The Genetic Code

One codon, AUG serves two related functions:

• it signals the start of translation
• it codes for the incorporation of the amino acid methionine (Met) into the growing polypeptide chain

The genetic code can be expressed as either RNA codons or DNA codons. RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation). But each mRNA molecule acquires its sequence of nucleotides by transcription from the corresponding gene. Because DNA sequencing has become so rapid and because most genes are now being discovered at the level of DNA before they are discovered as mRNA or as a protein product, it is extremely useful to have a table of codons expressed as DNA. So here are both.

Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second nucleotide, and the last column gives the third nucleotide.

The RNA Codons

The DNA Codons

These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of DNA (3' to 5') as the template. [Discussion]

This table could well be called the Rosetta Stone of life.

The Genetic Code (DNA)

Codon Bias

All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different codons. However, the genome of most organisms reveals that certain codons are preferred over others. In humans, for example, alanine is encoded by GCC four times as often as by GCG. This probably reflects a greater translation efficiency by the translation apparatus (e.g., ribosomes) for certain codons over their synonyms. [More]

Exceptions to the Code

Mitochondrial genes

The reason: these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic machinery, synthesis stops where Trp should have been inserted.

In addition, most

• animal mitochondria use AUA for methionine not isoleucine and
• all vertebrate mitochondria use AGA and AGG as chain terminators.
• Yeast mitochondria assign all codons beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).

Nuclear genes

A few unicellular eukaryotes, notably among the ciliates, have been found that use one or two or even all three of their STOP codons for amino acids. Only those STOP codons occurring close to the poly(A) tail trigger chain termination.

Nonstandard Amino Acids

The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically altered, e.g. by phosphorylation, at a later time.

• selenocysteine. This amino acid is encoded by UGA. UGA is still used as a chain terminator, but the translation machinery is able to discriminate when a UGA codon should be used for selenocysteine rather than STOP. This codon usage has been found in certain Archaea, eubacteria, and animals (humans synthesize 25 different proteins containing selenium).
• pyrrolysine. In several species of Archaea and bacteria, this amino acid is encoded by UAG. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known.