The Mechanism of Protein Synthesis

Our understanding of the mechanism of protein synthesis in plants comes mainly from studies on cell-free (in vitro) systems derived from seeds—by far the most popular material has been the isolated wheat embryo and commercially-produced wheat germ. 

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There were also less concrete considerations. In the early 1950s glycogenolysis was still believed to be completely reversible. UTP dependency and the glycogen synthase reactions had not yet been discovered nor had phosphofructokinase been shown to act irreversibly. The mechanism of protein synthesis was still a mystery. Laboratories studying proteolysis had shown that the peptide bond could be resynthesized by peptidases, although under very restricted conditions. Reversibility seemed to be an accepted property of the major metabolic pathways. 

One could plunge into the steric problems posed by the mechanism of protein synthesis on the ribosome 25 26)> or consider the steric fit of the hormone insulin to its acceptor in the cell membrane 27>. Or one could delve into the beautiful intricacy of terpenoid, squalene and steroid metabolism, or get lost in double bond formation, or in the steric problems posed by the branched chain fatty acids and their derivatives 28-34). 

Work with the carcinogen acetylaminofluorene found that residues of the compound in ribosomal RNA may correlate more closely with liver tumor formation than residues in DNA. Direct interactions with the mechanisms of protein synthesis, or with DNA and RNA polymerase enzymes, can also be seen as possible mechanisms. For instance, a modification of the polymerase enzymes by a carcinogen, either directly or indirectly, could lead to the erroneous replication of DNA or RNA and hence the permanent incorporation of a mutation. 

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 structure of nucleic acids is discussed in Appendix 5.2, while Appendix 5.6 gives details of how information can be stored in the cell in the form of DNA, genes, plasmids, and of the mechanisms of protein synthesis. 

Lipids also show asymmetrical distributions between the inner and outer leaflets of the bilayer. In the erythrocyte plasma membrane, most of the phosphatidylethanolamine and phosphatidylserine are in the inner leaflet, whereas the phosphatidylcholine and sphingomyelin are located mainly in the outer leaflet. A similar asymmetry is seen even in artificial liposomes prepared from mixtures of phospholipids. In liposomes containing a mixture of phosphatidylethanolamine and phosphatidylcholine, phosphatidylethanolamine localizes preferentially in the inner leaflet, and phosphatidylcholine in the outer. For the most part, the asymmetrical distributions of lipids probably reflect packing forces determined by the different curvatures of the inner and outer surfaces of the bilayer. By contrast, the disposition of membrane proteins reflects the mechanism of protein synthesis and insertion into the membrane. We return to this topic in chapter 29. 

The adaptors were theoretically predicted by Francis Crick in order to explain the mechanics of protein synthesis, but they are necessary structures in all organic codes. They are the molecular fingerprints of the organic codes, and their presence in a biological process is a sure sign that that process is based on a code. 

On the basis of current ideas on the mechanism of protein synthesis it is difficult to rationalize the occurrence of analogous structures of inverted sequence sense, and their significance in terms of structural regularity is in itself highly debatable. Their discussion in this context should be regarded as purely phenomenological. 

The answer is c. (Murray, pp 452-467. Scriver, pp 3-45. Sack, pp 1-40. Wilson, pp 101-120.) In a general sense, the mechanism of protein synthesis in eukaryotic cells is similar to that found in prokaryotes however, there are significant differences. Cycloheximide inhibits elongation of proteins in eukaryotes, while erythromycin causes the same effect in prokaryotes. Thus, one is an antibiotic beneficial to humans, while the other is a poison. Cytoplasmic ribosomes of eukaryotes are larger, sedimenting at SOS instead of 70S. While eukaryotic cells utilize a specific tRNA for initiation, it is not formylated as in bacteria. Finally, eukaryotic mRNA always specifies only one polypeptide, as opposed to prokaryotic mRNA, which may specify the synthesis of more than one gene product per mRNA. 

Very often found within the nucleus is a small densely stainin body called the nucleolus the number of these vary in differer cell types they are full of a particular class of RNA. Some RNA i also present in the nucleus in the form of ribosomes, althoug these are mainly to be found in the cytoplasm (see below). Th whole of the nucleus is constrained by a well-defined boundary the nuclear membrane, which has the same type of lipoproteii bilayer structure as the cell membrane, except that it is perforatei by pores whose role is obscure but which are believed to allow th passage of RNA into the cytoplasm (Plate 2). The significance o many of these structures and arrangements will become cleare when we discuss the mechanisms of protein synthesis in Chapte 10. 

The mechanism of protein synthesis inhibition exhibited by aminoglycosides other than SM differ in particular details. It was shown that KM, NM, and GM have multiple ribosomal binding sites rather than the single site to which SM binds. Translocation on bacterial ribosomes is also inhibited by these agents. 

More detailed information on the mechanism of protein synthesis in eukaryotes as well as on the structures and functions of their ribosomes can be found in several reviews [18, 82-85]. 

Nomura, M., Mizushima, S., Ozaki, M., Traub, R, and Lowry, C. V. (1969). Structure and function of ribosomes and their molecular components. In The Mechanism of Protein Synthesis, The Cold Spring Harbor Symposia on Quantitative Biology, Vol. XXXIV, pp. 49-61. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 

The antimicrobial drugs reviewed in this chapter (Figure 44—1) selectively inhibit bacterial protein synthesis. The mechanisms of protein synthesis in microorganisms are not identieal to those of mammalian cells. Bacteria have 70S ribosomes, whereas mammalian cells have SOS ribosomes. Differences exist in ribosomal subunits and in the chemical composition and functional specificities of component nucleic acids and proteins. Such differences form the basis for the selective toxicity of these drugs against microorganisms without causing major effects on protein synthesis in mammalian cells. 

Density-gradient separations of cytoplasmic fractions from liver have been carried out to study the distribution of activity of several enzymes (Thomson, 1959). Ribosomes and polysomes have been fractionated to elucidate the mechanisms of protein synthesis (Watson, 1964), Various viruses have been studied with the density-gradient technique polio virus (Levintow and Darnell, 1960), Rous sarcoma virus (Crawford, 1960), Shope papilloma virus (Williams et ai, 1960), and adenoviruses (Allison et ai, 1960). Density-gradient fractionation has been particularly useful for separation of DNA molecules from various species of bacteria (Rolfe and Meselson, 1959) and from animal cells (Kit, 1961), Other types of molecules, e.g., antibodies, lipoproteins, and rheumatoid factor have been isolated by density-gradient methods [see Charlwood (1966) for examples]. 

Ribonucleic acid (RNA) (Sections 25.1 and 25.5) One of the two classes of molecules (the other is DNA) that carry genetic information in cells. RNA molecules transcrihe and translate the information from DNA for the mechanics of protein synthesis. 

Regulatory mechanisms at the level of mRNA translation could also lead to gross metabolic changes. The mechanism of protein synthesis has been exhaustively studied [5], and many components have been implicated. Changes in each of these components—ribosomes, factors involved in the ribosomal binding of mRNA, in the initiation and termination of protein synthesis, and in polypeptide chain elongation, tRNA, and the components responsible for its acylation and subsequent transfer to the polysomal complex—could potentially lead to alteration in the rate, extent, or fidelity of protein synthesis. 

In the preceding paragraphs, we have reviewed the evidence establishing that the genetic information is stored in the DNA molecule, then later described the mechanism of protein synthesis. Now the flow of information from DNA to the protein molecule will be discussed [173-179]. 

The schematic presentation of the mechanism of protein synthesis that we have just presented immediately raises a number of problems. 

Zamecnik, P.C., Keller, E.B., Hoagland, M.B., Littlefield, J.W., Loft-field, R.B. Studies on the mechanism of protein synthesis. In Ionizing radiations and cell metabolism (Wolfstenholme, G.E.W., and O Connor, C., eds.). Ciba Found. Symp., p. 161-173. Boston Little, Brown and Company 1956... 

The mechanism of protein synthesis discussed above does not involve addition of amino acids to preformed peptides synthesis starts with an amino acid and a polypeptide chain is synthesised by the successive addition of single amino acids. Unless all the amino acids required to synthesise the peptide are present at the right time, synthesis will not take place and the amino acids that are present are removed and may be catabolised. Considerable wastage of amino acids may thus take place if an incomplete mixture is presented for synthesis. 

The mechanism of protein synthesis involves the transfer of information from one of the chains of the DNA helix to a molecule of RNA (ribonucleic acid) that is a complement of the DNA chain. RNA contains the sugar ribose... 

P. Chapeville, in The Mechanism of Protein Synthesis and Its Regulation (L. Bosch, ed.), p. 5. North-Holland Publ., Amsterdam, 1972. 

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