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Spirin A.S. Ribosomes (1998)(337s).pdf |
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G
UU G Cs y UC G p U A O al G U G Tp G r CU G CC G CA G CG G AU G AC G AA G AG G GU G GC G GA G GG G Ag r U C A G U C A G U C A G U C A G...
3 . 2 . 2 . S e c o n d a r y Structure
An analysis of even the first tRNA primary structure (i.e. tRNAAla of yeast) revealed a number of interesting features concerning possible chain folding into the secondary structure. First of all, the 5'terminal section (positions 1 to 7) has a marked complementarity with the 3'-end-adjacent section (positions 66 to 72) if the sections are arranged in an antiparallel fashion. In addition, three inner sections of the tRNA chain display self-complementarity when folded upon themselves; because of this they are capable of forming hairpin-like structures. Pairing these complementary sequences results in the structure schematically presented in Fig. 3.1, commonly called a cloverleaf structure. It is remarkable that without exception the nucleotide sequences of all the tRNA species studied so far reveal similar selfcomplementarity features and correspondingly can be folded into very similar cloverleaves. The parts of the cloverleaf structure have been designated as follows: the acceptor stem (AA stem), with the universal 3'-terminal sequence CCA which accepts an amino acid residue; the dihydrouridylic arm (D arm), with the corresponding loop varying somewhat in length and containing, as a rule, between one and five dihydrouridylic acid residues; the anticodon arm (AC arm), with an anticodon loop of constant length equal to seven nucleotides; and the thymidyl-pseudouridylic arm (TΨ arm), which has a loop with the universal GTΨCGA or GTΨCAA sequence. In addition, the cloverleaf contains a variable loop (V loop) between the anticodon and TΨ arms; in tRNAAla this loop is only five nucleotides long whereas in other tRNA species it may reach 15 to 20 nucleotide residues in length (the latter is the case for tRNALeu, tRNASer, and bacterial tRNATyr). In animal mitochondrial tRNAs D-arm or T-arm may be reduced or fully absent....
Figure 3.5. Base pairing in RNA double helices: ball-and-stick drawing. Top to bottom, A:U and U:A; G:C and C:G; G:U and U:G. Solid circles are carbons, shaded circles - nitrogens, large open circles - oxygens, and small open circles - hydrogens; solid sticks are N-glycosidic bonds between the base and ribose....
Figure 3.8. Schematic drawing of the three-dimensional structure of yeast tRNAPhe. (Redrawn, with minor modifications, from S.-H. Kim, Nature 256, 679–681, 1975, with permission; see also A. Rich & S.-H. Kim, Scientific American 238, 52062, 1978)....
SCSase:(Pyridoxal-P)-Aminoacryloyl-tRNASec + H2O. SCSase:(Pyridoxal- P)- Aminoacryloyl- tRNASec + Se-P SCSase:(Pyridoxal-P)-Selenocysteinyl-tRNASec + Pi. SCSase:(Pyridoxal- P)- Selenocysteinyl- tRNASec SCSase:Pyridoxal-P + Selenocysteinyl-tRNASec....
Figure 4.2. Electron micrograph of ribosomes on an ultra-thin section of a rat liver cell. Fixation with glutaraldehyde. Ribosomes on the membranes of rough endoplasmic reticulum, as well as some clusters of free ribosomes, are seen. (Courtesy of Yu.S. Chentsov, Moscow State University)....
Figure 4.5. Electron micrograph showing predominantly circular, and sometimes spiral “G-like”, polyribosomes on the rough endoplasmic reticulum of somatotrope cytoplasm from the rat pituitary. (Fig. 2 from A.K. Christensen, L.E. Kahn & C.M. Bourne, Amer. J. Anat. 178, 1–10, 1987; reproduced with permission)....
Figure 5.1. Electron micrograph of the 70S ribosomes isolated from Escherichia coli. To achieve the contrast necessary for the particles to be seen in the electron microscope, the isolated 70S ribosomes are applied on an ultra-thin carbon film; the film with attached particles is treated by uranyl acetate solution and dried in air. The particles become embedded in uranyl acetate that fills cavities and grooves. The ribosomal particles having lower electron density than uranyl acetate appear negatively stained against the background of uranyl acetate. The arrows indicate the L7/L12 stalk described in the text. (Original photo by V. D. Vasiliev)....
Different electron microscopic projections of the bacterial (Escherichia coli) ribosomal 30S subunit and the corresponding crude morphological model are shown in Fig. 5.5. The 30S subunit is somewhat elongated, and its length is about 230 Å. The subunit may be subdivided into lobes which are referred to as the “head” (H), “body” (B), and “side bulge” or “platform” (SB). The groove separating the head from the body is quite distinct. The eukaryotic 40S subunit has a similar morphology, although two additional details of structure may be mentioned. The first is a protuberance, or “eukaryotic bill” on the head. Second, the end of the body distal to the head appears to be bifurcated due to the presence of some additional mass; this bifurcation is referred to as the “eukaryotic lobes” (Fig. 5.6). More reliable information about ribosomal subunits can be derived from electron microphotographs if averaged images rather than individual ones are examined. Averaging allows the statistical noise on electron microphotographs to be eliminated. This contributes towards a better visualization of the common features in the images of a given particle type. For such an averaging a set of particle images in the same projection is digitized using microdensitometer and processed with computer. The images are aligned precisely with respect to each other and then summed together to give an “average” image. All non-reproducible details of original images such as resulted from variations of stain distribution around the particle, radiationinduced structural alterations, variations in the background support film, are removed, leaving the common elements remained on the averaged image. Examples of such an averaging for negatively stained 30S subunits of Escherichia coli are given in Fig. 5.7 A. All three projections show that the head is separated from the remainder of the subunit by a distinct deep groove, the ‘neck’ being rather thin. An example of the averaging for negatively stained 40S subunits of rat liver ribosomes is presented in Fig. 5.7 B. Again, the “neck” is thin, and the bill of the head can be seen clearly in two of the...
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