Phenylalanine-tRNA

Transfer RNA (tRNA) Transfer RNAs are relatively small nucleic acids containing only about 70 nucleotides They get their name because they transfer ammo acids to the ribosome for incorporation into a polypeptide Although 20 ammo acids need to be transferred there are 50-60 tRNAs some of which transfer the same ammo acids Figure 28 11 shows the structure of phenylalanine tRNA (tRNA ) Like all tRNAs it IS composed of a single strand with a characteristic shape that results from the presence of paired bases m some regions and their absence m others... 

Page 1176 (Figure 28 11) is adapted from crystallographic coordinates deposited with the Protein Data Bank PDB ID 6TNA Sussman J L Holbrook S R Warrant R W Church G M Kim S H Crystal Structure of Yeast Phenylalanine tRNA I Crystallographic Refinement / Mol Biol 1978 126 607 (1978)... 

FIGURE 12.37 Tertiary interactions in yeast phenylalanine tRNA. The molecnle is presented in the conventional cloverleaf secondary strnctnre generated by intrastrand hydrogen bonding. Solid lines connect bases that are hydrogen-bonded when this cloverleaf pattern is folded into the characteristic tRNA tertiary strnctnre (see also Figure 12.36). 

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

FIGURE 28.11 Phenylalanine tRNA from yeast, (a) A schematic drawing showing the sequence of bases. Transfer RNAs usually contain a number of modified bases ( gray circles). One of these is a modified guanosine (G ) in the anticodon. Hydrogen bonds, where present, are shown as dashed lines, (b) The structure of yeast tRNAphe as determined by X-ray crystallography. 

Figure 25-26 (a) Generalized representation of a tRNA molecule. Each segment represents a nucleotide, the actual number and sequence of nucleotides varies with the tRNA. There are regions of intrachain basepairing (dashed lines). The nucleotide at the long end has a ribose with a free 3 -OH. The nucleotide at the short end is phosphorylated at 5 -OH. The three nucleotides of the anticodon loop pair with the appropriate bases in mRNA. (b) Three-dimensional picture of a tRNA to show the manner in which the chain is coiled. An excellent review article on the determination of the structure of phenylalanine tRNA by x-ray diffraction has been published, J. L. Sussman and S.-H. Kim, Science 192, 853 (1976). 

The tertiary structure of yeast phenylalanine tRNA. (a) The full tertiary structure. Purines are shown as rectangular slabs, pyrimidines as square slabs, and hydrogen bonds as lines between slabs. (Source From G. J. Quigley and A. Rich, Structural domains of transfer RNA molecules, Science, 194 796, 1976.) (b) Nucleotide sequence. Residues... 

When yeast phenylalanine tRNA is digested with a small amount of RNase (partial digest) such as T2 RNase, almost all of the cleavage sites are found in the anticodon loop. Explain this observation. 

Codons that specify the same amino acid are called synonyms. Most synonyms differ only in the third base of the codon for example GUU, GUC, GUA and GUG all code for valine. During protein synthesis, each codon is recognized by a triplet of bases, called an anticodon, in a specific tRNA molecule (see Topics G10 and H2). Each base in the codon base pairs with its complementary base in the anticodon. However, the pairing of the third base of a codon is less stringent than for the first two bases (i.e. there is some wobble base-pairing ) so that in some cases a single tRNA may base-pair with more than one codon. For example, phenylalanine tRNA, which has the anticodon GAA, recognizes both of the codons UUU and UUC. The third position of the codon is therefore also called the wobble position. 

Phenylalanine-tRNA ligase ALANINE-TRNA-LIGASE-RXN 0.1781820... 

When tRNA acylation kinetics was studied on ttyptophanyl-ARS-( tRNA) and lysil-ARS-(LystRNA) pairs, linear dependence between the aminoacylation reaction and the incubation period was identified just as in the preceding case. Phenylalanine tRNA acylation kinetics also testified to linear dependence. The results of this series of experiments are presented in Fig. 1 (A, B, and C) and Fig. 2 (A, B and C). In Fig. 1, also, are presented ES effects, and in Fig. 2 the influences of IPG on the protein-synthesizing cell mechanism is presented. Figure 2 demonstrates that ES and IPG... 

FIGURE 10.1 An electron density map section from a yeast phenylalanine tRNA crystal showing contour lines drawn about areas of high electron density. In the map can be seen what appear to be broken lengths of continuous chains of density. When electron density sections above and below are included, the chains assume greater continuity. 

FIGURE 10.15 A model of yeast phenylalanine tRNA built according to an electron density map computed using 2.8 A resolution X-ray data. The model is constructed of Kendrew parts connected together by tiny screws. It required several months to build and is roughly 6 feet by 4 feet by 3 feet in size. It was constructed at MIT in 1972 by the author. 

Tricyclic hypermodified nucleosides are found in archaeal and eukaryotic tRNAs and are frequently observed at position 34 (wobble base) or position 37 (adjacent to the anticodon). Position 37 typically contains a hypermodified nucleoside such as N -threonylcarbamoyladenosine (t A), 2-methylthio-N -isopentenyl-ade-nosine (ms i A-37), or wybutosine (yW). yW and its derivatives occur at position 37 in archaeal and eukaryotic phenylalanine tRNA (tRNAphe). The modifications serve to maintain the correct translational reading frame via hydrophobic interactions, which reinforce codon—anticodon pairing and prevent incorrect Watson—Crick base-pairing. Studies have shown that unmodified tRNA leads to translational defects that have been implicated in different pathological states. ... 

SWI/PAW] Swiatek, J., Pawlowski, T., Polarographic study of Ni and Zn ion interaction with tRNAs of wheat germ. Lupine phenylalanine tRNA and related subunits, J. Inorg. Biochem., 44, (1991), 163-171. Cited on pages 205, 206, 421. 

FIGURE 27.28 Phenylalanine tRNA. (a) A schematic drawing showing the sequence of bases. RNAs usually contain modified bases (green boxes), slightly different from those in other RNAs. The anticodon for phenylalanine is shown in red, and the CCA triplet which bears the phenylalanine is in blue. (6) The experimentally determined structure for yeast phenylalanine tRNA. Complementary base-pairing is present in some regions, but not in others. 

R. S. Brown, ]. C. Dewan and A. Klug, Crystallographic and biochemical investigation of the lead (11)-catalyzed hydrolysis of yeast phenylalanine tRNA, Biochemistry 1985, 24, 4785-4801 (pdb ltn2). 

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