Biochemistry

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "BiochemistryOntology" v1.0

ENTITY BiochemistryOntology {
  TYPE: BiologicalOntology
  DOMAIN: Biochemistry
  SUBJECT: Biochemistry
  PURPOSE: FormalSemanticRepresentation
}

PAGE {
  TITLE: "Biochemistry"
  PARENT_DOMAIN: "Biological Ontologies"
  CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biochemistry.html"
  AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Biochemistry {
  STUDIES: [Biomolecules, ChemicalReactions, Metabolism, Enzymes, MolecularInteractions, EnergyTransfer, CellularChemistry]
}

ENTITY Biomolecule {
  MAY_BE: [Protein, NucleicAcid, Carbohydrate, Lipid, Metabolite]
  PARTICIPATES_IN: BiochemicalProcess
}

ENTITY BiologicalSystem {
  MAY_BE: [Cell, Organelle, Tissue, Organism]
}

ENTITY Molecule {
  COMPOSED_OF: Atoms
  HAS: ChemicalStructure
}

ENTITY FunctionalGroup {
  PART_OF: Molecule
  INFLUENCES: ChemicalReactivity
}

ENTITY Protein {
  IS_A: Biomolecule
  COMPOSED_OF: AminoAcid
  HAS: [Sequence, Structure, Function]
}

ENTITY Enzyme {
  IS_A: BiologicalCatalyst
  CATALYSES: BiochemicalReaction
  BINDS: Substrate
  HAS: ActiveSite
}

PROCESS EnzymeCatalysis {
  INPUT: Substrate
  CATALYST: Enzyme
  OUTPUT: Product
  LOWERS: ActivationEnergy
}

RULE CatalystRule {
  IF Enzyme catalyses Reaction
  THEN Enzyme IS_NOT stoichiometrically_consumed_by Reaction
}

ENTITY EnzymeKinetics {
  DESCRIBES: ReactionRateBehaviour
  DEPENDS_ON: [SubstrateConcentration, EnzymeConcentration, Temperature, pH, Inhibitors, Activators]
}

ENTITY NucleicAcid {
  IS_A: Biomolecule
  COMPOSED_OF: Nucleotide
  MAY_BE: [DNA, RNA]
}

ENTITY Carbohydrate {
  IS_A: Biomolecule
  MAY_BE: [Monosaccharide, Oligosaccharide, Polysaccharide]
  MAY_FUNCTION_IN: [EnergyStorage, Structure, Recognition]
}

ENTITY Lipid {
  IS_A: Biomolecule
  MAY_FUNCTION_IN: [MembraneStructure, EnergyStorage, Signalling]
}

ENTITY Metabolite {
  IS_A: SmallBiomolecule
  PARTICIPATES_IN: MetabolicReaction
  MAY_BE: [Substrate, Intermediate, Product, Cofactor]
}

PROCESS BiochemicalReaction {
  CONVERTS: Reactant
  TO: Product
  OBEYS: ChemicalStoichiometry
  MAY_BE_CATALYSED_BY: Enzyme
}

RULE MassBalanceRule {
  IF Reaction IS_BALANCED
  THEN atoms_and_charge SHOULD_BE conserved
  SUBJECT_TO reaction_representation
}

ENTITY GibbsFreeEnergy {
  SYMBOL: DeltaG
  DESCRIBES: ThermodynamicDrivingPotential
}

ENTITY Enthalpy { SYMBOL: DeltaH }
ENTITY Entropy { SYMBOL: DeltaS }

RULE GibbsRelation {
  DeltaG := DeltaH - Temperature * DeltaS
}

RULE SpontaneityRule {
  IF DeltaG < 0
  THEN process IS_THERMODYNAMICALLY_FAVOURABLE
  UNDER specified_conditions
}

RULE CatalystThermodynamicsConstraint {
  Enzyme changes_activation_energy
  BUT DOES_NOT_CHANGE equilibrium_DeltaG
}

ENTITY ATP {
  IS_A: NucleotideTriphosphate
  FUNCTIONS_AS: CellularEnergyCarrier
}

PROCESS EnergyCoupling {
  LINKS: ExergonicReaction
  TO: EndergonicReaction
}

PROCESS Oxidation { INVOLVES: ElectronLoss }
PROCESS Reduction { INVOLVES: ElectronGain }

ENTITY NAD {
  MAY_EXIST_AS: [NADPlus, NADH]
  PARTICIPATES_IN: RedoxReaction
}

RULE RedoxRule {
  Oxidation MUST_BE_COUPLED_WITH Reduction
  IN complete_redox_reaction
}

ENTITY Metabolism {
  COMPOSED_OF: MetabolicPathways
  INCLUDES: [Catabolism, Anabolism]
}

PROCESS Catabolism {
  BREAKS_DOWN: Molecules
  MAY_RELEASE: UsableEnergy
}

PROCESS Anabolism {
  BUILDS: ComplexMolecules
  REQUIRES: EnergyAndPrecursors
}

ENTITY MetabolicPathway {
  COMPOSED_OF: OrderedBiochemicalReactions
  HAS: [Inputs, Intermediates, Outputs]
}

PROCESS Glycolysis {
  CONVERTS: Glucose
  TO: Pyruvate
  PRODUCES: [ATP, NADH]
}

PROCESS CitricAcidCycle {
  OXIDIZES: AcetylCoA
  PRODUCES: ReducedElectronCarriers
}

PROCESS OxidativePhosphorylation {
  USES: ElectronTransportChain
  DRIVES: ATPProduction
}

ENTITY BiologicalMembrane {
  COMPOSED_PRIMARILY_OF: [Lipids, Proteins]
  CONTROLS: MolecularTransport
}

PROCESS MembraneTransport {
  MOVES: MoleculeOrIon
  ACROSS: BiologicalMembrane
  MAY_BE: [PassiveTransport, ActiveTransport]
}

ENTITY pH {
  DESCRIBES: HydrogenIonActivityScale
  AFFECTS: BiomolecularState
}

ENTITY Buffer {
  RESISTS: pHChange
  WITHIN: BufferingRange
}

ENTITY MolecularInteraction {
  OCCURS_BETWEEN: MolecularEntities
  MAY_BE: [ProteinProteinInteraction, ProteinLigandInteraction, ProteinDNAInteraction, ProteinRNAInteraction]
}

ENTITY BindingAffinity {
  DESCRIBES: StrengthOfBinding
}

PROCESS SignalTransduction {
  RECEIVES: Signal
  TRANSMITS: MolecularInformation
  MAY_CHANGE: CellularResponse
}

PROCESS BiochemicalRegulation {
  MAY_CONTROL: [EnzymeActivity, MetabolicFlux, GeneExpression, MolecularTransport, Signalling]
}

PROCESS FeedbackInhibition {
  OCCURS_WHEN: PathwayProductInhibitsEarlierStep
}

ENTITY Cofactor {
  ASSISTS: BiochemicalFunction
  MAY_BE: [MetalIon, OrganicCofactor]
}

ENTITY Coenzyme {
  SUBCLASS_OF: OrganicCofactor
  PARTICIPATES_IN: EnzymeCatalysis
}

PROCESS Biosynthesis {
  BUILDS: Biomolecule
  FROM: Precursors
  MAY_REQUIRE: Energy
}

PROCESS Degradation {
  BREAKS_DOWN: Biomolecule
  MAY_RECYCLE: Components
}

ENTITY BiochemicalHomeostasis {
  MAINTAINS: MolecularConditions
  WITHIN: FunctionalRange
}

PROCESS BiochemicalMeasurement {
  MAY_MEASURE: [Concentration, ReactionRate, BindingAffinity, EnzymeActivity, MetaboliteAbundance, ProteinAbundance]
}

ENTITY ExperimentalContext {
  MAY_INCLUDE: [organism, tissue, cell_type, temperature, pH, ionic_strength, concentration, assay_method]
}

RULE ExperimentalContextRule {
  IF biochemical_measurements ARE_COMPARED
  THEN ExperimentalContext MUST_BE preserved
}

ENTITY Evidence {
  TYPES: [BiochemicalEvidence, StructuralEvidence, KineticEvidence, MetabolomicEvidence, ProteomicEvidence, MolecularEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
  IF IndependentEvidenceSources AGREE
  THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
  IF EvidenceSources CONFLICT
  THEN {
    PRESERVE competing_assertions
    RECORD molecular_entities
    RECORD reaction_conditions
    RECORD assay_method
    RECORD biological_context
    RECORD provenance
    REDUCE confidence
    REQUIRE further_validation
  }
}

RELATION Biomolecule PARTICIPATES_IN BiochemicalProcess
RELATION Enzyme CATALYSES BiochemicalReaction
RELATION Substrate CONVERTED_TO Product
RELATION Metabolite PARTICIPATES_IN MetabolicPathway
RELATION ATP PARTICIPATES_IN EnergyCoupling
RELATION Protein HAS ProteinFunction
RELATION MolecularInteraction MAY_FORM MolecularComplex
RELATION MetabolicPathway PART_OF Metabolism

SEMANTIC_EQUIVALENCE {
  "biochemistry" ~= "chemistry of biological systems"
  "biochemical reaction" ~= "biological chemical reaction"
  "metabolic pathway" ~= "biochemical pathway" WHEN metabolism_context_is_defined
  "enzyme activity" ~= "catalytic activity" WHEN enzyme_context_is_defined
  "metabolite" ~= "small molecule metabolic intermediate or product" WHEN metabolic_context
}

RULE EquivalenceConstraint {
  IF terms ARE semantic_equivalents
  THEN preserve_molecular_identity()
  AND preserve_reaction_context()
  AND preserve_cellular_context()
  AND preserve_experimental_conditions()
  AND prevent_false_identity()
}

CONFIDENCE BiochemistryAssertion {
  INPUTS: [experimental_support, biochemical_support, kinetic_support, structural_support, analytical_quality, reproducibility, source_independence, contextual_consistency, semantic_consistency]
  SCORE := weighted_sum(INPUTS)
  LEVEL :=
    IF SCORE >= 0.90 THEN "very_high"
    ELSE IF SCORE >= 0.75 THEN "high"
    ELSE IF SCORE >= 0.55 THEN "moderate"
    ELSE IF SCORE >= 0.35 THEN "low"
    ELSE "uncertain"
}

RULE EnzymeReactionInference {
  IF Enzyme catalyses Reaction
     AND Reaction converts Substrate TO Product
  THEN Enzyme HAS_FUNCTION catalysis_of(Reaction)
}

RULE PathwayInference {
  IF ReactionA produces Intermediate
     AND ReactionB consumes same_Intermediate
  THEN ReactionA MAY_PRECEDE ReactionB
  IN compatible_pathway_context
}

RULE CausalityConstraint {
  IF molecular_association IS_OBSERVED
  THEN DO_NOT_INFER causal_biological_effect
  WITHOUT functional_evidence
}

QUERY BiochemistryEntityLookup(entity_identifier) {
  RETURN [entity_type, molecular_structure, biochemical_function, reactions, pathways, interactions, cellular_location, experimental_measurements, evidence, confidence]
}

QUERY BiochemicalReactionLookup(reaction_identifier) {
  RETURN [reactants, products, stoichiometry, enzymes, cofactors, thermodynamics, kinetics, pathway_context, evidence, confidence]
}

QUERY MetabolicPathwayLookup(pathway_identifier) {
  RETURN [inputs, reactions, enzymes, intermediates, outputs, energy_balance, regulation, cellular_context, evidence, confidence]
}

UPDATE_MODEL {
  ON new_biochemical_evidence:
    validate_provenance()
    identify_organism_and_cellular_context()
    normalize_molecular_identifiers()
    normalize_reaction_identifiers()
    validate_stoichiometry()
    capture_temperature_pH_and_assay_conditions()
    map_enzymes_substrates_products_and_cofactors()
    compare_existing_assertions()
    preserve_conflicting_evidence()
    recalculate_confidence()
    regenerate_pathway_and_interaction_links()
    update_flow_hash()
}

AI_CONSUMPTION {
  MODE: FormalSemanticReasoning
  PARSE_AS: ExecutableFlowAlgebra
  PRIORITIES: [molecular_identity, reaction_identity, stoichiometry, enzyme_context, thermodynamics, kinetics, pathway_context, cellular_context, evidence_provenance, confidence]
  REQUIREMENTS: [
    distinguish_substrate_from_product,
    distinguish_enzyme_from_reaction,
    preserve_molecular_identity,
    preserve_cellular_context,
    preserve_temperature_and_pH,
    preserve_assay_conditions,
    distinguish_thermodynamic_favourability_from_reaction_rate,
    distinguish_binding_from_catalysis,
    distinguish_observed_from_inferred_function,
    avoid_unsupported_causal_inference
  ]
}

VALIDATE {
  REQUIRE Biochemistry
  REQUIRE Biomolecule
  REQUIRE BiochemicalReaction
  REQUIRE Enzyme
  REQUIRE Metabolism
  REQUIRE MetabolicPathway
  REQUIRE GibbsFreeEnergy
  REQUIRE ATP
  REQUIRE MolecularInteraction
  REQUIRE Evidence
  REQUIRE CONFIDENCE
  REQUIRE SEMANTIC_EQUIVALENCE
  REQUIRE UPDATE_MODEL
  REQUIRE AI_CONSUMPTION

  ASSERT Enzyme != BiochemicalReaction
  ASSERT thermodynamic_favourability != reaction_rate
  ASSERT binding != catalysis
  ASSERT molecular_association != causal_function
}

FLOW_HASH {
  ALGORITHM: SHA-256
  INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
  PURPOSE: integrity_and_version_tracking
}

END flow "BiochemistryOntology"