Evolution and Structure of Mitochondria

Mitochondria (Fig. 19-1) arose about 2 billion years ago when a Bacterium fused with an archaeal cell or established a symbiotic relationship with a primitive eukaryotic cell (see Fig. 2-5 and associated text). The details are not preserved in the fossil record, but the bacterial origins of mitochondria are apparent in their many common features (Fig. 19-2). The closest extant relatives of the Bacterium that gave rise to mitochondria are Rickettsia, aerobic α-proteobacteria with a genome of 1.1 megabase pairs. These intracellular pathogens cause typhus and Rocky Mountain spotted fever. However, some evidence argues that the actual progenitor bacterium had the genes required for both aerobic and anaerobic metabolism.

Figure 19-1 cellular distribution and structure of mitochondria. A, Fluorescence light micrograph of a Cos-7 tissue culture cell with mitochondria labeled with green fluorescent antibody to the β-subunit of the F1-ATPase and microtubules labeled red with an antibody. B, Electron micrograph of a thin section of a mitochondrion.

(A, Courtesy of Michael Yaffee, University of California, San Diego. B, Courtesy of Don Fawcett, Harvard Medical School, Boston, Massachusetts.)

Figure 19-2 The compartments of a mitochondrion (A–B) compared with a Bacterium (C–D). Respiratory chain complexes I to IV are labeled with roman numerals.

As primitive eukaryotes diverged from each other, most of the bacterial genes were lost or moved to the nuclei of the host eukaryotes. The pace of the gene transfer to the nucleus varied considerably depending on the species, but all known mitochondria retain some bacterial genes. A very few eukaryotes, such as Entamoeba, that branched well after their ancestors acquired mitochondria lost the organelle, leaving behind a few mitochondrial genes in the nucleus.

Chromosomes of contemporary mitochondria vary in size from 366,924 base pairs (bp) in the plant Arabidopsis to only 5966bp in Plasmodium. These small, usually circular genomes encode RNAs and proteins that are essential for mitochondrial function, including some subunits of proteins responsible for adenosine triphosphate (ATP) synthesis. The highly pared-down human mitochondrial genome with 16,569bp encodes only 13 mitochondrial membrane proteins, two ribosomal RNAs, and just enough tRNAs (22) to translate these genes. The number of proteins encoded by other mitochondrial genomes ranges from just 3 in Plasmodium to 97 in a protozoan. Nuclear genes encode the other 600 to 1000 mitochondria proteins, including those required to synthesize proteins in the matrix. All mitochondrial proteins that are encoded by nuclear genes are synthesized in the cytoplasm and subsequently imported into mitochondria (see Figs. 18-2 and 18-3).

Mitochondria consist of two membrane-bounded compartments, one inside the other (Fig. 19-2). The outer membrane surrounds the intermembranous space. The inner membrane surrounds the matrix. Each membrane and compartment has a distinct protein composition and functions. Porins in the outer membrane provide channels for passage of molecules of less than 5000D, including most metabolites required for ATP synthesis. The highly impermeable inner membrane is specialized for converting energy provided by breakdown of nutrients in the matrix into ATP. Four complexes (I to IV) of integral membrane proteins use the transport of energetic electrons to create a gradient of protons across the inner membrane. The F1F0 ATP synthase (see Fig. 8-5) utilizes the proton gradient to synthesize ATP. The area of inner membrane available for these reactions is increased by folds called cristae that vary in number and shape depending on the species, tissue, and metabolic state. Cristae may be tubular or flattened sacs. Contacts between the inner and outer membranes are sites of protein import (see Fig. 18-4). Proteins in the intermembranous space participate in ATP synthesis but, when released into the cytoplasm, trigger programmed cell death (see Fig. 46-15).

Biogenesis of Mitochondria

Mitochondria grow by importing most of their proteins from the cytoplasm and by internal synthesis of some proteins and replication of the genome (Fig. 19-3). Targeting and sorting signals built into the mitochondrial proteins that are synthesized in the cytoplasm direct them to their destinations (see Fig. 18-4).

Figure 19-3 biogenesis of mitochondria. The drawing shows the relative contributions of nuclear and mitochondrial genes to the protein composition.

Similar to cells, mitochondria divide, but unlike most cells, they also fuse with other mitochondria. These fusion and division reactions were first observed nearly one hundred years ago. Now it is appreciated that a balance between ongoing fusion and division determines the number of mitochondria within a cell. Both fusion and division depend on proteins with guanosine triphosphatase (GTPase) domains related to dynamin (see Fig. 22-11). In fact, eukaryotes might have acquired their dynamin genes from the bacterium that became mitochondria.

One dynamin-related GTPase is required for division of mitochondria. This GTPase self-assembles into spirals that appear to pinch mitochondria in two. During apoptosis (see Chapter 46), this GTPase also participates in the fragmentation of mitochondria.

Fusion involves two GTPases, one anchored in the outer membrane and the other in the inner membrane, both linked by an adapter protein in the intermembrane space. Fusion of the outer membranes requires a proton gradient across the inner membrane, while fusion of the inner membranes depends on the electrical potential across the inner membrane. Loss of function mutations in fusion proteins lead to cells with numerous small mitochondria, some lacking a mtDNA molecule. Human mutations in the genes for fusion proteins result in defects in the myelin sheath that insulates axons (one form of Charcot-Marie-Tooth disease) and the atrophy of the optic nerve. Mitochondrial fusion proteins are also required for apoptosis.

Synthesis of ATP by Oxidative Phosphorylation

Mitochondria use energy extracted from the chemical bonds of nutrients to generate a proton gradient across the inner membrane. This proton gradient drives the F1F0 ATP synthase to synthesize ATP from ADP and inorganic phosphate. Enzymes in the inner membrane and matrix cooperate with pumps, carriers, and electron transport proteins in the inner membrane to move electrons, protons, and other energetic intermediates across the impermeable inner membrane. This is a classic chemiosmotic process (see Fig. 11-1).

Mitochondria receive energy-yielding chemical intermediates from two ancient metabolic pathways, glycolysis and fatty acid oxidation (Fig. 19-4), that evolved in the common ancestor of living things. Both pathways feed into the equally ancient citric acid cycle of energy-yielding reactions in the mitochondrial matrix:

Figure 19-4 metabolic pathways supplying energy for oxidative phosphorylation. A, Glycolysis. B, Citric acid cycle. Production of acetyl-CoA by the glycolytic pathway in cytoplasm and fatty acid oxidation in the mitochondrial matrix drive the citric acid cycle in the mitochondrial matrix. This energy-yielding cycle is also called the Krebs cycle after the biochemist H. Krebs. NADH and FADH₂ produced by these pathways supply high-energy electrons to the electron transport chain. C, Overview of metabolic pathways. Note energy-rich metabolites (yellow).

Breakdown of acetyl-CoA during one turn of the citric acid cycle produces three molecules of NADH, one molecule of FADH₂, and two molecules of carbon dioxide. Energetic electrons donated by NADH and FADH₂ drive an electron transport pathway in the inner mitochondrial membrane that powers a chemiosmotic cycle to produce ATP (Fig. 19-5). Electrons use two routes to pass through three protein complexes in the inner mitochondrial membrane. Starting with NADH, electrons pass through complex I to complex III to complex IV. Electrons from FADH₂ pass through complex II to complex III to complex IV. Along both routes, energy is partitioned off to transfer multiple protons (at least 10 electrons per NADH oxidized) across the inner mitochondrial membrane from the matrix to the inner membrane space. The resulting electrochemical gradient of protons drives ATP synthesis (see Fig. 8-5).

Figure 19-5 chemiosmotic cycle of the respiratory electron transport chain and atp synthase. a, left panel, A mitochondrion for orientation. Right panel, The electron transport system of the inner mitochondrial membrane. Note the pathway of electrons through the four complexes (red and yellow arrows) and the sites of proton translocation between the matrix to the intermembranous space (black arrows). The stoichiometry is not specified, but at the last step, four electrons are required to reduce oxygen to water. ATP synthase uses the electrochemical proton gradient produced by the electron transport reactions to drive ATP synthesis. B, The available atomic structures of the electron transport chain are shown. In the cytochrome bc₁ complex III, the 3 of 11 mitochondrial subunits used by bacteria are shown as ribbon models. The supporting subunits found in mitochondria are shown as cylinders. The four subunits of complex IV encoded by the mitochondrial genome are shown as ribbon models. They form the functional core of the complex, which is supported by additional subunits shown as cylinders. See Figure 8-4 for further details of ATP synthase (complex V).

(B, Images of complex III and complex IV courtesy of M. Saraste, European Molecular Biology Laboratory, Heidelberg, Germany. Reference: Zhang Z, Huang L, Schulmeister VM, et al: Electron transfer by domain movement in cytochrome bc₁. Nature 392:677–684, 1998. PDB file: 1BCC. Reference: Yoshikawa S, Shinzawα-Itoh K, Nakashima R, et al: Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science 280:1723–1729, 1998. PDB file: 2OCC.)

This process is called oxidative phosphorylation, since molecular oxygen is the sink for energy-bearing electrons at the end of the pathway and since the reactions add phosphate to ADP. Eukaryotes that live in environments with little or no oxygen use other acceptors for these electrons and produce nitrite, nitric oxide, or other reduced products rather than water. Oxidative phosphorylation is understood in remarkable detail, thanks to atomic structures of ATP synthase and three of the four electron transfer complexes. Nuclear genes encode most of the protein subunits of these complexes, but mitochondrial genes are responsible for a few key subunits.

Bacteria and mitochondria share homologous proteins for the key steps in oxidative phosphorylation (Fig. 19-2), but the machinery in mitochondria is usually more complex. Thus, bacteria are useful model systems with which to study the common mechanisms. Plasma membranes of bacteria and inner membranes of mitochondria have equivalent components, and the bacterial cytoplasm corresponds to the mitochondrial matrix (Fig. 19-2).

Energy enters this pathway in the form of electrons that are produced when NADH is oxidized to NAD⁺, releasing one H⁺ and two electrons (Fig. 19-5). If the proton and electrons were to combine immediately with oxygen, their energy would be lost as heat. Instead, these high-energy electrons are separated from the protons and then passed along the electron transport pathway before finally recombining to reduce molecular oxygen to form water. Along the pathway, electrons associate transiently with a series of oxidation/reduction acceptors, generally metal ions associated with organic cofactors, such as hemes in cytochromes and iron-sulfur centers (2Fe2S) and copper centers in complex IV. Electrons move along the transport pathway at rates of up to 1000s⁻¹. To travel at this rate through a transmembrane protein complex spanning a 35-nm lipid bilayer, at least three redox cofactors are required in each complex, because the efficiency of quantum mechanical tunneling of electrons between redox cofactors falls off rapidly with distance. Two cofactors, even with optimal orientation, would be too slow.

Step by step, electrons give up energy as they move along the transport pathway. In three complexes along the pathway, this energy is used to pump protons from the matrix to the inner membrane space. This establishes an electrochemical proton gradient across the inner mitochondrial membrane that is used by ATP synthase to drive ATP production. Direction is provided to the movements of electrons by progressive increases in the electron affinity of the acceptors. The final acceptor, oxygen (at the end of the pathway), has the highest affinity.

The first component of the electron transport pathway is called complex I (or NADH:ubiquinone oxidoreductase). Vertebrate mitochondrial complex I with 46 different protein subunits is more complex than bacterial complex I with 14 subunits. NADH donates two electrons to flavin mononucleotide associated with protein subunits located on the matrix side of the inner membrane. A crystal structure of the cytoplasmic domain of the bacterial complex shows the path for the electrons from flavin mononucleotide through seven iron sulfur clusters to quinone in the lipid bilayer. For each molecule of NADH oxidized, the transmembrane domains of complex I transfer four protons from the matrix into the inner membrane space.

The second component of the electron transport pathway is complex II or succinate:ubiquinone reductase, a transmembrane enzyme that makes up part of the citric acid cycle. Complex II couples oxidation of succinate (a four-carbon intermediate in the citric acid cycle) to fumarate with reduction of flavin adenine dinucleotide (FAD) to FADH₂. Complex II does not pump protons but transfers electrons from FADH₂ to ubiquinone. Reduced ubiquinone carries these electrons to complex III.

The third component of the electron transport pathway is complex III, also called cytochrome bc₁. This well-characterized, transmembrane protein complex consists of 11 different subunits. The homologous bacterial complex has only three of these subunits, the ones that participate in energy transduction in mitochondria. Eight other subunits surround this core. Complex III couples the oxidation and reduction of ubiquinone to the transfer of protons from the matrix across the inner mitochondrial membrane. Energy is supplied by electrons that move through the cytochrome b subunit to a subunit with a 2Fe2S redox center. This subunit then rotates into position to transfer the electron to cytochrome c₁, another subunit of the complex. Cytochrome c₁ then transfers the electron to the water-soluble protein cytochrome c in the intermembranous space (or periplasm of bacteria).

Cytochrome oxidase, complex IV, takes electrons from four cytochrome c molecules to reduce molecular oxygen to two waters as well as to pump four protons out of the matrix. Mitochondrial genes encode the three subunits that form the core of this enzyme, carry out electron transfer, and translocate protons. Nuclear genes encode the surrounding 10 subunits.

The electrochemical proton gradient produced by the electron transport chain provides energy to synthesize ATP. Chapter 8 explained how the rotary ATP synthase (complex V) can either use ATP hydrolysis to pump protons or use the transit of protons down an electrochemical gradient to synthesize ATP (see Figs. 8-5 and 8-6). The proton gradient across the inner mitochondrial membrane drives rotation of the γ-subunit. The rotating mg-subunit physically changes the conformations of the α- and β-subunits, bringing together ADP and inorganic phosphate to make ATP. An antiporter in the inner membrane exchanges cytoplasmic ADP for ATP synthesized in the matrix (see Fig. 9-2A).

Mitochondria and Disease

As expected from the central role of mitochondria in energy metabolism, mitochondrial dysfunction contributes to a remarkable diversity of human diseases (Fig. 19-6) including seizures, strokes, optic atrophy, neuropathy, myopathy, cardiomyopathy, hearing loss, and Type 2 diabetes mellitus. These disorders arise from mutations in genes for mitochondrial proteins encoded by both mitochondrial DNA (mtDNA) and nuclear DNA. More than half of the known disease-causing mutations are in genes for mitochondrial transfer RNAs.

Figure 19-6 Mutations in both mitochondrial and nuclear genes for mitochondrial proteins cause a variety of diseases by compromising the function of particular mitochondrial subsystems. FBSN, familial bilateral striatal necrosis; LHON, Leber hereditary optic neuropathy; MILS, maternally inherited Leigh syndrome; NARP, neurogenic muscle weakness, ataxia, retinitis pigmentosa.

(Adapted from Schon EA: Mitochondrial genetics and disease. Trends Biochem Sci 25:555–560, 2000.)

The existence of about 1000 copies of mtDNA per vertebrate cell influences the impact of deleterious mutations. A mutation in one copy would be of no consequence, but segregation of mtDNAs may lead to cells in which mutant mtDNAs predominate, yielding defective proteins. For example, a recurring point mutation in a subunit of complex I causes some patients to develop sudden onset of blindness in middle age owing to the death of neurons in the optic nerve. Patients with the same mutation in a larger fraction of mtDNA molecules suffer from muscle weakness and mental retardation as children. Mutations in the genes for subunits of ATP synthase cause muscle weakness and degeneration of the retina. Slow accumulation of mutations in mtDNA may contribute to some symptoms of aging.

Mutations in nuclear genes for mitochondrial proteins cause similar diseases (Fig. 19-6A). A mutation in one subunit of the protein import machinery (see Fig. 18-5), Tim8, causes a type of deafness.

Structure and Evolution of Photosynthesis Systems

Photosynthetic Bacteria and chloroplasts of algae and plants (Fig. 19-7) use chlorophyll to capture the remarkable amount of energy carried by single photons to boost electrons to an excited state. These high-energy electrons drive a chemiosmotic cycle to make NADPH and ATP, energy currency that is used by all cells. Photosynthetic organisms use ATP and the reducing power of NADPH to synthesize three-carbon sugar phosphates from carbon dioxide. Glycolytic reactions (Fig. 19-4) running backward use this three-carbon sugar phosphate to make six-carbon sugars and more complex carbohydrates for use as metabolic energy sources and structural components. Some Archaea, such as Halobacteria halobium, and some recently discovered Bacteria use a completely different light-driven pump lacking chlorophyll to generate a proton gradient to synthesize ATP. Retinol associated with bacteriorhodopsin absorbs light to drive proton transport (see Fig. 8-3).

Figure 19-7 morphology of chloroplasts and cyanobacteria. A, Electron micrograph of a thin section of a spinach chloroplast. B, Chloroplast. C–D, Comparison of the machinery in the photosynthetic membranes of chloroplasts and cyanobacteria. E, Drawing of a cyanobacterium illustrating the internal folds of the plasma membrane to form photosynthetic thylakoids.

(A, Courtesy of K. Miller, Brown University, Providence, Rhode Island.)

Photosynthesis originated approximately 3.5 billion years ago in a Bacterium, most likely a gram-negative purple bacterium (see Fig. 2-4). These bacteria evolved components to assemble a transmembrane complex of proteins, pigments, and oxidation/reduction cofactors called a reaction center (Fig. 19-8). Reaction centers absorb light and initiate an electron transport pathway that pumps protons out of the cell. Such photosystems turn sunlight into electrical and chemical energy with 40% efficiency, better than any human-made photovoltaic cell. Given their alarming complexity and physical perfection, it is remarkable that photosystems emerged only a few hundred million years after the origin of life itself.

Figure 19-8 comparison of photosynthetic components, electron transport pathways, and chemiosmotic cycles to make atp. a–b, Type II photosystem only. C–D, Type I photosystem only. E–F, Both photosystem II and photosystem I. Right diagrams, The energy levels of electrons in the three types of photosynthetic organisms, showing excitation of an electron by an absorbed photon (vertical arrows), electron transfer pathways through each reaction center (arrows sloping right), and electron transfer steps outside the reaction centers (arrows sloping left).

(A, C, and E, Reference: Kramer DM, Schoepp B, Liebl U, Nitschke W: Cyclic electron transfer in Heliobacillus mobilis. Biochemistry 36:4203–4211, 1997. B, D, and F, Reference: Allen JP, Williams JC: Photosynthetic reaction centers. FEBS Lett 438:5–9, 1998.)

Broadly speaking, photosynthetic reaction centers of contemporary organisms can be divided into two different groups (Fig. 19-8). The reaction centers of purple bacteria and green filamentous bacteria utilize the pigment pheophytin and a quinone as the electron acceptor, similar to photosystem II of cyanobacteria and chloroplasts. The reaction centers of green sulfur bacteria and heliobacteria have iron-sulfur centers as electron acceptors, similar to photosystem I of cyanobacteria and chloroplasts.

Cyanobacteria are unique among Bacteria in that they have both types of photosystems as well as a manganese enzyme that splits water, releasing from two water molecules four electrons, four protons, and oxygen (Fig. 19-7E). Coupling this enzyme to photosynthesis was a pivotal event in the history of the earth, as this reaction is the source of most of the oxygen in the earth’s atmosphere.

Chloroplasts of eukaryotic cells arose from a symbiotic cyanobacterium (see Fig. 2-8). Much evidence indicates that this event occurred just once, giving all chloroplasts a common origin. However, to account for chloroplasts in organisms that diverged prior to the acquisition of chloroplasts, one must also postulate lateral transfer of chloroplasts from, for example, a green alga to Euglena. Less likely, but not ruled out conclusively, cyanobacteria may have colonized eukaryotic cells on up to three different occasions, giving rise to organelles that evolved into chloroplasts.

Chloroplasts have retained up to 250 original bacterial genes on circular genomes, whereas many bacte-rial genes were lost or moved to the nucleus of host eukaryotes. Chloroplast genomes encode subunits of many proteins responsible for photosynthesis and chloroplast division, ribosomal RNAs and proteins, and a complete set of tRNAs. Chloroplast proteins encoded by nuclear genes are transported posttranslationally into chloroplasts (Fig. 18-6) after their synthesis in cytoplasm.

The organization of cyanobacterial membranes ex-plains the architecture of chloroplasts (Fig. 19-7C-E). In cyanobacteria, light-absorbing pigments, as well as protein complexes involved with electron transport and ATP synthesis, are concentrated in invaginations of the plasma membrane. The F1 domain of ATP synthase faces the cytoplasm, and the lumen of this membrane system is periplasmic. This internal membrane system remains in chloroplasts but is separated from the inner membrane (the former plasma membrane). These thylakoid membranes contain photosynthetic hardware and enclose the thylakoid membrane space. Like the bacterial plasma membrane, the chloroplast “inner membrane” is a permeability barrier, containing carriers for metabolites. The inner membrane surrounds the stroma, the cytoplasm of the original symbiotic bacterium, a protein-rich compartment devoted to synthesis of three-carbon sugar phosphates, chloroplast proteins, and all plant fatty acids. The stroma also houses the genomes and stores starch. The outer membrane, like the comparable bacterial and mitochondrial membranes, has large pore channels that allow free passage of metabolites.

Light and Dark Reactions

Photosynthetic mechanisms capture energy from photons to drive two types of reactions:

All photosynthetic systems use similar mechanisms to capture energy from photons (Fig. 19-8). Pigments associated with transmembrane proteins in photosynthetic reaction centers absorb photons and use the energy to boost electrons to a high-energy, excited state. Subsequent electron transfer reactions partition this energy in several steps to generate a proton gradient across the membrane. Generation of this proton electrochemical gradient and chemiosmotic produc-tion of ATP are similar to oxidative phosphorylation (Fig. 19-5).

Specific photosynthetic systems differ in the complexity of the hardware, the source of electrons, and the products (Fig. 19-8). Most photosynthetic bacteria use either a type I photosystem or a type II photosystem to create a proton gradient to synthesize ATP. Cyanobacteria and green plants use both types of reaction cen-ters in series to raise electrons to an energy sufficient to make NADPH in addition to ATP. These advanced systems also use water as the electron donor and produce molecular oxygen as a by-product.

Energy Capture and Transduction by Type II Photosystems and Photosystem II

The reaction center from the purple bacterium Rhodopseudomonas viridis (Fig. 19-9A) is a model for the more complex photosystem II of cyanobacteria and chloroplasts. This bacterial reaction center consists of just four subunits. A cytochrome subunit on the periplasmic side of the membrane donates electrons. Two core subunits form a rigid transmembrane framework to bind 10 cofactors in orientations that favor transfer of high-energy electrons from two “special” bacteriochlorophylls through chlorophyll b and bacteriopheophytin b.

Figure 19-9 structures of photosystem hardware. A, Ribbon diagram of type II photosystem from the purple bacterium Rhodopseudomonas viridis, with ball and stick models of bacteriochlorophyll and other cofactors to the right in their natural orientations. Similar core subunits L and M each consists of five transmembrane helices. This pair of subunits binds four molecules of chlorophyll b (Clb), two molecules of bacteriopheophytin b (Phb), one nonheme iron (Fe), two quinones (Q_A, Q_B), and one carotenoid (Car) in a rigid framework. A cytochrome with four heme groups binds to the periplasmic side of the core subunits. Subunit H associates with the core subunits via one transmembrane helix and with their cytoplasmic surfaces. The atomic structure of this photosynthetic reaction center was the Nobel Prize work of J. Diesenhoffer, R. Huber, and H. Michel. B, Ribbon diagram of photosystem I of Synechococcus elongatus, with ball and stick models of chlorophyll and other cofactors to the right in their natural orientations. This trimeric complex consists of three identical units, each composed of 11 polypeptide chains. Within each of these units, this 4-å resolution structure includes 43 α-helices, 89 chlorophylls, a quinone, and three iron-sulfur centers, but other details (e.g., amino acid side chains) are not resolved. The photosynthetic reaction center consists of the C-terminal halves of the two central subunits (PsaA/PsaB, red-brown) associated with six chlorophylls, one or two quinones, and a shared iron-sulfur cluster. Plastocyanin or cytochrome c₆ on the lumen side donates electrons to reduce the P700 special pair chlorophylls (eC₁) of the reaction center. Light energizes an electron, which passes successively through two other chlorophylls, a quinone, and the shared iron-sulfur cluster (red), F_x. The electron then transfers to the iron-sulfur clusters of the accessory subunit PsaC on the stromal side of the membrane. The surrounding eight subunits (red, gray), associated with about 80 chlorophylls, compose the core antenna system, forming a nearly continuous ring of α-helices around the reaction center. Absorption of light by additional light-harvesting complexes and these antenna subunits puts chloroplast electrons into an excited state. This energy passes from one pigment to the next until it eventually reaches the reaction center.

(A, Copyright of Diesenhoffer & Michel, Nobel Foundation, 1988. Reference: Diesenhoffer J, Michel H: The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis. Science 245:1463–1473, 1989. PDB file: 1PRC. A 3.5 å crystal structure [PDB file: 1IZL] of the PSII complex from the cyanobacterium Thermosynechococcus elongatus including 19 subunits is now available. Reference: Ferreira KN, Iverson TM, Maghlaoui K, et al: Architecture of the photosynthetic oxygen-evolving center. Science 303:1831–1838, 2004. B, PDB file: 2PPS. Reference: Schubert W-D, Klukas O, Krauss N, et al: Photosystem I of Synechococcus elongatus at 4 å resolution: Comprehensive structure analysis. J Mol Biol 272:741–769, 1997.)

Photosynthesis begins with absorption of a photon by the special pair bacteriochlorophylls. Photons in the visible part of the spectrum are quite energetic, 40 to 80kcalmol⁻¹, enough to make several ATPs. The purple bacterium reaction center absorbs relatively low-energy, 870-nm red light. The energy elevates an electron in the special pair bacteriochlorophylls to an excited state (Fig. 19-8B). In an organic solvent, the excited state would decay rapidly (10⁹s⁻¹), and the energy would dissipate as heat or emission of a less energetic photon by fluorescence or phosphorescence. However, reaction centers are optimized to transfer excited-state electrons rapidly and efficiently from the special pair bacteriochlorophylls to bacteriopheophytin (3 × 10⁻¹²s) and then to tightly bound quinone A (200 × 10⁻¹²s). Transfer is by quantum mechanical tunneling right through the protein molecule. Because the tunneling rate falls off quickly with distance, four redox centers must be spaced close together to allow an energetic electron to transfer across the lipid bilayer faster than spontaneous decay of the excited state.

On the cytoplasmic side of the membrane, two electrons transfer from quinone A to loosely bound quinone B (100 × 10⁻⁹s), where they combine with two protons to make a high-energy reduced quinone, QH₂ (Fig. 19-8A). In purple bacteria, these cytoplasmic protons are taken up through water-filled channels in the reaction center, contributing to the proton gradient.

QH₂ has a low affinity for the reaction center and diffuses in the hydrophobic core of the bilayer to the next component in the pathway, the chloroplast equivalent of the mitochondrial cytochrome bc₁ complex III (Fig. 19-8A). As in mitochondria, passage of energetic electrons through this complex releases protons from QH₂ on the periplasmic side of the membrane, adding to the electrochemical gradient. The electron circuit is completed by transfer of low-energy electrons from complex bc₁ to a soluble periplasmic protein, cytochrome c₂. Electrons then move to the cytochrome subunit of the reaction center, which supplies special pair chlorophylls with electrons for the photosynthetic reaction cycle.

The net result of this cycle is the conversion of the energy of two photons into transport of three protons to the periplasm. A diagram of the energy levels of the various intermediates in the cycle (Fig. 19-8B) shows how energy is partitioned after an electron is excited by a photon and then moves, step by step, through protein-associated redox centers back to the ground state.

The proton electrochemical gradient established by photosynthetic electron transfer reactions is used to drive an ATP synthase (see Fig. 8-5) similar to those of nonphotosynthetic prokaryotes and mitochondria.

Light Harvesting

Reaction center chlorophylls absorb light themselves, but both chloroplasts and bacteria increase the efficiency of light collection with proteins that absorb light and transfer the energy to a reaction center. Most of these light-harvesting complexes are small, transmembrane proteins that cluster around a reaction center, although some bacteria and algae also have soluble light-harvesting proteins. Transmembrane, light-harvesting proteins consist of a few α-helices associated with multiple chlorophyll and carotenoid pigments (Figs. 19-8A and C and 19-9B). The use of different pigments broadens the range of wavelengths absorbed. Multiple pigments increase the efficiency of photon capture. Leaves are green because chlorophylls and carotenoids absorb purple and blue wavelengths (<530nm) as well as red wavelengths (>620nm), reflecting only yellow-green wavelengths in between.

Light that is absorbed by light-harvesting proteins boosts pigment electrons to an excited state. This energy (but not the electrons) moves without dissipation by fluorescence resonance energy transfer from one closely spaced pigment molecule to another and eventually to the special pair chlorophylls of a reaction center. This rapid (10⁻¹²s), efficient process transfers energy captured over a wide area to a reaction center to initiate a cycle of electron transfer and energy transduction.

Energy Capture and Transduction by Photosystem I

The reaction centers of green sulfur bacteria and heliobacteria are similar to photosystem I of cyanobacteria and chloroplasts. Generation of a proton gradient by photosystem I has many parallels with photosystem II. Direct absorption of light or resonance energy transfer from surrounding light-harvesting complexes excites special pair chlorophylls in photosystem I (Fig. 19-8C-D). Excited-state electrons move rapidly within the reaction center from these chlorophylls through two accessory chlorophylls and to an iron-sulfur center. The pathway includes a quinone in cyanobacteria and chloroplasts. Electrons then move to the iron-sulfur center of a subunit on the cytoplasmic side of the membrane. The subsequent events in green sulfur bacteria and heliobacteria are still under investigation but are thought to include electron transfer by the soluble protein ferridoxin to an NAD reductase, followed by transfer by a lipid intermediate to cytochrome bc complex, and then back to the reaction center via a cytochrome c.

Oxygen-Producing Synthesis of NADPH and ATP by Dual Photosystems

Chloroplasts and cyanobacteria combine photosystem II and photosystem I in the same membrane to form a system capable of accepting low-energy electrons from the oxidation of water and producing both a proton gradient to drive ATP synthesis and reducing equivalents in the form of NADPH (Fig. 19-8E-F). Both photosystems are more elaborate in dual systems than in single systems. Although plant photosystem II, with more than 25 protein subunits, is much more complicated than is the homologous reaction center of purple bacteria, the arrangement of transmembrane helices and chlorophyll cofactors in the core of the plant reaction center is similar to the simple reaction center of purple bacteria.

Photosynthesis involves a tortuous electron transfer pathway powered at two way stations by absorption of photons. This process begins when the special pair chlorophylls of photosystem II are excited by direct aβ-sorption of light or by resonance energy transfer from surrounding light-harvesting complexes (Fig. 19-8E-F). Electrons come from splitting two waters into molecular oxygen and four protons. Excited-state electrons tunnel through the redox cofactors and combine with protons from the stroma (or cytoplasm in bacteria) to reduce quinone QB to QH₂, a high-energy electron donor. QH₂ diffuses to complex b_6-f, the chloroplast equivalent of the mitochondrial bc₁ complex. Passage of electrons through complex b_6-f releases protons from QH₂ into the thylakoid lumen (or bacterial periplasm), contributing to the proton gradient across the membrane.

Complex b_6-f donates electrons from QH₂ to photosystem I. Direct absorption of 680-nm light or resonance energy transfer from surrounding light-harvesting complexes boosts special pair chlorophyll electrons to a very high-energy, excited state (Fig. 19-8F). Excited-state electrons pass through chlorophyll and iron-sulfur centers of photosystem I to the iron-sulfur center of the redox protein, ferridoxin, on the cytoplasmic/stromal surface of the membrane. The enzyme NADP reductase combines electrons from ferridoxin with a proton to form NADPH, the final product of this tortuous electron transfer pathway powered at two way stations by absorption of photons. Uptake of stromal protons during NADPH formation contributes to the transmembrane proton gradient for the synthesis of ATP. Antiporters in the inner membrane exchange ATP for ADP, as in mitochondria.

Synthesis of Carbohydrates

ATP and NADPH produced by light reactions drive the unfavorable conversion of carbon dioxide into sugars. This is the first step in the earth’s annual production of about 10¹⁰ tons of carbohydrates by photosynthetic organisms. This process is very expensive, consuming three ATPs and two NADPHs for each carbon dioxide added to the five-carbon sugar ribulose 1,5-bisphosphate. The responsible enzyme, ribulose phosphate carboxylase (called RUBISCO), is the most abundant protein in the stroma and might be the most abundant protein on the earth. The products of combining the five-carbon sugar with carbon dioxide are two molecules of the three-carbon sugar 3-phosphoglycerate.

An antiporter in the inner chloroplast membrane exchanges 3-phosphoglycerate for inorganic phosphate, so 3-phosphoglycerate can join the glycolytic pathway in the cytoplasm (Fig. 19-4). Driven by this abundant supply of 3-phosphoglycerate, the glycolytic pathway runs backward to make six-carbon sugars, which are used to make disaccharides such as sucrose to nourish nonphotosynthetic parts of the plant, the glucose polymer starch to store carbohydrate, and cellulose for the extracellular matrix (see Figs. 3-25A and 32-12).