The Mechanism of Protein Biosynthesis

The primary cellular function of mRNA is to direct biosynthesis of the thousands of diverse peptides and proteins required by an organism—perhaps 100,000 in a human. The mechanics of protein biosynthesis take place on ribosomes, small granular particles in the cytoplasm of a cell that consist of about 60% ribosomal RNA and 40% protein. 

The intensive studies on the genetic code and on the proteins in recent years have led to a fairly good understanding of the mechanism of protein biosynthesis . The biosynthetic mechanism involved in the formation of peptides has not yet been studied in equal detail. Some physiologically active peptides like bradykinin and angiotensin are known to be derived from proteins by a specific enzymatic hydrolysis. Other peptides, like glutathione - , ophthalmic acid , the nucleotide-pentapeptide from Staph, aureus and y-polyglutamic acid have been shown to require for their synthesis only a soluble enzyme system. Their biosynthetic mechanism is therefore entirely different from that of the proteins. Such a different type of mechanism has also been demonstrated lately to be involved in the synthesis of peptide antibiotics. 

Elucidation of the biosynthesis of gramicidin S and of tyrocidin (Fig. 12), an additional component in Dubos tyrothricin, represents an important period in the development of our understanding of biochemistry. It took place at the time when the mechanism of protein-biosynthesis had just been recognized. In the 1950s, P. Zamecnik discovered that the synthesis of proteins in the cell occurs in organelles, later designated as ribosomes. Then M. Hoagland found a type of RNA, the transfer RNAs (t-RNAs) to which, in the presence of ATP, amino acids are attached in activated form. H.G. Zachau, G. Acs and F. Lipmann identified the mode of activation as esters of an adenosin residue in the t-RNA [30]. 

Ochoa s current work is directed toward further elucidating the mechanisms of protein biosynthesis, in prokaryotic and in the intriguingly complex brine shrimp, Artemia salina, which provides an interesting biological model to approach the study of biological differentiation. 

The mechanism of protein biosynthesis occurs in three consecutive phases initiation, elongation and termination. In prokaryotes and eukaryotes, differences exist in the mechanisms employed. These differences relate to ... 

We may now inquire as to the biochemical basis of the adaptive response and the biochemical defects responsible for the failure of adaptation to environmental factors, i.e., the defects that lead to abnormal structure or amounts of enzymes and nonenzymatic proteins. Fig. 5 depicts in simplified fashion the mechanism of protein biosynthesis. 

Figure 5. Simplified scheme of the mechanism of protein biosynthesis showing the intricate feedback mechanisms, the structural genes and their controls, and the regulatory gene.

The experiments described above indicated amino acids were oxidatively deaminated in liver and their a-amino groups converted to urea. A start on investigations of the mechanism of urea biosynthesis was made by Schultzen and Nenki (1869) who concluded that amino acids gave rise to cyanate which might combine with ammonia from proteins to produce urea. Von Knieren (1873) demonstrated that when he drank an ammonium chloride solution, or gave it to a dog, there was an increase in the formation of urea, without any rise in urinary ammonia. His results were consistent with the cyanate theory but did not eliminate the possibility that urea arose from ammonium carbonate which could be dehydrated to urea ... 

Naturally, if such materials are going to be useful as antibiotic drugs, we require a selective action. We need to be able to inhibit protein biosynthesis in bacteria, whilst producing no untoward effects in man or animals. Although the mechanisms for protein biosynthesis are essentially the same in prokaryotes and eukaryotes, there are some subtle differences, e.g. in the nature of the ribosome and how the process is initiated. Without such differences, the agent would be toxic to man as well as to bacteria. 

Because they often function as virulence factors, the enzymes involved in siderophore biosynthesis are potential targets for developing antimicrobial strategies. The mechanisms of siderophore biosynthesis follow the same fundamental biosynthetic logic involving similar protein machinery, which we describe in greater detail in Chapter 5 for fatty acid biosynthesis. It is also used in the microbial biosynthesis of many important natural products polyketides and peptides (including many antibiotics). Essentially, as is illustrated in Fig. 4.20, for enterobactin, it involves... 

The protein kinase H RI (heme regulated eIF-2 kinase) was first identified in studies on the regulation of protein biosynthesis in erythroid cells. A decrease in the heme concentration in reticulocytes leads to inhibition of globin synthesis at the level of translation. This regulation mechanism ensures that only so much globin is produced as is heme available. If the level of heme drops, then HRI becomes activated. The activated HRI phosphorylates the eIF-2a subunit, which in turn shuts off protein biosynthesis (Fig. 1.48). The mechanism of regulation of HRI kinase by heme is not well understood. Heme binding sites have been identified on the N-terminus and the kinase domain of HRI. 

In contrast to these results, the process of tyrocidine and gramicidin biosynthesis has been compared to protein synthesis, but this evidence was obtained in cell-free systems of B. brevis . Yet a difference in the mechanism of protein and antibiotic synthesis has also been reported for gramicidin polymyxin and mycobacillin and seems now to be... 

Thermophilic inteins were among the first inteins discovered and played a key role in establishing protein splicing as a fundamental method of protein biosynthesis. The proof that inteins were spliced from precursor proteins rather than from precursor RNAs and the mechanism of protein splicing were initially demonstrated using archaeal inteins. Since their discovery in 1990, inteins have been harnessed to perform numerous protein engineering processes. 

Sion of special morphogenetic problems in cases when, in order to explain some of the molecular "genetic mechanisms of morphogenesis, facts and concepts dealing with mechanisms of protein biosynthesis are mentioned. 

In principle, inherent catalytic function should be susceptible to quantum biochemical analysis. However, such an endeavor is beyond the ability of present methods (Scheiner and Kem, 1978). The activation-inactivation mechanisms are, at least in part, hormone mediated. The amount of enzyme present is dependent on the rate of protein biosynthesis versus the rate of degradation. These processes, in turn, are dependent on the effect of substrate on the protein biosynthetic mechanism necessary for the manufacture of the glycolytic, gluconeogenetic, and degradative enzymes. 

The information contained in genes is expressed, in part, by the proteins that are within a cell. The genes contain information for their own replication, for the synthesis of other nucleic acids and proteins including enzymes, and for the various control mechanisms of protein biosynthesis. 

Miller, D. L., and Weissbach, H., 1977, Factors involved in the transfer of aminoacyl-tRNA to the ribosome, in Molecular Mechanisms of Protein Biosynthesis (H. Weissbach and S. Pestka, eds.), pp. 323-373, Academic Press, New Yoik. 

Rohdich, F., Zepeck, F., Adam, P. et al. (2003) The deoxyxylulose phosphate pathway of isoprenoid biosynthesis studies on the mechanisms of the reactions catalyzed by IspG and IspH protein. Proceedings of the National Academy of Sciences of the United States of America, 100, 1586-1591. 

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