Codon → Chemistry → Organism Reassignment + Etymology

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)

CodonStandardFormulaNatural reassignment + organisms (with etymology)
UUUPhe / FC₉H₁₁NO₂
UUCPhe / FC₉H₁₁NO₂
UUALeu / LC₆H₁₃NO₂
UUGLeu / LC₆H₁₃NO₂
UCUSer / SC₃H₇NO₃
UCCSer / SC₃H₇NO₃
UCASer / SC₃H₇NO₃
UCGSer / SC₃H₇NO₃
UAUTyr / YC₉H₁₁NO₃
UACTyr / YC₉H₁₁NO₃
UAA (ochre)Stop
UAG (amber)Stop→ Pyrrolysine (Pyl, O) C₁₂H₂₁N₃O₃ in: Desulfitobacterium hafnienseDesulfitobacterium “sulfite-removing rod” (de- + sulfitum + bacterium); hafniense from Hafnia (Lat. Copenhagen). Methanosarcina barkeri/mazeiMethanosarcina “methane + fleshy (aggregates)”; barkeri/mazei honor Harold Barker/Jules Maze.
UGUCys / CC₃H₇NO₂S
UGCCys / CC₃H₇NO₂S
UGA (opal)Stop→ Selenocysteine (Sec, U) C₃H₇NO₂Se in: Escherichia coliEscherichia honors Theodor Escherich; coli “of the colon.” Clostridium spp. — Greek kloster “spindle” + dim. -idion (spindle-like endospores). Treponema pallidumtrepo “turn” + nema “thread”; pallidum “pale.” Methanococcus jannaschiimethan + kokkos “berry”; jannaschii honors Holger Jannasch. Methanopyrus kandlerimethan + pyr “fire”; kandleri honors Johannes Kandler.
UGGTrp / WC₁₁H₁₂N₂O₂

C-row (CXX)

CodonStandardFormulaNatural reassignment + organisms
CUULeu / LC₆H₁₃NO₂
CUCLeu / LC₆H₁₃NO₂
CUALeu / LC₆H₁₃NO₂
CUGLeu / LC₆H₁₃NO₂
CCUPro / PC₅H₉NO₂
CCCPro / PC₅H₉NO₂
CCAPro / PC₅H₉NO₂
CCGPro / PC₅H₉NO₂
CAUHis / HC₆H₉N₃O₂
CACHis / HC₆H₉N₃O₂
CAAGln / QC₅H₁₀N₂O₃
CAGGln / QC₅H₁₀N₂O₃
CGUArg / RC₆H₁₄N₄O₂
CGCArg / RC₆H₁₄N₄O₂
CGAArg / RC₆H₁₄N₄O₂
CGGArg / RC₆H₁₄N₄O₂

A-row (AXX)

CodonStandardFormulaNatural reassignment + organisms
AUUIle / IC₆H₁₃NO₂
AUCIle / IC₆H₁₃NO₂
AUAIle / IC₆H₁₃NO₂
AUGMet / M (Start)C₅H₁₁NO₂S
ACUThr / TC₄H₉NO₃
ACCThr / TC₄H₉NO₃
ACAThr / TC₄H₉NO₃
ACGThr / TC₄H₉NO₃
AAUAsn / NC₄H₈N₂O₃
AACAsn / NC₄H₈N₂O₃
AAALys / KC₆H₁₄N₂O₂
AAGLys / KC₆H₁₄N₂O₂
AGUSer / SC₃H₇NO₃
AGCSer / SC₃H₇NO₃
AGAArg / RC₆H₁₄N₄O₂
AGGArg / RC₆H₁₄N₄O₂

G-row (GXX)

CodonStandardFormulaNatural reassignment + organisms
GUUVal / VC₅H₁₁NO₂
GUCVal / VC₅H₁₁NO₂
GUAVal / VC₅H₁₁NO₂
GUGVal / VC₅H₁₁NO₂
GCUAla / AC₃H₇NO₂
GCCAla / AC₃H₇NO₂
GCAAla / AC₃H₇NO₂
GCGAla / AC₃H₇NO₂
GAUAsp / DC₄H₇NO₄
GACAsp / DC₄H₇NO₄
GAAGlu / EC₅H₉NO₄
GAGGlu / EC₅H₉NO₄
GGUGly / GC₂H₅NO₂
GGCGly / GC₂H₅NO₂
GGAGly / GC₂H₅NO₂
GGGGly / GC₂H₅NO₂

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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