Full integrated master chart that ties the genetic code (mRNA codons) to the amino-acid chemistry and flags all known natural codon reassignments, with the organism etymologies right beside them. Strict standard code everywhere; only UGA (→ Selenocysteine) and UAG (→ Pyrrolysine) get natural reassignments.
Columns: Codon • Standard assignment (3-letter / 1-letter) • Chemical formula • Natural reassignment + organisms (with etymology)
U-row (UXX)
| Codon | Standard | Formula | Natural reassignment + organisms (with etymology) |
|---|---|---|---|
| UUU | Phe / F | C₉H₁₁NO₂ | — |
| UUC | Phe / F | C₉H₁₁NO₂ | — |
| UUA | Leu / L | C₆H₁₃NO₂ | — |
| UUG | Leu / L | C₆H₁₃NO₂ | — |
| UCU | Ser / S | C₃H₇NO₃ | — |
| UCC | Ser / S | C₃H₇NO₃ | — |
| UCA | Ser / S | C₃H₇NO₃ | — |
| UCG | Ser / S | C₃H₇NO₃ | — |
| UAU | Tyr / Y | C₉H₁₁NO₃ | — |
| UAC | Tyr / Y | C₉H₁₁NO₃ | — |
| UAA (ochre) | Stop | — | — |
| UAG (amber) | Stop | — | → Pyrrolysine (Pyl, O) C₁₂H₂₁N₃O₃ in: Desulfitobacterium hafniense — Desulfitobacterium “sulfite-removing rod” (de- + sulfitum + bacterium); hafniense from Hafnia (Lat. Copenhagen). Methanosarcina barkeri/mazei — Methanosarcina “methane + fleshy (aggregates)”; barkeri/mazei honor Harold Barker/Jules Maze. |
| UGU | Cys / C | C₃H₇NO₂S | — |
| UGC | Cys / C | C₃H₇NO₂S | — |
| UGA (opal) | Stop | — | → Selenocysteine (Sec, U) C₃H₇NO₂Se in: Escherichia coli — Escherichia honors Theodor Escherich; coli “of the colon.” Clostridium spp. — Greek kloster “spindle” + dim. -idion (spindle-like endospores). Treponema pallidum — trepo “turn” + nema “thread”; pallidum “pale.” Methanococcus jannaschii — methan + kokkos “berry”; jannaschii honors Holger Jannasch. Methanopyrus kandleri — methan + pyr “fire”; kandleri honors Johannes Kandler. |
| UGG | Trp / W | C₁₁H₁₂N₂O₂ | — |
C-row (CXX)
| Codon | Standard | Formula | Natural reassignment + organisms |
|---|---|---|---|
| CUU | Leu / L | C₆H₁₃NO₂ | — |
| CUC | Leu / L | C₆H₁₃NO₂ | — |
| CUA | Leu / L | C₆H₁₃NO₂ | — |
| CUG | Leu / L | C₆H₁₃NO₂ | — |
| CCU | Pro / P | C₅H₉NO₂ | — |
| CCC | Pro / P | C₅H₉NO₂ | — |
| CCA | Pro / P | C₅H₉NO₂ | — |
| CCG | Pro / P | C₅H₉NO₂ | — |
| CAU | His / H | C₆H₉N₃O₂ | — |
| CAC | His / H | C₆H₉N₃O₂ | — |
| CAA | Gln / Q | C₅H₁₀N₂O₃ | — |
| CAG | Gln / Q | C₅H₁₀N₂O₃ | — |
| CGU | Arg / R | C₆H₁₄N₄O₂ | — |
| CGC | Arg / R | C₆H₁₄N₄O₂ | — |
| CGA | Arg / R | C₆H₁₄N₄O₂ | — |
| CGG | Arg / R | C₆H₁₄N₄O₂ | — |
A-row (AXX)
| Codon | Standard | Formula | Natural reassignment + organisms |
|---|---|---|---|
| AUU | Ile / I | C₆H₁₃NO₂ | — |
| AUC | Ile / I | C₆H₁₃NO₂ | — |
| AUA | Ile / I | C₆H₁₃NO₂ | — |
| AUG | Met / M (Start) | C₅H₁₁NO₂S | — |
| ACU | Thr / T | C₄H₉NO₃ | — |
| ACC | Thr / T | C₄H₉NO₃ | — |
| ACA | Thr / T | C₄H₉NO₃ | — |
| ACG | Thr / T | C₄H₉NO₃ | — |
| AAU | Asn / N | C₄H₈N₂O₃ | — |
| AAC | Asn / N | C₄H₈N₂O₃ | — |
| AAA | Lys / K | C₆H₁₄N₂O₂ | — |
| AAG | Lys / K | C₆H₁₄N₂O₂ | — |
| AGU | Ser / S | C₃H₇NO₃ | — |
| AGC | Ser / S | C₃H₇NO₃ | — |
| AGA | Arg / R | C₆H₁₄N₄O₂ | — |
| AGG | Arg / R | C₆H₁₄N₄O₂ | — |
G-row (GXX)
| Codon | Standard | Formula | Natural reassignment + organisms |
|---|---|---|---|
| GUU | Val / V | C₅H₁₁NO₂ | — |
| GUC | Val / V | C₅H₁₁NO₂ | — |
| GUA | Val / V | C₅H₁₁NO₂ | — |
| GUG | Val / V | C₅H₁₁NO₂ | — |
| GCU | Ala / A | C₃H₇NO₂ | — |
| GCC | Ala / A | C₃H₇NO₂ | — |
| GCA | Ala / A | C₃H₇NO₂ | — |
| GCG | Ala / A | C₃H₇NO₂ | — |
| GAU | Asp / D | C₄H₇NO₄ | — |
| GAC | Asp / D | C₄H₇NO₄ | — |
| GAA | Glu / E | C₅H₉NO₄ | — |
| GAG | Glu / E | C₅H₉NO₄ | — |
| GGU | Gly / G | C₂H₅NO₂ | — |
| GGC | Gly / G | C₂H₅NO₂ | — |
| GGA | Gly / G | C₂H₅NO₂ | — |
| GGG | Gly / G | C₂H₅NO₂ | — |
Notes & cross-links (your recursive lenses)
- Chemistry layerFormulas correspond to the free amino acids; once polymerized, each residue is minus H₂O at the peptide bond.
- Grammar layerOnly two stops are naturally “polysemous” in the wild code: UGA (Sec) and UAG (Pyl). UAA stays a period.
- Pragmatics layerBoth reassignments require contextual machinery (SECIS + tRNA⁽Sec⁾/SelB or pyl operon + tRNA⁽Pyl⁾/PylRS) that blocks release factors, turning punctuation into a “word.”
- Etymology layerNames encode meaning too—Methan- (methane), -coccus (berry/sphere), -pyr- (fire/heat), honorific epithets (jannaschii, barkeri, mazei), and place names (hafniense ← Hafnia/Copenhagen).
Letterscope – SolveForce Communications
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