Re: questions regarding mRNA codons

Most of the answers to your questions were answered in my previous post, " Re: Some questions about protein synthesis..." Before going into the history of the discovery of the Genetic Code, I will address your questions regarding the amino acids. Firstly, the term "amino acid" applies to any chemical with both an amino group and an acidic group. Thus many biochemicals, like g-amino-butyric acid (GABA: a neurotransmitter) and creatine (a phosphate transporter in muscle metabolism), are classified as "amino acids", even though they cannot be used as protein building blocks. In terms of amino acids used in proteins, there are certainly more than the 20 essential amino acids, though not that many more. There are two mechanisms for organisms to use these other amino acids: they can be coded for in place of one of the stop codons; or they can be added after the protein is translated. This latter mechanism is probably the most prevalent, since post-translational modifications of amino acids, including hydroxylation, phosphorylation, and dimerization, are essential to almost all cellular activities. Again, refer to the above link for more on how amino acids are used.

Now, on to the history of the Genetic Code. With the discoveries of Griffith, Avery, Watson and Crick, and Beadle and Tatum, it was known that genes were made of double-stranded DNA, and that the sequence of each gene determined the sequence of its corresponding protein. By the end of the 1950's, the search for the actual mechanism of this "translation" was underway, as was the code used to convert the genetic information into functional enzymes. In 1961, Marshall Nirenberg and Johann Matthaei took the first steps in cracking the code. They had developed a cell-free extract which would convert the code from any RNA added to it into its corresponding protein (this in vitro translation is now a common experimental procedure), and then synthesized polyuridylic acid (poly-U RNA) to use as an input. When this was added, their extract produced a protein composed entirely of the amino acid, phenylalanine (Phe). Similarly, polyguanidylic acid (poly-G RNA), polyadenylic acid (poly-A RNA), and polycytidylic acid (poly-C RNA) gave proteins composed solely of glycine, lysine, and proline, respectively. Thus, the sequence of bases was being directly cconverted into the sequence of amino acids. They then tested RNA's composed of two bases randomly mixed. When added to their extracts, these random RNA's produced proteins composed of random sequences of between 4 and 8 different amino acids, demonstrating that each codon had to be a triplet.

The greatest leap was made in 1967, when Nirenberg began collaborating with Har Gobind Khorana, who had developed a system for synthesizing nucleotide strands with exact, known sequences (still in wide use today). Using Khorana's RNA's in Nirenberg's extracts, they were able to test every polymer of triplet subunits conceivable, and by 1970, their compiled data encompassed the entire genetic code. In 1968, Nirenberg and Khorana shared the Nobel Prize in Physiology or Medicine with Robert W. Holley (who worked on tRNA) "for their interpretation of the genetic code and its function in protein synthesis."