Polypeptide chain synthesis

Transfer RNA (Mr s= 25,000) functions as an adapter in polypeptide chain synthesis. It comprises 10-20 percent of the total RNA in a cell, and there is at least one type of tRNA for each type of amino acid. Transfer RNAs are unique in that they contain a relatively high proportion of nucleosides of unusual structure (e.g., pseudouridine, inosine, and 2 -0-methylnucleosides) and many types of modified bases (e.g., methylated or acetylated adenine, cytosine, guanine, and uracil). As examples, the structures of pseudouridine and inosine are shown below. Inosine has an important role in codon-anticodon pairing (Chap. 17). 

Polypeptide Chain Synthesis The Elongation-Translocation Cycle... 

Analogues of methionine merit a special interest because the biological functions of methionine (Met) in the cell are multiple (1) it is the main methyl group donor via S-adenosylmethionine (2) it plays a key rdle in the initiation of polypeptide chain synthesis as N-formylmethionine-(transfer RNA) and (3) the methyla-tion of transfer-RNAs bases may be important in conferring the specific coding properties (see Sect B. Para. 8.1.2). 

Figure 6. Major steps in initiation of polypeptide chain synthesis. Reproduced, by kind permission of the authors and Grune and Stratton, from "The biosynthesis of hemoglobin" by Benz and Forget (1974), Semin. Hematol. 11 463-523.

Most reactions in cells are carried out by enzymes [1], In many instances the rates of enzyme-catalysed reactions are enhanced by a factor of a million. A significantly large fraction of all known enzymes are proteins which are made from twenty naturally occurring amino acids. The amino acids are linked by peptide bonds to fonn polypeptide chains. The primary sequence of a protein specifies the linear order in which the amino acids are linked. To carry out the catalytic activity the linear sequence has to fold to a well defined tliree-dimensional (3D) stmcture. In cells only a relatively small fraction of proteins require assistance from chaperones (helper proteins) [2]. Even in the complicated cellular environment most proteins fold spontaneously upon synthesis. The detennination of the 3D folded stmcture from the one-dimensional primary sequence is the most popular protein folding problem. 

PRA-isomerase lGP-synthase, a bifunctional enzyme from E. coli that catalyzes two reactions in the synthesis of tryptophan (Figure 4.6), has a polypeptide chain that forms two a/p barrels. The stmcture of this enzyme, solved at 2.8 A in the laboratory of Hans Jansonius in Basel, Switzerland, showed that residues 48-254 form one barrel with IGP-synthase activity, while residues 255-450 form the second barrel with PRA-isomerase activity (Figure 4.7). 

Transfer RNA (tRNA) serves as a carrier of amino acid residues for protein synthesis. Transfer RNA molecules also fold into a characteristic secondary structure (marginal figure). The amino acid is attached as an aminoacyl ester to the 3 -terminus of the tRNA. Aminoacyl-tRNAs are the substrates for protein biosynthesis. The tRNAs are the smallest RNAs (size range—23 to 30 kD) and contain 73 to 94 residues, a substantial number of which are methylated or otherwise unusually modified. Transfer RNA derives its name from its role as the carrier of amino acids during the process of protein synthesis (see Chapters 32 and 33). Each of the 20 amino acids of proteins has at least one unique tRNA species dedicated to chauffeuring its delivery to ribosomes for insertion into growing polypeptide chains, and some amino acids are served by several tRNAs. For example, five different tRNAs act in the transfer of leucine into... 

ATP synthase actually consists of two principal complexes. The spheres observed in electron micrographs make up the Fj unit, which catalyzes ATP synthesis. These Fj spheres are attached to an integral membrane protein aggregate called the Fq unit. Fj consists of five polypeptide chains named a, j3, y, 8, and e, with a subunit stoichiometry ajjSaySe (Table 21.3). Fq consists of three hydrophobic subunits denoted by a, b, and c, with an apparent stoichiometry of ajbgCg.ig- Fq forms the transmembrane pore or channel through which protons move to drive ATP synthesis. The a, j3, y, 8, and e subunits of Fj contain 510, 482, 272, 146, and 50 amino acids, respectively, with a total molecular mass... 

In animals, the enzymes of fatty acid synthesis are components of one long polypeptide chain, the fatty acid synthase, whereas no similar association exists for the degradative enzymes. (Plants and bacteria employ separate enzymes to carry out the biosynthetic reactions.)... 

Changes in the quantities of the various normal hemoglobin components during developmental stages can be explained in terms of ill-defined regulatory mechanisms which control the rate of synthesis of the polypeptide chains. Such mechanisms have to... 

The reactions of fatty acid synthesis all occur on one enzyme—fatty acid synthase.1 This enzyme has multiple catalytic activities on one polypeptide chain. The intermediates of the reaction are not released until... 

Successive amino acids are joined together during protein synthesis via a peptide (i.e. amide) bond (Figure 2.2). This is a condensation reaction, as a water molecule is eliminated during bond formation. Each amino acid in the resultant polypeptide is termed a residue , and the polypeptide chain will display a free amino (NH2) group at one end and a free carboxyl (COOH) group at the other end. These are termed the amino and carboxyl termini respectively. 

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