2.2.2: Genetic Code

Another example of mapping unused patterns into legal values is provided by the Genetic Code, described in Section 2.7. A protein consists of a long sequence of amino acids, of 20 different types, each with between 10 and 27 atoms. Living organisms have millions of different proteins, and it is believed that all cell activity involves proteins. Proteins have to be made as part of the life process, yet it would be difficult to imagine millions of special-purpose chemical manufacturing units, one for each type of protein. Instead, a generalpurpose mechanism assembles the proteins, guided by a description (think of it as a blueprint) that is contained in DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) molecules. Both DNA and RNA are linear chains of small “nucleotides;” a DNA molecule might consist of more than a hundred million such nucleotides. In DNA there are four types of nucleotides, each consisting of some common structure and one of four different bases, named Adenine, Cytosine, Guanine, and Thymine. In RNA the structure is similar except that Thymine is replaced by Uracil.

The Genetic Code is a description of how a sequence of nucleotides specifies an amino acid. Given that relationship, an entire protein can be specified by a linear sequence of nucleotides. Note that the coded description of a protein is not by itself any smaller or simpler than the protein itself; in fact, the number of atoms needed to specify a protein is larger than the number of atoms in the protein itself. The value of the standardized representation is that it allows the same assembly apparatus to fabricate different proteins at different times.

Since there are four different nucleotides, one of them can specify at most four different amino acids. A sequence of two can specify 16 different amino acids. But this is not enough – there are 20 different amino acids used in proteins – so a sequence of three is needed. Such a sequence is called a codon. There are 64 different codons, more than enough to specify 20 amino acids. The spare capacity is used to provide more than one combination for most amino acids, thereby providing a degree of robustness. For example, the amino acid Alanine has 4 codes including all that start with GC; thus the third nucleotide can be ignored, so a mutation which changed it would not impair any biological functions. In fact, eight of the 20 amino acids have this same property that the third nucleotide is a “don’t care.” (It happens that the third nucleotide is more likely to be corrupted during transcription than the other two, due to an effect that has been called “wobble.”)

An examination of the Genetic Code reveals that three codons (UAA, UAG, and UGA) do not specify any amino acid. These three signify the end of the protein. Such a “stop code” is necessary because different proteins are of different length. The codon AUG specifies the amino acid Methionine and also signifies the beginning of a protein; all protein chains begin with Methionine (although may be cleaved after expression). Many man-made codes have this property, that some bit sequences designate data but a few are reserved for control information.