Oxidative Phosphorylation and Electron Transport Chain: Structure, Function, and Mechanism

Oxidative Phosphorylation

Overview of Oxidative Phosphorylation

Oxidative phosphorylation is the final stage of aerobic metabolism, where the energy from the oxidation of nutrients is used to synthesize ATP. This process occurs in the mitochondria and involves the transfer of electrons from NADH and FADH2 to oxygen via the electron transport chain (ETC), generating a proton gradient that drives ATP synthesis.

• Definition: Oxidative phosphorylation is the process by which ATP is formed as electrons are transferred from NADH or FADH2 to O2 via a series of electron carriers.

• Location: Occurs in the inner mitochondrial membrane of eukaryotes.

• Chemiosmotic Theory: The energy from electron transfer is conserved by pumping protons across the inner membrane, creating a proton-motive force used for ATP synthesis.

• Key Reaction: Reduction of O2 to H2O.

The Mitochondria

Structure and Compartmentalization

Mitochondria are double-membraned organelles that serve as the site for oxidative phosphorylation and other metabolic pathways.

• Outer Membrane: Permeable to small molecules via porin channels.

• Inner Membrane: Impermeable to most small molecules, including protons; contains ETC complexes and ATP synthase.

• Matrix: Contains enzymes for the citric acid cycle, fatty acid oxidation, amino acid oxidation, and the pyruvate dehydrogenase complex.

• Cytosol: Site of glycolysis and gluconeogenesis.

Drugs and Toxins Impacting the TCA Cycle and ETC

Inhibitors and Their Mechanisms

Certain drugs and toxins can disrupt the TCA cycle and electron transport chain, affecting cellular energy production.

• Fluoroacetate: Blocks conversion of citrate to isocitrate in the TCA cycle.

• Bromopyruvate: Inhibits pyruvate dehydrogenase complex, preventing pyruvate entry into the Krebs cycle.

• Malonate: Competitive inhibitor of succinate dehydrogenase.

• Arsenic: Interferes with pyruvate dehydrogenase complex, preventing acetyl-CoA formation.

• Cyanide and Carbon Monoxide: Inhibit electron transport by binding to cytochrome c oxidase.

• Mercury: Affects enzymes such as α-ketoglutarate dehydrogenase.

Electron Carrying Molecules

Types and Functions

Five main types of electron carriers participate in the mitochondrial respiratory chain, facilitating electron transfer and energy conservation.

• NADH: Water-soluble, associates reversibly with dehydrogenases, cannot cross the inner membrane, transfers two electrons as a hydride ion and a proton.

• FADH2: Bound tightly to flavoproteins, can transfer one or two electrons.

• Ubiquinone (Coenzyme Q): Lipid-soluble benzoquinone, accepts one or two electrons, freely diffuses within the inner membrane.

• Cytochromes: Proteins with iron-containing heme groups; three classes (a, b, c) based on absorbance spectra; cytochrome c is soluble and moves between complexes.

• Iron-Sulfur Proteins: Contain iron associated with sulfur atoms and cysteine residues; participate in one-electron transfers; reduction potential depends on protein environment.

Structures of NAD+/NADP+ and FAD

Chemical Structures and Redox Properties

NAD+ and FAD are essential cofactors in redox reactions, with distinct chemical structures and absorbance properties.

• NAD+: Contains an adenine nucleotide and a nicotinamide ring; reduced to NADH during electron transfer.

• FAD: Contains a riboflavin (vitamin B2) moiety; can exist in oxidized, semiquinone, and fully reduced forms.

Ubiquinone (Coenzyme Q)

Role in Electron Transport

Ubiquinone is a mobile electron carrier within the inner mitochondrial membrane, shuttling electrons between complexes.

• Structure: Lipid-soluble benzoquinone.

• Redox States: Can accept one electron to form semiquinone (QH•) or two electrons to form ubiquinol (QH2).

• Function: Transfers electrons between less mobile carriers (complexes I/II and III).

Cytochromes

Classes and Functions

Cytochromes are heme-containing proteins that mediate electron transfer in the ETC.

• Classes: a, b, and c, distinguished by heme structure and absorbance spectra.

• Cytochrome c: Soluble protein, shuttles electrons between complexes III and IV.

• Reduction Potential: Depends on the protein environment surrounding the heme group.

Iron-Sulfur Proteins

Structure and Electron Transfer

Iron-sulfur proteins are involved in one-electron transfers within the ETC.

• Structure: Iron atoms coordinated with inorganic sulfur and cysteine residues.

• Types: Centers may contain one, two, or four iron atoms.

• Function: At least eight iron-sulfur proteins participate in mitochondrial electron transfer.

ETC Protein Complexes

Organization and Function

The electron transport chain consists of four main protein complexes and mobile carriers, each with distinct roles in electron transfer and proton pumping.

• Complex I (NADH dehydrogenase): Transfers electrons from NADH to ubiquinone; pumps 4 protons.

• Complex II (Succinate dehydrogenase): Transfers electrons from succinate to ubiquinone; does not pump protons.

• Complex III (Cytochrome bc1): Transfers electrons from ubiquinol to cytochrome c; pumps 4 protons.

• Complex IV (Cytochrome oxidase): Transfers electrons from cytochrome c to O2; pumps 2 protons and consumes 2 protons in water formation.

• Cytochrome c: Mobile electron carrier between complexes III and IV.

Enzyme Complex/Protein	Number of Subunits	Prosthetic Group(s)
NADH dehydrogenase (Complex I)	42	FMN, Fe-S
Succinate dehydrogenase (Complex II)	4	FAD, Fe-S
Cytochrome bc1 (Complex III)	11	Hemes, Fe-S
Cytochrome oxidase (Complex IV)	13	Hemes, Cu
Cytochrome c	1	Heme

Electron Flow in the ETC

Pathway of Electrons

Electrons from NADH and FADH2 are transferred through a series of carriers to oxygen, the final electron acceptor.

• NADH: Donates electrons to Complex I, then to CoQ, Complex III, cytochrome c, Complex IV, and finally O2.

• FADH2: Donates electrons to Complex II, then to CoQ, Complex III, cytochrome c, Complex IV, and O2.

Electricity Driven Proton Pumps

Proton Gradient Formation

Complexes I, III, and IV pump protons from the matrix to the intermembrane space, generating a proton-motive force.

• Complex I: Pumps 4 H+ per NADH oxidized.

• Complex III: Pumps 4 H+ per pair of electrons.

• Complex IV: Pumps 2 H+ per pair of electrons.

Complex I

Structure and Function

Complex I (NADH:ubiquinone oxidoreductase) is a large multi-subunit complex that initiates electron transfer from NADH to ubiquinone.

• Composition: 42 polypeptide chains, including FMN and iron-sulfur centers.

• Function: Transfers electrons from NADH to ubiquinone, pumps 4 protons.

• Reaction: $NADH + H^+ + Q + 4H^+_{matrix} \rightarrow NAD^+ + QH_2 + 4H^+_{intermembrane}$

Complex II

Structure and Function

Complex II (succinate dehydrogenase) links the TCA cycle to the ETC by transferring electrons from succinate to ubiquinone.

• Composition: At least four subunits; subunit A in the TCA cycle, subunits C and D embedded in the membrane.

• Function: Transfers electrons from succinate to FAD, then through Fe-S centers to ubiquinone.

• Does not pump protons.

Other Electron Carriers to Q

Alternative Pathways

Electrons can enter the ETC via other carriers, increasing the pool of reduced ubiquinone.

• ETF:Q oxidoreductase: Transfers electrons from fatty acid oxidation to ubiquinone.

• Glycerol 3-phosphate dehydrogenase: Channels electrons from cytosolic NADH into the ETC via ubiquinone.

Complex III

Structure and Function

Complex III (cytochrome bc1 or ubiquinone c oxidoreductase) transfers electrons from ubiquinol to cytochrome c and pumps protons.

• Composition: Contains hemes and Rieske iron-sulfur protein.

• Function: Couples electron transfer from QH2 to cytochrome c with the transport of 4 protons.

• Cytochrome c: Soluble protein that moves electrons to Complex IV.

The Q Cycle

Mechanism of Electron and Proton Transfer

The Q cycle describes the mechanism by which Complex III transfers electrons from QH2 to cytochrome c, while pumping protons across the membrane.

• QH2: Donates two electrons; one goes to cytochrome c, the other recycles through cytochrome b.

• Proton Pumping: 2 H+ per QH2 oxidized are pumped into the intermembrane space.

• Net Reaction: $QH_2 + Q + 2cyt~c_{(oxidized)} + 2H^+_{matrix} \rightarrow Q + QH_2 + 2cyt~c_{(reduced)} + 4H^+_{intermembrane}$

Complex IV

Structure and Function

Complex IV (cytochrome oxidase) catalyzes the final electron transfer to oxygen, forming water and pumping protons.

• Composition: 13 subunits; subunit II contains two Cu ions (CuA), subunit I contains two hemes (a and a3) and another Cu ion (CuB).

• Function: Transfers electrons from cytochrome c through Cu and heme centers to O2.

• Proton Pumping: 2 H+ pumped per 2 electrons; 2 H+ consumed in water formation.

• Reaction: $2cyt~c_{(red)} + 4H^+_{matrix} + 1/2O_2 \rightarrow 2cyt~c_{(ox)} + 2H^+_{intermembrane} + H_2O$

Energy Conservation and Proton-Motive Force

Free Energy and ATP Synthesis

The energy released by electron transfer is used to pump protons, creating a gradient that drives ATP synthesis via ATP synthase.

• Standard Free Energy Change: $\Delta G^\circ$ for NADH to O2 is -220 kJ/mol; for FADH2 is -150 kJ/mol.

• Proton-Motive Force: The gradient of protons across the inner membrane stores energy.

• Equation for Proton Gradient: $\Delta G = RT \ln \left( \frac{C_2}{C_1} \right) + ZF\Delta \Psi = 2.3RT\Delta pH + F\Delta \Psi$

• ATP Synthesis: The energy in the proton gradient (220 kJ/mol per electron pair) is sufficient to drive ATP formation (about 50 kJ/mol).

• ATP Synthase: F1-F0 ATP synthase couples proton flow back into the matrix to ATP synthesis.

Summary Table: ETC Complexes and Functions

Complex	Electron Donor	Electron Acceptor	Proton Pumping
Complex I	NADH	Ubiquinone (Q)	4 H+
Complex II	Succinate	Ubiquinone (Q)	None
Complex III	QH2	Cytochrome c	4 H+
Complex IV	Cytochrome c	O2	2 H+

Example: Inhibition of ETC by Cyanide

Cyanide binds to cytochrome oxidase (Complex IV), preventing electron transfer to oxygen and halting ATP synthesis, which can be fatal due to cellular energy failure.

Additional info:

• All equations are provided in LaTeX format for clarity.

• Tables are reconstructed from the original notes and may include inferred content for completeness.