Learning paths

Learning paths

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Learning path

Full curriculum

Full curriculum
  1. Amino acid structure, chirality and side-chain chemistry
  2. RNA strand structure, base pairing and folding
  3. The genetic code, codons and reading frames
  4. ATP hydrolysis, phosphoryl transfer and energetic coupling
  5. tRNA charging and codon-anticodon decoding
  6. Ribosome-catalyzed translation of mRNA into polypeptide
  7. DNA sequence substitutions, insertions and deletions
  8. Coding-sequence consequences of base substitutions
  9. Coding-sequence consequences of insertions and deletions

Unit content

The genetic code, codons and reading frames

In protein-coding messenger RNA (mRNA), nucleotide sequence is interpreted in groups of three bases called codons. Each codon specifies an amino acid or a translation stop signal.

Because RNA has four common bases, there are

$$4^3=64$$

possible codons.

The genetic code is redundant or degenerate: several codons can specify the same amino acid. But within the standard code, a particular codon does not normally specify several different amino acids.

Start and stop codons

The codon AUG commonly serves as a translation start codon and specifies methionine. The standard stop codons are

UAA   UAG   UGA

Stop codons do not encode an amino acid. They signal termination of translation.

Reading frame

A nucleotide sequence can be divided into triplets in different ways depending on where counting begins. A reading frame is one particular grouping into consecutive codons.

For example,

5'-AUG GCU UAC UGA-3'

read from the first base gives

AUG | GCU | UAC | UGA
Met | Ala | Tyr | Stop

where Met, Ala and Tyr abbreviate methionine, alanine and tyrosine.

Starting one nucleotide later would produce a different set of codons and therefore a different interpretation.

During translation, the ribosome establishes a reading frame at initiation and then advances along the mRNA codon by codon in the $5'\rightarrow3'$ direction.

The code connects two molecular alphabets

Codons are nucleotide sequences; amino acids are chemically different molecules. The genetic code is therefore a mapping between the nucleotide alphabet of RNA and the amino-acid alphabet of proteins.

The codon table does not itself explain how an amino acid is physically matched to a codon. That molecular decoding step is performed through transfer RNAs and aminoacyl-tRNA synthetases.