Peptides, synthesis using aminoacyl-tRNA

Write out in detail, using structural formulas, the chemical mechanism of synthesis of an aminoacyl-tRNA and of incorporation of the aminoacyl group into a peptide chain being formed by a ribosome. 

Nonribosomal peptide synthesis means that the peptide is not produced by the tRNA-mRNA mechanism described in Chapter 28, Section 28.6. Each amino acid found in 224 is directly selected for incorporation into the growing peptide chain by one of the domains of surfactin synthetase, shown with the pendant SH groups. Substrate activation occurs after binding the amino acid, and the enzyme catalyzes the formation of an aminoacyl adenylate intermediate using Mg2+-ATP and release of a cofactor. Subsequently, the amino acid-O-AMP oxoester is converted into a thioester by a nucleophilic attack of the free thiol-bound cofactor of an adjacent PCP domain. (Note that ATP is adenosine triphosphate and AMP is adenosine monophosphate see Chapter 28, Section 28.5.)... 

As shown in Scheme 12.71, and as affirmed by labeling experiments, an amino acid (shown using phenylalanine [Phe, F] as an example in the scheme) to be added to the growing peptide (protein) chain is activated for reaction by attachment at the carboxylate to adenosine triphosphate (ATP) to make an anhydride of the amino acid with adenosine monophosphate (and the loss of inorganic phosphate). Then, in the next step, the activated amino acid is esterified by the C-2 or the C-3 hydroxyl of a ribosyl unit of AMP, which is attached via phosphate at the 5 carbon to the aminoacyl transfer end of tRNA. If attachment is to C-2, rearrangement to C-3 follows and the aminoacyl-tRNA is activated and ready to be added to the growing peptide chain at the synthesis site on the ribosome. 

The energy for the reaction (two high-energy phosphate bonds) is provided by ATP and stored in the ester bond of the aminoacyl-tRNA to be used subsequently for peptide bond synthesis. 

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