of them to generate the products of ATP and NADPH in the proportions needed to serve the light-independent reaction.

10. The ATP molecules generated in the light-dependent reaction are too unstable chemically to serve as an energy source for the heterotrophic (animal) life-forms in the biosphere.

11. The light-independent pathway uses ATP energy and electrons from NADPH to capture energy-poor carbon dioxide and uses it to generate stable energy-rich carbohydrates.

12. In terrestrial plants, carbon dioxide enters the stomata on the underside of leaves; it then diffuses into plant cells, then into chloroplasts, where, in the stroma, it becomes chemically bound to existing carbohydrates.

13. The light-independent pathway is a cyclic series of chemical reactions that rearrange, cut, and paste carbohydrate molecules.

14. The pathway generates free carbohydrate energy sources and regenerates the five-carbon sugar that accepts carbon dioxide at the beginning of the cycle.

Let's conclude our analysis of energy's "driving effect" on life processes by comparing the two processes of photosynthesis and respiration (see Figures 6.15, 6.20). You must have noticed by now that the summary reactions for these two processes are materially precisely the reverse of each other. What does that fact mean functionally and energet​ically? Photosynthesis and respiration are comple​mentary processes within a global cycle called the carbon cycle. The major reservoirs of carbon in this cycle are atmospheric carbon dioxide, the Earth's water supply with its dissolved carbon dioxide, the organic matter in all of the living things on the sur​face of the planet, and all the residue of once-living organisms. This last category includes all coal and oil deposits (see Figure 6.30).

Photosynthesis is essentially an endergonic pro​cess. It requires the sun's energy to drive the uptake of energy-poor molecules—CO2 and H20—from their respective reservoirs and convert them into energy-rich organic molecules (like glucose) with the elaboration of free oxygen. The energy-rich glucose is then burned by heterotrophs like us.

We can't make our own fuel photosynthetically—we must depend on the autotrophs that can. The free oxygen they provide in photosynthesis can then be the final electron acceptors, pulling elec​trons off of energy-rich food molecules during the exergonic reactions of respiration.

Now that we've appreciated at least a bit of life's biochemical complexity, we dare to ask: How did all of this glorious machinery originate? Let's suppose, as many have, that metabolism evolved slowly from single chemical reactions to more com​plex pathways. We must imagine an early version of photosynthesis: just a few membrane-bound compounds that transfer electrons and that some​how learn to generate ATP as a result of electron transfer (see Figure 6.31). We next imagine that a

carbon cycle—the circulation of carbon within the biosphere, sometimes as carbon dioxide, and at other times within organic molecules such as glikose; photosynthesis and respiration are cen​tral processes in this circulation.

Figure 6.30 The Big Picture. The energy of the sun drives photosynthesis; the energy of glucose drives respiration. Respiration occurs in all higher plants and animals while photosynthesis occurs only in autotrophic forms. While matter cycles continuously between the two processes, energy flows vertically from light to chemical energy to heat.

Figure 6.31 Evolutionary Origin

of Photosynthesis and Respiration. Microfossils and layers of rock that show the effects of free oxygen are demonstrable features of sedimentary rocks. Beyond these hard evidences most of the lower portion of this figure is conjectural. It is based on the assumption that evolution takes us from what is simple to what is more complex. The photographs here show both modern cells of the blue-green cyanobacterium, and fossil forms of these bacteria. We can't know what these fossil forms were capable of metabolically.

more complex (non-cyclic) version of photosynthe​sis developed—one that generated oxygen. Our as​sumption further forces us to postpone arrival of cells capable of respiration until complex photo-synthesizers fill the atmosphere with this oxygen. It is difficult to force current evidence to require this progression of pathway development. The oldest known fossil microbes look like early members of Phylum Cyanobacteria (see Figure 6.31). Modern cyanobacteria possess the more complex form of photosynthesis although they are capable of running just the simpler version. Since these ancient cyano​bacteria exist only as fossils, they can't tell us what their metabolic abilities were. Yet if we assume life must have evolved from simple to complex, then we will assume that cyanobacteria came to have their present appearance well before they were capable of generating oxygen and NADPH since they are practically the earliest fossils we possess. So the simple-to-complex paradigm moves us to assume that respiring forms came far later than early pho​tosynthetic forms even though geologic evidence for early oxygen accumulation begins at about

the same time as unequivocal evidence for the first cyanobacterial cells.

But for a moment, let's stop trying to derive one form from another. Let's turn our attention away from when these early forms began life and ask what a Designer might have had in mind for them. A truly fascinating functional divide in nature is-observed. It is as though a Designer determined that one set of organisms—autotrophic bacteria and plants—would specialize in both energy capture and energy utilization. With their broad enzymatic capabilities, these "servant organisms" would be supremely adept in the whole business of energy handling, generating far more C–H bond energy than they would ever utilize (see Figure 6.32). Then, a whole range of heterotrophs from mini​mal microbes to the magnificence of man could,

cyanobacteria—prokaryotic cells, often colonial forms, that use chlorophyll to carry out photosynthesis with oxygen as a by-product; blue-green algae.

Figure 6.32 Independence and Dependence. Two highly sophisticated species each supremely adapted to its own role in nature. One is highly efficient at generating excessive amounts of stable chemical energy. The other simply utilizes that excess energy to work and to worship.

with a much simpler energy metabolism, fill either humbler or more exalted roles in the biosphere with stable carbohydrate energy always available

to support them. The one organism that we know has the ability to be proud is, upon study, given the knowledge that it he totally dependent on organ​isms that are completely independent of him. How fitting.

Each life-form, whether respiring, fermenting or photosynthesizing, complements every other life-form in nature. Each living thing supplies the global carbon cycle with precisely the molecules needed to render each other life-form a dynamic part of the biosphere. Powerful solar energy drives this wonderfully integrated machinery of life! How on earth could such a wondrous set of relationships originate? What would a biologist who knows St. Paul's writings answer to a ques​tion like that? There is only one answer—found in Romans 11:

"Oh the depths of the riches of the wisdom

and knowledge of God....

How unsearchable are His judgments

and His (metabolic) pathways beyond tracing out!"

IN OTHER WORDS

1. Photosynthesis uses solar energy and chlorophyll to convert energy-poor water and carbon dioxide to energy-rich carbohydrate with the evolution of free oxygen.

2. Respiration uses energy-rich carbohydrates to build up ATP resources, returning energy-poor water and carbon dioxide to the carbon cycle for photosynthesis to operate on again.

3. Evolutionary theorists believe that electron transport systems were the earliest elements of both respira​tory and photosynthetic machinery.

4. The earliest fossil forms are similar to modern cyanobacteria that currently do both photosynthesis and respiration; they are some of the most metabolically capable cells that exist.

5. The contrast between heterotrophic and autotrophic life-forms appears to be one of the most basic dis​tinctions in the mind of the Designer.

6. The man with the greatest faith attributes the wisdom inherent in the carbon cycle to environmental selec​tive forces he is entirely unable to rigorously quantitate.

QUESTIONS FOR REVIEW

1. List some specific examples (from previous chapters if necessary) where movement occurs within a living cell.

2. State the two laws that govern the behavior of energy in living things.

3. Solar energy enters life-forms and most of it is lost as heat energy. How would you describe

where the useful energy is retained within living systems?

4. Bonding two amino acids together while mak​ing a protein is an endergonic process. What does this term tell you about the process?

5. Why does glucose accumulate in grape cells but get used up in muscle cells?

6. Glucose can be degraded to energy-poor carbon 17. dioxide and water using either enzymes or a match. If the cell could withstand high tempera​tures, why would the enzyme approach still be 18. more useful to the cell?

7. What is the purpose of a metabolic pathway? Why must individual chemical reactions be linked together in such pathways?

8. If a product at the end of a pathway accumulates 19. to a high concentration, what effect will that have on the reaction generating the product?

9. How many binding sites does an allosteric enzyme have? What are their functions? 20.

10. Why are you perpetually breathing out carbon dioxide? Where does it originate? 21.

11. Write out a summary equation (reaction) for the whole process of aerobic respiration.

12. In what form does energy emerge from glycolysis? 22.

13. What is the connecting link between the Krebs cycle and the electron transfer compounds?

14. Once protons have been pumped across the inner mitochondrial membrane, what would 23. cause them to tend to flow back to the interior? What would keep them from doing so? What enables them to do so?

15. If respiration is so much more efficient than fer​mentation at deriving ATP energy from glucose, why does fermentation exist at all? 24.

16. List the reactants and products of the light-dependent pathway of photosynthesis; then do the same for the light-independent pathway.

Of what value are accessory pigments if chlorophyll molecules can themselves absorb photo energy and excite electrons with it? Draw a slice through a chloroplast showing its interior structure. Label the following terms: thylakoid, stroma, photosystem, ATPase, site of light-dependent reaction, and site of light-independent reaction.

Explain in your own words why you and I cannot simply absorb, digest, and utilize ATP generated by the light-dependent reaction of photosynthesis.

Why is the light-independent reaction pathway so named?

How many times must the light-independent cycle of reactions turn to generate one molecule of glucose? Why?

Why would a thylakoid sometimes use just one photosystem and generate only ATP when the electrons involved could simply go on, given sunlight, to generate more NADPH as well?

Draw your own diagram of the carbon cycle using figures from this chapter and the follow​ing terms: carbon dioxide, glucose, water, oxy​gen, mitochondrion, chloroplast, autotrophs, heterotrophs, atmosphere, dissolved carbon dioxide, and fermentation.

Metabolically, which of the following organisms is most independent of any other organism: man, cats, heterotrophic bacteria, eagles, cyano​bacteria, or mushrooms? Explain why.

QUESTIONS FOR THOUGHT

1. Consider a membrane within a cell where ions are being moved from one side of the membrane to the other (where they are already in higher concentration). Why would this require more energy than doing the same thing with glucose molecules?

2. Besides the water circulated by a water pump, what other critical substance in an automobile engine reminds us that most of combustion's energy ends up as heat?

3. Large "No Smoking" signs are found on gaso​line pumps everywhere. Use the term activation energy to explain why.

4. In terms of atoms, electrons, and covalent bonds, explain how an enzyme's active site low​ers a reaction's activation energy.

5. What is the advantage to a cell to have a met​abolic pathway that is subject to feedback inhibition?

6. Why do we say that ATP is an energy-rich mol​ecule when energy is actually required to break any covalent bond, including the phosphate bond of the ATP molecule?

7. Is respiration one metabolic pathway or is it three pathways? Explain your choice.

8. The process that causes bread to rise (found within the yeast Saccharomyces) is exactly the same fermentation pathway used to make wine. Why don't we get drunk eating bread?

9. Use an Internet search engine to answer these questions: How can some autotrophs make energy-rich molecules deep in the ocean depths

where no solar energy exists at all? What is their energy source? Hint: They are called chemoau​totrophs. Land plants are photoautotrophs.

10. If you believe in evolution, which of the follow​ing systems would have evolved first: respiratory pathways, photosynthetic pathways, or proton pumping? Why?

GLOSSARY

accessory pigments—organic compounds such as carotenoids that absorb wavelengths of light not readily absorbed by chlorophyll; they transfer the energy of that absorption to nearby chlorophyll molecules, enhancing their excitation of electrons.

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.

activation energy—an amount of energy necessary to break bonds in a reactant thus getting a chemical reaction started.

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.

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 re​actant end up combining with oxygen to form water.

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.

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

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 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 phosphorylate ADP making energy-rich ATP molecules.

autotroph—any organism capable of taking in car​bon dioxide gas from nature and using it to generate energy-rich carbohydrates.

biosynthesis—the building up of biomolecules or biological structures within a living cell; a process that requires energy.

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

carbon cycle—the circulation of carbon within the biosphere, sometimes as carbon dioxide, and at other times within organic molecules such as glu​cose; photosynthesis and respiration are central pro​cesses in this circulation.

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.

chlorophyll—a green pigment biomolecule capable of absorbing solar photons and using the resultant energy to break and form covalent bonds.

cyanobacteria—prokaryotic cells, often colonial forms, that use chlorophyll to carry out photosyn‑ thesis with oxygen as a by-product; blue-green algae.

electrical potential—a difference in charge across a membrane based on a difference in the concen​tration of positive and/or negative ions across the membrane.

electromagnetic spectrum—the entire range of radiation extending in frequency from approxi​mately 10213 centimeters to infinity and includ​ing cosmic-ray photons, gamma rays, X-rays, ultraviolet radiation, visible light, infrared radiation, microwaves, and radio waves.

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

energy—the capacity to do work; the capacity to make changes of importance to a living thing.

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

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

ethanol—a two-carbon alcohol formed when elec​trons on NADH are transferred to a molecule of ac​etaldehyde; beverage alcohol.

exergonic—descriptive of a chemical reaction in which free energy is given off; a spontaneous reaction.

FADH2 (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.

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 ca​talysis by an enzyme earlier in the pathway.

fermentation—a short metabolic pathway in which electrons transferred to NADH carrier molecules are finally accepted, not by oxygen but by some organic molecule.

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

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.

Life Is Energy Driven—one of 12 principles of life on which this book is based.

light-dependent pathway—a sequence of reactions within photosynthesis that utilize light energy to generate ATP molecules and to transfer electrons to NADP generating NADPH.

light-independent pathway—a cyclical sequence of reactions within photosynthesis that utilize ATP bond energy and electrons from NADPH to gener​ate energy-rich carbohydrates.

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