Bases codon

Three-base codons on die mRNA corresponding to specific amino acids direct the sequence of building a protein. These codons are recognized by tRNAs (transfer RNAs) carrying die appropriate amino acids. Ribosomes are the machinery for protein syn diesis. 

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

The mRNA is bound to the smaller 30S subunit of the bacterial ribosome. The mRNA is a transcription of one of the genes of DNA, and carries the information as a series of three-base codons. The message is read (translated) in the 5 to 3 direction along the mRNA molecule. The aminoacyl-tRNA anticodon (UAC) allows binding via hydrogen bonding to the appropriate codon (AUG) on mRNA. In prokaryotes, the first amino acid encoded in the sequence is A-formylmethionine (fMet). Although the codon for initiation (A-formylmethionine) is the same as... 

Codons are usually presented in the messenger RNA language of adenine (A), guanine (G), cytosine (C), and uracil (U). Their nudeotide sequences are always written from the 5 -end to the 3 -end. The four nucleotide bases are used to produce the three-base codons. There are, therefore, 64 different combinations of bases, taken three at a time as shown in Figure 31.2. 

Anticodon (first base) Codon (third base)... 

Anticodon First Base Codon Third Base ... 

Hohsaka T, Ashizuka Y, Taira H, Murakami H, Sisido M. Incorporation of normatural amino acids into proteins by using various four-base codons in an escherichia coU in vitro translation system. Biochemistry 2001 40 11060-11064. 

The fidelity of protein synthesis requires the accurate recognition of three-base codons on messenger RNA. Recall that the genetic code relates each amino acid to a three-letter codon (Section 5.5.1). An amino acid cannot itself recognize a codon. Consequently, an amino acid is attached to a specific tRNA molecule that can recognize the codon by Watson-Crick base pairing. Transfer RNA serves as the adapter molecule that binds to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain. 

Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since three bases code for one... 

In case when CGGG was decoded as the tour-base codon... 

It is argued that the extension of the lengths of codons and anticodons might cause steric overcrowding between the tRNAs in the ribosomal A site and P site. The overcrowding in ribosome, however, has been avoided by a bend of mRNA chain at the junction between the A and P sites [52]. Because of this bend, the main bodies of the two tRNAs are well separated, while the two anticodons as well as the amino acid and the peptide C-terminal are close to each other. Indeed, even five-base codons [53] and a tandem four-base codon [54] have been reported to be successful. 

Similar to the amber codon method, four-base codon method has been shown to work in living cells [55]. 

K. Taira, M. Sisido, Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/anticodon pairs, J. Am. Chem. Soc. 2002, 124, 14586-14589. 

M. Sisido, Four-base codon-mediated incorporation of nonnatural amino acids into proteins in a eukaryotic cell-free translation system, J. Biosci. Bioeng. 2005, 99, 473-476. 

H. Murakami, M. Sisido, Five-base codons for incorporation of nonnatural amino acids into proteins, Nucleic Acids Res. 2001, 29, 3646-3651. 

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