Codon pairing with anticodon

Table 6.1 shows the relationship between the codon sequence in mRNA and its corresponding amino acid in the new protein. Because there are 64 (43) different anticodon combinations and only 20 encoded amino acids, some different anticodon sequences encode for the same amino acid. Generally, all the anticodons matching a given amino acid will have the same first two nucleotides. Exceptions are arginine, serine, and isoleucine. For example, the codon for proline will always start with CC, but the arginine codon may start with either AG or CG. The 3 end of the tRNA anticodon pairs with the 5 end of the mRNA codon. In other words, the codon and anticodon align and bind in an antiparallel fashion. 

When the 70S initiation complex has been formed, the ribosome is ready for the elongation phase of protein synthesis. The fMet-tRNAf molecule occupies the P site on the ribosome. The other two sites for tRNA molecules, the A site and the E site, are empty. Formylmethionyl-tRNAf is positioned so that its anticodon pairs with the initiating AUG (or GUG) codon on mRNA. This interaction sets the reading frame for the translation of the entire mRNA. 

There are 64 different three-letter codons, but we don t have to have 64 different tRNA molecules. Some of the anticodon loops of some of the tRNAs can recognize (bind to) more than one condon in the mRNA. The anticodon loops of the various tRNAs may also contain modified bases that can read (pair with) multiple normal bases in the RNA. This turns out to be the reason for the wobble hypothesis, in which the first two letters of a codon are more significant than the last letter. Look in a codon table and you ll see that changing the last base in a codon often doesn t change the identity of the amino acid. A tRNA that could recognize any base in codon position 3 would translate all four codons as the same amino acid. If you ve actually bothered to look over a codon table, you realize that it s not quite so simple. Some amino acids have single codons (such as AUG for Met), some amino acids have only two codons, and some have four. 

Figure 3 Cognate and near-cognate codon-anticodon interactions. The anticodon ioop of tRNA is shown as an example interacting with various codons on the mRNA. In correct, cognate codon-anticodon pairings, two Watson-Crick base pairs can be formed in the first two positions while the third position contains either a Watson-Crick or a wobble base pair.

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).

Each tRNA has an anticodon sequence that allows it to pair with the codon for its cognate amino acid in the mRNA. Because base pairing is involved, the orientation of this interaction wEl be complementary and antiparallel as shown in Figure T4-6. The arg-tRNA 8 has an anticodon sequence, UCG, allowing it to pair with the arginine codon CGA. 

The third position of the codon does not always need to be paired with the anticodon (e.g., it is allowed to wobble in some cases). 

The charged initiator tRNA becomes bound to the AUG start codon on the messt e through base pairing with its anticodon. The initiator tRNA in prokaryotes carries fmet, whereas the initiator tRNA in eukaryotes carries Met. 

These experiments make it clear that removing competition with release factors leads to more efficient incorporation of the desired amino acid. Unfortunately, the technology to incorporate nonstandard nucleotides into mRNAs coding for full-length proteins is not yet available. Alternatives that have been tested include using (i) a 4-nucleotide codon-anticodon pair, dubbed frame-shift suppression (Sect. 6.1), (ii) a rare codon, and (iii) cell-free extracts from organisms that are either deficient in a release factor (Sect. 5.1) or unable to translate one or more codons (Sect. 6.2). 

In an effort to reduce the competition encountered with naturally occurring tRNAs, even when rare codons are used, Hardesty and co-workers have devised a strategy based on 4-nucleotide codon-anticodon pairs [48]. An extra thymidine was inserted either 5 or 3 to the rare arginine codon AGG to yield TAGG... 

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