Protein synthesis aminoacyl-tRNA formation

Figure 13.3 The process of protein synthesis on the ribosome. The strand of mRNA is shown associated with the small subunit of the ribosome. The aminoacyl-tRNA molecules are shown associated with the large subunit of the ribosome and base-paired with mRNA codons. A peptide bond is in the process of formation between the two associated amino acids, extending the growing polypeptide chain by one unit. On the left, a tRNA is shown leaving the ribosome, having donated its amino acid to the growing chain. On the right, an aminoacyl-tRNA molecule is shown entering the ribosome. It is next in line to contribute its amino acid to that chain.

The ribosome is both the site of protein synthesis and an active participant in the process. The eukaryotic ribosome is constructed from two subunits the smaller 40S subunit and the larger 60S subunit. Basically, the 40S subunit binds the mRNA and monitors the recognihon between the mRNA codon and tRNA anticodon. The 60S subunit has the binding sites for aminoacyl-tRNAs and catalyzes the formation of peptide bonds. Remarkably, the catalytic entity for peptide bond formahon in the 60S subunit is the RNA component, not the protein component. Therefore, the 60S subunit acts as a ribozyme. 

Chloramphenicol (Chloromycetin) is a nitrobenzene derivative that affects protein synthesis by binding to the 50S ribosomal subunit and preventing peptide bond formation. It prevents the attachment of the amino acid end of aminoacyl-tRNA to the A site, hence the association of peptidyltransferase with the amino acid substrate. Resistance due to changes in the ribosomebinding site results in a decreased affinity for the drug, decreased permeability, and plasmids that code for enzymes that degrade the antibiotic. 

The answer is b. (Hardman, p 1131.) Chloramphenicol inhibits protein synthesis in bacteria and, to a lesser extent, in eukaryotic cells. The drug binds reversibly to the SOS ribosomal subunit and prevents attachment of aminoacyl-transfer RNA (tRNA) to its binding site. The amino acid substrate is unavailable for peptidyl transferase and peptide bond formation. 

Proofreading by Aminoacyl-tRNA Synthetases The amino-acylation of tRNA accomplishes two ends (1) activation of an amino acid for peptide bond formation and (2) attachment of the amino acid to an adaptor tRNA that ensures appropriate placement of the amino acid in a growing polypeptide. The identity of the amino acid attached to a tRNA is not checked on the ribosome, so attachment of the correct amino acid to the tRNA is essential to the fidelity of protein synthesis. 

Amino acids are activated by specific aminoacyl-tRNA synthetases in the cytosol. These enzymes catalyze the formation of aminoacyl-tRNAs, with simultaneous cleavage of ATP to AMP and PPj. The fidelity of protein synthesis depends on the accuracy of this reaction, and some of these enzymes carry out proofreading steps at separate active sites. In bacteria, the initiating aminoacyl-tRNA in all proteins is A-formylmethionyl-tRNAfMet. 

Initiation of protein synthesis involves the assembly of the components of the translation system before peptide bond formation occurs. These components include the two ribosomal subunits, the mRNA to be translated, the aminoacyl-tRNA specified by the first codon in the message, GTP (which provides energy for the process), and initiation factors that facilitate the assembly of this initiation complex (see Figure 31.13). [Note In prokaryotes, three initiation factors are known (IF-1, IF-2, and IF-3), whereas in eukary- otes, there are at least ten (designated elF to indicate eukaryotic origin).] There are two mechanisms by which the ribosome recognizes the nucleotide sequence that initiates translation ... 

Overview of reactions in protein synthesis. (aab aa2, aa3 = amino acids l, 2, 3.) Protein synthesis requires transfer RNAs for each amino acid, ribosomes, messenger RNA, and a number of dissociable protein factors in addition to ATP, GTP, and divalent cations. First the transfer RNAs become charged with amino acids, then the initiation complex is formed. Peptide synthesis does not start until the second aminoacyl tRNA becomes bound to the ribosome. Elongation reactions involve peptide bond formation, dissociation of the discharged tRNA, and translocation. The elongation process is repeated many times until the termination codon is reached. Termination is marked by the dissociation of the messenger RNA... 

This overall reaction is reversible but is driven to completion by the subsequent hydrolysis of PP, to two equivalents of P through the action of ubiquitous pyrophosphatases. Thus, the formation of aminoacyl-tRNA consumes two equivalents of ATP. The energy that ultimately drives the formation of the peptide linkage during protein synthesis is derived from the ester linkage that joins amino acids to tRNA. 

After the correct aminoacyl-tRNA has been placed in the A site, the transfer of the polypeptide chain from the tRNA in the P site is a spontaneous process, driven by the formation of the stronger peptide bond in place of the ester linkage. However, protein synthesis cannot continue without the translocation of the mRNA and the tRNAs within the ribosome. The mRNA must move by a distance of three nucleotides as the deacylated tRNA moves out of the P site into the E site on the 30S subunit and the peptidyl-tRNA moves out of the A site into the P site on the 30S subunit. The result is that the next codon is positioned in the A site for interaction with the incoming aminoacyl-tRNA. 

C. mRNA supplies the codons, aminoacyl-tRNA and GTP provide energy, peptidyl transferase catalyzes the formation of peptide bonds, and elongation factor 2 translocates the peptidyl-tRNA. Formylmethionyl-tRNA is involved in initiation of protein synthesis in prokaryotes. 

The answer is b. (Murray, pp 452-467. Scriver, pp 3-45. Sack, pp 1-40. Wilson, pp 101-120.) During the course of protein synthesis on a ribosome, peptidyl transferase catalyzes the formation of peptide bonds. However, when a stop codon such as UAA, UGA, or UAG is reached, aminoacyl-tRNA does not bind to the A site of a ribosome. One of the proteins, known as a release factor, binds to the specific trinucleotide sequence present. This binding of the release factor activates peptidyl transferase to hydrolyze the bond between the polypeptide and the tRNA occupying the P site. Thus, instead of forming a peptide bond, peptidyl transferase catalyzes the hydrolytic step that leads to the release of newly synthesized proteins. Following release of the polypeptide, the ribosome dissociates into its major subunits. 

Enzymes involved in protein synthesis also possess potential, e.g. aminoacyl-tRNA-synthetase-aminoadenylate complex 1791, the arginyl-tRNA protein arginyl-transferase11801, and nonribosomal poly- or multienzyme complexes1721 which require ATP or GTP to activate the carboxyl group of an amino acid, and seem to accept various amino acid nucleophiles for peptide bond formation. Flowever, the application of these enzyme systems for generally practical peptide bond formation is rather limited. 

The previous sections have introduced the major participants in protein synthesis—mRNA, aminoacylated tRNAs, and ribosomes containing large and small rRNAs. We now take a detailed look at how these components are brought together to carry out the biochemical events leading to formation of polypeptide chains on ribosomes. Similar to transcription, the complex process of translation can be divided into three stages—initiation, elongation, and termination—which we consider in order. We focus our description on translation in eukaryotic cells, but the mechanism of translation is fundamentally the same in all cells. 

The activity of blasticidin S involves primarily the inhibition of fungal protein synthesis. In the presence of blasticidin S, the incorporation of amino acids into protein is reduced by 80-90% (Gottlieb et al., 19SS Misato et al., 1%1 Huang et al.. 1964a). It was foimd that blasticidin S reduces the formation of aminoacyl-tRNA. Hence the next step, the incorporation of the amino acid, is also block. The site of primary action is not yet known. 

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