Translation peptide bond formation

In addition to illustrating the mechanics of translation Figure 28 12 is important m that It shows the mechanism of peptide bond formation as a straightforward nude ophilic acyl substitution Both methionine and alanine are attached to their respective tRNAs as esters The ammo group of alanine attacks the methionine carbonyl displac mg methionine from its tRNA and converting the carbonyl group of methionine from an ester to an amide function... 

Post-translation modification Changes that occur to proteins after peptide-bond formation has occurred, e.g. glycosylation and acylation. 

Nucleophilic attack by the amino group of the neighbouring aminoacyl thioester is catalysed by the C domain, and this results in amide (peptide) bond formation. Enzyme-controlled biosynthesis in this manner is a feature of many microbial peptides, especially those containing unusual amino acids not encoded by DNA and where post-translational modification (see Section 13.1) is unlikely. 

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 ... 

Amino acids must be activated for translation to occur. Activation ensures that the correct amino acid will be recognized and fiiat there is sufficient energy for peptide bond formation. Activation is the covalent coupling of amino acids to specific adapter molecules. The adapter molecules are called transfer RNA (tRNA). There is atleast one tRNA for each of the 20 naturally occurring amino acids. The tRNA recognize the codons carried by the mRNA and position them to facilitate peptide bond formation. 

When codon-anticodon base pairing occurs the amino acid attached to the tRNA is correctly positioned within the ribosome for peptide bond formation. As each peptide bond is formed, the newly incorporated amino acid is released from its tRNA and the mRNA moves relative to the ribosome so that a new codon enters the catalytic site. The latter process is called translocation. Translation continues one codon at a time until a special base sequence, called a termination or stop codon, is reached. The polypeptide is then released from the ribosome, and folds into its biologically active conformation. Depending on the type of polypeptide, it may then bind to other folded polypeptides to form larger complexes. 

No matter what the organism, translation consists of three phases initiation, elongation, and termination. The elongation reactions, which include peptide bond formation and translocation, are repeated many times until a stop codon is reached. Posttranslational reactions and targeting processes vary according to cell type. 

Translation is relatively rapid in prokaryotes. For example, an E. coli ribosome can incorporate as many as 15 to 20 amino acids per second. (The eukaryotic rate, at about 50 residues per minute, is significantly slower.) Recall that prokaryotic ribosomes are composed of a 50S large subunit and a 30S small subunit. The large subunit contains the catalytic site for peptide bond formation. The small subunit serves as a guide for the translation factors required to regulate the process. Figure 19.5 provides a three-dimensional reconstruction of a functioning E. coli ribosome. 

The first event is binding of an aminoacyl-tRNA molecule to the empty A-site. Next, peptide bond formation occurs. This is catalyzed by an enzyme on the ribosome called peptidyl transferase. Now the peptide chain is shifted to the tRNA that occupies the A-site. Finally, the tRNA in the P-site falls away, and the ribosome changes positions so that the next codon on the mRNA occupies the A-site. This movement of the ribosome is called translocation. The process shifts the new peptidyl tRNA from the A-site to the P-site. The chain elongation stage of translation requires the hydrolysis of GTP to GDP and Pj. Several elongation factors are also involved in this process. 

The last stage of translation is termination. There are three termination codons— UAA, UAG, and UGA—for which there are no corresponding tRNA molecules. When one of these "stop" codons is encountered, translation is terminated. A release factor binds the empty A-site. The peptidyl transferase that had previously catalyzed peptide bond formation hydrolyzes the ester bond between the peptidyl tRNA and the last amino acid of the newly s)mthesized protein (Figure 24.19c). At this point the tRNA, the newly synthesized peptide, and the two ribosomal subunits are released. 

The translation step where proteins are assembled following the code of messenger RNA has a few instances of inhibition by alkaloids [361]. Emetine and tubulosine block peptide bond formation, acting similarly to the antibiotic cycloheximide by blocking translocation of the growing peptide chain from the A site to the P site of the ribosome. They evidently bind to a specific ribosomal site [362]. Homoharringtonine may act similarly [363]. Lycorine may act at the level of termination [364]. Narciclasine and related alkaloids of the Amaryllidaceae prevent binding of the 3 end of aminoacyl-tRNA to the peptidyl transferase site of the ribosome [365, 366]. Mescaline may act similarly [367]. 

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