9.1Aminoacyl-tRNA Synthesis

Amino acids are the substrate for protein synthesis, but they cannot be used directly. They must first bind tRNA in order to be used in protein synthesis.

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tRNA Structure

All tRNA share a common shape, and the majority of tRNA molecules have intramolecular double strands. This common shape is represented schematically by three loops and one stem (Fig. 9-1A). This figure shows a tRNA that binds phenylalanine. The anticodon loop contains an anticodon sequence that pairs with a codon on mRNA (code). Another characteristic of tRNA is that it contains rare bases (minor bases), such as D, T, Y, and ψ, in addition to the common bases A, C, G, and U (Fig. 9-1A). The 3′ terminus of all tRNA has a conserved CCA-3′ sequence to which amino acids bind. The actual three-dimensional structure of tRNA is compact, as shown in Fig. 9-1B.

Fig. 9-1 tRNA structure

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Aminoacyl-tRNA Synthetase

The correct binding of each amino acid to tRNA that has a corresponding anticodon is critically important in accurately translating the mRNA sequence information into amino acid sequence information; this is similar to dictionaries that are important in translation. Aminoacyl-tRNA synthetase catalyzes the correct binding of a specific amino acid to tRNA to form aminoacyl-tRNA. This enzyme recognizes the amino acid and tRNA structure and performes this reaction. Minor bases play a role in the recognition of tRNA structure.

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When a protein is synthesized, the first amino acid codon is for methionine. However, the first amino acid in eubacteria is formylmethionine (fMet), which is formylated methionine.*1 Two types of tRNA bind to methionine, tRNAMet and tRNAfMet. Methionine binds with tRNAfMet to form Met-tRNAfMet, which is formylated to form fMet-tRNAfMet. Met-tRNAMet is not formylated but is used for methionine located inside the protein. In archaea and eukaryotes, formylation does not occur, and different Met-tRNAMet molecules are used to add the first and subsequent methionines, respectively.

*1 formyl group (–CHO) binds to the molecule. During methionine formylation, one of the hydrogen (–H) atoms of the amino group of methionine is replaced by a formyl group. This region in the formylated methionine acquires a structure resembling a –CO-NH- peptide bond.


The 21st Amino Acid

The amino acid cysteine contains a sulfur atom. Another amino acid called selenocysteine is a minor element that contains selenium instead of sulfur, and it plays an important role as a component of a range of enzymes and proteins. This does not mean that the amino acid is modified to contain selenium once it is incorporated into the protein. Selenocysteinyl-tRNASec is produced by a particular converting enzyme and used in the ribosome for protein synthesis. tRNASec recognizes UGA on mRNA, which is normally a termination codon. A particular sequence is located immediately downstream of UGA, and selenocysteinyl-tRNASec is used through the activity of a special protein called translation factor to synthesize a protein containing selenocysteine.

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