I am working on a project in computer science related to proteins.
The materials I have consulted always present the coding table of amino acids without explaining how several different codons can represent the same amino acid. For instance, arginine is encoded by 6 different codons. But surely two different sequences of 3 nucleotides do not constitute the same chemical substance. Are there any chemical processes taking place that make the different codons equivalent?
Different codons can produce the same amino acid due to the way they bind to transfer RNA (tRNA). Different organisms use different codons. So in theory, as you say, arginine can be coded for by 6 different codons. However, in practice, not all of those are used in a single organism - it depends on the tRNA they express. Codon usage databases exist online which will allow you to find the known codon usage from any given organism.
Codon usage has important implications for molecular biology studies. For example, many gene function studies use a luciferase reporter gene to make it easy to visualise where a protein resides in a cell, or whether you can switch a gene on or off using different treatments or environmental conditions. However, that luciferase gene most likely originates from an organism with a different codon usage (G. princeps for example). We would, therefore, "humanise" the gene sequence to allow for optimal codon usage in a human cell line. Failure to do so would lead to poor protein production as our human cell line wouldn't have the correct tRNA to bind to each codon.
we have more than 64 than amino acids which are 20. Including a terminator codon, as you know we only need only 21 that including terminator codon, but there are 4^3 = 64 possibilities .wobble hypothesis by Crick, explains that the 3rd codon position is relatively less crucial as the 1st and 3nd are more involved in specificity so for example experiments show that the third base for amino acid valine does not have any distinctive function so we can cal it a 2 of 3 reading way.
Thank you all for your help.
As Crick's Wobble Hypothesis pertains only to the 3rd nucleobase in mRNA, I was initially confused as to the degeneracy in the 1st and 2nd bases of some amino acids. However I do understand now that different codons can be associated with one and the same anticodon of tRNA. So, in effect, indeed only the 3rd base undergoes wobble pairing. And so there have to be at least 3 different anticodons to take care of all 6 codons of arginine.
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