Codons, standard

Codon Standard Code Nuclear-Encoded Proteins Mammals Drosophila Mitochondria Neurospora Yeasts Plants... 

Figure 1 shows the standard code in DNA language (i. e., as a sequence of triplets in the sense strand of DNA, read in the 5 3 direction see p. 84), represented as a circular diagram. The scheme is read from the inside to the outside. For example, the triplet CAT codes for the amino acid histidine. With the exception of the exchange of U for T, the DNA codons are identical to those of mRNA. 

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. 

A standard version of the genetic code for the triplet codons on a messenger RNA is given in Table 2.2. 

Examples of standard (a) and wobble (b and c) base pairs formed between the first base in the anticodon and the third base in the codon. 

The genetic code differs very little between species. By contrast, considerable differences occur between species in the anticodon translation system of tRNA, as evidenced by the mitochondrial tRNA system. In all systems the bases in the anticodon-codon complex run antiparallel, as in standard double-helix pairing, and in all cases only Watson-Cricklike base pairing occurs between the first two bases in the codon and the opposing bases in the anticodon segment of the tRNA. However, for the 3 base in the codon, the rules for pairing vary with the species and with the base in question. These rules, summarized in table 29.4, are as follows. 

Fig. 10.2. Screenshots of die GUI after obtaining results for die problem of equimolar mixtures of amino acids, i. e., 5% of each amino acid and 0% of stop codons, (a) Standard one-pot syndiesis (b) two-pot syndiesis (c) diree-pot syndiesis (d) one-pot syndiesis using E. coli codon usage. Input fields are white and inactive fields are light gray. Computed fields are light blue and stop codons are light green (in die copy of diis figure on die CD diat accompanies diis book).

Mitochondria of various organisms use different genetic code. Search the Internet site to obtain information for the mitochondrial codons from either vertebrates or invertebrates. Discuss usage differences between the standard codons and mitochondrial codons. 

Clone a DNA fragment encoding a foreign protein into appropriate sites of pFastBacl vector in correct orientation with respect to the polyhedrin promotor. The fragment must contain its own initiator codon followed by an open reading frame and terminator codon. Prepare recombinant donor plasmid DNA from E. coli using the standard procedure (e. g., alkaline lysis method). 

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