Punctuated genetic code

THE GENETIC CODE IS DEGENERATE, UNAMBIGUOUS, NONOVERLAPPING, WITHOUT PUNCTUATION, UNIVERSAL... 

There are 64 ways to order four things three at a time when the order in which they are taken (permutations) matters n = 4 = 64. So there are 64 words in the language of DNA. This is more words than we need to specify the 20 amino acids of proteins. A few of these words are used as punctuation marks—start and stop signals. Beyond that, most of the amino acids are specified by more than one word. The genetic code is provided in table 12.1. Note that the code words in table 12.1 refer to those in messenger RNA, mRNA, the complement to the code words in DNA. 

Nonoverlapping and commaless The genetic code is nonoverlapping and commaless, that is, the code is read from a fixed starting point as a continuous sequence of bases, taken three at a time. For example, ABCDEFGHIJKL is read as ABC/DEF/GHI/JKL without any "punctuation" between the codons. 

The genetic code is degenerate (several codons have the same meaning), specific (each codon specifies only one amino acid), and universal (with a few exceptions each codon always specifies the same amino acid). In addition, the genetic code is nonoverlapping and without punctuation (i.e., mRNA is read as a continuous coding sequence). 

Stop codons are the "punctuation marks" of the genetic code that cause a ribosome to stop making protein when they are encountered in the process of translation. Though there are rare variations in the sequence of nucleotides making up stop codons, the stop codons for almost all organisms are UAA, UAG, and UGA. 

FIGURE 12.2 Theoretically possible genetic codes, (a) An overlapping versus a nonoverlapping code, (b) A continuous versus a punctuated code. 

Proteins are linear polymers of amino acids. The sequence of a protein s constituent amino acids determines its biochemical function. The mRNA sequence is read in groups of three, called codons. Because there are four bases in DNA or RNA, there are 64 (4 ) codons. Only 20 amino acids are specified by translation, so there is more than one codon per amino acid. In other words, the genetic code is redundant. The code also contains punctuation marks. Three codons, UAG, UAA, and UGA, specify stop signals (like the periods in a sentence). One amino acid, methionine, coded by AUG, is used to initiate each protein (like a capital letter at the beginning of a sentence). Just as a letter that starts a sentence can also appear in an uncapitalized form inside the sentence, so methionine also appears internally in proteins. See Table 4-1. 

Note that the gaps in the alignment are not actually represented in the Bioseqs as dashes. A fundamental property of the genetic code is that it is commaless (Crick et al., 1961). That is, there is no punctuation to distinguish one codon from the... 

The triplets of nucleotides (the codons) on mRNA are the genetic code (see Table 25.2). The code must be in the form of three bases, not one or two, because there are 20 different amino acids used in protein synthesis but there are only four different bases in mRNA. If only two bases were used, there would be only 4, or 16, possible combinations, a number too small to accommodate all of the possible amino acids. However, with a three-base code, 4, or 64, different sequences are possible. This is far more than are needed, and it allows for multiple ways of specifying an amino acid. It also allows for sequences that punctuate protein synthesis, sequences that say, in effect, start here and end here. ... 

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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