Polypeptide chain termination mechanism

On the whole, our present understanding of archaeal translation is far from being complete. There is a considerable dearth of information on such essential aspects of archaeal biochemistry as the structure and sequences of the aminoacyl-tRNA synthethases, the mechanism of polypeptide chain termination and release, the number and complexity of the initiation factors the possibility that the archaea may resemble eucarya in having a more complex set of initiation factors than exists in bacteria is, in fact, suggested by the identification in archaea of hypusine-containing proteins (see section 2.4). The development of efficient and accurate cell-free systems using natural messenger RNAs is an obvious priority in order to elucidate these points. 

Mechanism of action of puromycin. Puromycin is able to enter the ribosome A site and function as an aminoacyl tRNA analogue, resulting in polypeptide chain termination in both... 

Non-corrin cobalt has a number of interesting applications in the chemical industry, for example in the hydroformylation (OXO) reaction between CO, H2 and olefins. A number of non-corrin Co-containing enzymes have been described, including methionine aminopep-tidase, prolidase, nitrile hydratase and glucose isomerase. We describe the best characterized of these, namely the E. coli methionine aminopeptidase, a ubiquitous enzyme, which cleaves N-terminal methionine from newly translated polypeptide chains. The active site of the enzyme (Figure 15.13) contains two Co(II) ions that are coordinated by the side-chain atoms of five amino acid residues. The distance between the two Co2+ is similar to that between the two Zn2+ atoms in leucine aminopeptidase, and indeed the catalytic mechanism of methionine aminopeptidase shares many features with other metalloproteases, in particular leucine aminopeptidases. 

There are five distinct families of zinc proteases, classified by the nature of the zinc binding site. These families, and their variously proposed mechanisms, have recently been reviewed in depth.143 The most studied member is the digestive enzyme bovine pancreatic carboxypeptidase A, which is a metalloenzyme containing one atom of zinc bound to its single polypeptide chain of 307 amino acids and Mr 34 472. It is an exopeptidase, which catalyzes the hydrolysis of C-terminal amino acids from polypeptide substrates, and is specific for the large hydrophobic amino acids such as phenylalanine. The closely related carboxypeptidase B catalyzes the hydrolysis of C-terminal lysine and arginine residues. The two en-... 

The start of protein synthesis is signalled by specific codon-anticodon interactions. Termination is also signalled by a codon in the mRNA, although the stop signal is not recognized by tRNA, but by proteins that then trigger the hydrolysis of the completed polypeptide chain from the tRNA. Just how the secondary and tertiary structures of the proteins are achieved is not yet clear, but certainly the mechanism of protein synthesis, which we have outlined here, requires little modification to account for preferential formation of particular conformations. 

The molecular mechanism of translation in eukaryotes is very similar to that in bacteria. The activation of amino acids and attachment to tRNAs and the steps of initiation, elongation, and termination of polypeptide chains are essentially the same in overall terms. The small and large ribosomal subunits of bacteria and eukaryotes are equivalent with respect to their roles in initiation and elongation of chains. 

The mechanism of N-acetylation of a-crystallin is quite interesting. The N-terminal residue has been identified as N-acetyl methionine. This methionine residue is derived from Met-tRNA et which is responsible for the initiation of the polypeptide chain and not Met-tRNAmet which incorporates the methionine residue in the growing polypeptide chain. It is clear that the N-acetylation is a true posttranslational process since acetyl Met-tRNA cannot replace formyl Met-tRNA et. Moreover, N-acetylation occurs when the polypeptide chain has reached a length consisting of approximately 25 amino acid residues. Other proteins, such as ovalbumin, are also acetylated during the early stages of polymerization on the polysome, and the protein acetyltransferase activity must therefore be associated with the protein-synthesizing apparatus. 

Figure 3. The mechanism ofa irin s effect on platelets The 599 amino acid polypeptide chain of PGH synthase (center wavy line NHj-terminal methionine-1, COOH-terminal leucine-599) exerts cyclo-oxygenase activity as shown above (oxygenation/cycli-zation of arachidonate to PGGj) and interacts with aspirin as shown below. The serine residue located at position 529 of the polypeptide chain of cyclo-oxygenase is acetylated through transfer of aspirin s acetyl groiq> as indicated in bold face. Covalently-modified, acetylated PGH synthase carries a single acetyl group in its active site and lacks all cyclo-oxygenase activity.

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. 

In peptides, amino acids are joined by peptide bonds to form the polypeptide chain. The e q, OH, and H radicals react with the amino acids and with the polypeptide chain with high rate coefficients that are close to the diffusion limit. OH radicals and, less frequently, H atoms abstract a hydrogen atom from the polypeptide chain (from the carbon atoms) or from the side chains, but they can also add to the rings of the aromatic amino acids. The radical site produced on the main chain may move along the chain by an internal hydrogen abstraction mechanism. If the H atom is abstracted from an S-H bond the radical migration stops, since the S-H bond is much weaker than the G-H bonds. This reaction is the basis of repair mechanism. The radicals may terminate in radical-radical reactions. 

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