Biomolecular parts list: amino acids, nucleobases, sugars, lipids, cofactors, vitamins.
Biochemistry Foundations
Glycine (Gly, G)
Smallest proteinogenic amino acid; achiral. Essential structural residue of collagen (Gly-X-Y repeat) and major inhibitory neurotransmitter…
Alanine (Ala, A)
Simplest chiral proteinogenic amino acid. Major gluconeogenic substrate via the alanine (Cahill) cycle; D-Ala features in bacterial…
Valine (Val, V)
Branched-chain amino acid (BCAA). Sickle-cell disease results from Glu→Val substitution at position 6 of hemoglobin β.
Leucine (Leu, L)
Most abundant residue in most proteins. Branched-chain amino acid; principal amino-acid signal activating mTORC1 via the GATOR2-Sestrin2…
Isoleucine (Ile, I)
Branched-chain amino acid with two stereocenters; only (2S,3S)-Ile is proteinogenic. Most hydrophobic amino acid by the Kyte-Doolittle…
Proline (Pro, P)
Only proteinogenic imino acid (secondary amine). Constrains Ramachandran φ and acts as a helix/strand breaker; cis-trans isomerization is…
Phenylalanine (Phe, F)
Aromatic amino acid. Precursor to tyrosine via BH4-dependent phenylalanine hydroxylase; PAH loss-of-function causes phenylketonuria.
Tyrosine (Tyr, Y)
Aromatic amino acid with ionizable phenolic OH. Key phospho-site for SH2 binding; precursor to catecholamines, thyroid hormones, and…
Tryptophan (Trp, W)
Indole-ring aromatic amino acid; least abundant proteinogenic residue and single-codon (UGG). Dominates protein UV absorbance at 280 nm;…
Serine (Ser, S)
Polar amino acid with hydroxyl side chain. Active-site nucleophile in serine proteases; major phosphorylation and O-glycosylation site;…
Threonine (Thr, T)
Polar amino acid with β-hydroxyl (second stereocenter; only 2S,3R proteinogenic). Common phospho-site; last canonical amino acid discovered…
Cysteine (Cys, C)
Thiol-bearing amino acid. Forms disulfide (cystine) crosslinks; thiolate is a potent nucleophile (pKa ≈ 8.2); coordinates Zn in zinc…
Methionine (Met, M)
Sulfur-containing amino acid. Start codon AUG in the standard genetic code; S-adenosylmethionine (SAM) is the universal biological methyl…
Asparagine (Asn, N)
First amino acid ever isolated (Vauquelin & Robiquet 1806, asparagus juice). Amide side chain; major N-linked glycosylation site via the…
Glutamine (Gln, Q)
Most abundant free amino acid in plasma and muscle. Nitrogen carrier via glutamine synthetase; CAG-repeat expansions cause Huntington…
Lysine (Lys, K)
Basic ε-amino amino acid. Substrate for the bulk of histone PTMs (acetylation, methylation, ubiquitination, SUMOylation, and >10 acyl…
Arginine (Arg, R)
Basic guanidinium amino acid; charged across all physiological pH. Substrate for NOS-catalyzed nitric oxide synthesis; key histone…
Histidine (His, H)
Imidazole-bearing amino acid with side-chain pKa ≈ 6. Uniquely able to act as both H+ donor and acceptor at physiological pH — central to…
Aspartic acid / Aspartate (Asp, D)
Acidic carboxylate amino acid. General acid/base in many enzyme active sites (serine-protease triad, HIV-protease Asp25-Asp25' dyad).
Glutamic acid / Glutamate (Glu, E)
Acidic amino acid. Principal excitatory neurotransmitter in the vertebrate CNS; central hub of transamination (partners with…
Selenocysteine (Sec, U) — 21st amino acid
Co-translationally inserted at UGA when a SECIS element is present. Found in selenoproteins (GPX, TrxR, deiodinases); selenolate is more…
Pyrrolysine (Pyl, O) — 22nd amino acid
Co-translationally inserted at UAG by dedicated tRNA^Pyl + PylRS, without an accessory element. Found in methanogenic archaea…
Adenine (A)
Purine nucleobase. Pairs with thymine (DNA) / uracil (RNA) via two hydrogen bonds. Core of ATP, cAMP, NAD+/NADP+, FAD, CoA, SAM.
Guanine (G)
Purine nucleobase. Pairs with cytosine via three hydrogen bonds (GC pair more thermostable than AT). Core of GTP, cGMP;…
Cytosine (C)
Pyrimidine nucleobase. Pairs with guanine. Deamination to uracil is a common spontaneous lesion — repaired by uracil DNA glycosylase.…
Thymine (T)
Pyrimidine nucleobase specific to DNA. The 5-methyl group distinguishes it from uracil and provides a signal that uracil arising from…
Uracil (U)
Pyrimidine nucleobase specific to RNA (pairs with adenine). Intermediate in nucleotide metabolism; deamination product of cytosine, marking…
Monosaccharide
Single sugar unit (triose through heptose). Exists as open-chain aldehyde/ketone in equilibrium with furanose/pyranose ring forms; α/β…
Glucose (biochemical hub)
C6H12O6 aldohexose; β-D-glucopyranose is the physiological ring form. Universal metabolic currency: entry point of glycolysis, storage as…
Fatty acid
Long-chain aliphatic carboxylic acid. Saturated, monounsaturated, or polyunsaturated; chain length (short/medium/long/very-long) and…
Phospholipid (membrane context)
Glycerol- or sphingosine-based amphipath with a phosphate-linked polar head group. Bilayer-forming lipid class; head-group identity (PC,…
Cholesterol
27-carbon tetracyclic sterol. Modulates membrane fluidity and thickness, forms lipid rafts, precursor to all steroid hormones, bile acids,…
NAD+/NADH and NADP+/NADPH
Nicotinamide-adenine-dinucleotide redox cofactor pair. NAD+/NADH drives catabolic oxidation (high NAD+:NADH in cytosol and matrix);…
Coenzyme A (CoA)
Thiol-bearing acyl carrier built from pantothenate (vitamin B5), cysteamine, and 3'-phosphoadenosine. Acetyl-CoA / acyl-CoA are the…