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Bacterial ribosomes contain about 65% rRNA and about 35% protein. They have a diameter ofabout 18 nm and a sedimentation coefficient of 70S.Bacterial ribosomes consist of two subunits of unequal size (Fig.26-12), the larger having a sedimentation coefficient of 50S and thesmaller of 30S. The 50S subunit contains one molecule of 5S rRNA,one molecule of 23S rRNA, and 34 proteins. The 30S subunit containsone molecule of 16S rRNA and 21 proteins.
The proteins are designatedChapter 26 Protein Metabolism909Figure 26-13 Predicted folding patterns in E. coli16S and 5S rRNAs, based on maximizing the potential intrastrand base pairing.by numbers. Those in the large 50S subunit are numbered LI to L34 (Lfor large) and those in the smaller subunit SI to S21 (S for small).
Allthe ribosomal proteins of E. coli have been isolated and many havebeen sequenced. Their variety is enormous, with molecular weightsfrom about 6,000 to 75,000.The sequences of nucleotides in the rRNAs of many organismshave been determined. Each of the three single-stranded rRNAs ofE. coli has a specific three-dimensional conformation conferred by intrachain base pairing.
Figure 26-13 shows a postulated representationof the 16S and 5S rRNAs in a maximally base-paired conformation.The rRNAs appear to serve as a framework to which the ribosomalproteins are bound.In a method pioneered by Masayasu Nomura, the ribosome can bebroken down into its RNA and protein components, then reconstitutedin vitro. When the 21 different proteins and the 16S rRNA of the 30Ssubunit are isolated from E.
coli and then mixed under appropriateexperimental conditions, they spontaneously reassemble to form 30Ssubunits identical in structure and activity to native 30S subunits.Similarly, the 50S subunit can assemble itself from its 34 proteins andits 5S and 23S rRNAs, providing the 30S subunit is also present. Eachof the 55 proteins in the bacterial ribosome is believed to play a role inthe synthesis of polypeptides, either as an enzyme or as a structuralcomponent in the overall process. However, the detailed function ofonly a few of the ribosomal proteins is known.The two ribosomal subunits have irregular shapes.
The threedimensional structures of the 30S and 50S subunits of E. coli ribosomes (Fig. 26-12) have been deduced from x-ray diffraction, electronmicroscopy, and other structural methods. The two oddly shaped subunits fit together in such a way that a cleft is formed through which themRNA passes as the ribosome moves along it during the translationprocess and from which the newly formed polypeptide chain emerges(Fig. 26-14).The ribosomes of eukaryotic cells (other than mitochondrial andchloroplast ribosomes) are substantially larger and more complex thanbacterial ribosomes (Fig. 26-12).
They have a diameter of about 23 nmand a sedimentation coefficient of about 80S. They also have two subunits, which vary in size between species but on average are 60S and40S. The rRNAs and most of the proteins of eukaryotic ribosomes havealso been isolated. The small subunit contains an 18S rRNA, and thelarge subunit contains 5S, 5.8S, and 28S rRNAs. Altogether, eukaryotic ribosomes contain over 80 different proteins. (In contrast, the ribosomes of mitochondria and chloroplasts are somewhat smaller andsimpler than bacterial ribosomes.)Figure 26-14 Two different views of models of anE. coli ribosome, showing the relationship betweenthe 30S and 50S subunits. The arrow indicates thecleft between the subunits.5S rRNAMasayasu Nomura910Part IV Information PathwaysTransfer RNAs Have Characteristic Structural FeaturesRobert W.
Holley1922-1993To understand how tRNAs can serve as adapters in translating thelanguage of nucleic acids into the language of proteins, we must firstexamine their structure in more detail. As shown in Chapter 12, tRNAsare relatively small and consist of a single strand of RNA folded into aprecise three-dimensional structure (see Fig. 12-27a). In bacteria andin the cytosol of eukaryotes, tRNAs have between 73 and 93 nucleotideresidues, corresponding to molecular weights between 24,000 and31,000. (Mitochondria contain distinctive tRNAs that are somewhatsmaller.) As we have noted earlier in this chapter, there is at least onekind of tRNA for each amino acid; for some amino acids there are twoor more specific tRNAs. At least 32 tRNAs are required to recognize allthe amino acid codons (some recognize more than one codon), but somecells have many more than 32.Many tRNAs have been isolated in homogeneous form.
In 1965,after several years of work, Robert W. Holley and his colleaguesworked out the complete nucleotide sequence of alanine tRNA(tRNA^*1) from yeast. This, the very first nucleic acid to be sequencedin its entirety, was found to contain 76 nucleotide residues, ten ofwhich have modified bases. Its complete base sequence is shown inFigure 26-15.Since Holley's pioneering studies, the base sequences of manyother tRNAs from various species have been worked out and have revealed many common denominators of structure. Eight or more of thenucleotide residues of all tRNAs have unusual modified bases, many ofwhich are methylated derivatives of the principal bases. Most tRNAshave a guanylate (pG) residue at the 5' end, and all have the trinucleotide sequence CCA(3') at the 3' end.
All tRNAs, if written in a form inwhich there is maximum intrachain base pairing through the allowedSite for amino acidattachmentFigure 26-15 The nucleotide sequence of yeasttRNAAla as deduced by Holley and his colleagues.The cloverleaf conformation shown here is that inwhich intrastrand base-pairing is maximal. In addition to A, G, U, and C, the following symbols areused for the modified nucleotides: ip, pseudouridine;I, inosine; T, ribothymidine; DHU, 5,6-dihydrouridine; m1!, 1-methylinosine; mxG, 1-methylguanosine; m2G, A^-dimethylguanosine.
The modifiedbases are shaded in red, and most are illustrated inFig. 25-25. The blue lines between the parallel sections indicate base pairs. The anticodon is capableof recognizing three codons for alanine (GCA, GCU,and GCC). Other features of tRNA structure areshown in Fig. 26-16. Note the presence of G=Ubase pairs in both the amino acid arm (top) and theDHU arm (left), signified by a blue dot to indicatea non-Watson-Crick pairing. In RNAs guanosine isoften found base-paired with uridine, although theG=U pair is not as stable as the Watson—CrickG=C pair (Chapter 12)Anticodontriplet911Chapter 26 Protein MetabolismFigure 26-16 General structure of all tRNAsWhen drawn with maximum intrachain base pairing, all tRNAs show the cloverleaf structure.
Thelarge dots on the backbone represent nucleotideresidues, and the blue lines represent base pairings. Characteristic and/or invariant residues common to all tRNAs are shaded in red. TransferRNAs differ in length, from 73 to 93 nucleotides.Extra nucleotides occur in the extra arm or in theDHU arm. At the end of the anticodon arm is theanticodon loop, which always contains seven unpaired nucleotides. The DHU arm contains up tothree DHU residues, depending on the tRNA. Insome tRNAs the DHU arm has only three hydrogen-bonded base pairs In addition to the symbols explained in Fig.
26-15: Pu, purine nucleotide;Py, pyrimidine nucleotide; Gx, guanylate or 2-0methylguanylate.pairs A=U, G=C, and G=U (see Fig. 12-26), form a cloverleaflikestructure with four arms; the longer tRNAs have a short fifth or extraarm (Fig. 26-16; also evident in Fig. 26-15). The actual three-dimensional structure of a tRNA looks more like a twisted L than a cloverleaf(Fig. 26-17).Two of the arms of a tRNA are critical for the adapter function. Theamino acid or AA arm carries a specific amino acid esterifled by itscarboxyl group to the 2'- or 3'-hydroxyl group of the adenosine residueat the 3' end of the tRNA. The anticodon arm contains the anticodon.The other major arms are the DHU or dihydrouridine arm, whichcontains the unusual nucleotide dihydrouridine, and the Ti/fC arm,which contains ribothymidine (T), not usually present in RNAs, andpseudouridine (i/0, which has an unusual carbon-carbon bond betweenthe base and pentose (see Fig.
25-25). The functions of the DHU andT(//C arms have not yet been determined.Ti/rC armAmmoacid arm56DHUarm(residues10-25)20Anticodonarm32Anticodon3'AC Amino acidContainstwo or moreDHU residuesat differentpositions^ Extra armVariable in size,not present inall tRNAsAnticodonarmWobbleposition5'3'AnticodonFigure 26—17 The three-dimensional structure ofyeast tRNAphe deduced from x-ray diffraction analysis. It resembles a twisted L. (a) A schematic withthe various arms identified in Fig. 26-16 shaded indifferent colors (b) A space-filling model. Colorcoding is the same in both representations.
Thethree bases of the anticodon are shown in red andthe CCA sequence at the 3' end (the attachmentpoint for amino acids) is shown in orange. The T*//Cand DHU arms are blue and yellow, respectivelyPart IV Information Pathways912HJ\—+IIO—P—0—P—O—P—O—CHIIINH 3 OAmino acidHR—C+11OFigure 26—18 Aminoacylation of a tRNA by aminoacyl-tRNA synthetases. The first step is formationof aminoacyl adenylate, which remains bound tothe active site. In the second step the aminoacylgroup is transferred to the tRNA.
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