TRNA cloverleaf

The bases within the base-paired region of each arm of the tRNA cloverleaf stack in a manner similar to the base stacking described in Chapter 25 for DNA. In addition to the base stacking within base-paired regions, there is also stacking of one helix on top of another in the tRNA molecule. In particular, the acceptor stem stacks with the T PC stem and loop to form one nearly continuous stacked double helix. 

Second, the tRNA must be able to recognize the appropriate codon on the mRNA that calls for that amino acid. This is mediated through a sequence of three bases called the anticodon, which is located at the bottom of the tRNA cloverleaf (refer to Figure 24.10). The anticodon sequence for each tRNA is complementary to the codon on the mRNA that specifies a particular amino acid. As you can see in Figure 24.11, the anticodon-codon complementary hydrogen bonding will bring the correct amino acid to the site of protein synthesis. 

F. 14.17. The tRNA cloverleaf. Bases that commonly occur in a particular position are indicated by letters. Base-pairing in stem regions is indicated by lines between the strands. The locations of the modified bases dihydrouridine (D), ribothymidine (T), and pseudouridine ( F) are indicated. 

The other arms of the tRNA cloverleaf also have distinctive conserved features. The modified base dihydrouridine (D) is typically present in the loop that closes off a short 3- or 4-bp stem following the acceptor stem. This stem and loop are therefore called the D-arm. The anticodon arm consists of a 5-bp helix closed by a loop that contains the trinucleotide anticodon. Following the anticodon arm is the variable loop, which can contain 3-21 nucleotides, with a stem as long as 7 bp, depending on the particular tRNA. The modified bases pseudouridine (4>) and ribo-thymidine (T) are usually present in the loop of the T FC arm, so named because of the presence of this highly conserved sequence. 

FIGURE 1.20 Structures of tRNA. Cloverleaf model of secondary structure and 3-D structure of yeast tRNA " (A) In the cloverleaf model, the bases that form base-base tertiary H-bonds are connected by lines. Circles and parentheses indicate conserved and semiconserved bases, respectively. (B) In this schematic representation of a 3-D structure, the ribose-phosphate backbone is shown as a continuous tube. Base pairs are presented by long connected bars and single bases by short bars. Tertiary base-base H-bonds are indicated by filled bars between the two bases. Adapted from S. R. Holbrook, J. L. Sussman, R. W. Warrant, and S. H. Kim (1978). JMB 123, 631, with permission. 

Among the 76 bases in the tRNA molecule, only 4 bases (D16, D17, G20, and U47) are not involved in base stacking. Some of the bases are invariant in all tRNA sequences, and they are mainly involved in the tertiary interactions. The yeast tRNA cloverleaf contains 20 bp consisting of 52 H-bonds. The tertiary interactions contribute at least 40 additional H-bonds to the structure. All the tertiary H-bonds are of the non-Watson-Crick type and are highly twisted and bent. Due to extensive base pairing and stacking in tRNA, all the bases except the S terminal CCA and the three anticodon bases are inaccessible to solvent. 

FIGURE 12.36 The complete nncleodde sequence and cloverleaf strnctnre of yeast alanine tRNA. 

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). 

Figure 4.16 The structure of yeast tRNAplle (a) the cloverleaf form of the base sequence tertiary base-pairing interactions are represented by thin red lines connecting the participating bases. Bases that are conserved in all tRNAs are circled by solid and dashed lines, respectively. The different parts of the structure are colour-coded, (b) The X-ray structure showing how the different base-paired stems are arranged to form an L-shaped molecule. The sugar-phosphate backbone is represented as a ribbon with the same colour scheme as in (a). (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

The tRNAs are 65-110 nucleotides long and their backbones fold back to allow for intramolecular hydrogen binding (base pairing or hybridization) to form a cloverleaf secondary structure. 

FIGURE 27-8 Pairing relationship of codon and anticodon, (a) Alignment of the two RNAs is antiparallel. The tRNA is shown in the traditional cloverleaf configuration, (b) Three different codon pairing relationships are possible when the tRNA anticodon contains inosinate. 

Figure 5-30 Schematic cloverleaf structure of a phenylalanine-specific transfer RNA (tRNA he) of yeast. The dots represent pairs or triplets of hydrogen bonds. Nucleosides common to almost all tRNA molecules are circled. Other features common to most tRNA molecules are also marked. The manner in which the anticodon may be matched to a codon of mRNA is indicated at the bottom.

The complete tRNA contains 75 nucleotides. Sketch the rest of the molecule in the cloverleaf representation. Label the 5 and 3 ends and the dihydrouridine and T /C loops. What are the last three nucleotides at the 3 end ... 

The first surprise was that these molecules are much longer than seems necessary for the formation of adapters. In addition, 10-20% of their bases are modified greatly from their original form.171 Another surprise was that the anticodons are not all made up of "standard" bases. Thus, hypoxanthine (whose nucleoside is inosine) occurs in some anticodons. Conventional "cloverleaf" representations of tRNA, which display their secondary structures, are shown in Figs. 5-30 and 29-7. However, the molecules usually have an L shape rather than a cloverleaf form (Figs. 5-31 and 29-6),172 and the L form is essential for functioning in protein synthesis as indicated by X-ray and other data.173 Three-dimensional structures, now determined for several different tRNAs,174 175 are all very similar. Structures in solution are also thought to be... 

Cloverleaf and L forms. Interconversion between the cloverleaf and L forms of tRNA molecules can be pictured as in Eq. 29-2. Notice that in the L... 

Figure 29-7 (A) Generalized cloverleaf diagram of all tRNA sequences except for initiator tRNAs numbered as in yeast tRNAae (Fig. 5-30). Invariant bases A, C, G, T, U, and semivariant bases Y (pyrimidine base), R (purine base), H (hypermodified purine base). The dotted regions (a, P, variable loop) contain different numbers of nucleotides in various tRNA sequences. See Rich.179 (B) L form of the yeast phenyl-alanine-specific tRNAphe. The structure is the same as that in Fig. 5-31 but has recently been redetermined at a resolution of 0.20 nm.175 The new data revealed the presence of ten bound Mg2+ ions (green circles) as well as bound spermine (green).

The processing steps of E. coli tyrosine tRNATyr are diagrammed in figure 28.15. The initial transcript has, in addition to the 85 nucleotide residues of the final product, 41 residues at the 5 end and 225 residues at the 3 end it probably folds to form the typical cloverleaf structure of the mature tRNA prior to processing. Processing begins when a specific endonuclease called RNaseF cleaves the precursor... 

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... 

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