In protein biosynthesis

The discovery of nbozymes (Section 28 11) in the late 1970s and early 1980s by Sidney Altman of Yale University and Thomas Cech of the University of Colorado placed the RNA World idea on a more solid footing Altman and Cech independently discovered that RNA can catalyze the formation and cleavage of phosphodiester bonds—exactly the kinds of bonds that unite individual ribonucleotides in RNA That plus the recent discovery that ribosomal RNA cat alyzes the addition of ammo acids to the growing peptide chain in protein biosynthesis takes care of the most serious deficiencies in the RNA World model by providing precedents for the catalysis of biologi cal processes by RNA... 

A major sorting decision is made early in protein biosynthesis, when specific proteins are synthesized either on free or on membrane-bound polyribosomes. This results in two sorting branches called the cytosolic branch and the rough endoplasmic reticulum (R R) branch (Figure 46-1). This sorting occurs because proteins synthesized on membrane-bound polyribosomes contain a signal peptide that mediates their attachment to the membrane of the ER. Further details on... 

In diphtheria, the organism C. diphtheriae eonfmes itself to epithelial surfaces of the nose and throat and produces a powerfiil toxin which affects the elongation factor involved in protein biosynthesis. The heart and peripheral nerves are particularly affected resulhng in myocarditis (inflammation of the myocardium) and neuritis (inflammation of a nerve). Little damage is produeed at the infective site. 

In ah of today s living systems, RNA is involved in processes which are very old from an evolutionary point of view. RNA occurs in protein biosynthesis in three different forms, and thus with three different functions tRNA, mRNA and rRNA. 

As already mentioned, a continual inflow of energy is necessary to maintain the stationary state of a living system. It is mostly chemical energy which is injected into the system, for example by activated amino acids in protein biosynthesis (see Sect. 5.3) or by nucleoside triphosphates in nucleic acid synthesis. Energy flow is always accompanied by entropy production (dS/dt), which is composed of two contributions ... 

Whereas DNA is mostly located in the nucleus of cells in higher organisms (with some also in mitochondria and in plant chloroplasts), RNA comes in three major and distinct forms, each of which plays a crucial role in protein biosynthesis in the cytoplasm. These are, respectively, ribosomal RNA (rRNA), which represents two-thirds of the mass of the ribosome, messenger RNA (mRNA), which encodes the information for the sequence of proteins, and transfer RNAs (tRNAs) which serve as adaptor molecules, allowing the 4-letter code of nucleic acids to be translated into the 20-letter code of proteins. These latter molecules contain a substantial number of modified bases, which are introduced enzymatically. 

In extant organisms, aa-tRNAs are mostly used in the synthesis of polymers of amino acid residues (proteins) that takes place on ribosomes. In certain microorganisms, some aa-tRNAs used in protein biosynthesis are formed... 

The final step in protein biosynthesis is chain termination. Natural mRNA molecules contain termination codons UAA, UGA, or UAG There are no tRNAs that have anticodons which are complementary to these codons. When the growing peptide chain encounters one of these termination codons, the peptidyl-tRNAis transferred to water instead of another aminoacyl-tRNA. The peptidyl-tRNA is hydrolyzed to free the completed protein and the tRNA. Chain termination completes protein synthesis. 

Before looking at these five stages in detail, we must examine two key components in protein biosynthesis the ribosome and tRNAs. 

The activity of a very weak active mutant measured by steady state kinetics could result from traces of a wild-type or more active mutant in the preparation either as a contaminant or because of natural errors of misincorporation. The error rate in protein biosynthesis can be as high as one part in 100 or one part in 1000.10 The presence of a small amount of wild-type enzyme in an inactive mutant would give a low value of kcat (which is directly proportional to the concentration of wild type) but the KM value for the wild-type enzyme. Thus, the finding of a low value of kcat and the wild-type KM for a mutant is very suspicious. 

Many of the chaperones double as heat shock-proteins (Hsp). When a cell is put under stress that can cause proteins to denature, such as too high a temperature, it produces heat-shock proteins. Their names are abbreviated to Hsp plus their subunit molecular mass in kDa. Hsp70, for example, is a ubiquitous heat-shock protein in eukaryotes. It is known in E. coli as DnaK for historical reasons because it was first discovered from a supposed role in DNA replication. Hsp70 is also important in protein trafficking and the conveying of proteins across membranes, because the denatured state is important in these processes. In protein biosynthesis, the unfolded state of the nascent polypeptide chain is passed on to DnaK, which maintains it in an extended form. The chain, under the influence of ATP and co-chaperones such as DnaJ and GrpE, is handed over to GroEL. 

Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain.

Amino acyl 5 -adenylates have been known as products in the first stage of activation for the amino acids in protein biosynthesis before they are coupled to t-RNA. The... 

Janiak, F., Dell, V. A., Abrahamson, J. K., Watson, B. S., Miller, D. L., and Johnson, A. E. (1990). Fluorescence characterization of the interaction of various transfer RNA species with elongation factor Tu.GTP Evidence for a new functional role for elongation factor Tu in protein biosynthesis. Biochemistry 29, 4268—4277. 

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