TRNA molecules folded

Transfer RNA comes in many different types that can be distinguished by details in their nucleotide sequence. Regardless of sequence differences, all tRNA molecules fold up into the same general structure with several short double-helical regions... 

After synthesis, the pre-tRNA molecule folds up into the characteristic stem-loops structures (Fig. 1) and non-tRNA sequence is cleaved from the 5 and 3 ends by ribonucleases. In prokaryotes, the CCA sequence at the 3 end of the tRNA (which is the site of bonding to the amino acid) is enclosed by the tRNA gene but this is not the case in eukaryotes. Instead, the CCA is added to the 3 end after the trimming reactions by tRNA nucleotidyl transferase. Another difference between prokaryotes and eukaryotes is that eukaryotic pre-tRNA molecules often contain a short intron in the loop of the anticodon arm (Fig. 4). 

A tRNA molecule displays a three-base anticodon that is complementary to the codon on one end of its folded structure and carries the corresponding amino acid on the opposite end (Figure 12-1). 

The general structure of a tRNA molecule, (a) Representation in the form of a cloverleaf, which is the simplest way of observing the secondary structure, (b) A more realistic drawing of the three-dimensional folded structure. Color coding shows how the various loops in the cloverleaf structure correspond to the parts of the folded... 

In one of the earliest examples of the application of AUC to study RNA folding, Henley et al. (1966) demonstrated that the s2o,w values of tRNA molecules (unfractionated tRNAs from yeast) decreased with... 

E. coli contains clusters of up to seven tRNA genes separated by spacer regions, as well as tRNA genes within ribosomal RNA transcription units. Following transcription, the primary RNA transcript folds up into specific stem-loop structures and is then processed by ribonucleases D, E, F and P in an ordered series of reactions to release the individual tRNA molecules. 

While RNA molecules usually exist as single chains, they often form hairpin loops consisting of double helices in the A conformation (Moore, 1999). The best-known forms of RNA are the low-molecular-weight tRNA molecules. In all of them the bases can be paired to form a cloverleaf structure with three hairpin loops and sometimes a fourth. The cloverleaf structure of tRNA is further folded into an T-shape conformation with the anticodon triplet and the aminoacyl attachment CCA forming the two ends. 

RNA molecules form secondary structure by folding their polynucleotide chains via hydrogen bond formations between AU pairs and GC pairs. The thermochemical stability of forming such hydrogen bonds provides useful criterion for deducing the cloverleaf secondary structure of tRNAs that is, tRNA molecules are folded into DFI... 

Both fluorescence and NMR techniques have been used in studies involving lanthanide-RNA interactions. Fluorescence enhancement of several hundred fold was observed on interaction of Tb3+ and Eu3+ with tRNA from E. coli. Enhancement was not observed in the case tRNA from yeast. From the fluorescence measurements the conclusion [105] that there are four tight equivalent sites for Eu3+ per tRNA molecule containing approximately 80 nucleotides with Kd of 6 x 10-6 M. X-ray studies [61] also indicate four lanthanide binding sites on tRNA. 

At least one aminoacyl-tRNA synthetase exists for each amino acid. The diverse sizes, subunit composition, and sequences of these enzymes vv ere be vildering for many years. Could it be that essentially all synthetases evolved independently The determination of the three-dimensional structures of several synthetases follo ved by more-refined sequence comparisons revealed that different synthetases are, in fact, related. Specifically, synthetases fall into tvv o classes, termed class I and class II, each of vv hich includes enzymes specific for 10 of the 20 amino acids (Table 29.2). Glutaminyl-tRNA synthetase is a representative of class I. The activation domain for class I has a Rossmann fold (Section 16.1.101. Threonyl-tRNA synthetase (see Figure 29.11) is a representative of class II. The activation domain for class II consists largely of P strands. Intriguingly, synthetases from the tvv o classes bind to different faces of the tRNA molecule (Figure 29.14). The CCA arm of tRNA adopts different conformations to accommodate these interactions the arm is in the helical conformation observed for free tRNA (see Figures 29.5 and 29.6) for class II enzymes and in a hairpin conformation for class I enzymes. These two classes also differ in other ways. 

In standard tRNA molecules, each of these bases participates in bonds that produce the folded L-shaped molecule. Thus, the mitochondrial tRNA molecule seems to be stabilized by fewer interactions. The three-dimensional configurations of these molecules are not known with certainty possibly they differ from the standard L-shape, and mitochondrial tRNA engages in a different type of interaction with the ribosome than standard tRNA molecules do. 

Figure 4.1 depicts the cloverleaf structure of a tRNA the bars represent base pairs in the stems. There are four arms and three loops - the acceptor, D, T pseudouridine C, and anticodon arms, and D, T pseudouridine C, and anticodon loops. Sometimes tRNA molecules have an extra or variable loop (shown in yellow in Fig. 4.1). The synthesis of transfer RNA proceeds in two steps. The body of the tRNA is transcribed from a tRNA gene. The acceptor stem is the same for all tRNA molecules and added after the synthesis of the main body. It is replaced often during lifetime of a tRNA molecule. The 3-D structure of a yeast tRNA molecule, which can code for the amino acid serine, shows how the molecule is folded with the...

After the ribosome has read a codon off the mRNA strand, a transfer RNA (tRNA) molecule coimects to the mRNA codon, A tRNA molecule mainly contains a three-base section, the anticodon, which is complementary to a specific codon at the mRNA, and the associated amino acid residue. Thus the tRNA molecules serve as translators between the base codons and the amino acids. The ribosome separates the amino acid from the tRNA and attaches it to the already synthesized part of the protein sequence. This process continues until a stop codon is reached. Eventually, the protein is released into the aqueous solvent within the cell. It is widely believed that in this moment the protein is still unstructured and the formation of the functional structure is a spontaneous folding process. Larger proteins that would exhibit an increased tendency to misfold in the complex and crowded environment are often encapsulated in chaperons that assist in the folding process. 

Transfer RNA (tRNA) serves as a carrier of amino acid residues for protein synthesis. Transfer RNA molecules also fold into a characteristic secondary structure (marginal figure). The amino acid is attached as an aminoacyl ester to the 3 -terminus of the tRNA. Aminoacyl-tRNAs are the substrates for protein biosynthesis. The tRNAs are the smallest RNAs (size range—23 to 30 kD) and contain 73 to 94 residues, a substantial number of which are methylated or otherwise unusually modified. Transfer RNA derives its name from its role as the carrier of amino acids during the process of protein synthesis (see Chapters 32 and 33). Each of the 20 amino acids of proteins has at least one unique tRNA species dedicated to chauffeuring its delivery to ribosomes for insertion into growing polypeptide chains, and some amino acids are served by several tRNAs. For example, five different tRNAs act in the transfer of leucine into... 

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