Student’s Corner
Codes
The standard genetic code is a table with a history. This bench lets you read it instead of photographing it.
How to read a codon
Messenger RNA is read three bases at a time, in the 5′ to 3′ direction. Those three bases are a codon. In the standard code, 61 codons specify amino acids and 3 mean stop. AUG specifies methionine and is the usual start. The code is degenerate: leucine, arginine, and serine have six codons each, while methionine and tryptophan have one. Several codons for the same amino acid often share their first two letters, which is why a mutation in the third position is frequently silent.
The table below is the nuclear code used in most textbooks. Paste a coding sequence: the DNA strand that looks like the message, or the RNA itself. Thymine is read as uracil. This bench does not reverse-complement a template strand. If you paste the template, you will get a confident wrong protein.
Codon bench
Click any cell in the table. Matching cells are outlined.
Paste a coding sequence, using T or U. The bench reads it 5′ to 3′.
Poly-U is the message Marshall Nirenberg and Heinrich Matthaei translated in 1961: a run of phenylalanine. The teaching peptide is invented for this page, Met–Gly–Phe–Ser–Asp–Stop. It is not a gene from a real organism. Do not cite it as one.
The table
- Nonpolar
- Polar uncharged
- Acidic
- Basic
- Stop
- AUG, also the usual start
The full table and the translator use a small script. With scripts off, use the examples above and a printed codon table from a textbook. The groupings are still as stated.
Letter codes
Each amino acid has a three-letter name and a one-letter name. The one-letter code is what alignments and the translator’s protein line use. Stop is written as an asterisk. Histidine is grouped here with the basic amino acids; near neutral pH its side chain is only partly charged, which is why biochemists sometimes discuss it on its own.
Limits
Mitochondria and some microbes use variant codes. A real messenger RNA also has untranslated regions, a start that must be recognized in context, and introns that have already been spliced out of the mature message. This bench translates whatever coding sequence you give it, in the frame you choose. It does not find genes, and it is not a clinical interpreter of variants.
The history of filling this table is on the discoveries page and in Khorana’s note. When you want to be tested on it, use the quiz.