Genetic code codon assignments

Table 38-1. The genetic code (codon assignments in mammalian messenger RNA)J...

The genetic code (codon assignments in messenger RNA. (Reproduced, with permission, from Murray RK, Granner DK, Mayes PA, Rodwell VW Harper s Biochemistry, 25/e. New York, McGraw-Hill, 2000 453.)... 

An important factor in the evolution of the genetic code is certainly provided by the aminoacyl-tRNA synthetases (see Sect. 5.3.2). It is clear that the two synthetase classes are not randomly distributed across the matrix of the amino acid assignment of the genetic code. For example, with one exception, all XUX codons code for class 1 synthetases, while all XCX codons code for class 2 aminoacyl-tRNA synthetases. A possible explanation could be that the synthetases and the genetic code evolved simultaneously. However, it is more likely that these enzymes evolved when the genetic code had already been established (Wetzel, 1995). 

The following table indicates the standard codons that serve as the basis of the genetic code. Note (a) Stop codons have no amino acids assigned to them (b) Met indicates the AUG start codon. 

Note Presented here is a summary of data from one of the early experiments designed to elucidate the genetic code. A synthetic RNA containing only A and C residues in a 5 1 ratio directed polypeptide synthesis, and both the identity and the quantity of incorporated amino acids were determined, Based on the relative abundance of A and C residues in the synthetic RNA, and assigning the codon AAA (the most likely codon) a frequency of 100, there should be three different codons of composition A2C, each at a relative frequency of 20 three of composition AC2, each at a relative frequency of 4,0 and CCC at a relative frequency of 0.8. The CCC assignment was based on information derived from prior studies with poly(C), Where two tentative codon assignments are made, both are proposed to code for the same amino acid. 

Consolidation of the results from many experiments permitted the assignment of 61 of the 64 possible codons. The other three were identified as termination codons, in part because they disrupted amino acid coding patterns when they occurred in a synthetic RNA polymer (Fig. 27-6). Meanings for all the triplet codons (tabulated in Fig. 27-7) were established by 1966 and have been verified in many different ways. The cracking of the genetic code is regarded as one of the most important scientific discoveries of the twentieth century. 

Table 17.1. Codon-Amino Acid Assignments of the Genetic Code...

Figure 14.5. The standard genetic code minimizes the effects of point mutation better than the vast majority of alternative plausible genetic codes that could assign 20 amino acids to 64 codons in synonymous codon blocks (adapted from Freeland and Hurst 1998 [94]).

Recently, an asymmetric codon assignment rule was proposed. Evidence was found for a rapid early evolution of the Code via successive binary choices of 16 X X2N codons. It was claimed that the other scenarios (listed above in points 1-5) could have played a role in different periods of the evolving Genetic Code. 

The second key step for the expansion of the biosynthesizing system to introduce nonnatural amino acids is the expansion of the genetic codes. Schultz [38] and Chamberlin [39] first assigned an amber (UAG) stop codon to a nonnatural amino acid (aa ). By adding an aa -tRNA with a CUA anticodon as a suppressor of the amber codon, they successfully introduced the nonnatural amino acid at that position. Since then, the amber suppression method has been employed by a number of researchers. This method is advantageous in that an unsuccessful decoding of the UAG codon automatically leads to... 

C-labeled histidine-tRNA. Only the aminoacyl-tRNA whose binding is directed by the trinucleotide codon will become bound to the ribosomes and retained on the nitrocellulose filter. The amount of radioactivity retained by the filter is a measure of trinucleotide-directed binding of a particular labeled aminoacyl-tRNA by ribosomes. Use of this binding assay to test the 64 possible codon trinucleotides against the 20 different amino acids quickly enabled researchers to assign triplet code words to the individual amino acids. The genetic code was broken. 

This version of GeneDesign uses the standard genetic code future versions will be more flexible about codon to residue assignment. 

The information contained in the base sequence of the mRNA template is interpreted in sequences of three bases called codons each codon represents one amino acid. Therefore, the unit of information is the codon. Since there are four major bases in mRNA, 4 (i.e. 64) different codons are possible. The 64 triplets constitute the genetic code (Table 17.1). All codons have been assigned to amino acids or punctuation signals. Three triplets (UAA, UAG and UGA) are not complemented by anticodons on tRNAs and serve to signal that the polypeptide chain has been completed. Of the other 61 triplets which have complementary tRNAs, two (AUG and GUG) have additional roles in the initiation of protein synthesis. Since there are only 20 amino acids, most amino acids are specified by more than one codon, i.e. the code is degenerate. The genetic code applies to prokaryotes and eukaryotic nuclear and chloroplast mRNAs but not to... 

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