Energy, Enzymes, Cellular Respiration and Photosynthesis

A living cell is a chemical factory that never shuts down: it pulls energy out of food or sunlight, stores it briefly in ATP, and spends it to build, move and copy itself. This chapter follows that energy from the laws of thermodynamics through the enzymes that control every reaction, the breakdown of glucose in cellular respiration, and the capture of light in photosynthesis. Once you see how these pathways connect, much of physiology, nutrition, agriculture and medicine becomes far easier to understand.

Section 1Energy, free energy and ATP

Metabolism and the forms of energy

Metabolism is the sum of all the chemical reactions in an organism, organized into metabolic pathways in which each step is catalyzed by a specific enzyme. Catabolic pathways break complex molecules down and release energy (cellular respiration is the classic example); anabolic pathways consume energy to build complex molecules, such as proteins from amino acids. The energy released by catabolism pays for anabolism.

Energy is the capacity to cause change, or to do work. Kinetic energy is the energy of motion, and thermal energy is the kinetic energy of randomly moving molecules; when it is transferred between objects we call it heat. Potential energy is energy stored by location or structure, such as water behind a dam or a proton gradient across a membrane. Chemical energy is the potential energy in the arrangement of atoms in molecules; glucose has much more of it than the carbon dioxide and water it can become.

The laws of thermodynamics

Thermodynamics is the study of energy transformations. An organism is an open system that exchanges energy and matter with its surroundings.

The first law of thermodynamics states that energy can be transferred and transformed but not created or destroyed. A plant converts light energy into chemical energy; an animal converts the chemical energy in food into movement, gradients, new bonds and heat.

The second law of thermodynamics states that every energy transfer or transformation increases the entropy (disorder, or the dispersal of energy) of the universe. No transformation is perfectly efficient; some energy is always lost as heat the cell cannot use. Living things build ordered structures only by taking in organized energy (food or light) and releasing heat and simple, low energy molecules to the surroundings, so the entropy of organism plus surroundings always rises.

Free energy and spontaneous change

To predict whether a reaction can occur without an outside input of energy, biologists use free energy (G), the portion of a system's energy that can do work when temperature and pressure are uniform, as they are in a cell. The change in free energy during a reaction is

ΔG = ΔH − TΔS

where ΔH is the change in enthalpy (total energy, essentially the energy in bonds), ΔS is the change in entropy, and T is the absolute temperature in kelvins. A reaction with a negative ΔG loses free energy and is spontaneous, meaning it is energetically favorable and can proceed without an energy input. In biology the word spontaneous says nothing about speed. The oxidation of a sugar cube in air has a large negative ΔG, yet the cube sits on the table for years, because a barrier called activation energy (Section 2) keeps the reaction from starting.

Reactions are classified by the sign of ΔG:

• An exergonic reaction releases free energy (ΔG is negative). The products have less free energy than the reactants. The complete oxidation of one mole of glucose, C6H12O6 + 6 O2 → 6 CO2 + 6 H2O, has a standard ΔG of about −686 kcal/mol (−2,870 kJ/mol).
• An endergonic reaction absorbs free energy (ΔG is positive). It is not spontaneous, and the energy must come from somewhere else. Photosynthesis, the reverse of glucose oxidation, is strongly endergonic; its energy comes from light.

At chemical equilibrium the forward and reverse reactions occur at the same rate, ΔG is zero, and the system can do no work. A cell at metabolic equilibrium would be dead, so living cells keep their pathways far from equilibrium: products are constantly pulled away by the next reaction and fresh substrates constantly arrive.

ATP: the cell's energy currency

Cells do three main kinds of work: chemical work (pushing endergonic reactions, such as building polymers), transport work (pumping substances across membranes against their gradients), and mechanical work (beating cilia, contracting muscle, moving chromosomes). Most of this work is powered, directly or indirectly, by ATP (adenosine triphosphate).

ATP is a nucleotide made of adenine, the sugar ribose, and a chain of three phosphate groups joined by phosphoanhydride bonds. These are often called "high energy bonds," but the bonds are not unusually strong. The three negatively charged phosphates repel one another, and the products of hydrolysis are far more stable. Removing the terminal phosphate yields ADP plus inorganic phosphate (P_i) and releases about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions, and closer to 13 kcal/mol under cellular conditions.

Energy coupling and phosphorylation

Energy coupling is the use of an exergonic process to drive an endergonic one. The overall ΔG of two coupled reactions is the sum of their individual ΔG values, so as long as the sum is negative, the pair proceeds. The cell rarely just hydrolyzes ATP and lets the energy escape as heat. Instead, an enzyme transfers the terminal phosphate from ATP to another molecule, a step called phosphorylation. The phosphorylated intermediate is less stable (has more free energy) than the original molecule, so its next reaction becomes exergonic.

Consider the synthesis of glutamine from glutamate and ammonia (ΔG about +3.4 kcal/mol). The enzyme first phosphorylates glutamate using ATP, and the phosphorylated intermediate then reacts readily with ammonia. The coupled reaction has an overall ΔG of about −3.9 kcal/mol (+3.4 − 7.3). Transport and mechanical work follow the same logic: the sodium potassium pump changes shape when phosphorylated, and motor proteins such as myosin change shape as they bind and hydrolyze ATP.

ATP is a renewable resource. The ATP cycle regenerates ATP from ADP, an endergonic reaction paid for by catabolism. A working muscle cell recycles its whole ATP pool in about a minute, some 10 million molecules per second, and an adult turns over roughly his or her body weight in ATP each day. ATP is a currency spent as fast as it is earned; long-term storage is the job of glycogen, starch and fat.

Oxidation, reduction and electron carriers

Much of the energy flow in metabolism is the movement of electrons. A reaction that transfers electrons from one substance to another is an oxidation reduction reaction, or redox reaction. Losing electrons is oxidation; gaining electrons is reduction (the mnemonic is OIL RIG: oxidation is loss, reduction is gain). The electron donor is the reducing agent and the electron acceptor is the oxidizing agent. In biology, electrons often travel with protons, as hydrogen atoms, so a molecule that loses hydrogen atoms is usually being oxidized.

Electrons release energy when they move from a less electronegative atom to a more electronegative one. In glucose they are shared evenly between carbon and hydrogen; in CO2 and water they are pulled close to oxygen. The cell does not let them fall to oxygen all at once, as in a fire, but hands them in small steps to electron carriers.

The most important carrier is the coenzyme NAD⁺ (nicotinamide adenine dinucleotide, from the vitamin niacin). Dehydrogenase enzymes remove two hydrogen atoms from a fuel, give both electrons and one proton to NAD⁺, and release the other proton, forming NADH. A related carrier, FAD (from riboflavin), becomes FADH2. Photosynthesis uses NADP⁺, which becomes NADPH; NADH mainly feeds energy harvest, while NADPH supplies reducing power for synthesis.

Section 2Enzymes and their regulation

Activation energy and catalysis

Every reaction must pass through an unstable transition state in which old bonds are strained and new ones partly formed. The energy needed to reach it is the activation energy (E_A). At body temperature few molecules collide hard enough to get over this barrier, and heating the cell would denature proteins and speed every reaction indiscriminately.

A catalyst is a substance that speeds a reaction without being consumed. Biological catalysts are enzymes, nearly all of them proteins (a few are RNA molecules called ribozymes, such as the ribosomal RNA that forms peptide bonds). Enzymes speed reactions, often by factors of a million or more, by lowering the activation energy. They do not change ΔG, they do not change the position of equilibrium, and they cannot make an endergonic reaction exergonic. They simply let the reaction reach equilibrium faster, and because each enzyme catalyzes only one reaction or a small set of reactions, they let the cell decide which reactions happen.

The active site and induced fit

The reactant an enzyme acts on is its substrate. The substrate binds to a pocket or groove on the enzyme, the active site, usually formed by only a handful of amino acids brought together by the protein's folding. The shape and chemistry of the active site make enzymes highly specific: sucrase hydrolyzes sucrose but not maltose, even though both are disaccharides. When the substrate enters, the enzyme changes shape slightly so that the active site grips the substrate more snugly, an effect called induced fit. The older "lock and key" picture captures specificity but misses this flexibility.

Within the enzyme substrate complex, the active site lowers the activation energy in several ways:

• It acts as a template that holds two or more substrates in the correct orientation to react.
• It strains the substrate's bonds, bending it toward the transition state.
• It provides a favorable microenvironment, for example a pocket of acidic side chains that can donate protons.
• Amino acid side chains can participate directly, briefly forming covalent bonds with the substrate before the product is released.

The enzyme is unchanged by the reaction and may handle thousands of substrate molecules per second. The rate rises with substrate concentration until every enzyme molecule is busy; the enzyme is then saturated and the reaction runs at its maximum velocity, V_max. The substrate concentration giving half of V_max is the Michaelis constant, K_m; a low K_m means high affinity for the substrate.

Effects of the environment

Because an enzyme's activity depends on its shape, anything that changes shape changes activity. Each enzyme has an optimal temperature and optimal pH. Warming speeds collisions and the rate rises, until the weak bonds holding the protein's shape break and the enzyme denatures. Most human enzymes work best near 37°C, while enzymes of hot spring bacteria work best at 70°C or higher (one of them, Taq polymerase, makes the polymerase chain reaction possible). Pepsin in the stomach has a pH optimum near 2; trypsin in the small intestine works best near pH 8.

Many enzymes need nonprotein helpers called cofactors. Inorganic cofactors are metal ions such as zinc, iron, copper and magnesium. Organic cofactors are called coenzymes, and most vitamins are needed in the diet because they are coenzymes or their precursors: niacin for NAD⁺, riboflavin for FAD, pantothenic acid for coenzyme A, thiamine for the coenzyme of pyruvate dehydrogenase.

Enzyme inhibitors

Chemicals that selectively block enzymes are called inhibitors. If an inhibitor attaches by covalent bonds, the inhibition is usually irreversible; if it attaches by weak bonds, it is reversible.

• Competitive inhibitors resemble the normal substrate and compete for the active site. Because binding is reversible, adding more substrate can outcompete the inhibitor. A competitive inhibitor raises the apparent K_m (more substrate is needed to reach half speed) but leaves V_max unchanged. Statin drugs, which lower cholesterol, are competitive inhibitors of HMG-CoA reductase.
• Noncompetitive inhibitors bind elsewhere on the enzyme and change its shape so that the active site works less effectively. Adding substrate cannot overcome them. They lower V_max; in the classic pure form K_m is unchanged.
• Irreversible inhibitors bond covalently to the enzyme. Nerve gases such as sarin bind a serine in the active site of acetylcholinesterase; penicillin permanently disables the bacterial enzyme that cross links the cell wall; aspirin acetylates cyclooxygenase.

Allosteric regulation and feedback inhibition

Cells control which pathways run by switching enzymes on and off. In allosteric regulation, a regulatory molecule binds an allosteric site separate from the active site and stabilizes either the active or the inactive shape of the enzyme, which is usually built of several subunits. An activator stabilizes the active form and an inhibitor the inactive form; because binding is reversible, activity tracks the regulators' concentrations.

In cooperativity, substrate binding at one active site shifts the other subunits to their active shape, raising their affinity and giving an S shaped (sigmoidal) rate curve. Hemoglobin is not an enzyme, but its cooperative oxygen binding works the same way.

The most common control logic is feedback inhibition, in which a pathway's end product inhibits an early enzyme, often the first committed step. In some bacteria, isoleucine is made from threonine in five steps; accumulating isoleucine binds an allosteric site on threonine deaminase, the first enzyme, and shuts the pathway down until isoleucine is used up. Section 4 shows the same principle at phosphofructokinase.

Cells also regulate enzymes by adding or removing phosphate groups (Chapter 4), by controlling how much enzyme is made, and by localizing enzymes in particular compartments, such as the citric acid cycle enzymes in the mitochondrial matrix.

Section 3Glycolysis, the citric acid cycle and oxidative phosphorylation

An overview of cellular respiration

Cellular respiration is the catabolic process that extracts energy from organic fuel by oxidizing it, ideally all the way to carbon dioxide and water. In aerobic respiration the final electron acceptor is oxygen. Some prokaryotes carry out anaerobic respiration, using a different inorganic final acceptor such as sulfate or nitrate. Glucose is the fuel textbooks follow, but fats and proteins feed into the same pathways (Section 4). The overall equation for glucose is

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy (ATP and heat)

In this reaction glucose is oxidized to carbon dioxide and oxygen is reduced to water. Respiration has three stages:

1. Glycolysis, in the cytosol, splits glucose into two molecules of pyruvate.
2. Pyruvate oxidation and the citric acid cycle, in the mitochondrial matrix (in the cytosol of prokaryotes), finish the oxidation of the fuel to carbon dioxide.
3. Oxidative phosphorylation, at the inner mitochondrial membrane, uses an electron transport chain and chemiosmosis to make most of the ATP.

ATP is made in two ways. In substrate level phosphorylation, an enzyme transfers a phosphate group directly from a phosphorylated substrate to ADP. This happens in glycolysis and in the citric acid cycle and accounts for only about 4 ATP per glucose. In oxidative phosphorylation, the energy of electrons passed down the transport chain builds a proton gradient that drives ATP synthase; this accounts for about 26 to 28 ATP per glucose, nearly 90 percent of the total.

Glycolysis

Glycolysis ("sugar splitting") is a sequence of ten enzyme catalyzed reactions in the cytosol that breaks one six carbon glucose into two three carbon molecules of pyruvate. It does not require oxygen and occurs in nearly every living organism, which suggests it evolved very early, before oxygen was abundant in the atmosphere and before eukaryotic organelles existed. Its steps fall into two phases.

In the energy investment phase (steps 1 to 5), the cell spends 2 ATP. Hexokinase phosphorylates glucose to glucose 6-phosphate, which traps it in the cell because the charged molecule cannot cross the membrane. After an isomerization to fructose 6-phosphate, the enzyme phosphofructokinase (PFK) adds a second phosphate, forming fructose 1,6-bisphosphate. This is the committed step of glycolysis and its main control point. Aldolase then splits the six carbon sugar into two three carbon sugars, glyceraldehyde 3-phosphate (G3P) and dihydroxyacetone phosphate, which is converted to a second G3P.

In the energy payoff phase (steps 6 to 10), each G3P is oxidized by a dehydrogenase that transfers electrons to NAD⁺, producing NADH, while a phosphate from solution is attached. Two later steps transfer phosphates to ADP by substrate level phosphorylation; the last, catalyzed by pyruvate kinase, produces pyruvate. Because everything after the split happens twice per glucose, the payoff phase yields 4 ATP and 2 NADH.

The net result of glycolysis per glucose is 2 pyruvate, 2 ATP (4 made minus 2 invested) and 2 NADH. No carbon dioxide is released. Glycolysis captures only a small fraction of the energy in glucose; most of it remains in the two pyruvate molecules, waiting to be extracted in the mitochondrion.

Pyruvate oxidation

In eukaryotes, pyruvate enters the mitochondrion by active transport. There, a large multienzyme complex, pyruvate dehydrogenase, carries out three linked steps for each pyruvate: it removes the carboxyl group as CO2 (the first carbon dioxide released in respiration), oxidizes the remaining two carbon fragment while reducing NAD⁺ to NADH, and attaches the resulting acetyl group to coenzyme A, forming acetyl CoA. Per glucose, this link step produces 2 acetyl CoA, 2 CO2 and 2 NADH. Acetyl CoA is a crossroads molecule: it can enter the citric acid cycle for energy or, when energy is plentiful, be used to make fatty acids.

The citric acid cycle

The citric acid cycle (Krebs cycle) in the mitochondrial matrix completes the oxidation of the fuel in eight steps. First, the two carbon acetyl group joins the four carbon oxaloacetate to form the six carbon citrate. Two carbons are then removed as CO2, and the remaining four carbon molecules are oxidized and rearranged until oxaloacetate is regenerated. The succinate dehydrogenase step, the only one catalyzed by an enzyme in the inner membrane, transfers electrons to FAD.

Each turn of the cycle (one acetyl CoA) produces 2 CO2, 3 NADH, 1 FADH2 and 1 ATP (in animal cells, often made first as GTP and then transferred to ADP). Because one glucose yields two acetyl CoA, the cycle turns twice per glucose: 4 CO2, 6 NADH, 2 FADH2 and 2 ATP. Notice that the cycle itself does not use oxygen, but it stops quickly without oxygen because it depends on a supply of NAD⁺ and FAD that only the electron transport chain can regenerate.

The electron transport chain

By the end of the citric acid cycle, glucose has been completely oxidized to CO2, but only 4 ATP have been made. Most of the energy is held in the electrons carried by 10 NADH and 2 FADH2. The electron transport chain releases that energy in small, usable steps. In eukaryotes it is a series of protein complexes embedded in the folded inner mitochondrial membrane (the cristae, whose folding provides enormous surface area); in prokaryotes it lies in the plasma membrane. Most carriers are proteins with tightly bound prosthetic groups, such as iron sulfur clusters and the heme groups of proteins called cytochromes.

NADH donates its electrons to complex I (NADH dehydrogenase). FADH2, bound in complex II (succinate dehydrogenase), adds its electrons at a lower energy level. Both complexes pass electrons to ubiquinone (Q), a small, mobile, lipid soluble carrier that moves within the membrane. Q delivers electrons to complex III, which hands them to cytochrome c, a small mobile protein on the outer face of the inner membrane. Cytochrome c carries them to complex IV (cytochrome oxidase), which passes them to oxygen, the final electron acceptor. Oxygen picks up a pair of hydrogen ions and becomes water. Each carrier is more electronegative than the one before, so electrons fall step by step down an energy gradient of about 53 kcal/mol from NADH to oxygen.

The chain itself makes no ATP. Its job is to use the energy of falling electrons to pump hydrogen ions (protons) from the matrix across the inner membrane into the intermembrane space. Complexes I, III and IV act as proton pumps; complex II does not, which is one reason FADH2 yields less ATP than NADH.

Chemiosmosis and ATP synthase

Proton pumping creates a proton motive force: a higher H⁺ concentration and positive charge in the intermembrane space. Protons cannot cross the lipid bilayer, so their only route back is through ATP synthase. As protons flow through it, they turn a rotor and internal rod, and the rotation changes the shape of the catalytic knob in the matrix so that it joins ADP and P_i into ATP. Using a hydrogen ion gradient across a membrane to drive cellular work is called chemiosmosis; it also makes ATP in chloroplasts and powers bacterial flagella.

Each NADH supplies enough proton pumping to make about 2.5 ATP, and each FADH2 about 1.5 ATP. The two NADH from glycolysis are made in the cytosol and must pass their electrons into the mitochondrion through a shuttle; depending on the cell type the shuttle delivers them to NAD⁺ (full value) or to FAD (lower value). This is why the total is given as a range: about 30 to 32 ATP per glucose (older books quote 36 to 38, based on earlier estimates). Respiration captures roughly 34 percent of the energy in glucose as ATP; the rest is released as heat, which helps mammals and birds keep a constant body temperature.

Section 4Fermentation and the regulation of respiration

Why cells need to regenerate NAD⁺

Without oxygen, the electron transport chain stops and NADH accumulates. Glycolysis can still make 2 ATP per glucose without oxygen, but it needs a steady supply of NAD⁺, and the cell holds only a small pool. Cells solve this problem either by anaerobic respiration, in which a prokaryote uses a transport chain with a final acceptor other than oxygen, or by fermentation, in which NADH simply hands its electrons to pyruvate or a derivative of it.

Lactic acid and alcohol fermentation

Fermentation consists of glycolysis plus one or two reactions that regenerate NAD⁺ by transferring electrons from NADH to an organic molecule. It makes no additional ATP; its only purpose is to keep glycolysis running. The two most common types differ in what accepts the electrons.

In lactic acid fermentation, lactate dehydrogenase reduces pyruvate directly to lactate, oxidizing NADH to NAD⁺; no CO2 is released. Lactic acid bacteria do this when they turn milk into yogurt and cheese. Human skeletal muscle switches to lactic acid fermentation when it uses ATP faster than oxygen arrives, as in a sprint, and the liver later converts the lactate back to glucose. Lactate is not the cause of next day soreness, which reflects small injuries to muscle fibers.

In alcohol fermentation, pyruvate first loses CO2 to become acetaldehyde, which is then reduced by NADH to ethanol, regenerating NAD⁺. Yeasts carry out alcohol fermentation; the CO2 raises bread dough and the ethanol is the basis of brewing and winemaking.

Comparing fermentation, anaerobic and aerobic respiration

All three processes use glycolysis to make a net 2 ATP per glucose with NAD⁺ as the oxidizing agent. They differ in the final electron acceptor: an organic molecule in fermentation, oxygen or another inorganic molecule in respiration. Aerobic respiration yields about 16 times more ATP per glucose than fermentation, so fermenting cells must consume glucose much faster.

Organisms differ in their dependence on oxygen. Obligate anaerobes, such as the Clostridium species that cause tetanus and botulism, cannot use oxygen and are often poisoned by it. Facultative anaerobes, such as yeasts, E. coli and human muscle cells, switch between respiration and fermentation depending on oxygen supply. Obligate aerobes require oxygen.

Other fuels feed the same pathways

Glycolysis and the citric acid cycle are metabolic hubs. Free glucose is only one of many fuels. Starch and glycogen are hydrolyzed to glucose, and other sugars such as fructose and galactose are converted into glycolytic intermediates.

• Proteins are digested to amino acids, which are used mostly to build new proteins. Excess amino acids are deaminated: the amino group is removed and excreted (in mammals, as urea made in the liver), and the remaining carbon skeleton enters glycolysis or the citric acid cycle as pyruvate, acetyl CoA or a cycle intermediate.
• Fats are split into glycerol and fatty acids. Glycerol is converted to G3P, a glycolytic intermediate. Fatty acids are broken down by beta oxidation in the mitochondrial matrix into two carbon fragments that enter the cycle as acetyl CoA; each round of beta oxidation also yields one NADH and one FADH2. Because fatty acids are highly reduced (rich in C to H bonds), a gram of fat yields more than twice as much ATP as a gram of carbohydrate (about 9 versus 4 kcal per gram). The 16 carbon fatty acid palmitate yields about 106 ATP.

Regulation of cellular respiration

Cells are thrifty: they make ATP when it is needed and slow down when it is plentiful. The main control mechanism is feedback inhibition of key enzymes by allosteric regulators (Section 2). The most important control point is phosphofructokinase (PFK), which catalyzes the committed step of glycolysis.

• PFK is inhibited by ATP. When ATP is abundant, respiration slows.
• PFK is activated by AMP (and ADP). AMP accumulates when ATP is being used up quickly, so a high AMP level is the cell's signal to speed up.
• PFK is inhibited by citrate, the first product of the citric acid cycle. If citrate builds up in the cytosol, the cycle is running faster than needed, and glycolysis slows to match it. This synchronizes the two stages.

Other control points act later: pyruvate dehydrogenase is inhibited by acetyl CoA and NADH, and oxidative phosphorylation slows automatically when ADP is scarce. Hormones such as epinephrine (Chapter 4) add another layer by mobilizing glucose from glycogen during exercise or stress.

Section 5Photosynthesis: light reactions, the Calvin cycle, C4 and CAM plants

The process that feeds the biosphere

Photosynthesis converts light energy into the chemical energy of sugars. Plants, algae and cyanobacteria are photoautotrophs: they make organic molecules from CO2 using light, and they are the producers of almost every ecosystem. Heterotrophs, including animals and fungi, obtain organic molecules by eating other organisms, so they depend on photosynthesis too.

The overall equation is commonly written

6 CO2 + 12 H2O + light energy → C6H12O6 + 6 O2 + 6 H2O

or, simplified, 6 CO2 + 6 H2O → C6H12O6 + 6 O2. Experiments using water labeled with the heavy oxygen isotope ¹⁸O showed that the O2 released comes from water, not from carbon dioxide: water is oxidized, and its light-energized electrons reduce CO2 to sugar.

Chloroplasts and pigments

In plants, photosynthesis occurs mainly in the mesophyll cells of leaves. CO2 enters and O2 exits through pores called stomata. A chloroplast has two outer membranes around a fluid, the stroma, which holds the Calvin cycle enzymes. Inside are flattened membrane sacs, thylakoids, stacked into grana; their interior is the thylakoid space. The pigment chlorophyll sits in the thylakoid membranes.

Light travels in packets called photons; the shorter the wavelength, the more energy each photon carries. Visible light spans roughly 380 to 750 nanometers. Chlorophyll absorbs violet blue and red light most strongly and reflects green. An absorption spectrum plots how much light a pigment absorbs at each wavelength, while an action spectrum plots how effectively each wavelength drives photosynthesis; the two match closely in the blue and red.

The main pigment is chlorophyll a. Chlorophyll b and the yellow and orange carotenoids are accessory pigments that broaden the wavelengths captured; carotenoids also provide photoprotection by dissipating excess light energy. When a pigment absorbs a photon, an electron is boosted to an excited state. In isolated chlorophyll it falls back, releasing heat and red fluorescence; in the membrane, the energy is put to work.

Photosystems and linear electron flow

Chlorophyll is organized into photosystems: a reaction center complex surrounded by light harvesting complexes that funnel absorbed energy to a special pair of chlorophyll a molecules. There an excited electron is transferred to a primary electron acceptor, the step that converts light energy into chemical energy.

There are two photosystems, numbered in order of discovery rather than action. Photosystem II (PS II) has the reaction center chlorophyll P680 (absorbing best at 680 nm), and photosystem I (PS I) has P700. Their main path, linear electron flow, runs as follows:

1. A photon excites PS II, and an excited electron from P680 passes to its primary acceptor, leaving P680⁺, the strongest biological oxidizing agent known.
2. An enzyme complex on the lumen side splits water into 2 electrons, 2 H⁺ and an oxygen atom. The electrons refill P680⁺, the protons stay in the thylakoid space, and two oxygen atoms combine to form O2, released as a by-product.
3. The excited electrons travel down an electron transport chain: plastoquinone (Pq), the cytochrome complex, and plastocyanin (Pc). As they pass through the cytochrome complex, their energy is used to pump protons from the stroma into the thylakoid space.
4. Meanwhile, light energy excites PS I, whose P700 passes an electron to its primary acceptor. The resulting P700⁺ is refilled by the electron arriving from PS II through plastocyanin.
5. The re-energized electrons pass through a short chain including the iron protein ferredoxin (Fd) to the enzyme NADP⁺ reductase, which reduces NADP⁺ to NADPH on the stroma side.

The thylakoid space gains protons from water splitting and from pumping by the cytochrome complex. This gradient drives ATP synthase, whose catalytic knob faces the stroma, so ATP is made where the Calvin cycle needs it. Light-driven chemiosmotic ATP synthesis is called photophosphorylation.

Cyclic electron flow and the comparison with mitochondria

In cyclic electron flow, excited electrons from PS I return from ferredoxin to the cytochrome complex instead of going to NADP⁺. They pass back to P700, pumping protons on the way. Cyclic flow uses only PS I, produces ATP but no NADPH and no O2. It matters because the Calvin cycle consumes more ATP than NADPH (a ratio of 18 to 12 per glucose), and linear flow alone does not supply enough ATP.

Chloroplasts and mitochondria both make ATP by chemiosmosis with similar electron transport chains and ATP synthases. Mitochondria take high energy electrons from food and pump protons from the matrix into the intermembrane space; chloroplasts take electrons from water, energized by light, and pump protons from the stroma into the thylakoid space, where the pH falls to about 5 while the stroma rises to about 8.

The Calvin cycle

The Calvin cycle uses the ATP and NADPH from the light reactions to build sugar from CO2. It is anabolic, and like the citric acid cycle it regenerates its starting material with each turn. Its direct product is not glucose but a three carbon sugar, glyceraldehyde 3-phosphate (G3P). To make one net molecule of G3P, the cycle must fix three molecules of CO2 and turn three times. It has three phases.

1. Carbon fixation. Each CO2 is attached to a five carbon sugar, ribulose bisphosphate (RuBP). The enzyme is rubisco (RuBP carboxylase oxygenase), probably the most abundant protein on Earth. The six carbon product is so unstable that it immediately splits into two molecules of 3-phosphoglycerate (3-PGA). Three CO2 therefore yield six 3-PGA.
2. Reduction. Each 3-PGA is phosphorylated by ATP and then reduced by electrons from NADPH, forming G3P. For six 3-PGA, this uses 6 ATP and 6 NADPH and produces 6 G3P. One of the six is the net gain; it leaves the cycle to be used by the plant cell.
3. Regeneration of RuBP. The other five G3P (15 carbons) are rearranged in a complex series of reactions into three RuBP (15 carbons), at a cost of 3 more ATP. The cycle is ready to fix more CO2.

For each net G3P the cycle consumes 9 ATP and 6 NADPH. Making one glucose (two G3P) requires 6 CO2, 18 ATP and 12 NADPH. G3P is then used to make glucose, sucrose, starch and cellulose.

Photorespiration: rubisco's weakness

Rubisco evolved when the atmosphere held almost no oxygen, and it cannot fully tell O2 from CO2. When it adds O2 to RuBP, it forms a two carbon compound that the plant salvages at a cost of ATP, releasing CO2 without making sugar. This is photorespiration. It becomes severe on hot, dry days, when plants close their stomata to save water: CO2 in the leaf is used up, O2 accumulates, and heat further favors the reaction with oxygen. In some crops photorespiration drains off as much as half of the fixed carbon.

Most plants, including rice, wheat and soybeans, are C3 plants, so named because the first stable product of carbon fixation is the three carbon 3-PGA. Two groups of plants have evolved ways to keep rubisco supplied with CO2.

C4 plants: separating steps in space

C4 plants, such as corn, sugarcane and many grasses, have Kranz anatomy: bundle sheath cells packed around each vein, surrounded by mesophyll cells. In the mesophyll, PEP carboxylase adds CO2 to phosphoenolpyruvate (PEP), forming the four carbon oxaloacetate, usually converted to malate. PEP carboxylase has a high affinity for CO2 and none for O2, so it keeps fixing carbon even when stomata are nearly closed. The four carbon compound moves into the bundle sheath cells and releases CO2, keeping CO2 high around rubisco and minimizing photorespiration. Regenerating PEP costs extra ATP, a price worth paying in hot, sunny climates.

CAM plants: separating steps in time

CAM plants (crassulacean acid metabolism), such as pineapples, cacti and other succulents, open their stomata at night, when less water evaporates. They fix CO2 with PEP carboxylase into organic acids stored in vacuoles. During the day, with stomata closed, the acids release CO2 to the Calvin cycle in the same cells. CAM plants trade growth rate for water conservation.

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