Transfer RNA in protein synthesis

Hatfield GW, Gurman GA (1992) Codon pair utilization bias in bacteria, yeast and mammals. In Hatfield DL, Lee BJ, Pirtle RM (eds) Transfer RNA in protein synthesis. CRC Press, Boca Raton, chap 7... 

What is the role of transfer RNA in protein synthesis Transfer RNA is relatively small, about 80 nucleotides long. It exhibits extensive intrachain hydrogen bonding, represented in two dimensions by a cloverleaf structure. Amino acids are brought to the site of protein synthesis bonded to transfer RNAs. 

All eukaryotic cells have four major classes of RNA ri-bosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). The first three are involved in protein synthesis, and snRNA is involved in mRNA splicing. As shown in Table 37-1, these various classes of RNA are different in their diversity, stability, and abundance in cells. 

Several different types of RNA, including ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA), are involved in protein synthesis. 

Transfer RNA (tRNA) RNA with a triplet nucleotide sequence that is complementary to the triplet nucleotide coding sequences of mRNA. tRNAs in protein synthesis bond with amino acids and transfer them to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA... 

In protein synthesis, there are three classes of RNA to worry about ribosomal RNA, rRNA messenger RNA, mRNA and transfer RNA, tRNA. All three classes of RNA play key roles in the final stage of the process the biosynthesis of proteins. However, we are going to take this one step at a time. We turn attention first to the... 

Transcription. For expression of a gene—i. e., synthesis of the coded protein—the DNA sequence information has to be converted into a protein sequence. As DNA itself is not involved in protein synthesis, the information is transferred from the nucleus to the site of synthesis in the cytoplasm. To achieve this, the template strand in the relevant part of the gene is transcribed into an RNA (hnRNA). The sequence of this RNA is thus complementary to that of the template strand (3), but— with the exception of the exchange of thy-... 

The final principal component of the cell is the nucleus. This is located in the center of the cell and is surrounded by a double membrane, the outer layer being derived from the ER of the cytoplasm and the inner layer coming from the nucleus itself. The two leaflets of the double membrane are fused in places, producing nuclear pores that enable the transfer of macromolecules from the cytoplasm to the nucleus. Two important components of the nucleus are chromatin and the nucleolus. Chromatin represents polymers of DNA complexed with protein. The nucleolus is a complex substructure, composed of ribonucleoprotein granules, that controls the synthesis of RNA destined to form the ribosomes of the cytoplasm. Cells engaged heavily in protein synthesis have... 

Messenger RNA is only one of several classes of cellular RNA. Transfer RNAs serve as adapter molecules in protein synthesis covalently linked to an amino acid at one end, they pair with the mRNA in such a way that amino acids are joined to a growing polypeptide in the correct sequence. Ribosomal RNAs are components of ribosomes. There is also a wide variety of special-function RNAs, including some (called ribozymes) that have enzymatic activity. All the RNAs are considered in detail in Chapter 26. The diverse and often complex functions of these RNAs reflect a diversity of structure much richer than that observed in DNA molecules. 

RNA has a variety of functions within a cell for each function, a specific type of RNA is required. Messenger RNA (mRNA) serves as intermediaries for carrying genetic messages from the DNA to the ribosomes where protein synthesis lakes place. Ribosomal RNA (rRNA) serves both structural and functional roles in the ribosome it is diverse, both in terms of its size and structure. Transfer RNAs (tRNAs) are small molecules that have a central role in protein synthesis. Other RNA molecules, called ribozymes, function as enzymes to catalyze chemical transformations. Although ribozymes most often catalyze cleavage of the... 

RNA consists of long strings of ribonucleotides, polymerised in a similar way to DNA, but the chains are considerably shorter than those of DNA. RNA contains ribose rather than deoxyribose and also contains uracil instead of thymidine. This has important connotations in the secondary structure of RNA which does not form the long helices found in DNA. RNA is usually much more abundant than DNA in the cell and its concentration varies according to cell activity and growth. This is because RNA has several roles in protein synthesis. There are three major classes messenger RNA (mRNA) ribosomal RNA (rRNA) and transfer RNA (tRNA). 

In prokaryotes DNA, RNA, and protein synthesis all take place in the same cellular compartment. In eukaryotes the DNA is compartmentalized in the cell nucleus, and it became clear long before the biochemistry of these three processes was understood that DNA synthesis takes place in the nucleus, whereas the bulk of protein synthesis takes place in the cytoplasm. From these observations on eukaryotes it was self-evident that DNA cannot be directly involved in the synthesis of protein but must somehow transmit its genetic information for protein synthesis to the cytoplasm. Careful experiments with radioactive labels were used to demonstrate that RNA synthesis takes place in the nucleus much of this RNA is degraded rather quickly, but the portion that survives is mostly transferred to the cytoplasm (fig. 28.1). From observations of this kind it became clear that RNA was the prime candidate for the carrier of genetic information for the synthesis of proteins. 

In eukaryotic cells the nuclear membrane separates the processes of RNA and protein synthesis. This can be demonstrated with radioactive substrates that are precursors of RNA and protein. Immediately after exposure of cells to labeled precursors, the RNA label becomes fixed in the nucleus, and the protein label becomes fixed in the cytoplasm. Eventually most of the labeled RNA becomes transferred to the cytoplasm, and a fraction of the labeled protein becomes transferred to the nucleus. 

Overview of reactions in protein synthesis. (aab aa2, aa3 = amino acids l, 2, 3.) Protein synthesis requires transfer RNAs for each amino acid, ribosomes, messenger RNA, and a number of dissociable protein factors in addition to ATP, GTP, and divalent cations. First the transfer RNAs become charged with amino acids, then the initiation complex is formed. Peptide synthesis does not start until the second aminoacyl tRNA becomes bound to the ribosome. Elongation reactions involve peptide bond formation, dissociation of the discharged tRNA, and translocation. The elongation process is repeated many times until the termination codon is reached. Termination is marked by the dissociation of the messenger RNA... 

Besides having a much lower molar mass than DNA, RNA generally forms only single-strand helices. RNA is often found associated with proteins inside cells. The most prevalent bases in RNA are the same as those in DNA, except that uracil is present instead of thymine. Three common types of RNA are ribosomal (rRNA), transfer (tRNA), and messenger RNA (mRNA). They are all involved in protein synthesis, controlling the sequence of amino acids that make up the primary structure. Thus the base sequence in RNA is related to the amino acid sequence in the protein that is made from it. 

According to this proposal, the incorporation of proline into collagen follows the acyl adenylate and acyl RNA stages now generally believed to occur in protein synthesis. A bound hydroxyproline intermediate is postulated, from which hydroxyproline is transferred to soluble RNA. We prefer to suggest that different RNA acceptor molecules exist for hydroxyproline and proline this would be consistent with recent work which indicates that the soluble RNA molecule contains the information for incorporation of a particular amino acid into protein (3). Although it is conceivable that there is hydroxylation of prolyl-sRNA to yield hydroxyprolyl-sRNA, an additional mechanism would be needed... 

Messenger RNAs (mRNAs) and transfer RNAs (tRNAs) participate directly in protein synthesis. The nucleotide sequence of one of the two DNA strands in the double-helix is transcribed by RNA polymerase to produce a mRNA that is complementary to it (see Experiment 22). A portion or all of this mRNA nucleotide sequence will then serve as the template for the ribosome, which will translate the mRNA molecule into a polypeptide or protein (see Experiment 23). Messenger RNAs, then, carry information contained in the DNA into the production of protein. 

The formation of IAA conjugates is widely believed to be a means for removal of excess IAA produced during certain times of plant development and also in mutant plants where indolic precursors and IAA metabolites accumulate.32 In all higher and many lower plants, applied IAA is rapidly conjugated to form IAA—aspartate.33 The ability of plant tissues to make aspartate conjugates of a variety of active auxins is induced by pretreatment with auxin,34 and this induction was shown to be blocked by inhibitors of RNA and protein synthesis. After almost 50 years of study, an in vitro system from plants was described that accounts for the formation of IAA amide conjugates35 via a mechanism where the acidic auxin is adenylated followed by acyl transfer to the amino acid. The gene for this reaction had been discovered almost 20 years before, when GH3 from soybean was shown... 

In addition to the bases oudined above, transfer RNA (tRNA) (involved in amino acid-specific codon recognition in protein synthesis) contains unusual chemically modified bases (e.g. 

This highly innovative hypothesis soon became established as fact. The adaptor in protein synthesis is transfer RNA. The structure and reactions of these remarkable molecules will be considered in detail in Chapter 29. For the moment, it suffices to note that tRNA contains an amino acidattachment site and a template-recognition site. A tRNA molecule carries a specific amino acid in an activated form to the site of protein synthesis. The carboxyl group of this amino acid... 

---