Figure 1
The genetic code (adopted from [19, 24, 36, 40]). A. The code table. Yellow and blue colors indicate the two modes of tRNA recognition by aaRSs - from the minor and major groove sides of the acceptor stem, respectively [21, 22]. The minor groove side of recognition represents mostly the class I aaRSs, the major groove side, class II aaRSs. Stop codons are shown in yellow because the known cases of their "capture" by amino acids are mostly from class I; AGG and AGA are assigned not to yellow Arg's codons (as they usually are) but to blue Ser's or Gly's codons (as they are in mitochondria) [68]. Lysine is colored in lighter shade of blue because some archaebacteria use class I synthetases for this amino acid [92]. B. The condensed version of the code representation when complementary codons are put vis-á-vis each other. This particular "yin-yang" version reveals otherwise invisible rules of the sub-code for two modes of tRNA aminoacylation described in [19, 36]. These rules when applied to the pairs of tRNAs with complementary anticodons flanked by 5'U and R3' minimize a risk of their confusion by aaRSs. Symbols: N and complementary И denote all four nucleotides, R purine (G or A), Y pyrimidine (C or U). For details see [19, 36]. C. The two-dimensional cloverleaf representation of a tRNA molecule (the E. coli tRNAAla with GGC anticodon is shown) [24]. The complementary halves are colored yellow (5' half) and blue (3' half), in accordance with the sub-code for two modes of tRNA aminoacylation (B). Arrows show the two sides from which the putative ribozymic precursors of class I and class II p-aaRSs recognized the proto-tRNAs.