| Molecule/Component | Domain/Context | Class | Formula/Composition | Immediate role | Upstream inputs | Downstream outputs | Material Class | Functional Property |
|---|---|---|---|---|---|---|---|---|
| Adenine | Genetic code | Nucleobase (purine) | C5H5N5 | DNA/RNA base; pairs with T/U | Purine biosynthesis | ATP, dATP, RNA, DNA | Biomaterial (small molecule) | Hydrogen bonding; information encoding |
| Guanine | Genetic code | Nucleobase (purine) | C5H5N5O | DNA/RNA base; pairs with C | Purine biosynthesis | GTP, dGTP, RNA, DNA | Biomaterial (small molecule) | Hydrogen bonding; information encoding |
| Cytosine | Genetic code | Nucleobase (pyrimidine) | C4H5N3O | DNA/RNA base; pairs with G | Pyrimidine biosynthesis | CTP, dCTP, RNA, DNA | Biomaterial (small molecule) | Hydrogen bonding; information encoding |
| Thymine | Genetic code | Nucleobase (pyrimidine) | C5H6N2O2 | DNA base; pairs with A | Pyrimidine biosynthesis | dTTP, DNA | Biomaterial (small molecule) | Hydrogen bonding; information encoding |
| Uracil | Genetic code | Nucleobase (pyrimidine) | C4H4N2O2 | RNA base; pairs with A | Pyrimidine biosynthesis | UTP, RNA | Biomaterial (small molecule) | Hydrogen bonding; information encoding |
| ATP | All domains | Nucleotide triphosphate | C10H16N5O13P3 | Energy currency | Respiration, photosynthesis | ADP + Pi, RNA synthesis | Biomaterial (energy carrier) | High-energy phosphoanhydride bonds |
| GTP | Genetic code | Nucleotide triphosphate | C10H16N5O14P3 | Translation energy, RNA synthesis | TCA cycle, kinases | GDP, RNA synthesis | Biomaterial (energy carrier) | GTPase-driven mechano-chemistry |
| Alanine | Genetic code | Amino acid | C3H7NO2 | Protein building block | Amino acid biosynthesis | Proteins | Biomaterial (monomer) | Polymerizable; acid-base buffering |
| Selenocysteine | Genetic code | Amino acid | C3H7NO2Se | Special amino acid at UGA codon | Ser-tRNA^Sec + Se | Selenoproteins | Biomaterial (monomer) | Redox-active selenol chemistry |
| Pyrrolysine | Genetic code | Amino acid | C12H21N3O3 | Special amino acid at UAG codon | Lysine derivatives | Pyl-containing enzymes | Biomaterial (monomer) | Expanded side-chain; methyl transfer catalysis |
| mRNA | Genetic code | RNA polymer | Variable | Codon carrier | DNA transcription | Protein synthesis | Polymer (biopolymer) | Programmable sequence; template function |
| tRNA | Genetic code | RNA polymer | Variable | Delivers amino acids | tRNA transcription + aminoacylation | Translation elongation | Polymer (biopolymer) | Folded nano-machine; specific recognition |
| Ribosome | Genetic code | Ribonucleoprotein | Variable | Translates mRNA | rRNA + ribosomal proteins | Proteins | Composite (RNA+protein) | Catalysis (ribozyme); mechano-chemical transducer |
| Chitin | Mycelium | Structural polysaccharide | (C8H13O5N)n | Fungal cell wall polymer | UDP-N-acetylglucosamine | Cell wall | Polymer (biopolymer) | High tensile strength; biodegradability |
| β-1,3-glucan | Mycelium | Structural polysaccharide | (C6H10O5)n | Cell wall strength | UDP-glucose | Glucan network | Polymer (biopolymer) | Viscoelastic network; pore regulation |
| Ergosterol | Mycelium | Sterol lipid | C28H44O | Membrane fluidity | Mevalonate pathway | Membrane rafts | Biomaterial (lipid) | Phase modulation; permeability control |
| Lignin peroxidase | Mycelium | Enzyme | Protein | Lignin degradation | Gene expression + heme | Aromatic breakdown products | Biomaterial (enzyme) | Redox catalysis; radical chemistry |
| Cellulose | Algae/Soil | Structural polysaccharide | (C6H10O5)n | Structural polymer | UDP-glucose | Microfibrils, glucose | Polymer (biopolymer) | High modulus; fiber formation |
| Agarose | Algae | Structural polysaccharide | Agarobiose units | Red algae cell wall | Galactose metabolism | Agar gel | Polymer (hydrogel) | Thermo-reversible gelation |
| Carrageenan | Algae | Sulfated polysaccharide | (C12H18O9S)n | Gel-forming wall polysaccharide | Galactose + sulfate | ECM gels | Polymer (polyelectrolyte hydrogel) | Ion-dependent gelation; viscosity control |
| Alginate | Algae | Structural polysaccharide | Mannuronic + guluronic acids | Brown algae matrix | Mannuronic acid biosynthesis | Alginate fibers/gels | Polymer (hydrogel) | Ca2+-crosslinked gel networks |
| Chlorophyll a | Algae | Pigment (porphyrin) | C55H72MgN4O5 | Primary photosynthetic pigment | Tetrapyrrole biosynthesis | Electron transfer | Metallo-organic (biomaterial) | Strong visible absorption; exciton transfer |
| Fucoxanthin | Algae | Carotenoid pigment | C42H58O6 | Accessory pigment | Isoprenoid pathway | Photoprotection | Biomaterial (pigment) | Triplet quenching; antioxidant |
| β-carotene | Algae | Carotenoid pigment | C40H56 | Antioxidant pigment | Isoprenoid pathway | Vitamin A | Biomaterial (pigment) | Conjugated π-system; light absorption |
| DMSP | Algae | Secondary metabolite | C5H10O2S | Osmolyte, sulfur cycle | Methionine metabolism | Dimethyl sulfide | Biomaterial (small molecule) | Volatile sulfur cycling; osmoprotection |
| Quartz | Inorganic minerals | Silicate mineral | SiO2 | Soil structure | Weathering of rocks | Soil framework | Ceramic (oxide) | High hardness; chemical resistance |
| Feldspar (orthoclase) | Inorganic minerals | Aluminosilicate mineral | KAlSi3O8 | K+, Al, Si source | Rock weathering | Clays, K+ | Ceramic (aluminosilicate) | Ion release on weathering |
| Feldspar (plagioclase) | Inorganic minerals | Aluminosilicate mineral | NaAlSi3O8–CaAl2Si2O8 | Na+, Ca2+ source | Rock weathering | Clays, Na+, Ca2+ | Ceramic (aluminosilicate) | Ion release on weathering |
| Kaolinite | Inorganic minerals | Clay mineral | Al2Si2O5(OH)4 | Stable clay, low CEC | Feldspar weathering | Clay fraction | Ceramic (phyllosilicate) | Low CEC; thermal stability |
| Calcite | Inorganic minerals | Carbonate mineral | CaCO3 | pH buffer, Ca2+ source | Limestone weathering | Ca2+, CO2 | Ceramic (carbonate) | Acid neutralization; Ca reservoir |
| Dolomite | Inorganic minerals | Carbonate mineral | CaMg(CO3)2 | Mg2+, Ca2+ source | Dolostone weathering | Ca2+, Mg2+ | Ceramic (carbonate) | Divalent cation supply |
| Gypsum | Inorganic minerals | Sulfate mineral | CaSO4·2H2O | Ca2+, S source | Evaporite dissolution | Ca2+, SO4^2- | Ceramic (sulfate) | Soil amendment; sodicity correction |
| Apatite | Inorganic minerals | Phosphate mineral | Ca5(PO4)3F/OH | P source | Rock weathering | PO4^3- | Ceramic (phosphate) | Slow-release phosphorus |
| Calcium oxalate | Organic minerals | Biomineral (organic acid salt) | CaC2O4·xH2O | Ca storage/regulation | Oxalic acid + Ca2+ | Crystals | Composite (biomineral) | Sequestration; crystal mechanics |
| Struvite | Organic minerals | Biomineral (organic phosphate salt) | MgNH4PO4·6H2O | Nutrient store | Mg2+ + NH4+ + PO4^3- | Fertilizer | Composite (biomineral) | Controlled nutrient release |
| Chlorophyll–Mg complex | Organic minerals | Metalloporphyrin | C55H72MgN4O5 | Photosynthesis | Tetrapyrrole + Mg2+ | Electron transfer | Metallo-organic | Light absorption; charge separation |
| Heme–Fe complex | Organic minerals | Metalloporphyrin | C34H32FeN4O4 | O2 transport | Porphyrin synthesis + Fe2+ | Oxyhemoglobin | Metallo-organic | Reversible ligand binding |
| Vitamin B12–Co complex | Organic minerals | Corrinoid | C63H88CoN14O14P | Cofactor | Corrin ring + Co2+ | Methylation reactions | Metallo-organic | Organometallic methyl transfer |
| Glucose | Organic chemicals | Monosaccharide | C6H12O6 | Energy source | Photosynthesis, hydrolysis | Glycolysis | Biomaterial (small molecule) | Reducing sugar; energy currency |
| Sucrose | Organic chemicals | Disaccharide | C12H22O11 | Transport sugar | Photosynthesis | Energy in sinks | Biomaterial (small molecule) | Osmotic transport; stability |
| Starch | Organic chemicals | Polysaccharide | (C6H10O5)n | Energy storage | Photosynthesis | Glucose | Polymer (biopolymer) | Granular storage; controlled hydrolysis |
| Fatty acids | Organic chemicals | Lipid | Variable | Membrane/energy | Acetyl-CoA | Lipids, β-oxidation | Biomaterial (lipid) | Hydrophobic packing; energy density |
| Triacylglycerol (TAG) | Organic chemicals | Lipid | Glycerol + 3 FAs | Energy storage | FA synthesis | FAs via lipases | Biomaterial (lipid) | Phase-separated energy reservoir |
| Phospholipids | Organic chemicals | Lipid | Variable | Membranes | FA + glycerol + phosphate | Bilayers | Composite (amphiphile) | Self-assembly; selective permeability |
| Sterols | Organic chemicals | Lipid | C27–C28 | Membrane fluidity, hormones | Isoprenoid biosynthesis | Hormones, vit D | Biomaterial (lipid) | Phase modulation; signaling precursor |
| Phenolic acids | Organic chemicals | Aromatic acids | Variable | Antioxidants | Phenylpropanoid pathway | Lignin, tannins | Biomaterial (small molecule) | Radical scavenging |
| Terpenes | Organic chemicals | Isoprenoid | C10–C15 | Signals, defense | Isoprenoid pathway | Aroma compounds | Biomaterial (volatile) | Volatility; ecological signaling |
| Water | Inorganic chemicals | Polar molecule | H2O | Solvent, reactant | Precipitation, metabolism | Hydrolysis products | Fluid | High heat capacity; hydrogen-bond network |
| Oxygen gas | Inorganic chemicals | Diatomic molecule | O2 | Respiration, oxidation | Photosynthesis | H2O, ROS | Gas | High redox potential; paramagnetism |
| Carbon dioxide | Inorganic chemicals | Linear molecule | CO2 | C source for photosynthesis | Respiration | Carbohydrates | Gas | Acid–base buffer (carbonic system) |
| Nitrogen gas | Inorganic chemicals | Diatomic molecule | N2 | N fixation source | Atmosphere | NH3, organic N | Gas | Triple bond inertness |
| Ammonia/Ammonium | Inorganic chemicals | Inorganic base | NH3 / NH4+ | N nutrient | N fixation, mineralization | Nitrate, amino acids | Ion/aqueous species | Acid–base equilibrium; nucleophilicity |
| Nitrate | Inorganic chemicals | Inorganic anion | NO3- | N nutrient | Nitrification | Organic N | Ion (aqueous) | High solubility; redox substrate |
| Phosphate | Inorganic chemicals | Inorganic oxyanion | PO4^3- | ATP/nucleic acids | Weathering, mineralization | Biomass P | Ion (aqueous) | Polymerization/energy transfer |
| Sulfate | Inorganic chemicals | Inorganic oxyanion | SO4^2- | S nutrient, e- acceptor | Weathering, mineralization | Sulfide | Ion (aqueous) | Redox couple member |
| Chloride | Inorganic chemicals | Inorganic anion | Cl- | Osmotic balance | Halite dissolution | Biomass Cl | Ion (aqueous) | Electrolyte; charge balance |
| Sodium | Inorganic chemicals | Inorganic cation | Na+ | Osmotic balance | Halite dissolution | Ion gradients | Ion (aqueous) | Electrochemical potential |
| Potassium | Inorganic chemicals | Inorganic cation | K+ | Nutrient | Feldspar/mica weathering | Biomass K | Ion (aqueous) | Enzymatic activation; osmoregulation |
| Calcium | Inorganic chemicals | Inorganic cation | Ca2+ | Cell wall, signaling | Calcite/dolomite weathering | Ca salts | Ion (aqueous) | Crosslinking; signaling |
| Magnesium | Inorganic chemicals | Inorganic cation | Mg2+ | Chlorophyll central atom | Dolomite/olivine weathering | Biomass Mg | Ion (aqueous) | Enzyme cofactor; coordination chemistry |
| Iron(II) | Inorganic chemicals | Inorganic cation | Fe2+ | e- donor, cofactor | Reducing mineral dissolution | Fe3+ | Ion (aqueous) | Redox activity |
| Iron(III) | Inorganic chemicals | Inorganic cation | Fe3+ | e- acceptor, cofactor | Fe2+ oxidation | Fe oxides | Ion (aqueous) | Redox activity; hydrolysis |
| Zinc | Inorganic chemicals | Inorganic cation | Zn2+ | Cofactor | Mineral weathering | Biomass Zn | Ion (aqueous) | Lewis acidity; structural cofactor |
| Copper | Inorganic chemicals | Inorganic cation | Cu+/Cu2+ | Electron transfer | Mineral weathering | Biomass Cu | Ion (aqueous) | Redox cycling; electron transfer |
| Cobalt | Inorganic chemicals | Inorganic cation | Co2+ | Cofactor (B12) | Mineral weathering | Corrinoids | Ion (aqueous) | Coordination chemistry; catalysis |
| Hydrogen ion | Inorganic chemicals | Inorganic ion | H+ | pH control, PMF | Acid dissociation | Water, gradients | Ion (aqueous) | Electrochemical gradient; catalysis |
| Hydroxide ion | Inorganic chemicals | Inorganic ion | OH- | pH control, base catalysis | Water autoprotolysis | Water, hydroxides | Ion (aqueous) | Nucleophilicity; precipitation |
Unified Categorical Language System – SolveForce Communications