Degenerate Code
More than one sequence of DNA nitrogenous bases can ultimately code for the insertion of the same type of amino acid into a protein's polypeptide chain during translation. For this reason, the genetic code is a degenerate code. In science, the term "degenerate" does not imply that something is abnormal or not fully functional. With specific regard to the genetic code, the code presents a tremendous stability and regularity to genetic processes. Moreover, there are important biological advantages to systems having a certain amount of flexibility and redundancy. In the case of the genetic code, this redundancy is reflected in the fact that at the DNA level, more than one triplet code (a sequence of three base pairs) is able to instruct the insertion of the same type of amino acid into the protein's polypeptide chain during translation at the ribosome. There are also redundant codes for certain instructions related to other genetic processes including the initiation and termination of protein synthesis.
The combination of four different nucleotide bases: adenine (A), thymine (T), cytosine (C), and guanine (G) into triplet (three base) sequences ultimately directs the insertion and sequence of twenty amino acids during protein synthesis. The degeneracy is not, however, the same for all amino acids. There are, for example, six different codes that direct the insertion of the amino acid leucine (leu), yet there are only two sequences or codes that direct the insertion of tyrosine (tyr). Only the amino acids trytophan (trp) and methionine (met) have unique codes.
The DNA sequence does not directly instruct the insertion of amino acids during protein synthesis. There are a number of intermediate molecules that convey the instructions contained in the genetic code from the nucleus to the appropriate protein synthesis complex associated with ribosomes that are located outside the nucleus in the cytoplasm. The genetic code is first carried by codons. A codon is a three base nucleotide sequence, constructed upon the DNA template, along a strand of messenger RNA (mRNA). Accordingly, codons are complimentary to base triplets in the DNA. The construction of codons is in strict accord with specific base pairing rules (A only with T, and C only with G), except for the fact that in RNA, the base uracil (U) substitutes for thymine (T). Accordingly, if the DNA code is GCA the corresponding codon on the mRNA strand will read CGU (a code for the amino acid arginine). Codons may also direct the termination of protein synthesis.
The codon library (the assignment of specific codon sequences to the insertion of specific amino acids) is also influenced by the fact that the third base in the sequence is less specific that the first two with regard to the insertion of a particular amino acid. For example, the a codon sequence starting with CU (cytosine-uracil) can be combined with any of the four base codes to produce CUA, CUG, CUU, or CUC--four of the six codes for the amino acid leucine.
The last code in a sequence (e.g., C in a ATC sequence) codes for the nucleotide (a base, phosphate and sugar) at the 3' hydroxyl end of the codon. According to wobble theory, a wobble or "looseness" of fit (in terms of the kinetics of molecular bonding) in the third nucleotide accounts for the diminished role of the third codon in code specificity.
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