Week+of+5-2-10

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While I do not know the exact codon that I am replacing, I can still make progress towards choosing the replacement amino acid. The codon for this amino acid must be of similar frequency to the lysine codon being replaced, but the exact codon can be established later. As stated in my previous posts, lysine has a positively charged side chain. We will replace it, then, with three other amino acids. One will be a non-polar amino acid to determine whether the region is involved in membrane adhesion. We must also test an amino acid with a negative side chain and one with another positively charged side chain. This will help determine if the region is directly involved in mediating reactions, which are more often specific to the amino acid in question. If both the negatively and positively charged amino acid replacements result in a functional protein, while the non-polar (hydrophobic) amino acid fails, then we will know almost certainly that the area is involved in a non-specific membrane reaction. In this way, we can look at not only which reaction works, but we can draw inferences by cross-referencing the results of multiple tests.


 * Alanine is the standard non-polar amino acid for this type of task, as it is relatively small and less likely to cause problems with the folding of the tertiary structure.
 * Arginine, is a very similar amino acid in structure and charge
 * Aspartic acid would likely be the best choice for a negative replacement

 I have had difficulty with finding the specific ratios at which the codons are used, but I am still making progress
 * Lysine has two codon variations, AAA and AAG
 * Alanine comes in four varieties: GCU, GCC, GCA, GCG
 * GCC is used about four times as often as GCG
 * Arginine has several codons: CGU, CGC, CGA, CGG, AGA, AGG
 * Aspartic acid's codons are GAU and GAC