Codon redundancy

To make things a little more complicated (or interesting), it is worth remembering that some amino acids are specified by more than one codon (termed redundancy, there are 20 basic amino acids and 64 available codons). Quite often, where an amino acid has associated codon redundancy, an organism will more frequently use one or more codons over the others to specify that particular amino acid (codon bias). 

Many amino acids are specified by more than one codon (redundancy). Frequently, a tRNA can translate more than one of these codons, sparing the ceE from making multiple tRNAs to carry the same amino acid. For instance, in Figure 1-4-6 the arg-tRNA shown can translate both the CGA and the CGG codons that specify arginine. This phenomenon is known as Wobble" and can be summarized as follows ... 

The same argument applies for RNA as for DNA except that there are 303 bases in the sequence. Again, any one of four bases may occur in each position of the 303 base sequence. Thus we would write, (1/4) = 10" . Of course, this again is more improbable than the 100 residue protein into which the RNA sequence is translated, but this number is again not quite so small due to codon redundancy. 

Also very early it was appreciated that the way to limit deletions was to utilize codon redundancy. For example, four different triplet base sequences encode for the glycine (Gly, G)... 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

A base substitution can also result in the formation of a new inappropriate terminator (or non-sense) codon, and are thus known as non-sense mutations. The polypeptide formed from such mutated genes will be shorter than normal and is most likely to be inactive. Owing to the redundancy of the genetic code, about a quarter of all possible base substitutions will not result in an amino acid replacement and will be silent mutations. 

Genetic code Start AUG (also codes for Met) Stop UAG,UGA,UAA Unambiguous (1 codon = 1 amino acid) Redundant (1 amino acid >1 codon) often differ at base 3 ... 

The sequence of bases in the polynucleotide chain is also important because it determines the exact sequence of amino acids used in the synthesis of a protein. Twenty amino acids are commonly found in proteins, while only four bases are used in the DNA molecule. Thus, more than one base must specify each amino acid. The genetic code is in fact read as triplets and there are 64 possible triplet combinations using 4 nucleotides. Each triplet of nucleotides is termed a codon, and given the redundancy, some amino acids are specified by more than one codon. 

The existence of 64 - 20 = 44 excess codons allows a valuable redundancy in the genetic code. It also permits the signaling for the start and end of the protein chain. 

The most common changes in mitochondria (and the only code changes that have been observed in cellular genomes) involve termination codons. These changes affect termination in the products of only a subset of genes, and sometimes the effects are minor because the genes have multiple (redundant) termination codons. 

The 3 terminal redundancy of the genetic code and its mechanistic basis were first appreciated by Francis Crick in 1966. He proposed that codons and anticodons interact in an antiparallel manner on the ribosome in such a way as to require strict Watson-Crick pairing (that is, A-U and G-C) in the first two positions of the codon but to allow other pairings in its 3 terminal position. Nonstandard base pairing between the 3 terminal position of the codon and the 5 terminal position of the anticodon alters the geometry between the paired bases Crick s proposal, labeled the wobble hypothesis, is now viewed as correctly describing the codon-anticodon interactions that underlie the translation of the genetic code. 

The sequence of bases (A, G, T, and C) in a strand of DNA specifies the order in which amino acids are assembled to form proteins. The genetic code is the collection of base sequences that correspond to each amino acid, codon. Since there are only four bases in DNA and twenty amino acids in protein, each codon must contain at least three bases.5 Two bases cannot serve as codons because there are only 42 possible pairs of four bases, but three bases can serve because there are 43 = 64 possible triplets. Since the number of possible triplets are more than enough, several codons designate the same ammo acid. In other words, the genetic code is highly redundant as shown in Table 7.1. For example, UCU, UCC, UCA, UCG, AGU, and AGC are all codes for serine. 

Consult Table 18.2. The codon UUU translates to the amino acid phenylalanine. If a UUU sequence were to be mutated to UCU (the codon for serine), the protein produced would have a Ser residue in place of the Phe. Since UCU and UCC both code for Ser, a UCU UCC mutation would not lead to a change in the protein sequence. Thus, the advantage of a redundant code is that not all mutations cause disadvantageous changes in protein structure. 

There are 20 naturally occurring amino acids that are assembled into proteins. If codons consisted of only two base pairs, each of which could be one of four nitrogenous bases, directions could be given for only 4x4= 16 amino acids. Using three bases per codon gives a total of 4 x 4 x 4 = 64 possibilities, which is more than sufficient. This provides for some redundancies for example, six different codons specify arginine. Codons also signal initiation and termination of a protein chain. 

Codon positions Selective weighting of first, second, and third codon positions in translated genes, because of redundancy of genetic code. A general rule is that third-codon positions are under less selective constraint than first and second and, as such, are more... 

Organism-biased codon usage can be remedied by manipulating the interplay between a codon and its encoded amino acid. It is evident that several codons encode a particular amino acid, but only one amino acid is encoded by a particular codon. This redundancy is, thus, unidirectional in this context. Consequently, one could either increase the availability of the amino acid corresponding to the rare codon or change the transcript sequence to reflect the codon preferences of the host (analogous to market forces, one can either manipulate the supply or the demand sides). 

The redundancy in the genetic code is settled on the tRNA anticodon side. For each codon on the mRNA, the first two nucleotides (counting from the... 

The genetic code is degenerate (redundant). There is at least 1 codon for each of the 20 common amino adds many amino adds have numerous codons. 

The number of mammalian mitochondrial tRNA molecules is 22, which is less than the minimum number (32) needed to translate the universal code. This is possible because in each of the fourfold redundant sets—e.g., the four alanine codons GCU, GCC, GCA, and GCG—only one tRNA molecule (rather than two, as explained above) is used. In each set of four tRNA molecules, the base in the wobble position of the anticodon is U or a modified U (not I). It is not yet known whether this U is base-paired in the codon-anticodon interaction or manages to pair weakly with each of the four possible bases. For those codon sets that are doubly redundant—e.g., the two histidine codons CAU and CAC—the wobble base always forms, a G-U pair, as in the universal code. The structure of the human mitrochondrial tRNA molecule is also different from that of the standard tRNA molecule (except for mitochondrial tRNA UUX). (X = any nucleotide.) The most notable differences are the following ... 

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