RNA, transfer

Transfer RNAs (tRNAs) have two functions that link the RNA and protein information systems. First, they must accept a specific amino acid, one of 20. They do this with accuracy greater than 99.99 percent, even distinguishing between chemically similar structures. But tRNAs share functions as well. The translating ribosome must be able to insert any of the 20 amino acids at the correct position in the growing polypeptide chain, with roughly the same efficiency. Otherwise, the number of proteins that a cell could make would be severely limited. This means that all tRNAs must have common structural features that are recognized by the ribosome. 

You can see the common structural features of tRNAs at both the secondary and tertiary levels. Only a few sequences or bases are common to all tRNAs. The common secondary structure of tRNAs is the cloverleaf pattern, where the 5 and 3 sequences are base-paired, and then the other three stem-loops of the cloverleaf are formed by 

Transfer RNA (tRNA) or soluble RNA (sRNA) molecules have been examined at high resolution (Rich, 1977). Transfer RNAs are relatively compact single strands of nucleic acid of 23-30kDa in size that contain 74-94 nucleotides (nt). Individual tRNA transport a covalently attached amino acid to the ribosome and facilitate its proper incorporation into a protein sequence, the latter of which is specified by the sequence of nucleotides read as a triplet code in the mRNA. Thus a tRNA molecule contains two key functional domains  

the site of covalent attachment for a particular amino acid and 

a triplet anticodon base sequence that is complementary to a codon in the mRNA. 

Each tRNA is specific for only one particular amino acid. However, the triplet code displays degeneracy and consequently there are often several different tRNA molecules (isoacceptor tRNAs (Sprinzl et al, 1991)) for one particular amino acid, each with a different three-base anticodon. Surprisingly, even though aU tRNA molecules are believed to adopt similar tertiary structures, the enzymatic attachment of the correct amino acid on to its cognate tRNA by an aminoacyl-tRNA synthetase is carried out with profound fidelity (Schimmel, 1987). Of particular interest is the determination of those features of a tRNA molecule that lead to the attachment of the proper amino acid. 

Transfer RNA from all organisms contains modified nucleosides. Most of them play an important role in the fine tuning of tRNA activity. The presence of a modified nucleoside improves the efficiency of the tRNA in the decoding event, and may affect the fidelity of protein synthesis and codon choice such as the modified nucleoside next to the 3 -side of the anticodon (position 37) and at the Wobble position (position 34). Modified nucleosides in the anticodon region, other than positions 34 and 37, may influence the translational efficiency and fidelity, whereas those outside the anticodon region may stabilize tRNA conformations. Useful information concerning modified nucleosides in RNA is available from RNA modification database at http //medlib.med.utah.edu/RNAmods. 

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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... 

The 1968 Nobel Prize in physiology or medicine was shared by Robert W Holley of Cornell University for determining the nucleotide sequence of phenylalanine transfer RNA... 

Transfer RNAs normally contain some bases other than AUG and C Of the 76 bases m tRNA for example 13 are of the modified variefy One of fhese marked G m Figure 28 11 is a modified guanosme m fhe anficodon Many of fhe modified bases including G are mefhylafed derivafives of fhe customary RNA bases... 

Transcription (Section 28 11) Construction of a strand of mRNA complementary to a DNA template Transfer RNA (tRNA) (Section 28 11) A polynucleotide of n hose that is bound at one end to a unique amino acid This ammo acid is incorporated into a growing peptide chain Transition state (Section 3 1) The point of maximum energy in an elementary step of a reaction mechanism Translation (Section 28 12) The reading of mRNA by van ous tRNAs each one of which is unique for a particular ammo acid... 

Cellular protein biosynthesis involves the following steps. One strand of double-stranded DNA serves as a template strand for the synthesis of a complementary single-stranded messenger ribonucleic acid (mRNA) in a process called transcription. This mRNA in turn serves as a template to direct the synthesis of the protein in a process called translation. The codons of the mRNA are read sequentially by transfer RNA (tRNA) molecules, which bind specifically to the mRNA via triplets of nucleotides that are complementary to the particular codon, called an anticodon. Protein synthesis occurs on a ribosome, a complex consisting of more than 50 different proteins and several stmctural RNA molecules, which moves along the mRNA and mediates the binding of the tRNA molecules and the formation of the nascent peptide chain. The tRNA molecule carries an activated form of the specific amino acid to the ribosome where it is added to the end of the growing peptide chain. There is at least one tRNA for each amino acid. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Figure 4.15 Schematic diagram of the enzyme tyrosyl-tRNA synthetase, which couples tyrosine to its cognate transfer RNA. The central region of the catalytic domain (red and green) is an open twisted a/p stmcture with five parallel p strands. The active site is formed by the loops from the carboxy ends of P strands 2 and S. These two adjacent strands are connected to a helices on opposite sides of the P sheet.

Transfer RNAs normally contain some bases other than A, U, G, and C. Of the 76 bases in tRNA , for example, 13 are of the modified variety. One of these, marked G in Figure 28.11, is a modified guanosine in the anticodon. Many of the modified bases, including G, are methylated derivatives of the customary RNA bases. 

Transfer RNA (tRNA) (Section 28.11) A polynucleotide of ri-bose that is bound at one end to a unique amino acid. This amino acid is incorporated into a growing peptide chain. 

Three-base codons on die mRNA corresponding to specific amino acids direct the sequence of building a protein. These codons are recognized by tRNAs (transfer RNAs) carrying die appropriate amino acids. Ribosomes are the machinery for protein syn diesis. 

In contrast, RNA occurs in multiple copies and various forms (Table 11.2). Cells contain up to eight times as much RNA as DNA. RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). With these basic definitions in mind, let s now briefly consider the chemical and structural nature of DNA and the various RNAs. Chapter 12 elaborates on methods to determine the primary structure of nucleic acids by sequencing methods and discusses the secondary and tertiary structures of DNA and RNA. Part rV, Information Transfer, includes a detailed treatment of the dynamic role of nucleic acids in the molecular biology of the cell. 

Transfer RNA also has a complex secondary structure due to many intrastrand hydrogen bonds. 

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... 

In the cytoplasm, the mRNA attaches to a ribosome and acts as a template for the construction of a protein with the proper amino acid sequence (a process known as translation ). Single amino acids are brought to the ribosome by transfer RNA molecules (tRNA) and added to the growing amino acid chain in the order instructed by the mRNA. Each time a nucleotide is added to the growing RNA strand, one molecule of ATP is broken down to ADP. Each time a tRNA binds an amino acid and each time the amino acid is added to the protein, additional ATP is broken down to ADP. Because proteins can contain many hundreds of amino acids, the cell must expend the energy in 1,000 or more ATP molecules to build each protein molecule. 

Transfer RNA (tRNA) transports amino acids to the ribosomes, where they are joined together to make proteins. 

Figure 28.7 A representation of protein biosynthesis. The codon base sequences on mRNA are read by tRNAs containing complementary anticodon base sequences. Transfer RNAs assemble the proper amino acids into position for incorporation into the growing peptide.

H Translation is the process by which mRNA directs protein synthesis. Each mRNA is divided into codons, ribonucleotide triplets that are recognized by small amino acid-carrying molecules of transfer RNA (tRNA), which deliver the appropriate amino acids needed for protein synthesis. 

Transcription (DNA), 1108-1109 coding strand in, 1108 primer strand in, 1108 promoter sites in, 1108 template strand in, 1108 Transfer RNA, 1108... 

Triterpenoid, 1071 tRNA, see Transfer RNA Trypsin, peptide cleavage with, 1033 Tryptophan, pKa of, 52... 

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