Specific tRNA

The D, T VC, and extra arms help define a specific tRNA. 

Activation of individual amino acids occurs in the synthesis of aminoacyl tRNA. This process bums two ATP equivalents (forms pyrophosphate and AMP) and connects a specific amino acid to a specific tRNA. 

The next process is similar in both eukaryotes and prokaryotes, and involves the translation of mRNA molecules into polypeptides. This procedure involves many enzymes and two further types of RNA transfer RNA (tRNA) and ribosomal RNA (rRNA). There is a specific tRNA for each of the amino acids. These molecules are involved in the transportation and coupling of amino acids into the resulting... 

How, in turn, does the synthetase recognize its specific tRNA From extensive mutagenesis studies, it appears that the aminoacyl-tRNA synthetases recognize particular regions of the tRNA molecule, most often in their anticodon loops and/or in their acceptor stems. 

The stem-loop structure in the noncoding 3 region of selenoprotein mRNAs has also been termed a SECTS element in mammals although it has a different overall structure. ° In silica analysis of the human genome sequence, using this consensus SECTS element along with the presence of the characteristic UGA codon within an exon, has led to the discovery of several new selenoproteins, including a selenium-dependent methionine sulfoxide reductase. It has been shown that a specific complex exists for selenoprotein synthesis that shuttles between the nucleus and the cytosol. This possibly protects the preformed complex for nonsense-mediated decay to allow for more efficient selenoprotein synthesis. The specific tRNA needed for selenocysteine... 

Cysteine and tyrosine are described as conditionally essential (see text). Selenocysteine is not always included in lists of amino acids but it obeys the definition of an amino acid, it is present in the diet, is present in some mammalian proteins, and it is incorporated directly into these proteins as selenocysteine during the normal process of translation there is a specific tRNA for this amino acid the anticodon is AGU. 

Selenium is present in meat, seafood and cereals. The former two contain the highest levels. It is present in soil as inorganic selenium that enters the food chain via plants. In plant protein, it is present as selenomethionine and in animals as selenocysteine this difference is due to the metabolism of selenomethionine in the liver as part of the normal catabolic pathway for methionine (Chapter 8). Somewhat surprisingly, selenocysteine is incorporated into protein via a specific tRNA which possesses a UCA anticodon for this amino acid. 

Each stage described above involves at least one critical RNA-RNA and/or RNA-protein interaction. Initiation of reverse transcription involves the binding of a specific tRNA, which is packaged in the viral particle, to a short sequence of the viral RNA. Transcription and accumulation of viral RNA is dependent upon the sequence-specific interaction between two essential viral regulatory proteins. Tat and Rev, with their respective RNA sites, TAR and RRE (Figure 10.1). Tat is a transcriptional activator, whereas Rev acts post-transcriptionally to increase the cytoplasmic accumulation of the viral gag-pol and env messenger RNAs. Viral assembly is initiated by formation of an RNA-RNA dimer where... 

Amino acids are supplied to the ribosome complex of mRNA by transport RNA (tRNA). There is a specific tRNA for each amino acid that must be included into the proteins being synthesized. Every tRNA is in turn specific with respect to one nucleotide region (nucleotide... 

The three termination or stop codons, UAA, UAG, and UGA, do not specify amino acids and thus do not base pair with specific tRNAs. 

At least one specific type of tRNA is required per amino acid. In humans, there are at least fifty species of tRNA, whereas bacteria contain thirty to forty species. Because there are only twenty different amino acids commonly carried by tRNAs, some amino acids have more than one specific tRNA molecule. This is particularly true of those amino acids that are coded for by several codons. 

In all tRNAs the bases can be paired to form "clover-leaf" structures with three hairpin loops and sometimes a fourth as is indicated in Fig. 5-30.329 331 This structure can be folded into the L-shape shown in Fig. 5-31. The structure of a phenylalanine-carrying tRNA of yeast, the first tRNA whose structure was determined to atomic resolution by X-ray diffraction, is shown.170/332 334 An aspartic acid-specific tRNA from yeast,335 and an E. coli chain-initiating tRNA, which places N-formyl-methionine into the N-terminal position of proteins,336,337 have similar structures. These molecules are irregular bodies as complex in conformation as globular proteins. Numerous NMR studies show that the basic... 

The aminoacyl-tRNA synthetases join amino acids to their appropriate tRNA molecules for protein synthesis. They have the very important task of selecting both a specific amino acid and a specific tRNA and joining them. The enzymes differ in size and other properties. However, they all appear to function by a common basic chemistry that makes use of cleavage of ATP at Pa (Eq. 12-48) via an intermediate aminoacyl adenylate and that is outlined also in Eq. 17-36. These enzymes are discussed in Chapter 29. ... 

The results of these efforts show that no method of tRNA recognition is universal.2443 In some cases, e.g., for methionine- or valine-specific tRNAs, the synthetase does not aminoacylate a modified tRNA if the anticodon structure is incorrect. Although the anticodon is 7.5 ran away from the CCA end of the tRNA, the synthetases are large enzymes. Many of them are able to accommodate this large distance between a recognition site and the active site (Fig. 29-9A). For some other tRNAs the anticodon is not involved in recognition 245 For yeast tRNAphe residues in the stem of the dihydrouridine loop and at the upper end of the amino acid acceptor stem seem to be critical.241... 

Soon after the discovery of RNase Ti, it was suggested (70, 71) that it would become an important tool for the elucidation of nucleotide sequence in RNA. Indeed, since 1962 several workers have tried to use the enzyme for the nucleotide sequence analysis of RNA, especially in highly purified specific tRNA s. Finally, the brilliant research of Holley and his associates in 1965 resulted in the first elucidation of the complete nucleotide sequence of an RNA, alanine specific yeast tRNA, using RNase Ti as a main tool (29). Since then many successful elucidations of nucleotide sequence of various RNA s, using RNase Ti as a main tool, followed, and now the enzyme is well-known as an essential tool for the structural analysis of RNA. 

Activation of the amino-acids. This stage takes place in the cytoplasm. Each of the 20 amino-acids is covalently attached to a specific tRNA at the expense of ATP hydrolysis (i.e. it is an energy-driven process). Each amino-acid has a specific enzyme for this reaction to ensure that the correct amino-acid is linked to the tRNA molecule. 

Protein synthesis involves more than 100 different proteins and more than 30 kinds of RNA molecules. The process begins by the attachment of amino acids to specific tRNA molecules. Subsequent steps take place on the ribosome amino acids are transported to the ribosome on their tRNA carriers, and they do not leave the ribosome until they have become an integral part of a polypeptide chain. 

Kothe, U., Paleskava, A., Konevega, A. L., and Rodnina, M. V. (2006). Single-step purification of specific tRNAs by hydrophobic tagging. Anal. Biochem. 356, 148—150. 

Romer, R., and Hach, R. (1975). tRNA conformation and magnesium binding. A study of a yeast phenylalanine-specific tRNA by a fluorescent indicator and differential melting curves. Eur.J. Biochem. 55(1), 271—284. 

Transfer RNA (tRNA) transports the required amino acids from the cell s amino acid pool to the ribosome. Each type of amino acid can only be transported by its own specific tRNA molecule. The tRNA, together with its amino acid residue, binds to the mRNA already bound to the ribosome. It recognizes the point on the mRNA where it has to deliver its amino acid through the use of a consecutive sequence of three bases known as an anticodon, which is found on one of the loops of the tRNA (Figure 1.33(b)). This anticodon binds to the complementary codon of the mRNA. Consequently, the amino acids can only be delivered to specific points on the mRNA, which controls the order in which amino acid residues are added to the growing protein. This growth occurs from the N-terminal end of the protein. 

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. 

S. cerevisiae converts inorganic Se to SeMet and incorporates it into the cellular protein in place of Met. The biosynthesis of SeMet proceeds via SeCys in analogy to that of Met, as was demonstrated in a study of a mutant strain of yeast requiring Met for growth due to a lack of homocysteine methyl transferase activity. When grown in Se-containing media, this strain produces SeCys, but no SeMet (Mason, 1994). While most of the SeCys is synthesized without involving Se-specific enzymes, recent studies indicate that some of the SeCys is also produced by a specific tRNA and incorporated into a 25 kDa... 

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