How cell controls the rate of protein synthesis

Olivia Judson is back in action on her blog, with a very interesting new post: Braking the Virus:

However -- and this is where the opportunity to rewrite genes comes in -- there is more than one way to specify most of the amino acids. Glutamine, for example, can also be written as CAA. Arginine can be written in six different ways; proline, in four. The reason for this is that the genetic code has a great deal of redundancy. Although there are 64 possible codons (4 different nucleotides for each of three positions), there are only 20 amino acids to be assigned to them. This means that the particular string of the three amino acids given above could be specified in 48 different ways.

Cells have evolved to take advantage of this by using different codons for different purposes. Genes for proteins that need to be made quickly tend to be composed of "favorite" codons -- the ones that the cell has evolved to use frequently. Genes for "slow" proteins tend to be made of disfavored codons -- the ones the cell uses rarely. The reason is that if a codon is rare, the cell takes longer to recognize it, so it gets translated more slowly. A protein from a gene made entirely of rare codons, or rare combinations of codons -- for the combinations can matter, too -- will thus be made with a fraction of the efficiency of the same protein made from favorite codons or codon combinations. (Certain codon combinations can slow down the cell's reading machinery.)

Of course, as I am interested in biological timing, this got my attention. But, the differences in rates of translation between 'slow' and 'fast' combinations of codons is so small it is not sufficient to slow down processes all the way to 24 hours. Thus, in circadian clocks, most of the slowing down appears to happen after the protein has been synthetized, using various methods of post-translational modifications. I need to catch up on reading on this - there has been a lot published lately - and perhaps write a post that summarizes it.

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