Oxidative phosphorylation

METPO:1000803 · CLASS · REVIEWED

A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient.

Oxidative phosphorylation chemiosmotic coupling

Evidence-backed causal sketch linking respiratory electron transfer, proton motive force, ATP synthase, and ATP production.

Oxidative phosphorylation chemiosmotic coupling Interactive directed graph showing evidence-backed causal relationships for Oxidative phosphorylation.

Edge evidence

  • Oxidative phosphorylation uses pathway electron transport chain

    Oxidative phosphorylation couples phosphorylation to respiratory electron transfer.

    • DOI:10.1038/191144a0 electron and hydrogen transfer Mitchell paper supports coupling electron/hydrogen transfer to phosphorylation.
  • electron transport chain localized to cellular membrane biolink:located_in

    Electron transfer and proton translocation are membrane-coupled.

    • DOI:10.1038/191144a0 Chemi-Osmotic Type of Mechanism Chemiosmotic mechanism requires a membrane-separated ion gradient.
  • electron transport chain generates proton motive force biolink:produces

    Respiratory electron transfer establishes a proton motive force.

    • DOI:10.1038/s41598-019-38564-0 proton motive force (pmf) established and maintained by respiratory chain enzymes Supports respiratory chain generation of pmf.
  • proton motive force regulates F1Fo ATP synthase RO:0002211

    Proton motive force energizes F1Fo ATP synthase.

    • DOI:10.1038/s41598-019-38564-0 energized by the proton motive force Supports pmf-driven ATP synthase.
  • F1Fo ATP synthase produces ATP METPO:2000202

    ATP synthase synthesizes ATP from ADP and phosphate.

    • DOI:10.1007/BF01923429 synthesis of ATP is also driven by a proton motive force ATP synthase review supports pmf-driven ATP synthesis.
  • NADH is oxidized by Complex I / NADH:quinone oxidoreductase (NDH-1)

    Complex I oxidizes NADH at the respiratory chain entry point.

    • DOI:10.3390/ijms252413421 complex I catalyzes the oxidation of NADH by ubiquinone (general prokaryotic claim).
  • Complex I / NADH:quinone oxidoreductase (NDH-1) reduces quinone pool METPO:2000017

    Complex I transfers electrons from NADH to the quinone pool.

    • DOI:10.3390/ijms252413421 oxidation of NADH by ubiquinone; reduces the membrane quinone pool.
  • Complex I / NADH:quinone oxidoreductase (NDH-1) translocates proton

    Complex I couples redox chemistry to transmembrane proton translocation.

    • DOI:10.3390/ijms252413421 coupled with the vectorial transmembrane transfer of four H+ ions.
  • succinate is oxidized by succinate dehydrogenase / Complex II

    Succinate dehydrogenase oxidizes succinate, reducing quinone.

    • DOI:10.1007/s10863-024-10041-y succinate dehydrogenase catalyzes the two-electron reduction of quinone by succinate.
  • proton translocation generates proton motive force biolink:produces

    Vectorial proton translocation establishes the proton motive force.

    • DOI:10.3390/ijms252413421 energy conservation in the form of an electrochemical gradient (proton motive force, pmf).
  • terminal oxidase reduces oxygen METPO:2000017

    Terminal oxidases catalyze four-electron reduction of O2 to water.

    • DOI:10.3390/ijms25021277 Terminal oxidases catalyze four-electron reduction of O2 to 2H2O (general bacterial claim).
  • heme-copper oxidase translocates proton

    Heme-copper oxidases act as proton pumps contributing to PMF.

    • DOI:10.3390/ijms25021277 Heme-copper oxidases are true proton pumps (general claim).

Provenance

Source
METPO (2025-11-25)
Author
Anthea Guo
Definition source
DOI:10.1038/191144a0

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000803 [-1.060, -0.950, -1.248, -0.351, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · ADDED_CAUSAL_GRAPH · codex

    Added DOI-backed causal graph for chemiosmotic coupling, proton motive force, ATP synthase, and ATP production.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:located_in×1, biolink:produces×1).

  5. · RENAME_PREDICATE_LABELS · claude

    Renamed 1 causal-edge predicate label(s) to align with existing groundings: drives → regulates ×1.

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002211×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1007500×1).

  8. · RETYPE_CAUSAL_NODES · claude

    Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum semantics: proton motive force: BIOLOGICAL_PROCESS → STATE ×1.

  9. · ENRICH_CAUSAL_GRAPH · claude

    Added 7 evidence-backed generic edges (10 new nodes) from the deep-research report.

  10. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000017×2, biolink:produces×1).

  11. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:24636×1).

  12. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A2U9ILE5×1).