Why the table has 64 rows

Proteins are built from 20 commonly occurring amino acids, and mRNA has an alphabet of only four letters, so the code has to group nucleotides. Doublets would not be enough: there are only 16 two-nucleotide combinations. Triplets give 4 cubed, which is 64 possible codons, comfortably more than 20. That surplus is why the genetic code is degenerate: a given amino acid can be encoded by more than one triplet. Three of the 64 codons terminate protein synthesis and release the polypeptide, and one, AUG, does double duty by specifying methionine and serving as the start codon that sets the reading frame near the 5′ end.

A worked example

Use a standard codon chart to translate the mRNA sequence 5′-AUGUUCGCAGGAUAA-3′ into a peptide, and say how many amino acids long the product is.

  1. Find the start. Translation begins at the AUG nearest the 5′ end, and that AUG sets the reading frame for everything after it. Here the sequence begins with AUG, so the frame starts at nucleotide 1.
  2. Split the sequence into non-overlapping triplets from that point: AUG, UUC, GCA, GGA, UAA. Fifteen nucleotides divide evenly into five codons, so no partial codon is left over.
  3. Look up each codon in turn. AUG is methionine (Met), UUC is phenylalanine (Phe), GCA is alanine (Ala), and GGA is glycine (Gly).
  4. Check the last codon before writing it down as an amino acid. UAA is one of the three stop codons, along with UAG and UGA, so it terminates translation and contributes no amino acid.
  5. Assemble the peptide in the order read: Met-Phe-Ala-Gly. Four codons specified amino acids and the fifth stopped the process, so the product is four amino acids long, not five.

= The peptide is Met-Phe-Ala-Gly, four amino acids long, with UAA acting as a stop codon rather than a fifth residue.

Where students go wrong

The frame is the usual casualty. Codons are read in non-overlapping groups of three from the start codon onward, so beginning one nucleotide early or late changes every amino acid downstream, which is precisely what Crick and Brenner demonstrated by inserting one, two or three nucleotides into a viral gene. The second common error is reading a DNA sequence straight off an mRNA chart; charts are written in RNA, so thymine has to become uracil first. The third is counting the stop codon as an amino acid, which inflates every peptide length by one.

Where this leads next

The chart is only useful once you know where its input comes from, which is transcription, and what happens to its output, which is the ribosome assembling the polypeptide. That whole sequence is the transcription and translation page. Underneath it sits the base difference between DNA and RNA, since uracil is what makes a codon chart an RNA table rather than a DNA one, and that is the DNA and RNA page. Degeneracy also explains why some point mutations change nothing at all, which is where mutation types pick up.

Common mistakes

  • Starting the reading frame at the wrong nucleotide. Codons are non-overlapping triplets counted from the AUG start codon, and a shift changes every amino acid after it.
  • Looking up a DNA sequence on an mRNA chart. Convert thymine to uracil first; codon charts are written in RNA.
  • Counting the stop codon as an amino acid. UAA, UAG and UGA end translation and add no residue.
  • Assuming each amino acid has one codon. The code is degenerate, and leucine, serine and arginine each have six.

Related concepts

  • DNA vs RNA: DNA and RNA are both polynucleotides, but DNA uses deoxyribose and the bases A, T, G and C, and forms an antiparallel double helix.
  • Punnett square: A Punnett square applies the rules of probability to predict the outcomes of a genetic cross.
  • Transcription vs translation: Transcription copies a gene's DNA sequence into messenger RNA, one nucleotide at a time.

Sources