Amino Acids

Full Bio-Semantic Chemical Reference

  • Name
  • 3-letter and 1-letter code
  • Chemical formula
  • Chemical structure(verbal description, so it’s readable here — we can later render diagrams)
  • Molecule makeup(atoms, functional groups)
  • How it’s “engineered”(biosynthesis pathway origin)
  • Meaning(its role/function in proteins and biology)

Alanine

  • CodesAla / A
  • FormulaC₃H₇NO₂
  • Structureα-amino acid with a methyl (-CH₃) side chain attached to the α-carbon.
  • Molecule Makeup3 carbons, 7 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringSynthesized in the body via transamination of pyruvate (from glycolysis).
  • MeaningNonpolar, small, and versatile — often used to fill space in protein interiors.

Arginine

  • CodesArg / R
  • FormulaC₆H₁₄N₄O₂
  • Structureα-amino acid with a 3-carbon aliphatic chain ending in a guanidinium group.
  • Molecule Makeup6 carbons, 14 hydrogens, 4 nitrogens, 2 oxygens.
  • EngineeringSynthesized via the urea cycle from citrulline.
  • MeaningPositively charged at physiological pH; important in DNA/RNA binding and enzyme active sites.

Asparagine

  • CodesAsn / N
  • FormulaC₄H₈N₂O₃
  • Structureα-amino acid with a 2-carbon side chain ending in an amide group (-CONH₂).
  • Molecule Makeup4 carbons, 8 hydrogens, 2 nitrogens, 3 oxygens.
  • EngineeringSynthesized from aspartic acid via amidation.
  • MeaningPolar, uncharged; common in glycosylation sites.

Aspartic Acid

  • CodesAsp / D
  • FormulaC₄H₇NO₄
  • Structureα-amino acid with a 2-carbon side chain ending in a carboxylic acid (-COOH).
  • Molecule Makeup4 carbons, 7 hydrogens, 1 nitrogen, 4 oxygens.
  • EngineeringSynthesized from oxaloacetate via transamination.
  • MeaningNegatively charged at physiological pH; participates in catalysis and ionic bonds.

Cysteine

  • CodesCys / C
  • FormulaC₃H₇NO₂S
  • Structureα-amino acid with a thiol (-SH) group in its side chain.
  • Molecule Makeup3 carbons, 7 hydrogens, 1 nitrogen, 2 oxygens, 1 sulfur.
  • EngineeringSynthesized from serine and methionine via cystathionine pathway.
  • MeaningForms disulfide bonds, stabilizing protein structures.

Glutamic Acid

  • CodesGlu / E
  • FormulaC₅H₉NO₄
  • Structureα-amino acid with a 3-carbon side chain ending in a carboxylic acid (-COOH).
  • Molecule Makeup5 carbons, 9 hydrogens, 1 nitrogen, 4 oxygens.
  • EngineeringSynthesized from α-ketoglutarate in the TCA cycle.
  • MeaningNegatively charged; key in neurotransmission (as glutamate).

Glutamine

  • CodesGln / Q
  • FormulaC₅H₁₀N₂O₃
  • Structureα-amino acid with a 3-carbon chain ending in an amide group.
  • Molecule Makeup5 carbons, 10 hydrogens, 2 nitrogens, 3 oxygens.
  • EngineeringSynthesized from glutamic acid by glutamine synthetase.
  • MeaningNitrogen donor in biosynthetic pathways; supports cell growth.

Glycine

  • CodesGly / G
  • FormulaC₂H₅NO₂
  • StructureSimplest amino acid; hydrogen as side chain.
  • Molecule Makeup2 carbons, 5 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringSynthesized from serine via hydroxymethyltransferase.
  • MeaningFlexible, fits in tight turns of protein structures.

Histidine

  • CodesHis / H
  • FormulaC₆H₉N₃O₂
  • StructureImidazole side chain capable of proton exchange.
  • Molecule Makeup6 carbons, 9 hydrogens, 3 nitrogens, 2 oxygens.
  • EngineeringSynthesized from ribose-5-phosphate through multi-step pathway.
  • MeaningCatalytic in enzyme active sites; pH sensor.

Isoleucine

  • CodesIle / I
  • FormulaC₆H₁₃NO₂
  • StructureBranched-chain α-amino acid; sec-butyl side chain.
  • Molecule Makeup6 carbons, 13 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringEssential amino acid obtained from diet.
  • MeaningHydrophobic; stabilizes protein cores.

Leucine

  • CodesLeu / L
  • FormulaC₆H₁₃NO₂
  • StructureBranched-chain α-amino acid; isobutyl side chain.
  • Molecule MakeupSame as isoleucine, different structure.
  • EngineeringEssential amino acid obtained from diet.
  • MeaningStimulates protein synthesis; major hydrophobic core residue.

Lysine

  • CodesLys / K
  • FormulaC₆H₁₄N₂O₂
  • StructureLong aliphatic chain ending in an amino group (-NH₂).
  • Molecule Makeup6 carbons, 14 hydrogens, 2 nitrogens, 2 oxygens.
  • EngineeringEssential amino acid obtained from diet.
  • MeaningPositively charged; interacts with DNA.

Methionine

  • CodesMet / M
  • FormulaC₅H₁₁NO₂S
  • StructureSulfur-containing thioether side chain.
  • Molecule Makeup5 carbons, 11 hydrogens, 1 nitrogen, 2 oxygens, 1 sulfur.
  • EngineeringEssential amino acid from diet; also start codon in translation.
  • MeaningInitiates protein synthesis; methyl donor in metabolism.

Phenylalanine

  • CodesPhe / F
  • FormulaC₉H₁₁NO₂
  • StructureBenzyl side chain.
  • Molecule Makeup9 carbons, 11 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringEssential amino acid from diet.
  • MeaningAromatic; absorbs UV light, useful in protein quantification.

Proline

  • CodesPro / P
  • FormulaC₅H₉NO₂
  • StructureSecondary amine; pyrrolidine ring linking side chain to backbone nitrogen.
  • Molecule Makeup5 carbons, 9 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringSynthesized from glutamate.
  • MeaningIntroduces kinks in proteins; disrupts α-helices.

Serine

  • CodesSer / S
  • FormulaC₃H₇NO₃
  • StructureSide chain contains hydroxymethyl group (-CH₂OH).
  • Molecule Makeup3 carbons, 7 hydrogens, 1 nitrogen, 3 oxygens.
  • EngineeringSynthesized from 3-phosphoglycerate.
  • MeaningPolar; site for phosphorylation and glycosylation.

Threonine

  • CodesThr / T
  • FormulaC₄H₉NO₃
  • Structureβ-hydroxy group (-CHOH-) in side chain.
  • Molecule Makeup4 carbons, 9 hydrogens, 1 nitrogen, 3 oxygens.
  • EngineeringEssential amino acid from diet.
  • MeaningPolar; supports hydrogen bonding in proteins.

Tryptophan

  • CodesTrp / W
  • FormulaC₁₁H₁₂N₂O₂
  • StructureIndole side chain.
  • Molecule Makeup11 carbons, 12 hydrogens, 2 nitrogens, 2 oxygens.
  • EngineeringEssential amino acid from diet.
  • MeaningAromatic; precursor to serotonin and melatonin.

Tyrosine

  • CodesTyr / Y
  • FormulaC₉H₁₁NO₃
  • StructurePhenolic side chain.
  • Molecule Makeup9 carbons, 11 hydrogens, 1 nitrogen, 3 oxygens.
  • EngineeringSynthesized from phenylalanine.
  • MeaningPolar aromatic; involved in signaling through phosphorylation.

Valine

  • CodesVal / V
  • FormulaC₅H₁₁NO₂
  • StructureBranched isopropyl side chain.
  • Molecule Makeup5 carbons, 11 hydrogens, 1 nitrogen, 2 oxygens.
  • EngineeringEssential amino acid from diet.
  • MeaningHydrophobic; important in stabilizing protein structure.
  1. ASCII schematic — a rough line-based representation of each amino acid’s structure so you can see atom connections in text form.
  2. Regular text format — the names, abbreviations, and formulas in clear list form to match against the chart.

1. ASCII Schematic (Simplified)

Alanine (Ala, A, C3H7NO2)
    H   O
    |  //
H2N-C--C
    |   \
   H-C-H  OH
    |
   CH3

Arginine (Arg, R, C6H14N4O2)
    H   O
    |  //
H2N-C--C
    |   \
   H-C-H  OH
    |
  (CH2)3-NH-C(NH2)2+

Asparagine (Asn, N, C4H8N2O3)
    H   O
    |  //
H2N-C--C
    |   \
   H-C-H  OH
    |
  CH2-C(=O)-NH2

Aspartic Acid (Asp, D, C4H7NO4)
    H   O
    |  //
H2N-C--C
    |   \
   H-C-H  OH
    |
  CH2-COOH

Cysteine (Cys, C, C3H7NO2S)
    H   O
    |  //
H2N-C--C
    |   \
   H-C-H  OH
    |
   CH2-SH

... (pattern repeats for all 20 amino acids) ...

2. Regular Text Format

  1. Alanine — Ala — A — C₃H₇NO₂
  2. Arginine — Arg — R — C₆H₁₄N₄O₂
  3. Asparagine — Asn — N — C₄H₈N₂O₃
  4. Aspartic acid — Asp — D — C₄H₇NO₄
  5. Cysteine — Cys — C — C₃H₇NO₂S
  6. Glutamic acid — Glu — E — C₅H₉NO₄
  7. Glutamine — Gln — Q — C₅H₁₀N₂O₃
  8. Glycine — Gly — G — C₂H₅NO₂
  9. Histidine — His — H — C₆H₉N₃O₂
  10. Isoleucine — Ile — I — C₆H₁₃NO₂
  11. Leucine — Leu — L — C₆H₁₃NO₂
  12. Lysine — Lys — K — C₆H₁₄N₂O₂
  13. Methionine — Met — M — C₅H₁₁NO₂S
  14. Phenylalanine — Phe — F — C₉H₁₁NO₂
  15. Proline — Pro — P — C₅H₉NO₂
  16. Serine — Ser — S — C₃H₇NO₃
  17. Threonine — Thr — T — C₄H₉NO₃
  18. Tryptophan — Trp — W — C₁₁H₁₂N₂O₂
  19. Tyrosine — Tyr — Y — C₉H₁₁NO₃
  20. Valine — Val — V — C₅H₁₁NO₂

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