Codon tables

There are 64 different three-letter codons, but we don t have to have 64 different tRNA molecules. Some of the anticodon loops of some of the tRNAs can recognize (bind to) more than one condon in the mRNA. The anticodon loops of the various tRNAs may also contain modified bases that can read (pair with) multiple normal bases in the RNA. This turns out to be the reason for the wobble hypothesis, in which the first two letters of a codon are more significant than the last letter. Look in a codon table and you ll see that changing the last base in a codon often doesn t change the identity of the amino acid. A tRNA that could recognize any base in codon position 3 would translate all four codons as the same amino acid. If you ve actually bothered to look over a codon table, you realize that it s not quite so simple. Some amino acids have single codons (such as AUG for Met), some amino acids have only two codons, and some have four. 

Some amino acids utilize only one codon of the 64 in the genetic code. Other amino acids use as many as six codons (Tables 5-5,5-6). What advantages to a cell is provided by utilization of several codons for a single amino acid ... 

As noted above, the genetic code used by cells is a triplet code, with every three-nucleotide sequence, or codon, being read from a specified starting point In the mRNA. Of the 64 possible codons in the genetic code, 61 specify individual amino acids and three are stop codons. Table 4-1 shows that most amino acids are encoded by more than one codon. Only two—methionine and tryptophan—have a single... 

Inspection of a codon table shows that in most instances of multiple codons for a single amino acid, the variation occurs in the third base of the codon (see Table 15.1). Crick noted that the pairing between the 3 -base of the codon and the 5 -base of the anticodon does not always follow the strict base-pairing rules that he and Watson had previously discovered (i.e., A pairs with U, and G with C). This observation resulted in the wobble hypothesis. 

Protein synthesis is initiated by START codons and terminated by STOP codons (Table 15.6). 

As described above, DNA determines the structure of mRNA. The mRNA has 64 possible triplet codons. However, there are only 20 amino acids. The code is actually highly degenerate most amino acid residues are designated by more than one triplet. Only Trp and Met are designated by single codons. Table 14.7 (95) provides the genetic code of protein biosynthesis. Note that three combinations indicate a termination of the translation and the carboxyl end of the protein chain. 

In addition to the frequencies that are determined by the choice of Codon Table, the user also has the opportunity to select a usage frequency Threshold. This is used as a cutoff, where any codon below the Threshold frequency is treated as if its frequency were zero, so it is never selected in backtranslation. This allows a user to exclude rare codons. 

During backtranslation, in some versions of the software, codons whose frequencies are above the Threshold will be chosen probabilistically at their relative frequencies in the Codon Table. Other versions of the software will iterate during backtranslation to approximate the frequencies defined in the Codon Table. 

Codons used for the initial gene population and for mutation at each generation of the genetic algorithm are chosen statistically according to the codon table settings. The degree to which the... 

To add organisms and codon tables, you can edit the gd organisms. txt file. Again, make sure that your additions follow the formatting rules. 

The simplest link between nucleic acid and protein components would have been a code with a one-to-one correspondence where each nucleotide dictated a particular amino acid. With only four nucleotides making up the information storage in cells, the resulting proteins synthesized in such a scenario would be limited to those having 4 different amino acids. Even a code of two nucleotides per amino acid would allow for only 16 amino acids. The standard genetic code instead makes use of trinucleotide sequences called codons these 64 codons are able to determine fully the 20 amino acids used in protein synthesis and also include start and stop codons (Table I). 

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