Codon-anticodon complex

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).

In order to allow for translocation of the tRNA-mRNA complex, the ribosome will have to undergo conformational changes as well. The contacts described above between the decoding center and the codon-anticodon helix as well as the base pairs between the SOS A and P loops and the tRNA acceptor stems will have... 

The wobble base pairs are displayed in Fig. 20.4. In comparison with Watson-Crick base pairs, the positions of the glycosyl links differ, but their directions are more or less retained so that the short codon-anticodon double helix is smooth. Pyrimidine-pyrimidine base pairs U - U and U - C, which could also form (Part II, Chap. 16) are considered to be unlikely since their C(l,) -C(r) distances are about 2 A shorter than the 10.5 A in a Watson-Crick base pair. The long A-1 base pair with C(l ) -C(r) distance of about 13.5 A, as actually observed in a comparable crystalline base-pairing complex [678], is too long to be accommodated in a smooth double helix. It has been suggested therefore that inosine in syn form could mimic the Watson-Crick geometry [679]. 

When codon-anticodon base pairing occurs the amino acid attached to the tRNA is correctly positioned within the ribosome for peptide bond formation. As each peptide bond is formed, the newly incorporated amino acid is released from its tRNA and the mRNA moves relative to the ribosome so that a new codon enters the catalytic site. The latter process is called translocation. Translation continues one codon at a time until a special base sequence, called a termination or stop codon, is reached. The polypeptide is then released from the ribosome, and folds into its biologically active conformation. Depending on the type of polypeptide, it may then bind to other folded polypeptides to form larger complexes. 

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. 

It has been accepted for some time that tetracycline interferes with proper tRNA binding to the A-site (57). A refinement of this model has the elongation factor Tu/tRNA complex docking correctly into the A-site, allowing the correct codon-anticodon interaction to take place, and the subsequent hydrolysis of GTP by EF-Tu (1 l)At this point a necessary rotation of the A-site tRNA is blocked by tetracycline, leading to the ejection of tRNA from the A-site without peptide bond formation. In this scenario, tetracycline extracts two payments from the cell, inhibition of protein synthesis and the unproductive hydrolysis of GTP. 

On the other hand, the inhibitory effect of erythromycin, a 14-membered-ring macrolide, on such a peptidyltransferase reaction is markedly diminished in terms of the character of a substrate. Erythromycin inhibits poly(A)-dependent polymerization of a transferred substrate such as lysine residue linked to tRNA but not other oligonucleotide-dependent polymerization of an amino acid linked either to tRNA or to oligonucleotides such as CACCA and UACCA. It has been shown that the transfer of A-acylaminoacyl residues to puromycin (puromycin reaction) is usually stimulated by erythromycin [88, 89, 95]. Igarashi et al. [96] have also confirmed these findings. That is to say, they found that erythromycin inhibits the release of a deacylated tRNA from the P site of ribosome. The release of such a deacylated tRNA from the P site and the translocation of peptidyl-tRNA from the A site to the P site of ribosome occurs concomitantly when EF-G catalyzes the GTP-dependent movement of the ribosome and the codon-anticodon-linked mRNA-peptidyl-tRNA complex. 

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