Standard genetic code

The standard genetic code words are universal in all species, with some minor deviations in mitochondria and a few single-celled organisms. 

The EDITSEQ application allows you to manually enter DNA or protein sequence information into your computer. This application has several features that make it useful to the research scientist. First, it can identify open reading frames (possible gene sequences) within a DNA sequence. Second, it can provide the percent base composition (A,G,C,T), the percent GC, the percent AT, and the melting temperature of the entire sequence or a small subset of that sequence. Third, EDITSEQ can translate a nucleotide sequence into a protein sequence. Finally, the application is capable of translating or reverse translating a nucleotide sequence of interest using codes other than the standard genetic code. 

Figure 14.2. The biochemistry of protein. Protein is another linear polymer in which each building block is an amino acid. Amino acids have a central ( alpha ) carbon to which an amino group, a carboxyl group, and a variable side chain are joined. Twenty amino acids are encoded within the standard 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]).

Perhaps, in the not-too-distant future, meaningful optimality studies will explore realistically the link between protein structure and the amino acid alphabet. Meanwhile, it would seem pertinent to extend optimality studies of the standard genetic code to explore the properties of codes with fewer, more, or different amino acids with respect to the canonical 20. 

A comprehensive review is given in S. J. Freeland, T. Wu and N. Keulmann. The case for an error minimizing standard genetic code. Origins of Life, and Evolution of Biospheres, 33 (2003), 457-77. 

W. Zhu and S. J. Freeland. The standard genetic code enhances adaptive evolution of proteins. Journal of Theoretical Biology, 239 (2006), 63-70. 

Since nucleic acids generally cannot go in and out of mitochondria, all mitochondria appear to code for their own rRNAs and tRNAs. For the same reason, only the mRNAs that have been transcribed from the mitochondrial genome are translated in the mitochondria. A unique feature of mitochondrial mRNAs is the lack of a m G cap at the 5 end (reviewed by Bag, 1991). There are only 22-25 tRNA species in the mitochondria, indicating that a single tRNA can recognize more than one codon. There are some structural and sequence differences in the mitochondrial tRNAs. Furthermore, deviations from the standard genetic code, for example, utilization of AUA as the initiation codon instead of AUG, and reading UGA as a tryptophan instead of a stop codon, are a unique feature of mitochondria (Lapointe... 

More than one codon or triplet signifying genetic instructions may exist for synthesizing each amino acid. This information is provided in terms of a tabulation of the standard genetic code, which is given in most biochemical textbooks. That is, it turns out that the number of codons may be one, four, or six, any one of which may serve to encode the instructions for producing a particular amino acid. 

As we discuss In Chapter 8, the structure of chloroplasts is similar In many respects to that of mitochondria. Like mitochondria, chloroplasts contain multiple copies of the organellar DNA and ribosomes, which synthesize some chloroplast-encoded proteins using the standard genetic code. Other chloroplast proteins are fabricated on c3rt osolIc ribosomes and are incorporated into the organelle after translation (Chapter 16). 

The genetic code of animal and fungal mtDNAs differs slightly from that of bacteria and the nuclear genome and varies between different animals and plants (see Table 10-3). In contrast, plant mtDNAs and chloroplast DNAs appear to conform to the standard genetic code. 

Translation of the consensus cDNA sequence using the standard genetic code results in a single open reading frame coding for human factor XII. The derived amino acid sequence agreed well... 

Transformation In genetic engineering, the genetic alteration of a cell as a result of inserting new genetic material into an organism s standard genetic code. 

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