TRNA, tertiary structure

Interactions of the same water molecules with RNA nucleotides (via H-bonding) and metal ions (via inner-sphere coordination) could stabilize specific metal ion-nucleic acid complexes (e.g. in Mg + -tRNA chelates) and also create the possibility for direct proton transfer through a water chain that could play a role in ribozyme-metal ion catalysis and in the mechanism of metal-dependent nucleases and polymerases. Similar types of H-bonds between different nucleotide residues have been found in tRNA tertiary structures, where they provide additional stabilization of tertiary interactions. 

FIGURE 12.7 Ribbon diagram of the tRNA tertiary structure. Numbers represent the consensus nucleotide sequence. The locations of... 

It was earlier considered that all the amino acid-activating synthetases were derived from a single primeval synthetase , so that all synthetases would have similar structures. Surprisingly, however, this is not the case. When the primary sequences, and in part the secondary and tertiary structures, of all the synthetases had been determined, clear differences in their construction became obvious. The aminoacyl-tRNA synthetases consist either of one single polypeptide chain (a) or of two or four identical polypeptides (ot2 or 04). In addition, there are heterogeneously constructed species with two sets of two identical polypeptide chains (OC2P2). This nomenclature indicates that, for each synthetase, a or P refers to a primary structure. The number of amino acids can vary from 334 to more than 1,000. 

To say that RNA molecules are single-stranded molecules is not the same as saying that they have no higher-order structures, hi fact they have several. The formation of Watson-Crick complementary base pairs is a driving force for formation of higher-order structures. These include the stem-loop and hairpin secondary structures, as well as more complex tertiary structures. Of particular note, are the complex structures for transfer RNAs, tRNAs. Examples are provided in figure 12.5 (note that there are several nnnsnal bases in these structnres this is typical of tRNAs but not of RNA molecnles in general). These strnctures are intimately related to the function of these molecnles as adaptors in the process of protein synthesis, as developed in the next chapter. 

In contrast to DNA, RNAs do not form extended double helices. In RNAs, the base pairs (see p.84) usually only extend over a few residues. For this reason, substructures often arise that have a finger shape or clover-leaf shape in two-dimensional representations. In these, the paired stem regions are linked by loops. Large RNAs such as ribosomal 16S-rRNA (center) contain numerous stem and loop regions of this type. These sections are again folded three-dimensionally—i.e., like proteins, RNAs have a tertiary structure (see p.86). However, tertiary structures are only known of small RNAs, mainly tRNAs. The diagrams in Fig. B and on p.86 show that the clover-leaf structure is not recognizable in a three-dimensional representation. 

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). 

RNA molecules are unable to form extended double helices, and are therefore less highly ordered than DNA molecules. Nevertheless, they have defined secondary and tertiary structures, and a large proportion of the nucleotide components enter into base pairings with other nucleotides. The examples shown here are 5S-rRNA (see p. 242), which occurs as a structural component in ribosomes, and a tRNA molecule from yeast (see p.82) that is specific for phenylalanine. 

Base stacking effects and some unusual forms of hydrogen bonding between the bases cause tRNAs to take on a tertiary structure that is roughly L-shaped. 

The structures of all the aminoacyl-tRNA synthetases of E. coli have been determined. Researchers have divided them into two classes (Table 27-7) based on substantial differences in primary and tertiary structure and in reaction mechanism (Fig. 27-14) these two classes are the same in all organisms. There is no evidence for a common ancestor, and the biological, chemical, or evolutionary reasons for two enzyme classes for essentially identical processes remain obscure. 

The start of protein synthesis is signalled by specific codon-anticodon interactions. Termination is also signalled by a codon in the mRNA, although the stop signal is not recognized by tRNA, but by proteins that then trigger the hydrolysis of the completed polypeptide chain from the tRNA. Just how the secondary and tertiary structures of the proteins are achieved is not yet clear, but certainly the mechanism of protein synthesis, which we have outlined here, requires little modification to account for preferential formation of particular conformations. 

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... 

The complex folded structures adopted by tRNAs illustrates the fact that nucleic acids with a properly adjusted primary sequence can adopt complex secondary and tertiary structures. Apropos of this, Francis Crick once said that transfer RNA is an RNA molecule trying to look like a protein. 

Removal of internal sequences in eukaryotes is not restricted to mRNA processing. It also occurs in the processing of rRNA and some tRNAs. In tRNAs the mechanism appears to be different in that the signal for splicing originates not from the primary sequence but from the secondary or tertiary structure of the pre-tRNA. 

Base-stacking interactions are an important stabilizing force in nucleic acid structures. Describe how base stacking contributes to the tertiary structure of the tRNA molecule. 

The D and t loops in tRNA interact with each other to form the tertiary structure, leaving only the anticodon with a single-stranded loop able to be cleaved by RNase. 

Unlike the double-stranded nature of DNA, RNA molecules usually occur as single strands. This does not mean they are unable to base-pair as DNA can. Complementary regions within an RNA molecule often base-pair and form complex tertiary structures, even approaching the three-dimensional nature of proteins. Some RNA molecules, such as transfer RNA (tRNA) possess several helical areas and loops as the strand interacts with itself in complementary sections. Other hybrid molecules such as the enzyme RNase P contain protein and RNA portions. The RNA part is highly complex with many circles, loops, and helical regions creating a convoluted structure. 

The tertiary structure of all tRNAs are likewise similar. All known tRNAs are roughly L-shaped, with the anticodon on one end of the L and the acceptor stem on the other. Each stem of the L is made up of two of the stems of the cloverleaf, arranged so that the base pairs of each stem are stacked on top of each other. The parts of the molecule that are not base-paired are involved in other types of interactions, termed tertiary interactions. The tertiary structures of tRNAs thus reflect the dual functions of the molecule The anticodons are well-separated from the acceptor stems. This feature allows two tRNA molecules to interact with two codons that are adjacent on an mRNA molecule. See Figure 10-4. 

The replacement of thymine by uracil has no significant effect on the hydrogen bonding, as RNA does not use base pairing to form complementary dimers it is of less importance than it would be for DNA, but the removal of the methyl group may have an influence on the tertiary structures that RNA can adopt. From this it is clear that DNA is a better method of storing information whereas RNA is more suited to turn that information into a protein sequence. This is done by the ribosome, composed of ribosomal RNA (rRNA), which translates the codons of the mRNA sequence into a protein by matching three base sequences to those of tRNA that have the appropriate amino acids attached. 

Just as main-chain NH 0=C hydrogen bonds are important for the stabilization of the a-helix and / -pleated sheet secondary structures of the proteins, the Watson-Crick hydrogen bonds between the bases, which are the side-chains of the nucleic acids, are fundamental to the stabilization of the double helix secondary structure. In the tertiary structure of tRNA and of the much larger ribosomal RNA s, both Watson-Crick and non-Watson-Crick base pairs and base triplets play a role. These are also found in the two-, three-, and four-stranded helices of synthetic polynucleotides (Sect. 20.5, see Part II, Chap. 16). 

Fig. 20.8. Three-dimensional structure of phenylalanine specific tRNA from yeast. Watson-Crick type base pairs indicated by slabs, nonstandard base-base interactions that stabilize the tertiary structure are denoted a to h. Invariant and semi-invariant nucleotides are shaded, the four double helical regions are indicated by a a-(amino add) arm, Tarm, D arm, a.c. (anticodon arm [696]...

Figure 6 Sites of specific binding of Mg + ions in yeast tRNA . (a) secondary structure. (Ref i49. Reproduced by permission of American Society for Biochemistry Molecular Biology) (b) tertiary structure. (Ref 150. Reproduced by permission of Oxford University Press)...

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