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📒 Mitochondrial Energetics: a summary

Mitochondrial Energetics: a summary

The mitpochodria are not only the powerhouse of the cell, but also participate in cell survival, signalling, urea cycle, redox reaction, calcium dynamics.

Abbreviations

  • Pyr: pyruvate
  • Mtx: (mitochondrial) matrix
  • PDH: pyruvate dehydrogenase
  • CoA: coenzyme A
  • AcCoA: Acetyl CoA
  • NAD(P) / NAD(P)H: (oxidized/ reduced) nicotinamide adenine dinucleotide (phosphate)
  • FAD / FADH₂: (oxidized/ reduced) flavin adenine dinucleotide
  • FMN / FMNH₂: (oxidized/ reduced) flavin mononucleotide
  • CAC: citric acid cycle, also called TriCarboxylic Acid Cycle (TCA cycle), Krebs cycle
  • SCS: succinyl-CoA synthatase, also called succinyl-CoA lyase, SL
  • Q: Coenzyme Q, ubiquinone
  • Glu: Glutamate
  • Glc: Glucose
  • AKG: alpha-keto glutarate
  • GDH: Glutamate degydrogenase
  • AST: aspartate transaminase
  • Asp: Aspartate
  • OAA: oxaloacetate
  • PEP: phosphoenolpyruvate
  • PEPCK-M: mitochondrial phosphoenolpyruvate carboxykinase
  • GABA: gamma-aminobutyric acid
  • ROS: reactive oxygen species
  • FeS: iron-sulfur clusters

Energy metabolism in the mitochondrial matrix

Pyruvate degydrogenation

Pyr (from glucolysis) + NAD + CoA -> (PDH) -> AcCoA + CO₂ + NADH

TCA cycle

  • Turns 1 AcCoA into 2 CO₂ molecules and reduces 3 NAD and 1 FAD per full cycle
  • 1 ATP or 1 GTP generated per full cycle, depending on the subunit of SCS
  • Anaplerosis: replenish TCA cycle intermediates by Pyr / amino acids
  • Cataplerosis: draws TCA cycle intermediates for amino acids / lipogenesis / gluconeogenesis

Branches and shunts

  • Glu + NAD(P) <- (GDH) -> AKG + ammonia + NAD(P)H
  • Pyr + HCO₃⁻ + ATP -> (pyruvate carboxylase, PC) -> OAA + ADP + Pi
  • OAA + GTP -> (PEPCK-M) -> PEP + GDP + CO₂
  • Asp + AKG <-(AST)-> OAA + Glu
  • Asp -> (Urea cycle) -> fumarate
  • Lipogenesis: citrate out -> (citrate lyase) -> AcCoA (cytosolic)
  • GABA shunt: AKG -> Glu -> (Glutamate decarboxylase) -> GABA -> (transaminase)-> succinate semialdehyde -> (dehydrogenase) -> succinate

Electron transport chain (ETC)

Complex I

NADH reduces ubiquinone: NADH + Q <-> NAD + QH₂

  • Redox centers: FMN, FeS
  • Pumps 4 protons per NADH oxidized
  • Inhibited by rotenone (blocking qunione site)
  • Forward electron transport (FET) vs reverse electron transport (RET, more ROS )

Complex II

Succinate reduces ubiquinone. succinate + Q <-> fumarate + QH₂

  • Redox centers: FAD, FeS
  • No proton pumping (Keq ≈ 1, almost no free energy drop)
  • Inhibited by malonate and oxaloacetate (competitive inhibition)
  • Associated with oxidative stress in ischemia-reperfusion injury (succinate overload)

Complex III

Ubiquinol reduces cytochrome c. 2QH₂ + 2c³⁺ <-> QH₂ + Q + 2c²⁺

  • Redox centers: cytochrome b (low potential and high potential), FeS
  • Protons are pumped indirectly with the Q cycle. (1 e⁻ per 1 cytochrome c reduced)
  • Q oxidation on the p (outer) side (Qo site) and reduction om the n (inner) side (Qi site)
  • Transient semiquinone radical @ Qo (responsible for superoxide generation) and more stable semiquinone radical @ Qi
    • Competing hypothesis for the machanism: semiforward vs semireverse
  • Inhibited by Antimycin A (blocking Qi)

Complex IV

Cytochrome c reduces O₂. 4c²⁺ + O₂ + 4H⁺ -> 4c³⁺ + 2H₂O, irreversible reaction.

  • Redox centers: cytochrome a’s, Fe-Cu centers
  • One proton pumped per electron transferred
  • Inhibited physiologically by NO. Also inhibited by H₂S, CO, and cyanide.
  • Photomodulation by near infrared (NIR) photons
  • No (physiological) ROS generation

ATP synthesis

By Complex V (ATP synthase)

  • Consumes proton motive force (pmf) and potassium motive force (kmf) (new)
  • Catalyzes ATP synthesis from ADP and phosphate. Mg + ADP + Pi -> MgATP
  • ~100 round per second at physiological conditions
  • Inhibited by oligomycin
  • Reversible during low ΔΨ (determined by Keq)
  • But the rate favors ATP synthesis (limited ATP hydrolysis for intact ATP synthase)

Ion flow

Calcium

  • In: mainly via mitochodrial clacium uniporter (MCU)
  • Out: via natrium-calcium-lithium exchanger (NCLX)
  • Bufferd by mitochondrial phosphate
  • Enhances NAD reduction (CAC enzymes) and ATP synthesis
  • Calcium buffer in the cell, coordinates with endoplasmic reticulum (the calcium reservior)
  • Overload: mPTP open and cell death

Natrium (sodium)

  • In: via NCLX
  • Out: via natrium-H exchanger (NHE)
  • Counter balance of mitochondrial calcium
  • In heart failure, increase in intrecellular sodium hinders mitochondrial calcium extrusion

Kalium (potassium)

  • In: mainly via mitochondrial ATP-inhibited potassium channel (mKATP) or ATP synthase
  • Out: by kalium-H exchanger (KHE)
  • Mitochondrial volume balance
  • Ischemic preconditioning

ROS scavenging and signaling

Superoxide

  • Byproduct of complex I, III
  • Consumed by superoxide dismutase (SOD), oxidized cytochrome c
  • May cross the IMM via inner mitochodnrial anion channel (IMAC), depolarizing the mitochondrial membrane potential (ΔΨ)
  • Group depolarization of mitochondria network

Hydrogen peroxide

  • Produced by SOD and complex I
  • Consumed by glutathione and thioredoxin systems (mito and cytosol), plus catalase in the cytosol
  • Assumed simple diffusion across the IMM

NADPH

  • The reducing equivalent
  • Produced by transhydrogenase (THD): NADP + NADH <-> NADPH + NAD
  • Levels affected by ΔΨ and NADH/NAD ratio

Superoxide dismutase (SOD)

  • Dismutate superoxide into O₂ and H₂O₂
  • Cytosolic (SOD1[Cu-Zn]), mitochondrial (SOD2[Mn]), and extracellular (SOD3 [Cu-Zn])
  • Inhibited by excessive H₂O₂?

Catalase

  • Dismutate H₂O₂ into H₂O and O₂
  • Inhibited by excessive H₂O₂

Glutathione (GSH) system

  • Electron flow: NADPH -> (GSH reductase) -> GSH -> (GSH peroxidase) -> H₂O₂
  • Repairs oxidized protein via glutaredoxin cycle

Thioredoxin (Trx) system

  • Electron flow: NADPH -> (Trx reductase) -> Trx -> (Trx peroxidase) -> H₂O₂
  • Parallel to the GSH system
  • Inhibited by excessive oxidation (to sulfate)
  • Repairs oxidized protein via itself