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Mitochondrial Bioenergetics – Lecture 1

Bioenergetics – The Grand Context

  • Bioenergetics = study of how cells acquire, convert and use energy.

  • Energy sources differ by organism:

    • Eukaryotes: carbohydrates (glycolysis), fatty acids (β-oxidation), amino acids → feed into mitochondria.

    • Prokaryotes: can use sunlight, methane, etc.

  • Despite diverse inputs, mitochondria (animals) and chloroplasts (plants) employ parallel principles: build an electrochemical (proton) gradient across an internal membrane and couple its dissipation to ATP formation.

Overview of Upcoming Lecture Block

  • Three-hour module focused on mitochondrial bioenergetics.

  • Major milestones to be covered (today is the foundation):

    1. Fundamental bioenergetics, anatomy & architecture of mitochondria.

    2. Evolution of the chemiosmotic/chemical coupling idea (Peter Mitchell).

    3. Molecular dissection of the Electron Transport Chain (ETC).

    4. ATP production mechanism of the F{1}F{0}-ATP synthase.

Endosymbiotic Origins of Mitochondria

  • Double membrane, their own circular DNA, bacterial-type transcription/translation machinery → supports endosymbiotic event.

  • Mitochondrial DNA (mtDNA): \approx 16 \,\text{kb}.

    • Encodes 13 respiratory chain polypeptides, rRNAs (large + small subunits) & tRNAs required for intramitochondrial translation.

  • Phylogenetic analyses: single ancestral engulfment event; the core gene set is conserved across eukaryotes.

Canonical Cartoon vs. Real Ultrastructure

  • Classical cartoon: outer membrane (OM), intermembrane space (IMS), inner membrane (IM) with cristae, matrix.

  • Modern electron-tomography: reveals highly folded lamellar/curved cristae with large IM surface area.

  • Guiding questions:

    • Why so much membrane?

    • How is curvature achieved and what energetic advantage results?

Matrix – Metabolic Hub Beyond the TCA Cycle

  • High-profile pathways:

    • Tricarboxylic Acid (TCA) cycle.

    • Fatty-acid β-oxidation.

  • Both primarily yield NADH (reducing equivalents) rather than ATP.

  • Additional matrix functions:

    • Urea cycle.

    • Amino-acid biosynthesis.

    • Heme/porphyrin synthesis (via succinyl-CoA).

    • Partial lipid & steroid synthesis (citrate export).

    • Mitochondrial protein synthesis (mito-ribosomes).

  • Implication: robust import/export systems required for many metabolites and cofactors.

Membrane Biochemistry—Composition Mirrors Function

  • Inner Mitochondrial Membrane (IMM)

    • Protein-dense (~\ge 70\% by mass); lipid-poor relative to other eukaryotic membranes.

    • Nearly devoid of cholesterol (contrast: most eukaryotic membranes 30$–$50\% cholesterol).

    • Enriched in cardiolipin (CL) \approx 18\% of phospholipids; also high in phosphatidylethanolamine (PE).

  • Cardiolipin traits

    • Four acyl chains + two phosphate headgroups → small head, large hydrophobic body; overall anionic.

    • Conical geometry forces negative curvature when packed → drives membrane bending (supports cristae formation & protein organization).

  • Outer Mitochondrial Membrane (OMM)

    • More typical lipid profile; still low cholesterol.

    • Houses porins (β-barrel VDACs) → relatively permeable to <∼5\,\text{kDa} solutes.

OMM – Transport & Signalling Gateway

  • Voltage-Dependent Anion Channel (VDAC)

    • Major porin; inner pore lined by basic residues → favours anionic substrates (ATP^{4-}, ADP^{3-}).

    • Helical plug shifts in/out → voltage-gated open vs. closed states.

    • Diffusive, not active transport; directionality follows concentration: ATP exits (matrix high), ADP enters.

  • OMM as signalling platform

    • Binds cytoskeleton, ER, endosomes.

    • Central in apoptosis: Bax/Bak pore formation, loss of potential, protein release.

Dynamic Positioning of Mitochondria – “Mobile Battery Packs”

  • Fluorescent microscopy (e.g.
    rhodamine-123) shows extensive mitochondrial network along microtubules.

  • Motion orchestrated by the Miro–Milton adaptor pair:

    • Miro (OMM GTPase) binds Milton → links to motor proteins.

    • Kinesin = anterograde (toward cell periphery).

    • Dynein = retrograde (toward nucleus).

  • Regulation knobs

    • \text{[Ca^{2+}]} rise → Ca^{2+} binds Miro → releases kinesin heavy chain → halts movement locally.

    • Parkin-mediated ubiquitination of Miro → irreversible disengagement (quality control / mitophagy).

  • Static anchoring possible via myosin–actin contacts—targets mitochondria to high-ATP-demand locales (e.g.
    ER, synapses).

ER–Mitochondria Contact Sites

  • Electron micrographs: ER tubules "gripping" mitochondria.

  • Molecular tethers (species-dependent):

    • Yeast: ERMES (Mmm1–Mdm10/12/34–Gem1).

    • Metazoans: VAPB-PTPIP51, VDAC-IP_{3}R/Grp75 etc.

  • Functions

    • Rapid lipid transfer (ER is lipid-biosynthetic hub; IMM needs unique lipids).

    • Local Ca^{2+} exchange.

    • Spatial coordination of ATP supply to protein-synthesis-rich ER regions.

IMM – Protein Toolkit

  • Electron Transport Chain (ETC) complexes I–IV.

    • Job: move high-energy electrons (NADH/FADH{2}) to O{2} while pumping protons from matrix → IMS.

  • F{1}F{0}-ATP synthase

    • F{0} membranous rotor + F{1} catalytic head.

    • Uses \Delta\mu_{H^{+}} (combined \Delta\Psi + \Delta pH) to phosphorylate ADP → ATP.

  • ADP/ATP Carrier (AAC) – electrogenic antiporter.

    • Alternating-access mechanism; six-TM repeat dimer (12 TM total).

    • Stoichiometry 1\,\text{ADP}{\text{cyto}} \leftrightarrow 1\,\text{ATP}{\text{matrix}} per cycle.

Sculpting Cristae – How Shape Emerges

  1. Protein crowding & dimerization

    • F{1}F{0}-ATP synthase forms angled dimers/rows → impose curvature; their absence flattens cristae.

  2. Cardiolipin clustering enhances negative curvature.

  3. MICOS (Mitochondrial Contact Site & Cristae Organizing System)

    • Two core subunits: • MIC10

      • 2 TM helices with glycine kink motifs → favour oligomeric packing.

      • Positively charged loop interacts with anionic cardiolipin.

      • Drives membrane invagination (“membrane sculpting”).
        • MIC60 (Mitofilin)

      • Creates IM–OMM contact sites; recruits protein import machinery (e.g.
        TOM, TIM complexes), VDAC, lipid transfer factors.

    • MICOS deletions → loss of crista junctions, appearance of onion-like stacked lamellae.

Functional Pay-Off of Elaborate Geometry

  • Crista junctions partition IMS into micro-compartments → extremely small volume.

    • Proton pumping here results in larger \Delta pH for same number of protons ((c \propto 1/\text{volume})).

  • Co-localisation of ETC complexes with adjacent rows of ATP synthase maximises efficiency:

    • Short diffusion distance for protons.

    • Evidence for “respirasomes” or supercomplexes (CI+CIII+CIV) docked near ATP synthase rows.

  • Geometry therefore enhances both generation and harvesting of the proton-motive force.

Summary – Key Takeaways

  • Mitochondria stem from a single bacterial ancestor; retain own DNA, ribosomes, double membrane.

  • Matrix is multifunctional: NADH factories (TCA, β-oxidation) + biosynthetic hub.

  • IMM is protein-dense, cardiolipin-rich, cholesterol-poor; OMM is porin-rich and signalling-active.

  • Mitochondria are highly dynamic, trafficked on microtubules via Miro/Milton–kinesin/dynein; position matches local energy demand.

  • ER–mitochondria contact sites mediate lipid, Ca^{2+} and metabolic crosstalk.

  • Cristae architecture is a product of:

    1. Cardiolipin-induced curvature.

    2. ATP synthase dimer rows.

    3. MICOS scaffolding & IM–OMM tethering.

  • Structural design boosts proton-motive force and couples ETC output directly to ATP production.

These insights transition us from textbook cartoons to a molecularly informed, dynamic view of mitochondria as modular, mobile, and architecturally specialised power-and-biosynthesis stations.