Transfer RNA molecules

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. 

C13-0105. Transfer-RNA molecules (tRNA) have a set of three bases at their tip that are exposed and can bind their complementary bases. What sequence of bases will be recognized by the following tRNA sequences (a) GAU, (b) AGG, and (c) CCU ... 

What is the importance of this enzyme family for the biogenesis problem These enzymes form the link between the protein world and the nucleic acid world . They catalyse the reaction between amino acids and transfer RNA molecules, which includes an activation step involving ATR The formation of the peptide bond, i.e., the actual polycondensation reaction, takes place at the ribosome and involves mRNA participation and process control via codon-anticodon interaction. 

Transfer RNA molecules are adaptors they adapt each amino acid to its triplet codon on messenger RNA. 

Protein synthesis means translation into a peptide chain of a genetic message first copied (transcribed) into m-RNA (p. 274). Amino acid (AA) assembly occurs at the ribosome. Delivery of amino acids to m-RNA involves different transfer RNA molecules (t-RNA), each of which binds a specific AA. Each t-RNA bears an anticodon nucleobase triplet that is complementary to a particular m-RNA coding unit (codon, consisting of 3 nucleobases. 

All ribosomes have two subunits, and each subunit contains several protein chains and one or more chains of RNA (ribosomal RNA, or rRNA). In the ribosome from E. coli, the smaller of the two subunits is known as the 30S subunit and the larger is referred to as the 50S subunit. (The unit S stands for Svedberg, a measure of how rapidly a particle sediments in a centrifuge.) The two subunits combine to form the active 70S ribosomal assembly. The special RNA molecules that are a part of the ribosome are quite distinct from messenger or transfer RNA molecules, and they play important roles in forming the overall ribosomal quaternary structure and in aligning mRNA and tRNA molecules during protein biosynthesis. 

Each triplet code, the codon, in the messenger RNA specifies a different amino acid, but there are more possible codons (64) than amino acids (20), and several codons can specify the same amino acid. To each codon, one molecule of transfer RNA becomes attached via a complementary anticodon. These transfer RNA molecules carry a single, specific amino acid. In this way a protein, comprising a chain of amino acids, can be built up (Fig. 6.38). 

Translation involves transfer RNA. (a) The structure of a transfer RNA molecule, with an anticodon at one end and an amino acid attachment site at the other end. (b) A highly simplified symbol for tRNA. The anticodon is a series of three nucleotides that complement the mRNA codon and code for a specific amino acid at the amino acid attachment site. 

Hoogsteen pairs were first observed in nature in transfer RNA molecules (Fig. 5-31). These molecules contain mostly Watson-Crick base pairs but there are also two reversed Hoogsteen pairs. One of them, between U8 and A14, is invariant in all tRNAs studied. Hoogsteen pairing also occurs in four-stranded DNA, which has important biological functions. A G quartet from a DNA tetraplex held together by Hoogsteen base pairs is shown in Fig. 5-8. 

How does a cell read the code This question is dealt with in detail in Chapters 28 and 29. A key step is the positioning of each amino acid on the ribosome in proper sequence. This is accomplished by the pairing of codons of messenger RNA with the anticodons of the appropriate transfer RNA molecules as is indicated at the bottom of Fig. 5-30. Each tRNA carries the appropriate "activated" amino acid at its 3 end ready to be inserted into the growing peptide. 

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... 

Transfer RNA molecules are notable for containing unusual nucleotides (Fig. 5) such as 1-methylguanosine (m G), pseudouridine OF), dihydrouridine (D), inosine (I) and 4-thiouridine (S4U). These are created by modification of guano-sine and uridine after tRNA synthesis. For example, inosine is generated by deamination of guanosine. 

The ribosome is the enzyme that catalyzes peptide bond formation. The bacterial ribosome is a large 2500 kDa ribonucleic acid/protein complex comprised of a large subunit (LSU or SOS subunit) and a small subunit (SSU or 30S subunit) (Fig. 4.1). The small ribosomal subunit binds to messenger RNA (mRNA) and reads the genetic code by aligning its base triplet codons with anticodons of transfer RNA molecules (tRNA). The large ribosomal subunit binds to opposite ends of tRNA molecules and catalyzes peptide bond formation. 

Transfer RNA molecules are the adaptors that associate an amino acid with its correct base sequence. Transfer RNA molecules are structurally similar to one another each adopts a three-dimensional cloverleaf pattern of base-paired groups (Figure 2,10). Subtle differences in structure enable the protein-synthesis machinery to distinguish transfer RNA molecules with different amino acid specificities. 

Figure 2.10. Cloverleaf Pattern of tRNA. The pattern of base-pairing interactions observed for all transfer RNA molecules reveals that these molecules had a common evolutionary origin.

S, and 28S ribosomal RNA (Section 29.3.1). The other ribosomal RNA molecule (5S rRNA, Section 29.3.1) and all the transfer RNA molecules (Section 29.1.2) are synthesized by RNA polymerase III, which is located in the nucleoplasm rather than in nucleoli. RNA polymerase II, which also is located in the nucleoplasm, synthesizes the precursors of messenger RNA as well as several small RNA molecules, such as those of the splicing apparatus (Section 28.3.5). Although all eukaryotic RNA polymerases are homologous to one another and to prokaryotic RNA polymerase, RNA polymerase II contains a unique carboxyl-terminal domain on the 220-kd subunit this domain is unusual because it contains multiple repeats of a YSPTSPS consensus sequence. The activities of RNA polymerase II are regulated by phosphorylation on the serine and threonine residues of the carboxyl-terminal domain. Another major distinction among the polymerases lies in their responses to the toxin a -amanitin, a cyclic octapeptide that contains several modified... 

Transfer RNA molecules (tRNAs), messenger RNA, and many proteins participate in protein synthesis along with ribosomes. The link between amino acids and nucleic acids is first made by enzymes called aminoacyl-tRNA synthetases. By specifically linking a particular amino acid to each tRNA, these enzymes implement the genetic code. This chapter focuses primarily on protein synthesis in prokaryotes because it illustrates many general principles and is relatively well understood. Some distinctive features of protein synthesis in eukaryotes also are presented. 

Protein Assembly. The ribosome, shown at the right, is a factory for the manufacture of polypeptides. Amino acids are carried into the ribosome, one at a time, connected to transfer RNA molecules (blue). Each amino acid is joined to the growing polypeptide chain, which detaches from the ribosome only once it is completed. This assembly line approach allows even very long polypeptide chains to be assembled rapidly and with impressive accuracy. [(Left) Doug Martin/ Photo Researchers.]... 

All known transfer RNA molecules have the following features ... 

Synthetases Recognize the Anticodon Loops and Acceptor Stems of Transfer RNA Molecules... 

Some Transfer RNA Molecules Recognize More Than One Codon Because of Wobble in Base-Pairing... 

Messenger RNA makes a mirror image copy of a stretch of the DNA molecule and then moves RNA out of the nucleus through the nuclear pores into the cytoplasm. There the RNA locates the ribosomes where it consumes the protein products with the help of transfer RNA molecules. 

GG CAA Initial steps Messenger RNA is bound to ribosome with the start codon (AUG) at the P site. A transfer RNA molecule with the amino acid methionine (M) and the anticodon UAC has bound to the exposed start codon. The codon UCA is exposed at the A site. 

GG CAA A second transfer RNA molecule, with the anticodon AGU and the amino acid serine (S) has bound to the A site. 

The leap from infonnation in mRNA to the sequence of amino acids in a polypeptide chain is bridged by transfer RNA. Transfer RNA molecules are relatively small, when compared to mRNA and proteins, and consist of only about 40 ribonucleotides. There exist about 40 distinct types of iRNA, and these share the task of aligning the 20 amino adds according to the sequence of ribonucleotide bases cKcurring in any molecule of mRNA. Since there exist more types of mRNA molecules about 40) than amino acids (20), one can see that the collection of tRNA molecules is also redundant or degenerate. 

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