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12 the Translation of Mrna: Protein Synthesis

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12 the Translation of Mrna: Protein Synthesis 12 The translation of mRNA: protein synthesis 12.1 AN OVERVIEW OF PROTEIN involves the successive reading of the codons BIOSYNTHESIS of the mRNA by the aminoacyl-tRNAs in an ordered manner, and the linking of the In the preceding chapters the reader has amino acids to form a polypeptide chain. already encountered the concept that the This is a complex process and takes place on mRNA (messenger RNA) is an intermedi­ an elaborate organelle, the ribosome. The ary in the expression of that portion of direction of growth of the polypeptide chain the genetic information in the DNA that is from the N-terminus to the C-terminus encodes proteins. The present chapter pre­ [2], and the direction of reading of the sents a detailed consideration of the process mRNA is 5' ~ 3' [3, 4]. Figure 12.1 provides of translation of the mRNA. Although this a schematic summary of the interactions of will be prefaced with a summary of the main mRNA, tRNA and ribosome. It represents a features of translation, the reader is directed stage in protein biosynthesis just before to suitable textbooks of biochemistry (e.g. the aminoacyl ester bond of the peptidyl­ [1]) for a more elementary account of this tRNA is broken and the polypeptide chain topic. transferred to the a-amino group of the In essence, protein biosynthesis involves aminoacyl-tRNA. Also represented in Fig. translating the information of the sequence 12.1 are two sites on the ribosome to which of the four different nucleotides of DNA or tRNA can bind, the A-site and the P-site, RNA into a protein sequence with twenty and the integral ribosomal enzymic activity different possible amino acid units. The that catalyses the formation of peptide genetic code provides the conceptual basis of bonds, peptidyltransferase. this in the relationship of single amino acids The overall length of the mRNA and the to groups of three nucleotides in the mRNA rate of initiation are usually such that a (triplet codons); whereas tRNA (transfer second ribosome can attach to the mRNA RNA) provides its physical basis through before the first one has completed its poly­ possessing an anticodon complementary to peptide chain. In fact, several ribosomes a mRNA codon, and a specific covalently are normally found on a given molecule attached amino acid. Protein biosynthesis of mRNA, translating different parts of it R. L. P. Adams et al., The Biochemistry of the Nucleic Acids © Roger L. P. Adams, John T. Knowler and David P. Leader 1992 516 The translation of mRNA N amino acids s-1 for globin chains in rabbit 50S reticulocytes [8] have been reported. These are, however, much lower than the rates estimated for DNA or RNA synthesis (800 and 50 nucleotides s-1, respectively, in pro karyotes). It should be mentioned that the synthesis of certain small bacterial peptides occurs in a manner not dependent on mRNA and ribosomes. The reader interested in this tRNA subject is directed elsewhere [9]. mRNA s' 12.2 THE GENETIC CODE 305 12.2.1 The standard genetic code Fig. 12.1 Diagrammatic representation of a The elucidation of the genetic code repre­ prokaryotic ribosome. Two tRNA molecules are bound to the ribosome in response to the mRNA sented one of the major breakthroughs codons designated n and n + 1. The tRNA in modern biology. Here we shall merely bearing the growing polypeptide chain is describe the features of the code, as accounts occupying the peptidyl site (rectangular area, of the history of the code are to be found in marked P), and the tRNA bearing an amino acid a number of reviews (e.g. [10-12]). the aminoacyl site (rectangular area, is occupying The genetic code is a triplet code with marked A). The peptidyltransferase centre, where the peptide bond formation is catalysed, is individual amino acids represented in the represented by the semicircular area, marked X. mRNA by code words (codons) of three Note the exaggeration of the amino acid (1 A - nucleotides. Although certain codons also 0.1 nm) relative to the tRNA (75 A- 7.5nm), specify initiation and termination signals, the shape of the and the misrepresentation of the code is uninterrupted, with no 'commas' ribosomal subunits (cf. Fig. 12.21). between codons, and these follow one another in succession and do not overlap. The code was at one time thought to be simultaneously, and such groups of ribo­ universal, i.e. each triplet codon had the somes are termed polyribosomes or poly­ same meaning, regardless of the species. somes (Fig. 12.2). The size of the polysomes This assumption derived from comparison increases with the size of the mRNA: poly­ between E. coli and higher mammals, where somes synthesizing haemoglobin P-chains initially it was shown that the tRNAs re­ (Mr = c. 16000) contain four to five ribo­ cognized the same codon triplets in vitro somes [5], whereas those synthesizing myosin [13], a result subsequently corroborated by heavy chains (Mr =c. 200000) contain about comparison of protein and nucleic acid 50-60 ribosomes [6]. sequences. It is now known that in certain The rates of protein synthesis in pro­ organisms and in the mitochondria of karyotes and eukaryotes appear to be quite eukaryotes the genetic code differs from similar: values of 15 amino acids s-1 for that first established in E. coli (section P-galactosidase in E. coli [7], and seven 12.2.3). However, the latter code is so wide- The genetic code 517 Fig. 12.2 Electron micrograph showing the translation of silk fibroin mRNA on polysomes. The extended fibrous fibroin molecules can be seen emerging from the ribosomes (dark irregular particles). The length of the fibroin molecules increases from the top right to the bottom left of the frame, indicating that this is the 5'- 3' direction along the mRNA (courtesy of Dr Steven L. McKnight and Dr Oscar L. Miller, Jr). spread (it is found in the vast majority of It can be seen from Fig. 12.3 that 20 dif­ prokaryotes and eukaryotes, animals and ferent amino acids are specified by the plants) that we shall refer to it as the standard genetic code. Other amino acids are found genetic code. It is presented in Fig. 12.3. in proteins, but almost all of these are 518 The translation of mRNA Second letter u c A G uuu } UAU } UGU u uuc Phe ucc UAC Tyr UGC l Cys c u UUA } ""]UCA Ser UAA } UGA StoP A UUG Leu UCG UAG Stop UGG Trp G CAU u ..... CAC l His ::r wulcue ccuCCC CGUCGC c -, c CUA Leu CCA lPro CGA lArg c. I... CAA } Gln A .....Q) ..... CUG CCG CAG CGG G ,...CD Q) ,... u CD ..... AUU AAU } AGU } -, en AUC l Ile AWlACC AAC Asn AGC Ser c I... A ACA Thr -u.. AUA AAA ) LYS AGA } Arg A AUG Met ACG AAG AGG G GAU u GAC l Asp G wuGUC l Val GCC~u l Ala GGUGGC l Gly c GUA GCA GAA J Glu GGA A GUG GCG GAG GGG G Fig. 12.3 The standard genetic code. Termination codons are indicated as 'Stop'. generated by post-translational enzymic ation codons. These tRNAs occur in the modification of these 20 genetically-defined 'suppressor' strains of E. coli, so called for amino acids. The one known exception is the their ability to suppress particular classes rare amino acid, selanocysteine, which is of 'nonsense' mutants. Nucleotide sequence encoded by UGA, otherwise a termination analysis of such a mutant of a tRNA Tyr from codon (see below). As this is not a complete an amber suppressor strain showed that its reassignment of the meaning of the codon, anticodon is changed from 3'-AUG-5' to 3'­ but an alternative translational possibility, AUC-5'. Thus, it is able to insert tyrosine thought to depend on the broader context of into a polypeptide chain in response to the the mRNA, we shall consider it in section termination codon UAG, rather than to the 12.9.6 with other examples of 'suppression' tyrosine codon UAC [14]. The reason that of termination codons. such suppressor mutants are viable, and do It is also apparent from Fig. 12.3 that not exhibit premature termination of the three ofthe codons (UAA, UAG and UGA, bulk of normal proteins, is because the designated 'Stop') do not normally specify mutations occur in the minor, otherwise an amino acid, but are all signals for the redundant, representatives of certain pairs termination of the polypeptide chain. For of isoaccepting tRNAs. historical reasons relating to the type of Although inspection of Fig. 12.3 does not suppressor mutations (see below) that reveal a codon, the sole role of which is to characterized them, UAG and UAA are specify the start of a polypeptide chain, the also referred to as 'amber' and 'ochre', codon AUG fulfills this role as well as that of respectively; and UGA is sometimes called encoding methionine residues in the body 'opal' or 'umber'. Although the termination of the polypeptide chain. In E. coli the process does not involve tRNA (section initiation of protein synthesis involves the 12.4.3), certain mutant tRNAs have been AUG codon being decoded by a unique found that can recognize individual termin- species, N-formylmethionyl-tRNA (fMet- The genetic code 519 tRNA) [15]. The tRNA that inserts the Triplets coding for the same amino acid are initiating fMet into polypeptide chains, not distributed at random, but are grouped tRNAret, has a different nucleotide together so that they generally share the sequence from the tRNA that inserts Met same 5' and middle base (although there are internally: tRNA~et [16, 17].
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