| Home / lib / B_Biology / | ||
Spirin A.S. Ribosomes (1998)(337s).pdf |
|
Size 4.4Mb Date Nov 14, 2004 |
A
UU A Tr y UC A c U A O hre A U G A ber A m CU A CC A CA A CG A AU A AC A AA A AG A GU A GC A GA A GG A Hs i Gn i An s Ls y Ap s Gu l...
Table 2.2. Variations in mitochondrial genetic code. Organism UGA Stop Trp Trp Trp Trp Trp Trp Trp Trp Trp Trp Trp AUA Ile Met Met — Met Met Met — ND Met — — AAA Lys — — Asn — — — Asn ND — — — AAA AGG Arg Stop Gly Ser Ser Ser Ser Ser — — — — CUN Leu — — — — — — — ND Thr — — UAA Stop — — — — — — Thr? ND — — —...
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....
Structurally, the paired (double-stranded) part of each arm of tRNA is a double helix. The RNA double helix contains 11 pairs of nucleotide residues per turn. The parameters of this helix are similar to hose of the A-form of DNA. The double helix is the main element of tRNA secondary structure. In addition to the canonical Watson–Crick base pairs G:C and A:U, the double-stranded regions of tRNA often contain the G:U pair, which is close by its steric parameters to the canonical pairs (Fig. 3.5). The secondary structure of unpaired regions, such as loops and the acceptor ACCA- or GCCA terminus, is of a different type. A single-helical arrangement of several residues maintained by base-stacking interactions can occur here. The structure of the anticodon loop is particularly interesting (Fig. 3.6); three anticodon bases and two subsequent bases adjacent to the anticodon from the 3'-side are stacked with each other and form a single-stranded, right-handed helix; the first base of the anticodon is located at the top of the helix, and the groups capable of forming hydrogen bonds of all three anticodon bases are exposed outward. Such an orientation of the anticodon bases is extremely important for interaction with the mRNA codon. The features of the primary structure of the anticodon loop contribute specifically to the maintenance of the spatial arrangement described: the hypermodified purine base directly adjacent to the anticodon from the 3'-side as well as the next base, usually also a purine, provides for stable stacking interactions in the single-stranded helix, while the two “small” pyrimidine bases at the 5'-side of the anticodon, and particularly the adjacent invariant U, make a sharp bend in the chain (between the anticodon and U) and...
AC arm Gm AA U Y Cm A AΨ G m5C AU CG V arm CG 2G m2 A G7 C m2G mG GC U A AU C GC A A U D arm G G G hU G hU C Ψ T G U G Um 5CU U A G G C Gp G m1A C C A C A G A A U U C G C A C C A OH U TΨ arm AA arm...
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....
The total energy balance of the overall reaction ∆G is equal to about –30 kcal per mole of amino acid or – 6000 kcal per mole of protein with a length of 200 amino acid residues. Here, only the chemical aspect of the process has been taken into account. It is important to analyze to what extent this estimate may be changed if we take into account entropy loss due to the ordered
0'...
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)....
Figure 5.11. Stereo representation of the three-dimensional density map of the E. coli 70S ribosome in the nonoverlap projection viewed from the L7/L12 stalk side (J. Frank, J. Zhu, P. Penczek, Y. Li, S. Srivastava, A. Verschoor, M. Radermacher, R. Grassucci, R.K. Lata & R.K. Agrawal, Nature 376, 441–444, 1995). The 3D reconstruction is based on so-called random-conical-tilt-series approach. This elegant approach exploits the random azimutal orientations of asymmetrical particles lined in one (or several) preferred orientation relative to the support film. It starts from a pair of micrographs showing the same field both from a high tilt angle and without tilt. The tilted-field image is recorded first and only particle images from this field enter the 3D reconstruction. The untilted-specimen images are used as references to convert the random planar particle orientations in the real definite projections. The first 3D reconstruction is then improved by iterative procedures. Finally, the orientation of each projection is determined individually by matching it to computed projections of the previous model. This 25Å 3D reconstruction of the 70S ribosome is obtained by combining 4300 individual images. (Courtesy of J. Frank, New York State Department of Health, Albany)....
Figure 5.12. Stereo representation of the three-dimensional reconstruction of the E. coli 70S ribosome in the nonoverlap projection viewed from the side opposite to the L7/L12 stalk (H. Stark, F. Miller, E.V. Orlova, M. Schatz, P. Dube, T. Erdemir, F. Zemlin, R. Brimacombe & M. van Heel, Structure 3, 815–821, 1995). The 3D reconstruction is based on “angular reconstruction” approach which allows to determine the relative angular orientations of the particles arbitrarily arranged within a vitreous ice matrix. This 23Å 3D reconstruction is derived from 2447 individual images. (Courtesy of M. van Heel and H. Stark, Fritz Haber Institute, the Max Planck Society, Berlin)....
| © 2007 eKnigu | ||