User:Am0833/Amino acid activation

Amino acid activation
Amino acid activation (also known as aminoacylation or tRNA charging) refers to the attachment of an amino acid to its respective Transfer RNA (tRNA). The reaction occurs in the cell cytosol and consists of two steps: first, the enzyme Aminoacyl tRNA synthetase catalyzes the binding of Adenosine triphosphate (ATP) to a corresponding amino acid, forming a reactive aminoacyl adenylate intermediate (AMP-amino acid) and releasing inorganic pyrophosphate (PPi). Subsequently, Aminoacyl tRNA synthetase binds the AMP-amino acid to a tRNA molecule, releasing AMP and attaching the amino acid to the tRNA. The resulting aminoacyl-tRNA is said to be charged.

Amino acid activation is a prerequisite to the initiation of translation and protein synthesis. Peptide bond formation is an endergonic, thermodynamically unfavorable process, so amino acids must be activated by covalent linkage to tRNA molecules. The energy stored within the aminoacyl-tRNA bond is used to drive peptide bond formation. Activation thus enhances the chemical reactivity of the amino acid and drives peptide bond synthesis. Moreover, the inorganic pyrophosphate released during the activation process is rapidly hydrolyzed in a highly exergonic reaction. The energy released by this hydrolysis helps drive the otherwise energetically unfavorable reaction forward. Following activation, the aminoacylated tRNA is ready to proceed to the initiation stage of translation, in which the aminoacyl-tRNA and mRNA transcript bind to the ribosome.

Mechanism
During amino acid activation, each amino acid (aa) is attached to its corresponding tRNA molecule. The coupling reaction is catalyzed by a group of enzymes called Aminoacyl-tRNA synthetases (named after the reaction product aminoacyl-tRNA or aa-tRNA). The coupling reaction proceeds in two steps:

First, the carboxyl group of the backbone of the amino acid is covalently linked to the α-phosphate of the ATP molecule, releasing inorganic pyrophosphate (PPi) and creating a 5’ aminoacyl adenylate intermediate (aa-AMP).

1.    aa + ATP ⟶aa-AMP + PPi

Second, the aminoacyl adenylate intermediate undergoes nucleophilic attack, attaching an aminoacyl group to the tRNA at the 3’-OH, and freeing an AMP molecule.

2.    aa-AMP + tRNA ⟶aa-tRNA + AMP

There are two classes of Aminoacyl t-RNA synthetases: class I and class II. Class I enzymes catalyze transfer of the aminoacyl group to the 2’-OH of the tRNA molecule, and a subsequent transesterification reaction moves the aminoacyl group to the 3’-OH of the tRNA. Class II enzymes catalyze transfer of the aminoacyl group directly to the 3’-OH of the tRNA in a single step. The active site for Class I enzymes is in a Rossman fold whereas the active site for Class II enzymes is in a different location made of a beta-structure with seven strands. The resulting aminoacyl-tRNA molecule is identical regardless of the enzyme class.

The net reaction is:

aa + ATP + tRNA ⟶ aa-tRNA + AMP + PPi

The amino acid is coupled to the penultimate nucleotide at the 3’-end of the tRNA (the A in the sequence CCA) via an ester bond. The formation of the ester bond conserves a considerable part of the energy from the activation reaction. This stored energy provides the majority of the energy needed for peptide bond formation during translation.

During activation, the tRNA functions as an adaptor molecule, as posited by Francis Crick’s Adaptor Hypothesis. Transfer RNA is an abundant noncoding protein, which forms a cloverleaf secondary structure to allow for activation. That is, the tRNA binds at one end to the specific amino acid of interest, and at the other end to the mRNA codon sequence. The tRNA molecule effectively acts as an intermediary between the two, enabling translation of the genetic code to an amino acid sequence.