Part III => METABOLISM and ENERGY 3.6 Oxidative Phosphorylation 3.6a Electron Transport 3.6b ATP Synthesis
Section 3.6a: Electron Transport
Synopsis 3.6a - During processes such as glycolysis and Krebs cycle, oxidation of macronutrients results in the release of electrons that are ultimately captured in the form of reduced NADH/FADH 2 - In order to recover the free energy of these electrons stored in NADH and FADH 2, they are funneled into a series of redox protein complexes collectively referred to as the electron transport chain (ETC) located within the inner mitochondrial membrane (IMM) - ETC in turn couples the free energy of incoming electrons with the transfer of protons (H + ) across the IMM culminating with the reduction of O 2 to H 2 O via a series of redox reactions the electrochemical energy stored in the resulting proton gradient across the IMM is then utilized to synthesize ATP directly from ADP and Pi - Simply put, the energy released from the oxidation of NADH and FADH 2 (ultimately from the nutrients) is coupled to phosphorylation of ADP directly with Pi (HPO 4 2- ) to generate ATP in a process referred to as Oxidative Phosphorylation - Oxidative phosphorylation (OP) is in stark contrast to substrate-level phosphorylation whereby the transfer of a phosphoryl group from a high-energy compound (eg phosphoenol pyruvate) to ADP is used to synthesize ATP (see 3.1 and 3.2) - Be aware that ETC and OP are often used synonymously, or sometimes considered as two distinct processes but, in reality, oxidative phosphorylation is ultimately an overall consequence of ETC!
Mitochondrion: The Cell s Power Plant OMM harbors large non-selective channels such as voltage-dependent anion channels /porins, which enable facilitated diffusion of most metabolites into the intermembrane space! IMM is much more restrictive with respect to the non-selective diffusion of metabolites but harbors metabolite-specific transporters! Both the Krebs cycle and oxidative phosphorylation occur within the mitochondrial matrix! IMM Inner (Mitochondrial) Membrane OMM Outer (Mitochondrial) Membrane
Oxidative Metabolism - NADH and FADH 2 produced during glycolysis and Krebs cycle enter the ETC - While glycolysis occurs in the cytosol, Krebs cycle and ETC take place within the mitochondrial matrix - How does glycolytic NADH enter the mitochondrial matrix so that it can inject its electrons into the ETC?
Regeneration of Cytosolic NAD + IMM Glycerol-3-phosphate Shuttle Glycolytic NADH cannot diffuse through IMM but transfers its electrons to: 1) Mitochondrial FAD, thereby reducing it to FADH 2 via the glycerol-3-phosphate shuttle 2) Mitochondrial NAD +, thereby reducing it to NADH via the malate-aspartate shuttle In each case, glycolytic NADH is reoxidized to cytosolic NAD + so that it can be reused in glycolysis while the resulting mitochondrial pools of FADH 2 and NADH enter the ETC
Coupling of ETC to ATP Synthesis NADH and FADH 2 essentially act like miniature batteries in that the flow of electrons from them powers up various transmembrane vehicles (eg complexes I, III and IV) that in turn pump protons across the IMM against their concentration gradient in a manner akin to active transporters (see 1.5) Krebs cycle V
ETC Components: A Closer Look ETC is primarily comprised of protein complexes I-IV, coenzyme Q (CoQ), and cytochrome c (CytC) all of which are highly dynamic and move freely within the IMM 2 2 NADH NAD + FADH 2 FAD Krebs cycle The efflux of protons (H + ) is associated with complexes I, III and IV (that essentially act as proton pumps) the free energy captured in the resulting electrochemical proton gradient is ultimately harnessed to synthesize ATP
ETC Components: Standard Reduction Potentials ( ) - ETC components are arranged such that their increases progressively from electron injectors NADH and FADH 2 to the terminal electron acceptor O 2 H 2 - ETC thus essentially acts like an electron gradient with the electrons having the tendency to flow downhill (in the direction of increasing ) in a manner akin to the rolling of a stone down a hill (or the flow of electrons across an electrochemical cell see 3.1) - The free energy resulting from the dissipation of such electron gradient is usurped to pump protons across the IMM thereby setting up a proton gradient, which is ultimately harnessed to synthesize ATP Direction of Electron Flow
/ V ETC Components: Points of ATP Synthesis Parallel Pathways for injecting electrons into ETC - NADH and FADH 2 do not directly donate electrons to O 2 but rather via a series of membrane-bound protein complexes called I-IV located within the IMM FADH 2 FAD (-0.040 V) Complex II = +0.085 V G = -16.4 kj.mol -1 - While NADH donates electrons to Complex I, Complex II serves as an electron acceptor for FADH 2 both cofactors ultimately donate their electrons to coenzyme Q (CoQ) - Electron transport from NADH and FADH 2 to O 2 via complexes I-IV is an highly exergonic process - Free energy ( G) of electron transport is coupled to the generation of a proton gradient across the IMM - Recall that G is given by (see 3.1): G = -zf
Complex I (NADH Dehydrogenase): Structure Peripheral arm Electron transport Transmembrane arm Proton pump Mitochondrial Matrix IMM Intermembrane Space
Complex I (NADH Dehydrogenase): Function - The peripheral arm of Complex I harbors various cofactors such as flavin mononucleotide (FMN) and nine iron-sulfur Clusters two conforming to [2Fe-2S] geometry (N1a and N1b), while the rest to [4Fe-4S] see 3.1 NADH - By virtue of such cofactors, the peripheral arm of Complex I facilitates the transfer of electrons from NADH to coenzyme Q (CoQ) also known as ubiquinone in a series of redox steps (from FMN via iron-sulfur clusters N1-N7) culminating with the overall reaction: NADH + CoQ + H + NAD + + CoQH 2 = +0.360V => G = -70 kj/mol - The reaction generates sufficient free energy to pump four protons across the IMM how?! - The transfer of electrons from NADH to CoQ via the peripheral arm of Complex I induces conformational changes within its transmembrane arm - Such structural transition is coupled to an alteration of hydrogen bonding network that allows protons to hop across the transmembrane arm of Complex I within the IMM from the mitochondrial matrix to the intermembrane space, thereby setting up a proton gradient that will be ultimately coupled to ATP synthesis (next section) CoQ
Complex II (Succinate Dehydrogenase): Structure Hydrophilic domain (electron transport) FAD(H 2 ) [2Fe-2S] [4Fe-4S] [3Fe-4S] Mitochondrial Matrix Heme b CoQ Transmembrane domain (facilitates electron transport by directly binding to CoQ) IMM Intermembrane Space
Complex II (Succinate Dehydrogenase): Function - The hydrophilic domain of Complex II harbors various cofactors such as flavin adenine dinucleotide (FAD) and three iron-sulfur clusters designated [2Fe-2S], [4Fe-4S], and [3Fe-4S] H 2 - Complex II catalyzes the oxidation of succinate to fumarate (Step 6 of Krebs cycle) by virtue of its succinate dehydrogenase activity coupled with the reduction of its FAD cofactor to FADH 2 - Next, Complex II facilitates the transfer of electrons from FADH 2 to CoQ in a series of redox steps (from FADH 2 via three iron-sulfur clusters) culminating with the overall reaction: FADH 2 + CoQ FAD + CoQH 2 = +0.085V => G = -16 kj/mol - This reaction does not generate sufficient free energy to pump protons across the IMM via the transmembrane domain of Complex II this step is however important in that it injects electrons directly into CoQ so that the energy carried by electrons can be utilized by Complexes III and IV in generating the proton gradient - Importantly, the transmembrane domain directly binds to CoQ and thus ensures its proximity to the iron-sulfur clusters which pass the electrons downhill to CoQ - Transmembrane domain also binds heme b, which is believed to attune electron transit between Complex II and CoQ
Complex III (Cytochrome c Reductase): Structure Homodimeric Complex IMM Mitochondrial Matrix CoQH2 Intermembrane Space Cytochrome b H Cytochrome b L Stigmatellin [2Fe-2S] Transmembrane domain Cytochrome c Cytochrome c 1
Complex III (Cytochrome c Reductase): Function - Complex III harbors four redox centers: cytochrome b H, cytochrome b L, cytochrome c 1, and a single [2Fe-2S] ironsulfur cluster within the so-called Rieske iron-sulfur protein (ISP) recall from 3.1 that cytochromes harbor heme (Fe 3+ ) cofactor! - Owing to such redox centers, Complex III mediates the transfer of electrons from CoQH 2 (QH 2 ) to cytochrome c (CytC) via a series of redox steps collectively referred to as the Q Cycle culminating with the overall reaction: CoQH 2 + 2CytC(Fe 3+ ) CoQ + 2CytC(Fe 2+ ) + 2H + = +0.190V => G = -37 kj/mol - The Q cycle is critical in that while CoQH 2 is a 2e - carrier, CytC (Fe 3+ ) is a 1e - carrier thus one molecule of CoQH 2 reduces TWO molecules of CytC! - In order to facilitate the above reaction, CytC transiently binds to Complex III on its intermembrane face lying between IMM and OMM - The free energy released by the above reaction is used to pump four protons across the IMM via Complex III how?! - Unlike Complex I, proton pumping by Complex III is primarily mediated by virtue of the ability of CoQ to act as a proton carrier across the IMM CytC CytC Q Cycle IMM
Complex IV (Cytochrome c Oxidase): Structure Cytochrome a Cytochrome a 3 Mitochondrial Matrix IMM CytC e- Intermembrane Space e - CytC Cu A Cu B Homodimeric Complex
Complex IV (Cytochrome c Oxidase): Function - Complex IV contains four redox centers: cytochrome a, cytochrome a 3, a single Cu + ion (Cu B ), and a pair of Cu + ions (Cu A ) recall from 3.1 that cytochromes harbor heme (Fe 3+ ) cofactor! Intermembrane Space e - CytC - Owing to such redox centers, Complex IV catalyzes the transfer of electrons from cytochrome c (CytC) to the terminal electron acceptor O 2 via a series of redox steps culminating with the overall reaction: 2CytC(Fe 2+ ) + 0.5O 2 + 2H + 2CytC(Fe 3+ ) + H 2 O = +0.580V => G = -112 kj/mol - The free energy released by the above reaction is used to reinforce proton gradient across the IMM in two ways by Complex IV: (1) Two protons are pumped across the IMM, thereby increasing proton concentration in the intermembrane space (2) Depletion of two matrix protons by supplying them for reduction of each half-molecule of O 2 e - e - Redox Centers - Like Complex I, proton pumping by Complex IV is mediated by conformational changes that facilitate protons to hop along the transmembrane domain to the intermembrane space Matrix
Exercise 3.6a - Describe the route followed by electrons from NADH/FADH 2 to O 2 - Write the net equation for electron transfer from NADH to O 2 - For each of the electron-transport complexes, write the overall redox reaction - Position the four electron-transport complexes on a graph showing their relative reduction potentials, and indicate the path of electron flow - List the types of cofactors in Complexes I, II, III, and IV - Describe the different mechanisms for translocating protons during electron transport
Section 3.6b: ATP Synthesis SPINDLE
Synopsis 3.6b - Free energy of electrons in the form of NADH/FADH 2 released via ETC is coupled to the generation of an electrochemical proton gradient across the IMM the electrochemical potential of such a proton gradient is subsequently harnessed to drive ATP synthesis directly from ADP and Pi (strictly, HPO 4 2- ) via oxidative phosphorylation - Coupling the free energy stored in the proton gradient to ATP synthesis is carried out by an enzyme called ATP synthase which can be essentially viewed as Complex V located downstream of Complexes I-IV in the ETC - Embedded within the IMM and protruding into the mitochondrial matrix, ATP synthase is comprised of two components: (1) Fo component (IMM-embedded) (2) F1 component (Matrix) - Fo (capitalized F subscripted with small letter o not zero!) component includes a c-ring whose rotation is driven by the dissipation of the proton gradient and drives conformational changes in the F1 component which in turn catalyzes ATP synthesis by the so-called binding change mechanism
Coupling of ETC to ATP Synthesis Complex V (ATP Synthase) Fo F1 - Coupling the free energy stored in the proton gradient to ATP synthesis is carried out by an enzyme called ATP synthase which can be essentially viewed as Complex V located downstream of Complexes I-IV in the ETC - ATP synthase can also act as an ATPase ie it can catalyze exergonic hydrolysis of ATP to pump protons against their electrochemical gradient! - Simply put, oxidative phosphorylation involves coupling the free energy released by the oxidation of nutrients to directly synthesize ATP from ADP and Pi (strictly, HPO 4 2- )
ATP Synthase: Mushroom-Like Structure Embedded within the IMM and protruding into the mitochondrial matrix, ATP synthase is comprised of two components: (1) IMM-embedded Fo component (2) Matrix F1 component Fo component (a 1 b 2 c 12 ) - 1 a subunit - 2 b subunits - 12 c subunits (but may vary) F1 component ( 3 3 ) - 3 subunits (catalytic) - 3 subunits (catalytic) - 1 subunit - 1 subunit - 1 subunit The b subunits together with the subunit form a peripheral stalk that tethers F1 to the a subunit of Fo a key feature that underscores the rotation of c12 subunits (called c- ring) of Fo relative to F1 Matrix IMM c 12 Intermembrane space
- ATP synthase can be envisioned as a: (1) Rotor (c 12 ) the C-ring (2) Spindle ( ) spinning inside the. (3) Stator (ab 2 3 3 ) so what sets the rotor spinning? ATP Synthase: Rotary Engine - Protons enter via a hydrophilic channel located between the a-subunit and the c-ring at the intermembrane space: Stator (1) Proton binding to one of the 12 c-subunits causes a conformational change that makes the c-ring rotate counter-clockwise (as viewed from the matrix) by one c-subunit (2) Binding of protons to successive c-subunits makes the c-ring spin smoothly and continuously IMM Spindle Matrix - Such rotary action converts electrochemical energy stored in the proton gradient across IMM a form of potential energy or the proton motive force (pmf) into mechanical energy of the spinning rotor - Spinning of the rotor is coupled to ATP synthesis occurring at the interface of the 3 3 catalytic subunits of F1 component (by virtue of yet another conformational change within 3 3 ) the mechanical energy is ultimately converted back to chemical energy! Hydrophilic channel c-ring Rotor Intermembrane space
ATP Synthase: Basis of Rotation - The conformational change that spins the rotor is driven by a mutual attraction between a cationic arginine on the a-subunit and an anionic aspartate on the c-subunit essentially a salt bridge or an ion pair - As the proton concentration rises in the intermembrane space (thanks to ETC), such union of opposites is disrupted by the entry of a proton since it competes with the arginine for binding to the aspartate via the hydrophilic channel Stator Spindle - Upon binding to aspartate, the proton induces a structural change within the c-subunit that drives it in a counter-clockwise manner (as viewed from the matrix side) so as to allow the next c-subunit to engage in an arginine-aspartate bridge with the stationary a-subunit IMM c-ring Matrix - The above process is repeated to drive the rotary action of the c-ring in a continuous manner until the proton gradient is fully discharged - How many protons are required to drive one full turn of the rotor (c-ring)?! Hydrophilic channel Rotor Intermembrane space
ATP Synthase: In Action - One full turn of the rotor (c-ring) requires 12 protons one for each c-subunit! - Each full turn produces 3 ATP molecules one by each of the three catalytic protomers of 3 3 subunits of F1 component - Simply put, 3/12 (or 0.25) ATP molecules are produced for the discharge of every proton during oxidative phosphorylation - How is the spinning of the rotor coupled to ATP synthesis occurring at the interface of the 3 3 catalytic subunits of F1 component? - Enter the binding change mechanism
ATP Synthase: Binding Change Mechanism In the so-called binding change mechanism, each of the three catalytic protomers of the 3 3 subunits of F1 component is envisioned to adopt three distinct conformations designated O, L and T that are in equilibrium exchange with each other: O catalytically-inactive / low affinity for ligands (ATP, ADP, Pi) L catalytically-inactive / moderate affinity for ligands T catalytically-active / high affinity for ligands (1) In the absence of the spinning action of the rotor (c 12 ), the protomer largely equilibrates between the O and L states it cannot synthesize ATP from ADP and Pi with the latter being able to accommodate ADP/Pi with moderate affinity (2) Upon the spinning action of the rotor (c 12 ), the free energy released shifts the conformational equilibrium of the protomers from the L state to the catalytically-active T conformation, enabling it to stick together ADP and Pi to generate ATP (3) Upon the synthesis of ATP, the T state undergoes conformational change to O state (with low affinity for ligands), thereby releasing ATP and enabling the protomer to return to its initial state in order to undergo another catalytic cycle
ATP Synthesis Via OP: Oxidation of Carbs Free energy of electron transport from NADH/FADH 2 drives ATP synthesis NADH Oxidation 10 H + /NADH pumped across the IMM 10 H + /NADH * 0.25 ATP/H + => 2.5 ATP/NADH FADH 2 Oxidation 6 H + /FADH 2 pumped across the IMM 6 H + /FADH 2 * 0.25 ATP/H + => 1.5 ATP/FADH 2 Aerobic Conditions Glycolysis Acetyl-CoA Synthesis Krebs Cycle Total => 7 ATP/glucose => 5 ATP/glucose => 20 ATP/glucose => 32 ATP/glucose Anaerobic Conditions Glycolysis Acetyl-CoA Synthesis Krebs Cycle Total => 2 ATP/glucose => 0 ATP/glucose => 0 ATP/glucose => 2 ATP/glucose
Palmitic Acid (16:0) ATP Synthesis Via OP: Oxidation of Fats Palmitoyl-CoA 6 - Palmitic acid is a saturated fatty acid harboring 16 carbon atoms (16:0) - It is the most commonly occurring fatty acid in living organisms - So how much energy does -oxidation of a single chain of palmitic acid (16 C atoms) generate? - Complete degradation of palmitic acid would require 7 rounds of -oxidation producing 7 FADH 2, 7 NADH and 8 acetyl-coa the final round produces 2 acetyl-coa! - Further oxidation of each acetyl-coa via the Krebs cycle produces 3 NADH, 1 FADH 2 and 1 GTP (enzymatically converted to ATP) per molecule (and there are 8 acetyl-coa!) see 3.5 - Oxidation of each NADH and FADH2 via the ETC respectively produces 2.5 and 1.5 molecules of ATP as noted in 3.4 8 Acetyl-CoA Krebs cycle -Oxidation 7 FADH 2 7 NADH 24 NADH 8 FADH 2 8 GTP ETC ETC ETC ETC 10.5 ATP 17.5 ATP Fat Is hypercaloric! 60 ATP 12 ATP 8 ATP Total Energy = 108 ATP
ATP Comparison: Carbs vs Fats Palmitate Glucose 6 M r = 256 g.mol -1 but: N A = 6x10 23 mol -1 thus: m = 256 g.mol -1 / 6x10 23 mol -1 m = 43x10-23 g M r = 180 g.mol -1 but: N A = 6x10 23 mol -1 thus: m = 180 g.mol -1 / 6x10 23 mol -1 m = 30x10-23 g Complete Oxidation via the Krebs cycle Glucose => 32 ATP => 32 ATP / 30x10-23 g => 1.07x10 23 ATP/g Plamitate => 108 ATP => 108 ATP / 43x10-23 g => 2.51x10 23 ATP/g - Fats generate more than two-fold greater ATP per unit mass compared to carbs ie they serve as more energy-efficient fuels - The energy-efficient nature of fats in particular is not lost on heart (virtually devoid of glycogen reserves) an organ that primarily uses fats to meet its energy needs (see 3.1)
Exercise 3.6b - Explain why an intact and impermeable IMM is essential for ATP synthesis - Describe the overall structure of the F1 and F0 components of ATP synthase. Which parts move? Which are stationary? Which are mostly stationary but undergo conformational changes? - Summarize the steps of the binding change mechanism - Describe how protons move from the intermembrane space into the matrix. How is proton translocation linked to ATP synthesis?