How are 32 ATP produced in electron transport chain?

The ETC Links Chemical Energy to H+ Pumping Out of the Mitochondria

The ETC consists of an array of proteins inserted in the inner mitochondrial membrane. The overall plan is this: NADH delivers two electrons to a series of chemicals that differ in their chemical affinity for these electrons (see Figure 2.10.7). This is expressed in their reduction potential (see above) which is related to their free energy. The energy is released gradually, in steps, and the ETC complexes use the decrease in free energy to pump hydrogen ions from the matrix space to the intermembrane space between the inner and outer mitochondrial membranes. This pumping of hydrogen ions produces an electrochemical gradient for hydrogen ions and the energy in this gradient is used to generate ATP from ADP and Pi.

8.5.3 Electron Transport Chain

The electron transport chain is the last step in the conversion of glucose into ATP, as illustrated in Figure 8.26. It involves a series of enzyme catalyzed chemical reactions that transfer electrons from (NADH+H+)andFADH2 (donor molecules) to acceptor molecules. Ultimately the electron transport chain produces 32 molecules of ATP from one molecule of glucose through hydrogen oxidation, and also regenerates NAD and FAD for reuse in glycolysis. The overall reaction is given by

(NADH+H+)+12O2+3ADP+3P⟶NAD++4H2O+3ATP

and

(8.113)FADH2+12O2+2ADP+2P⟶FAD+3H2O+2ATP

The electron transport chain activity takes place in the inner membrane and the space between the inner and outer membrane, called the intermembrane space. In addition to one molecule of ATP created during each Krebs cycle, three pairs of hydrogen are released and bound to 3NAD+ to create 3(NADH+H+), and one pair of hydrogen is bound to FAD to form FADH2 within the mitochondrial matrix. As described before, two cycles through the Krebs cycle are needed to fully oxidize one molecule of glucose, and thus 6(NA DH+H+) and 2FADH2 molecules are created.

The energy stored in these molecules of (NADH+H+)andFADH2 is used to create ATP by the release of hydrogen ions through the inner membrane and electrons within the inner membrane. The energy released by the transfer of each pair of electrons from (NADH+H+ )andFADH2 is used to pump a pair of hydrogen ions into the intermembrane space. The transfer of a pair of electrons is through a chain of acceptors from one to another, with each transfer providing the energy to move another pair of hydrogen ions through the membrane. At the end of the acceptor chain, the two electrons reduce an oxygen atom to form an oxygen ion, which is then combined with a pair of hydrogen ions to form H2O. The movement of the hydrogen ions creates a large concentration of positively charged ions in the intermembrane space and a large concentration of negatively charged ions in the matrix, which sets up a large electrical potential. This potential is used by the enzyme ATP synthase to transfer hydrogen ions into the matrix and to create ATP. The ATP produced in this process is transported out of the mitochondrial matrix through the inner membrane using carrier facilitated diffusion and diffusion through the outer membrane. In the following description, we assume all of the hydrogen and electrons are available from these reactions. In reality, some are lost and not used to create ATP. Other descriptions of the electron transport chain have additional sites and are omitted here for simplicity.

We first consider the use of (NADH+H+) in the electron transport chain. During the first step, a pair of electrons from NADH+H+ are transferred to the electron carrier coenzyme Q by NADH dehydrogenase (site 1 and Q in Figure 8.26), and using the energy released, a pair of hydrogen ions are pumped into the intermembrane space.

Next, the coenzyme Q carries the pair of electrons to the cytochrome bc1 complex (site 2 in Figure 8.26). When the pair of electrons are transfered from the cytochrome bc1 complex to cytochrome c (site C in Figure 8.26), the energy released is used to pump another pair of hydrogen ions into the intermembrane space through the cytochrome bc1 complex.

In the third step, cytochrome c transfers electrons to the cytochrome c oxidase complex (site 3 in Figure 8.26), and another pair of hydrogen ions are pumped through the cytochrome c oxidase complex into the intermembrane space. A total of 6 hydrogen ions have now been pumped into the intermembrane space, which will allow the subseqent creation of 3 molecules of ATP.

Also occuring in this step, the cytochrome oxidase complex transfers the pair of electrons within the inner membrane from the cytochrome c to oxygen in the matrix. Oxygen then combines with a pair of hydrogen ions to form water.

As described previously, the transfer of hydrogen ions into the intermembrane space creates a large concentration of positive charges and a large concentration of negative charges in the matrix, creating a large electrical potential across the inner membrane. The energy from this potential is used in this step by the enzyme ATP synthase (site 4 in Figure 8.26) to move hydrogen ions in the intermembrane space into the matrix and to synthesize ATP from ADP and P.

The ATP in the matrix is then transported into the intermembrane space and ADP is transported into the matrix using a carrier-mediated transport process (site 5 in Figure 8.26). From the intermembrane space, ATP diffuses through the outer membrane into the cytosol, and ADP diffuses from the cytosol into the intermembrane space.

In parallel with (NADH+H+), FAD H2 goes through a similar process but starts at coenzyme Q, where it directly provides a pair of electrons. Thus, FADH2 provides two fewer hydrogen ions than (NADH+H+).

The focus of this section has been the synthesis of ATP. Glycolysis and the Krebs cycle are also important in the synthesis of small molecules such as amino acids and nucleotides, and large molecules such as proteins, DNA, and RNA. There are other metabolic pathways to store and release energy that were not covered here. The interested reader can learn more about these pathways using the references at the end of this chapter and the website http://www.genome.jp.

5.3.4.1 Electron Transport Chains

Bacteria develop various electron transport chains (ETCs) to adjust diverse environmental circumstances [79,80] (Table 5.3.2). Redox reactions utilized for electron transport are catalyzed by various mechanisms linked with dehydrogenases and membrane protein complexes [79]. Soluble lipophilic electron carrying co-factors such as quinones and the proteins such as heme play important role in electron transport. The net energy advance in ETC is administered by the redox potential variance among electron donor and acceptor. About numerous electron donors and acceptors, some bacteria incline to integrate numerous electron transport chains concurrently, while some undergo single pathway as like Acetobacter woodii [81]. Therefore, to deploy the metabolic pathways of bacteria in a BES, a systematic extracellular electron transfer (EET) is obligatory. Even though abundant exoelectrogens were discovered, only a few known comprehensive EET mechanisms are available. Among these, dissimilatory metal-reducing bacteria were studied in detail and are recognized to respire unsolvable metals under anaerobic environments. The Geobacter sulfurreducens and S. oneidensis are two well-known classical bacteria having EET mechanisms through both direct and indirect electron transfer to electrodes [79]. These bacteria comprise outer membrane cytochromes that permit EET [82], though their mechanisms of electron transport vary from one another. In the case of Shewanella it expels soluble electron carriers which were absent in Geobacter sp. [83]. Thermincola, an obligate anaerobe similarly falls under the group of dissimilatory metal-reducing bacteria and are found to be accomplished by direct electron transfer via cell wall–related cytochromes [84]. Some bacteria such as C. ljungdahlii show EET property even with the absence of membrane-bound cytochromes [85].

Table 5.3.2. Electron Transport Mechanisms of Various Bacteria in BES

A, Acetobacterium; BES, bioelectrochemical system; G, Geobacter; M, Moorella; P, Pseudomonas; S1, Sporomusa; S, Shewanella.

Table was generated with information from F. Kracke, I. Vassilev, J.O. Krömer, Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems. Front. Microbiol. 6 (2015) 1–18.

Introduction

The paramount importance of metal ions in biological systems is illustrated in Fig. 1.1, which presents the abundance of the chemical elements (ppb by weight) in the human body (Winter, 2016). This study was carried out using inductively coupled plasma mass spectrometry (ICP-MS), which has sub-ppt detection limits, allowing the detection of virtually all naturally occurring elements in biological samples (Maret, 2016). However, as we will discuss in the next section, the presence of an element in a biological sample does not establish its essentiality. In this short introduction, we illustrate the biological importance of a few selected metal ions by a few examples.

The alkali metals Na+ and K+ play an important role in the human body as we will see later. In contrast, although Li+, Rb+ and Cs+ are present in small amounts, there is no evidence to suggest that they play any functional role in humans or any other living organism. The alkaline earth metal ions, Mg2+ and Ca2+, also play important roles in the human body, whereas Be2+, Sr2+, Ba2+ and Ra2+ do not.

The transition metals of the first row present particularly rich pickings with regard to their biological functions, notably on account of their capacity (with the exception of Zn2+) to exist in different oxidation states, and therefore to participate in redox reactions. We will consider V and Cr later, but already Mn as a major component of the oxygen-evolving complex (OEC) of photosystem II plays a star role in what is potentially the ultimate green energy production system. The OEC is a membrane-bound multisubunit protein–pigment complex found in cyanobacteria, algae and plants which catalyses the decomposition of water into protons, electrons and molecular oxygen (Eq. 1.1), and its catalytic centre (Fig. 1.2) is a cubane-like Mn4CaO5 cluster (Leslie, 2009; Cox et al., 2013).

(1.1)6CO2+6H2O→C6H12O 6+6O2

Confronted by the rapidly growing consumption of finite reserves of feedstocks (derived essentially from natural gas, hydrocarbon gas liquids, and petrochemical sources), both for generating energy and for the production of a variety of chemicals (organic chemicals; resins, synthetic rubber, and fibres; inorganic chemicals; and agricultural chemicals), we desperately need to find ways to permit us to maintain the sustainability of our society. The vast potential of photosynthetic systems to split water and reduce CO2 on a large scale for practical applications is clearly the ultimate goal towards worldwide sustainability. ‘If we are to fulfill our energy supply continuously and sufficiently, and to reduce the emission of carbon dioxide remarkably, we must learn from photosynthesis on how to obtain energy from the sun artificially and efficiently’ (Allakhverdiev and Shen, 2014).

The electrons produced by the OEC are used to generate the reducing equivalents required for the reduction of CO2, and the electron transfer chains involved contain both the transition metals Fe and Cu. However, the arrival of cyanobacteria capable of the water-splitting reaction had fundamental consequences as far as Fe and Cu were concerned. Until that moment in time, the atmosphere of our newly formed planet was essentially reducing. Fe in its Fe2+ form was readily available, whereas Cu+ in a sulphide-rich milieu was inaccessible. The advent of light-generated oxygen production inaugurated a drastic inversion of roles: Fe3+ in the increasingly aquatic environment became insoluble and difficult to acquire, whereas Cu2+, released from the shackles of insolubility was now readily bioavailable. The availability of dioxygen also opened the possibility to generate energy by the oxidation of organic molecules like glucose (Eq. 1.2), in the reversal of photosynthesis that we call respiration.

(1.2)C6 H12O6+6O2→6CO2+6H2O

This process also requires electron transport chains, which again involve Fe and Cu. Whereas Fe alone is involved in many of the electron transfer steps, the four-electron reduction of dioxygen to two molecules of water requires both Fe and Cu in the terminal component of the respiratory chain, cytochrome c oxidase (CCO).1 The global structure of bovine heart CCO and the arrangement of the haems a and a3:CuB and CuA in CCO are shown in Fig. 1.3. The dinuclear CuA centre is the entrance site for electrons from reduced cytochrome c. Electrons are subsequently passed to the low-spin, bis-His haem a and then to the heterodimetallic haem a3:CuB centre in Cox1 (transparent grey) where O2 reduction occurs.

As we will see in Chapter 15, Nickel and Cobalt: Evolutionary Relics, Co and Ni are particularly important in the metabolism of small molecules such as CO, H2 and CH4, which were thought to be abundant in the reducing atmosphere of early evolution, and are still utilized by a number of microorganisms. Although Co in the form of cobalamin derivatives of vitamin B12 is an essential element for humans, Ni proteins are virtually unheard of in higher eukaryotes, with the obvious exception of the plant enzyme urease.

The celebrated German chemist Richard Willstätter received the Chemistry Nobel Prize in 1915 for his pioneering investigations into plant pigments, especially his work on anthocyanins and chlorophylls, in the course of which he showed not only that Mg2+ was an essential component of the chlorophyll molecule but also that it was bound in a very similar way to that in which Fe is bound in haemoglobin. He also carried out studies on the isolation of enzymes, beginning in 1911. Despite obtaining enrichment of horse radish peroxidase by a factor of 12,000 and of yeast invertase by 3500-fold, Willstätter did not have the good fortune to obtain a crystalline enzyme (Huisgen, 1961), and concluded that enzymes were not proteins (Willstätter, 1926), and that the protein was only a carrier for the veritable catalytic centre (‘nur ein träger Substanz’). However, in 1926, the American James Sumner obtained crystals of urease, the enzyme which catalyses the decomposition of urea to ammonia and carbon dioxide, from jack bean. Subsequently in 1930, John Northrop crystallized pepsin and trypsin, thereby establishing conclusive proof of the protein nature of enzymes (they both received the Chemistry Nobel Prize in 1946). Some 50 years later, when analytical methods for the determination of metal ions in proteins had increased in sensitivity, Willstätter was partially vindicated by the demonstration in 1975 (Dixon et al., 1975) that urease is in fact a nickel-dependent enzyme, and that when the Ni is removed, urease loses its catalytic activity. The protein is indeed a carrier for the Ni, but a carrier which provides the right coordination sphere to bind the two Ni atoms in the right conformation (Fig. 1.4), as well as creating the right environment for the molecular recognition of the substrates, urea and water, and their binding in the right orientation to enable the dimetallic nickel site to carry out its catalysis (see chapter: Nickel and Cobalt: Evolutionary Relics for more details).

As we will see in Chapter 12, Zinc – Lewis Acid and Gene Regulator, Zn2+ is an important cofactor for a vast number of metalloproteins, where it is typically tightly bound and its cellular concentration is usually tightly regulated. However, remarkable changes in total intracellular Zn2+ content have been identified as key events in regulating the cell cycle in the mammalian egg (Kim et al., 2010). On 26 April 2016, the US News published the headline ‘Human eggs emit zinc sparks at moment of fertilization,’ complete with the stunning image of human eggs emitting sparks during conception (Fig. 1.5; Dicker, 2016). In the course of their meiotic maturation, oocytes take up over 20 billion zinc atoms. When a sperm cell enters and fertilizes a mature, zinc-enriched oocyte, this increases intracellular Ca2+ levels, and triggers the coordinated release of zinc into the extracellular space in a prominent ‘zinc spark,’ detectable by fluorescence (Que et al., 2015; Duncan et al., 2016), as illustrated in Fig. 1.5. This loss of zinc is necessary to mediate the egg-to-embryo transition.

Of the other transition metals present in humans, Zr has no known function nor has Au, whereas Mo, together with W, which is absent in humans, most certainly does as we will see in Chapter 17, Molybdenum, Tungsten, Vanadium and Chromium, and Cd appears to replace Zn2+ in the carbonic anhydrase of a marine diatom (Lane and Morel, 2000).

10.3 Partial electron transport reactions assayed with the O2 electrode and a conventional recording spectrophotometer

The reactions described below are illustrated in Figure 10.4. Intact chloroplasts are freshly shocked in the electrode vessel by dilution in 50 mM Tricine-KOH, 50 mM KCl, 5 mM MgCl2 (pH 7.6) to a final chlorophyll concentration of 20–50 μg ml−1. Additions are given below. Other media may be substituted provided that Mn is not included. Electron transport reactions catalysed by methyl viologen may be of indeterminate stoichiometry; consult Allen and Hall4 on this complex topic. See Chapter 7 for details of the oxygen electrode.

7-3-3 LIGHT ENERGY CONVERSION WITH CHLOROPHYLL ELECTRODES

If we regard the electron-transport chain in photosynthesis (Fig. 7.20) as a conducting wire, PS I and PS II (composed mainly of Chl a) can be simulated as a photocathode and a photoanode, respectively. It is hence expected that a Chl-deposited electrode connected to a counter electrode, immersed in an electrolyte solution, will drive a redox reaction under illumination, giving rise to a photocurrent through the external circuit. Based on this isea, several research groups have recently attempted to construct photoelectrochemical cells using Chl electrodes.

In vitro photoelectrochemical behavior of Chl has been studied for the first time by Tributsch and Calvin in 1971 [72]. Albrecht and coworkers [73, 74] investigated the photoelectric and photoelectrochemical properties of microcrystalline Chl a layers deposited on a metal substrate. The peak of photocurrents was observed at around 745 nm, being remarkably red-shifted from Chl a monomer absorption peak (ca. 660 nm). The photoactive species was confirmed to be a Chl a-H2O adduct. In their photoelectric cell, the Chl layer behaved like a p-type semiconductor, and the energy conversion efficiency and the quantum efficiency (under a bias of 2 V) were ca. 0.1% and 3%, respectively.

Fong and his coworkers [75, 76], in their attempt to simulate artificially the reaction centers in PS I and PS II, prepared two different Chl a-H2O adducts, (Chl a-H2O)2 and (Chl a-2H2O)n ≧2, and examined their photoelectrochemical properties using Pt as a substrate. Photocurrents were cathodic, having a maximum around 740 nm due to aggregation, and the quantum efficiency was on the order of 1%. Redox titration of (Chl a-2H2O)n demonstrated that its oxidation potential was near +0.9 V vs. NHE [76], which is reasonably more positive than that for water oxidation (+0.81 V vs. NHE at pH 7). Thus they expected the occurrence of “water splitting” into H2 and O2 at an illuminated (Chl a-2H2O)n electrode. This has been verified recently by mass spectrometric analyses [77]. Though the yield of water decomposition is still limited to a very low level, an improvement of the solar conversion system based on Ch a-H2O adducts could be promising.

From biological observations, it has been proposed that Chl molecules on thylakoid membranes assume a highly ordered structure, through hydrophobic interaction between phytol chains and lipids or proteins, and the Chl local concentration is relatively high (ca. 0.1 − 0.2 M) [64]. A monomolecular layer of Chl [78, 79], prepared on a suitable substrate by means of the Langmuir-Blodgett technique, will be closer to the biological system than the aggregated Chl layer used in investigations cited above. For this purpose a metal substrate is inappropriate, since an excited state of a molecule can be effectively quenched by free electrons in the latter. Taking these into account, we attempted to study photoelectrochemical behaviors of Chl a monomolecular layers deposited on an optically transparent SnO2 electrode [80, 81].

A high charge separation efficiency, due to rectifying characteristics of semiconductor solution interfaces (cf. 7-2-1), was expected with this system. On illumination to the Chl a electrode, anodic photocurrents and negative photovoltages were observed, in accordance with an electron injection from excited Chl molecules to the conduction band of SnO2, as schematically illustrated in Fig. 7.21. The injected electron reaching the counter electrode can reduce some solution species, leading possibly to fuel formation.

Figure 7.22 demonstrates that the action spectrum for the anodic photocurrent coincides well with the absorption spectrum of Chl a monolayer at the SnO2- electrolyte solution interface. These features are essentially the same as those observed in the spectral sensitization of semiconductor electrodes by organic dyes [82]. Quantum efficiency for photocurrent generation was measured with Chl a-stearic acid mixed monolayers and a value of around 15% was attained at the Chl a/stearic acid molar ratio of ca. 1.0. In a subsequent study [83] we replaced stearic acid by lecithin, which is more chemically insert than the former, as a diluent for the Chl a monolayer. With decreasing Chl a/lecithin molar ratio, the quantum efficiency of photo current tended to increase, due presumably to the suppression of Chl a-Chl a inter molecular energy transfer, and a maximum value of 25 ± 5 % was attained (Table 7.3). Owing to such high values of quantum conversion efficiency, these Chl a monolayer (or multilayer)-SnO2 electrodes would be promising for simulating PS II in photosynthesis as well as for constructing an artificial solar conversion system.

Table 7.3. Photocurrent quantum efficiencies at Chlorophyll a-lecithin mixed monolayers [83]

Aizawa et al. [84] recently constructed photoactive electrodes by incorporating magnesium Chl or manganese Chl into several liquid crystals spread on Pt substrates. They observed a cathodic photocurrent with the magnesium Chl and an anodic one with the manganese Chl, though the reason for such a difference remains to be clarified. Immobilization of the pigments by liquid crystals seems to play some role in generating stable photocurrents,

9.7.5 Respiration

The respiration reaction sequence is also known as the electron transport chain. The process of forming ATP from the electron transport chain is known as oxidative phosphorylation. Electrons carried by NADH + H+ and FADH2 are transferred to oxygen via a series of electron carriers, and ATPs are formed. Three ATPs are formed from each NADH + H+, and two ATPs are formed for each FADH2 in eukaryotes. The details of the respiratory (cytochrome) chain are depicted in Fig. 9.30. The major role of the electron transport chain is to regenerate NADs for glycolysis, and ATPs for biosynthesis. The term P/O ratio is used to indicate the number of phosphate bonds made (ADP + H3PO4 → ATP) for each oxygen atom used as an electron acceptor.

The cytochromes (cytochrome a and cytochrome b) and the coenzyme ubiquinone CoQn are positioned at, or near, the cytoplasmic membrane (or the inner mitochondrial membrane in eukaryotes). When electrons pass through the respiratory chain, protons are pumped across the membrane (in prokaryotes, it is the cytosolic membrane, and in eukaryotes, it is the inner mitochondrial membrane). When the protons reenter the cell (or the mitochondria) through the action of the enzyme F0F1-ATPase, as shown in Fig. 9.30, ADP may be phosphorylated to form ATP; therefore, the respiratory chain is often referred to as oxidative phosphorylation. The number of sites where protons can be pumped across the membrane in the respiratory chain depends on the organism. In many organisms there are three sites, and ideally 3 mol of ATP can be formed by the oxidation of NADH. FADH2 enters the respiratory chain at CoQn. The electrons, therefore, do not pass the NADH dehydrogenase; and therefore, the oxidation of FADH2 only results in the pumping of protons across the membrane at two sites. The number of moles of ATP formed for each oxygen atom used in the oxidative phosphorylation is normally referred to as the P/O ratio. The value of this stoichiometric coefficient indicates the overall thermodynamic efficiency of the process. If NADH were the only coenzyme formed in the catabolic reactions, the theoretical P/O ratio would be exactly 3, but since some FADH2 is also formed, the P/O ratio is always < 3. Furthermore, the proton and electrochemical gradient is also used for solute transport. Therefore, the overall stoichiometry for this process is substantially smaller than the upper value of 3. As the different reactions in the oxidative phosphorylation are not directly coupled, the P/O-ratio varies with growth conditions, and the overall stoichiometry is therefore written as:

(9.54)NADH+½O2+P/OADP+H++P/OH3PO4=NAD++1+P/O H2O+P/OATP

In many microorganisms, one or more of the sites of proton pumping are lacking, and this of course results in a substantially lower P/O-ratio.

Since the electron transport chain is located in the inner mitochondrial membrane in eukaryotes, and since NADH cannot be transported from the cytosol into the mitochondrial matrix, NADH formed in the cytosol needs to be oxidized by another route. Strain specific NADH dehydrogenases face the cytosol, and these proteins donate the electrons to the electron transport chain at a later stage than the mitochondrial NADH dehydrogenase. The theoretical P/O ratio for oxidation of cytoplasmic NADH is, therefore, lower than that for mitochondrial NADH. In order to calculate the overall P/O ratio, it is therefore necessary to distinguish between reactions in the cytoplasm and reactions in the mitochondria.

Formation of NADH + H+, FADH2, and ATP at different stages of the aerobic catabolism of glucose are summarized in Table 9.6. The overall reaction (assuming 3 ATP/NADH) of aerobic glucose catabolism in eukaryotes:

Table 9.6. Summary of NADH, FADH2, and ATP Formation During Aerobic Catabolism of Glucose (Based on the Consumption of One Mole of Glucose)

(9.55)glucose+36H3PO4+ 36ADP+6O2→6CO2+6H2O+36AT P

The energy deposited in 36 moles of ATP is 1100 kJ/mol-glucose. The free-energy change in the direct oxidation of glucose is 2870 kJ/mol-glucose. Therefore, the energy efficiency of glycolysis is 38% under standard conditions. With the correction for nonstandard conditions, this efficiency is estimated to be > 60%, which is significantly higher than the efficiency of man-made machines. The remaining energy stored in glucose is dissipated as heat. However, in prokaryotes the conversion of the reducing power to ATP is less efficient. The number of ATPs generated from NADH + H+ is usually ≤ 2, and only one ATP may be generated from FADH2. Thus in prokaryotes, a single glucose molecule will yield < 24 ATPs, and the P/O ratio is generally between 1 and 2.

5.1 Enzyme role

Menaquinone (29) plays a critical role in the electron transport chain (ETC) of mycobacteria, cycling between menaquinone and menaquinol in the membrane to shuttle electrons between the various redox enzymes involved. Menaquinone is synthesized from chorismate via a series of nine enzymes (MenA-I), in the order F → D → H → C → E → B → I → A → G. Some of these enzymes have become targets for small-molecule inhibitors.7,9 A further enzyme, MenJ, which catalyzes the hydrogenation of a single isoprene unit of menaquinone in M.tb, has been characterized, and an assay that would be amenable to high-throughput screening for inhibitors has also been developed.41

Ubiquinone (Coenzyme Q)

Ubiquinone (UQ) is a component of the membrane-bound electron transport chains and serves as a redox mediator in aerobic respiration via reversible redox cycling between ubiquinol (UQH2), the reduced form of UQ, and UQ. UQH2 possesses significant antioxidant properties and protects not only against lipid peroxidation but also against modification of integral membrane proteins, DNA oxidation, and strand breaks.

UQ is a lipid consisting of a quinone head group and a polyprenyl tail varing in length depending on the organism. The isoprenoid side chain from mevalonic acid and methyl and methoxyl groups derived from S-adenosylmethionine attached to the quinone ring derives from chorismate to biosynthesize UQ. The biosynthetic pathways of UQ in E. coli and S. cerevisiae diverge after the assembly of 3-polyprenyl-4-hydroxybenzoate derived from chorismate, but converge from 2-polyprenyl-6-methoxyphenol to UQH2. The composition of the quinone pool is highly influenced by the degree of oxygen availability in E. coli.

Genes Encoding Proteins Involved in Electron Transport and Oxidative Phosphorylation

The mitochondrial genome specifies components of complexes I–IV of the electron transport chain and complex V (ATP synthase). The genes corresponding to these various complexes are abbreviated nad (complex I), sdh (II), cob (III), cox (IV), and atp (V). The number of genes in each class varies among mitochondrial genomes, with the mtDNA of humans encoding seven nad, no sdh, one cob, three cox, and two atp genes (13 in total). The largest number of such genes (25) is found in the jakobid mitochondrial genome, whereas the smallest number (3) occurs in the mitochondrial genome of Plasmodium falciparum, the human malaria parasite, and related members of the protist phylum Apicomplexa (recently, the mitochondrial genome of a phototrophic relative of apicomplexan parasites, Chromera velia, was shown to contain just two genes, lacking the cob gene that is otherwise universal in mtDNA). In mitochondrial genomes harboring smaller numbers of respiratory chain genes, the missing genes are typically found in the nuclear genome, with their cytoplasmically synthesized protein products being imported into mitochondria.