Unified Mega Biochemical Matrix

Overview

Molecule/Component	Domain/Context	Class	Formula/Composition	Immediate role	Upstream inputs	Downstream outputs
Adenine	Genetic code	Nucleobase (purine)	C5H5N5	DNA/RNA base; pairs with T/U	Purine biosynthesis	ATP, dATP, RNA, DNA
Guanine	Genetic code	Nucleobase (purine)	C5H5N5O	DNA/RNA base; pairs with C	Purine biosynthesis	GTP, dGTP, RNA, DNA
Cytosine	Genetic code	Nucleobase (pyrimidine)	C4H5N3O	DNA/RNA base; pairs with G	Pyrimidine biosynthesis	CTP, dCTP, RNA, DNA
Thymine	Genetic code	Nucleobase (pyrimidine)	C5H6N2O2	DNA base; pairs with A	Pyrimidine biosynthesis	dTTP, DNA
Uracil	Genetic code	Nucleobase (pyrimidine)	C4H4N2O2	RNA base; pairs with A	Pyrimidine biosynthesis	UTP, RNA
ATP	All domains	Nucleotide triphosphate	C10H16N5O13P3	Energy currency	Respiration, photosynthesis	ADP + Pi, RNA synthesis
GTP	Genetic code	Nucleotide triphosphate	C10H16N5O14P3	Translation energy, RNA synthesis	TCA cycle, kinases	GDP, RNA synthesis
Alanine	Genetic code	Amino acid	C3H7NO2	Protein building block	Amino acid biosynthesis	Proteins
Selenocysteine	Genetic code	Amino acid	C3H7NO2Se	Special amino acid at UGA codon	Ser-tRNA^Sec + Se	Selenoproteins
Pyrrolysine	Genetic code	Amino acid	C12H21N3O3	Special amino acid at UAG codon	Lysine derivatives	Pyl-containing enzymes
mRNA	Genetic code	RNA polymer	Variable	Codon carrier	DNA transcription	Protein synthesis
tRNA	Genetic code	RNA polymer	Variable	Delivers amino acids	tRNA transcription + aminoacylation	Translation elongation
Ribosome	Genetic code	Ribonucleoprotein	Variable	Translates mRNA	rRNA + ribosomal proteins	Proteins
Chitin	Mycelium	Structural polysaccharide	(C8H13O5N)n	Fungal cell wall polymer	UDP-N-acetylglucosamine	Cell wall
β-1,3-glucan	Mycelium	Structural polysaccharide	(C6H10O5)n	Cell wall strength	UDP-glucose	Glucan network
Ergosterol	Mycelium	Sterol lipid	C28H44O	Membrane fluidity	Mevalonate pathway	Membrane rafts
Lignin peroxidase	Mycelium	Enzyme	Protein	Lignin degradation	Gene expression + heme	Aromatic breakdown products
Cellulose	Algae/Soil	Structural polysaccharide	(C6H10O5)n	Structural polymer	UDP-glucose	Microfibrils, glucose
Agarose	Algae	Structural polysaccharide	Agarobiose units	Red algae cell wall	Galactose metabolism	Agar gel
Carrageenan	Algae	Sulfated polysaccharide	(C12H18O9S)n	Gel-forming wall polysaccharide	Galactose + sulfate	ECM gels
Alginate	Algae	Structural polysaccharide	Mannuronic + guluronic acids	Brown algae matrix	Mannuronic acid biosynthesis	Alginate fibers/gels
Chlorophyll a	Algae	Pigment (porphyrin)	C55H72MgN4O5	Primary photosynthetic pigment	Tetrapyrrole biosynthesis	Electron transfer
Fucoxanthin	Algae	Carotenoid pigment	C42H58O6	Brown algae accessory pigment	Isoprenoid pathway	Photoprotection
β-carotene	Algae	Carotenoid pigment	C40H56	Antioxidant pigment	Isoprenoid pathway	Vitamin A
Dimethylsulfoniopropionate (DMSP)	Algae	Secondary metabolite	C5H10O2S	Osmolyte, sulfur cycle	Methionine metabolism	Dimethyl sulfide
Quartz	Inorganic minerals	Silicate mineral	SiO2	Soil structure	Weathering of rocks	Soil framework
Feldspar (orthoclase)	Inorganic minerals	Aluminosilicate mineral	KAlSi3O8	K+, Al, Si source	Rock weathering	Clays, K+
Feldspar (plagioclase)	Inorganic minerals	Aluminosilicate mineral	NaAlSi3O8–CaAl2Si2O8	Na+, Ca2+ source	Rock weathering	Clays, Na+, Ca2+
Kaolinite	Inorganic minerals	Clay mineral	Al2Si2O5(OH)4	Stable clay, low CEC	Feldspar weathering	Clay fraction
Calcite	Inorganic minerals	Carbonate mineral	CaCO3	pH buffer, Ca2+ source	Limestone weathering	Ca2+, CO2
Dolomite	Inorganic minerals	Carbonate mineral	CaMg(CO3)2	Mg2+, Ca2+ source	Dolostone weathering	Ca2+, Mg2+
Gypsum	Inorganic minerals	Sulfate mineral	CaSO4·2H2O	Ca2+, S source	Evaporite dissolution	Ca2+, SO4^2-
Apatite	Inorganic minerals	Phosphate mineral	Ca5(PO4)3F/OH	P source	Rock weathering	PO4^3-
Calcium oxalate	Organic minerals	Biomineral	CaC2O4·xH2O	Ca storage/regulation	Oxalic acid + Ca2+	Crystals
Struvite	Organic minerals	Biomineral	MgNH4PO4·6H2O	Nutrient store	Mg2+ + NH4+ + PO4^3-	Fertilizer
Chlorophyll–Mg complex	Organic minerals	Metalloporphyrin	C55H72MgN4O5	Photosynthesis	Tetrapyrrole + Mg2+	Electron transfer
Hemoglobin/heme–Fe complex	Organic minerals	Metalloporphyrin	C34H32FeN4O4	O2 transport	Porphyrin synthesis + Fe2+	Oxyhemoglobin
Vitamin B12–Co complex	Organic minerals	Corrinoid	C63H88CoN14O14P	Cofactor	Corrin ring + Co2+	Methylation reactions
Glucose	Organic chemicals	Monosaccharide	C6H12O6	Energy source	Photosynthesis, hydrolysis	Glycolysis
Sucrose	Organic chemicals	Disaccharide	C12H22O11	Transport sugar	Photosynthesis	Energy in sinks
Starch	Organic chemicals	Polysaccharide	(C6H10O5)n	Energy storage	Photosynthesis	Glucose
Fatty acids	Organic chemicals	Lipid	Variable	Membrane/energy	Acetyl-CoA	Lipids, β-oxidation
Triacylglycerol (TAG)	Organic chemicals	Lipid	Glycerol + 3 FAs	Energy storage	FA synthesis	FAs via lipases
Phospholipids	Organic chemicals	Lipid	Variable	Membranes	FA + glycerol + phosphate	Bilayers
Sterols	Organic chemicals	Lipid	C27–C28	Membrane fluidity, hormones	Isoprenoid biosynthesis	Hormones, vit D
Phenolic acids	Organic chemicals	Aromatic acids	Variable	Antioxidants	Phenylpropanoid pathway	Lignin, tannins
Terpenes	Organic chemicals	Isoprenoid	C10–C15	Signals, defense	Isoprenoid pathway	Aroma compounds
Water	Inorganic chemicals	Polar molecule	H2O	Solvent, reactant	Precipitation, metabolism	Hydrolysis products
Oxygen gas	Inorganic chemicals	Diatomic molecule	O2	Respiration, oxidation	Photosynthesis	H2O, ROS
Carbon dioxide	Inorganic chemicals	Linear molecule	CO2	C source for photosynthesis	Respiration	Carbohydrates
Nitrogen gas	Inorganic chemicals	Diatomic molecule	N2	N fixation source	Atmosphere	NH3, organic N
Ammonia	Inorganic chemicals	Inorganic base	NH3/NH4+	N nutrient	N fixation, mineralization	Nitrate, amino acids
Nitrate ion	Inorganic chemicals	Inorganic anion	NO3-	N nutrient	Nitrification	Organic N
Phosphate ion	Inorganic chemicals	Inorganic oxyanion	PO4^3-	ATP/nucleic acids	Weathering, mineralization	Biomass P
Sulfate ion	Inorganic chemicals	Inorganic oxyanion	SO4^2-	S nutrient, e- acceptor	Weathering, mineralization	Sulfide
Chloride ion	Inorganic chemicals	Inorganic anion	Cl-	Osmotic balance	Halite dissolution	Biomass Cl
Sodium ion	Inorganic chemicals	Inorganic cation	Na+	Osmotic balance	Halite dissolution	Ion gradients
Potassium ion	Inorganic chemicals	Inorganic cation	K+	Nutrient	Feldspar/mica weathering	Biomass K
Calcium ion	Inorganic chemicals	Inorganic cation	Ca2+	Cell wall, signaling	Calcite/dolomite weathering	Ca salts
Magnesium ion	Inorganic chemicals	Inorganic cation	Mg2+	Chlorophyll central atom	Dolomite/olivine weathering	Biomass Mg
Iron (ferrous) ion	Inorganic chemicals	Inorganic cation	Fe2+	e- donor, cofactor	Reducing mineral dissolution	Fe3+
Iron (ferric) ion	Inorganic chemicals	Inorganic cation	Fe3+	e- acceptor, cofactor	Fe2+ oxidation	Fe oxides
Zinc ion	Inorganic chemicals	Inorganic cation	Zn2+	Cofactor	Mineral weathering	Biomass Zn
Copper ion	Inorganic chemicals	Inorganic cation	Cu+/Cu2+	Electron transfer	Mineral weathering	Biomass Cu
Cobalt ion	Inorganic chemicals	Inorganic cation	Co2+	Cofactor (B12)	Mineral weathering	Corrinoids
Hydrogen ion	Inorganic chemicals	Inorganic ion	H+	pH control, proton motive force	Acid dissociation	Water, gradients
Hydroxide ion	Inorganic chemicals	Inorganic ion	OH-	pH control, base catalysis	Water autoprotolysis	Water, hydroxides

Notes:

Genetic Code system(nucleic acids, amino acids, ribosome machinery)
Mycelium(fungal structural/metabolic biochemistry)
Algae(photosynthetic pigments, storage polysaccharides, metabolites)
Soil(organic matter, biotic molecules)
Organic Minerals(organo-mineral complexes, biominerals, metallopigments)
Inorganic Minerals(primary & secondary mineral phases)
Organic Chemicals(general biological organics across domains)
Inorganic Chemicals(free ions & small molecules in biogeochemical cycles)

Key terms in plain language

Open a term for a concise explanation of language used on this page.

Cloud Computing

Computing resources—such as applications, servers, storage, or databases—delivered from remote infrastructure and scaled as requirements change.

Infrastructure as a Service (IaaS)

Cloud-based servers, storage, and networking that customers configure and manage without owning the underlying data-center hardware.

Software as a Service (SaaS)

Software accessed as an online service instead of being installed and maintained entirely on the customer’s own computers or servers.

Disaster Recovery (DRaaS)

A plan and service for restoring applications, data, and operations after an outage or disruption. DRaaS provides recovery infrastructure through a managed cloud service.

Identity and Access Management (IAM)

The systems and policies that determine who a user is, what resources they may access, and how that access is authenticated and reviewed.

API

An application programming interface is a defined way for software systems to exchange data or request functions from one another.