Protein anticodon bases

Figure 28.7 A representation of protein biosynthesis. The codon base sequences on mRNA are read by tRNAs containing complementary anticodon base sequences. Transfer RNAs assemble the proper amino acids into position for incorporation into the growing peptide.

Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain.

Although the accuracy of translation (approximately one error per 104 amino acids incorporated) is lower than those of DNA replication and transcription, it is remarkably higher than one would expect of such a complex process. The principal reasons for the accuracy with which amino acids are incorporated into polypeptides include codon-anticodon base pairing and the mechanism by which amino acids are attached to their cognate tRNAs. The attachment of amino acids to tRNAs, considered the first step in protein synthesis, is catalyzed by a group of enzymes called the aminoacyl-tRNA synthetases. The precision with which these enzymes esterify each specific amino acid to the correct tRNA is now believed to be so important for accurate translation that their functioning has been referred to collectively as the second genetic code. 

Several fluorescence and biochemical experiments reveal the detailed mechanism of translation and the contribution of KPR towards the fidelity of protein synthesis. The incorporation of an amino acid into the peptide is composed of two consecutive processes initial selection of tRNA at the A site of the ribosome followed by KPR [23]. Various factors affect the initial selection of tRNA such as the HB energy between the codon-anticodon base pairs, the specific interactions between the large subunit of the ribosome and aa-tRNA, etc. The contribution of the initial selection step to the overall error fraction for Escherichia coli is observed to be -1/6, compared to the overall error fraction -7 x 10 for cognate and near-cognate anticodons. As a consequence the contribution of KPR is expected to be 1/24 i.e. -80% of the observed fidelity comes from the KPR. The translation process occurs through the following mechanism (see Figure 13.2). 

Anticodon (Section 28.5) A sequence of three bases on tRNA that reads the codons on mRNA and brings the correct amino acids into position for protein synthesis. 

Codon (Section 28.5) A three-base sequence on a messenger RNA chain that encodes the genetic information necessary to cause a specific amino acid to be incorporated into a protein. Codons on mRNA are read by complementary anticodons on tRNA. 

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).

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

Figure 12-2. Formation of the initiation complex for protein synthesis. Several eukaryotic initiation factors (elFs) ensure proper assembly at each step. The initiator Met-tRNA is bound in the peptidyl site of the SOS complex with its anticodon (black stripes) base paired to the AUG start codon (gray box) of the mRNA.

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