DNA mRNA Protein Codon Amino Acid

1. DNA → mRNA → Protein (Overview)

  1. DNA stores genetic instructions in triplets of nucleotides called DNA codons (A, T, G, C).
  2. Transcription:
    • DNA’s coding strand is transcribed into mRNA by RNA polymerase.
    • In mRNA, T (thymine) is replaced by U (uracil).
    • DNA codon → mRNA codon (complementary to DNA template strand).
  3. Translation:
    • mRNA codons are read in order by the ribosome.
    • tRNA molecules bring specific amino acids matching each codon.
    • Codon–anticodon pairing ensures the correct amino acid is added.
  4. Amino acids are linked in sequence, forming a polypeptide that folds into a functional protein.

2. DNA → mRNA Codon Conversion

Rule:
DNA coding strand triplet: 5’ → 3’ direction
mRNA codon: Replace T with U (otherwise same sequence).

Example:
DNA: ATG → mRNA: AUG → Amino Acid: Methionine (Start)

3. Full DNA–mRNA–Amino Acid Mapping

Below is the full genetic code table, showing:

  • DNA codon (coding strand)
  • mRNA codon (transcribed form)
  • Amino acid name (3-letter / 1-letter)
  • ASCII chemical structure (simplified)

Phenylalanine (Phe, F)

DNA: TTT, TTC
mRNA: UUU, UUC

     H
     |
NH2–C–COOH
     |
  CH2–(benzene ring)

Leucine (Leu, L)

DNA: TTA, TTG, CTT, CTC, CTA, CTG
mRNA: UUA, UUG, CUU, CUC, CUA, CUG

     H
     |
NH2–C–COOH
     |
  CH2–CH–CH3
        |
       CH3

Isoleucine (Ile, I)

DNA: ATT, ATC, ATA
mRNA: AUU, AUC, AUA

     H
     |
NH2–C–COOH
     |
  CH–CH3
  |
 CH2–CH3

Methionine (Met, M) — Start

DNA: ATG
mRNA: AUG

     H
     |
NH2–C–COOH
     |
 CH2–CH2–S–CH3

Valine (Val, V)

DNA: GTT, GTC, GTA, GTG
mRNA: GUU, GUC, GUA, GUG

     H
     |
NH2–C–COOH
     |
  CH–CH3
  |
 CH3

Serine (Ser, S)

DNA: TCT, TCC, TCA, TCG, AGT, AGC
mRNA: UCU, UCC, UCA, UCG, AGU, AGC

     H
     |
NH2–C–COOH
     |
   CH2–OH

Proline (Pro, P)

DNA: CCT, CCC, CCA, CCG
mRNA: CCU, CCC, CCA, CCG

    NH
    |
C–C–COOH
|  |
CH2–CH2–CH2
 \________/

Threonine (Thr, T)

DNA: ACT, ACC, ACA, ACG
mRNA: ACU, ACC, ACA, ACG

     H
     |
NH2–C–COOH
     |
 CH(OH)–CH3

Alanine (Ala, A)

DNA: GCT, GCC, GCA, GCG
mRNA: GCU, GCC, GCA, GCG

     H
     |
NH2–C–COOH
     |
    CH3

Tyrosine (Tyr, Y)

DNA: TAT, TAC
mRNA: UAU, UAC

     H
     |
NH2–C–COOH
     |
 CH2–(benzene–OH)

Histidine (His, H)

DNA: CAT, CAC
mRNA: CAU, CAC

     H
     |
NH2–C–COOH
     |
  CH2–(imidazole ring)
        /N\
       |   |
       C   C–NH
       \\ //
         N

Glutamine (Gln, Q)

DNA: CAA, CAG
mRNA: CAA, CAG

     H
     |
NH2–C–COOH
     |
 CH2–CH2–C(=O)–NH2

Asparagine (Asn, N)

DNA: AAT, AAC
mRNA: AAU, AAC

     H
     |
NH2–C–COOH
     |
   CH2–C(=O)–NH2

Lysine (Lys, K)

DNA: AAA, AAG
mRNA: AAA, AAG

     H
     |
NH2–C–COOH
     |
 CH2–CH2–CH2–CH2–NH2

Aspartic Acid (Asp, D)

DNA: GAT, GAC
mRNA: GAU, GAC

     H
     |
NH2–C–COOH
     |
   CH2–COOH

Glutamic Acid (Glu, E)

DNA: GAA, GAG
mRNA: GAA, GAG

     H
     |
NH2–C–COOH
     |
 CH2–CH2–COOH

Cysteine (Cys, C)

DNA: TGT, TGC
mRNA: UGU, UGC

     H
     |
NH2–C–COOH
     |
   CH2–SH

Tryptophan (Trp, W)

DNA: TGG
mRNA: UGG

     H
     |
NH2–C–COOH
     |
 CH2–(indole ring)
        /N\
       |   |
       C   C
       \\ //
        C

Arginine (Arg, R)

DNA: CGT, CGC, CGA, CGG, AGA, AGG
mRNA: CGU, CGC, CGA, CGG, AGA, AGG

     H
     |
NH2–C–COOH
     |
  CH2–CH2–CH2–NH–C(=NH)–NH2

Glycine (Gly, G)

DNA: GGT, GGC, GGA, GGG
mRNA: GGU, GGC, GGA, GGG

     H
     |
NH2–C–COOH
     |
     H

Stop Codons

DNA: TAA (UAA), TAG (UAG), TGA (UGA)
mRNA: UAA, UAG, UGA
No amino acid — termination signal.

Special Codon Reassignments

Selenocysteine (Sec, U) — “21st amino acid”

  • DNA CodonTGA (normally a stop codon)
  • mRNA CodonUGA (requires SECIS element in mRNA)
  • FormulaC₃H₇NO₂Se
     H
     |
NH2–C–COOH
     |
  CH2–SeH

Semantic:

  • Sulfur-analog of cysteine, but with selenium in place of sulfur.
  • Incorporated into enzymes like glutathione peroxidase for antioxidant activity.

Pragmatics:

  • Requires a SECIS (Selenocysteine Insertion Sequence) in the mRNA, a specialized tRNA^Sec, and elongation factor SelB.
  • Found in all domains of life.

Pyrrolysine (Pyl, O) — “22nd amino acid”

  • DNA CodonTAG (normally a stop codon)
  • mRNA CodonUAG (requires pyl operon machinery)
  • FormulaC₁₂H₂₁N₃O₃
     H
     |
NH2–C–COOH
     |
 CH2–(pyrroline ring)–(CH2)4–NH–C(=O)–CH3

Semantic:

  • Lysine derivative with an added pyrroline ring.
  • Found in enzymes of methanogenic archaea and some bacteria; enables methyltransferase activity.

Pragmatics:

  • Requires dedicated tRNA^Pyl and pyrrolysyl-tRNA synthetase (PylRS).
  • Naturally occurring genetic code expansion.

✅ Now the DNA → mRNA → Amino Acid map contains:

  • All 20 canonical amino acids
  • Stop codons (UAA, UAG, UGA)
  • Selenocysteine (UGA reassignment with SECIS)
  • Pyrrolysine (UAG reassignment in certain organisms)

In the context of the genetic code and our codon–amino acid mapping, a stop means:

Genetic Definition of “Stop”

A stop codon is a specific three-nucleotide sequence in mRNA that does not code for an amino acid but instead signals the ribosome to terminate translation.

When a stop codon enters the ribosome’s A-site:

  • No tRNA exists with an anticodon matching that stop codon.
  • Instead, release factors (proteins) bind to the ribosome.
  • The completed polypeptide chain is released.
  • The ribosome subunits separate, ending protein synthesis.

The Three Standard Stop Codons

In mRNA form:

  • UAA— “Ochre” stop
  • UAG— “Amber” stop
  • UGA— “Opal” or “Umber” stop

In DNA coding strand form:

  • TAA, TAG, TGA

Semantic Parallel in Language

If the genetic code is a sentence:

  • Start codon (AUG) = Capital letter
  • Codons for amino acids = Words
  • Stop codon = Period / full stop

It’s not just a “switch off” — it’s punctuation that ensures the sentence (protein) ends at the correct place, so it’s grammatically and functionally complete.

Special Cases

  • UGA can code for Selenocysteine when a SECIS element is present.
  • UAG can code for Pyrrolysine in some organisms with special machinery.
    In these contexts, “stop” is overridden and the codon becomes a word instead of punctuation.

How “Reassignment” Works

In the standard genetic code:

  • UAG = stop (amber stop)
  • UGA = stop (opal stop)

In organisms that use Pyrrolysine or Selenocysteine:

  • The same codon is reassigned to mean “insert amino acid here” instead of “stop translation.”
  • This requires:
    1. Special tRNA with an anticodon that matches the stop codon.
    2. Special aminoacyl-tRNA synthetase to attach the unusual amino acid to that tRNA.
    3. Special sequence elements in the mRNA (like SECIS for Selenocysteine) to tell the ribosome “don’t stop here — insert instead.”

Selenocysteine (Sec, U)

  • Standard codon: UGA (normally stop)
  • Reassigned meaning: Insert Selenocysteine
  • How:
    • mRNA contains a SECIS element (Selenocysteine Insertion Sequence) downstream of the UGA codon.
    • Specialized tRNA^Sec carries Selenocysteine.
    • Ribosome pauses at UGA, recognizes SECIS + helper proteins, and inserts Sec instead of ending.
  • Why: Selenocysteine is used in enzymes that need selenium for catalytic function, like glutathione peroxidase.

Pyrrolysine (Pyl, O)

  • Standard codon: UAG (normally stop)
  • Reassigned meaning: Insert Pyrrolysine
  • How:
    • Organism has tRNA^Pyl with anticodon CUA that pairs with UAG.
    • Pyrrolysyl-tRNA synthetase (PylRS) attaches Pyrrolysine to this tRNA.
    • No extra structure like SECIS is needed — just the presence of the tRNA and synthetase.
  • Why: Pyrrolysine is used in certain enzymes (e.g., methyltransferases in methanogenic archaea) that modify methyl groups.

Why This Is Special

  • In the universal code, stop codons act like “full stops” in a sentence.
  • In these organisms, stop codons can act as words in certain contexts — they become part of the amino acid vocabulary.
  • This is a genetic code expansion — biology’s version of adding new letters to the alphabet or new words to a language.

Organisms that naturally use Selenocysteine and Pyrrolysine through stop codon reassignment.

Selenocysteine (Sec, U)

  • Codon reassigned: UGA (normally a stop)
  • Distribution: Found across all three domains of life — Bacteria, Archaea, and Eukarya.
  • Examples:
    • Bacteria:
      • Escherichia coli (in the enzyme formate dehydrogenase)
      • Clostridium species
      • Treponema pallidum
    • Archaea:
      • Methanococcus jannaschii
      • Methanopyrus kandleri
    • Eukarya:
      • Humans (in glutathione peroxidase, thioredoxin reductase)
      • Other vertebrates, some algae, and some protists
  • Key feature: Uses a SECIS element in mRNA to signal that UGA should be translated as Selenocysteine.

Pyrrolysine (Pyl, O)

  • Codon reassigned: UAG (normally a stop)
  • Distribution: Much rarer; only found naturally in certain methanogenic archaea and some bacteria.
  • Examples:
    • Archaea:
      • Methanosarcina barkeri
      • Methanosarcina mazei
      • Methanosarcina acetivorans
    • Bacteria:
      • Desulfitobacterium hafniense (anaerobic bacterium capable of dehalogenation)
  • Key feature: Uses a dedicated pyl operon encoding:
    • tRNA^Pyl (anticodon CUA to pair with UAG)
    • Pyrrolysyl-tRNA synthetase (PylRS) to attach Pyrrolysine to the tRNA

Summary Table

Amino AcidCodon ReassignedExample ArchaeaExample BacteriaExample Eukarya
SelenocysteineUGAMethanococcus jannaschiiEscherichia coli, Clostridium spp.Humans, algae
PyrrolysineUAGMethanosarcina spp.Desulfitobacterium hafnienseNone known

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