TRNA-Gly

The anticodon loop of one of the tRNA Gly molecules from E. coli is as follows. Identify the anticodon, reading from 3 to 5. This tRNA recognizes two different Gly codons. What are they Write them from 5 to 3. ... 

The structure of the isoleucyl-tRNA synthetase (IleRS) from Thermus ther-mophilus (1045 residues, Mr 120 000) has been solved, as well as its complexes with lie and Val.17 The protein contains a nucleotide binding fold (Chapter 1) that binds ATR The fold has two characteristic ATP binding motifs His-54-Val-55-Gly-56-His-57 and Lys-591-Met-592-Ser-593-Lys-594. In the L-Ile-IleRS complex, a single He is bound at the bottom of the ATP cleft, with the hydrophobic side chain in a hydrophobic pocket, surrounded by Pro-46, Trp-518, and Trp-558. L-Leucine cannot fit into this pocket because of the steric hindrance of one of its terminal methyl groups. Larger amino acids are similarly excluded from this site. In the l-Val-IleRS complex, Val is bound to the same site, but the... 

Retrieve nucleotide sequences (fasta files) of yeast cytosolic and mitochondrial Gly-tRNA and submit them to RNA folding to obtain their secondary (cloverleal) structures and thermochemical data of foldings. 

The process continues until a stop codon ends up in the A site at which point a protein release factor binds to the stop codon, the peptide (H3N+-fMet-Gly-Ser— HN-CH(R,i)COO )-tRNA bond is hydrolysed, the completed polypeptide is released and the ribosomal subunits separate. 

Several aaRSs possess amino acid editing domains, which hydrolytically clear mistakes in cis (3) (Table 1). Interestingly however, some archaeal and bacterial synthetases rely on paralogs of editing domains that hydrolyze mischarged products in tram (10, 11). These products include the YbaK and ProX (or PrdX), which edit Ala-tRNA , and AlaX that hydrolyzes mischarged Ser-tRNA and Gly-tRNA . 

The structure resembles that of a tRNA by molecular mimicry. The sequence Gly-Gly-Gln, present in both eukaryotes and prokaryotes, occurs at the end of the structure corresponding to the acceptor stem of a tRNA. This region binds a water molecule. Disguised as an aminoacyl-tRNA, the release factor may carry this water molecule into the peptidyl transferase center and, assisted by the catalytic apparatus of the ribosome, promote this water molecule s attack on the ester linkage, freeing the polypeptide chain. The detached polypeptide leaves the ribosome. Transfer RNA and messenger RNA remain briefly attached to the 70S ribosome until the entire complex is dissociated in a GTP-dependent fashion by ribosome release factor (RRF) and EF-G. Ribosome release factor is an essential factor for prokaryotic translation. 

Figure 29.31. Structure of a Release Factor. The structure of a eukaryotic release factor reveals atRNA-like fold. The acceptor-stem mimic includes the sequence Gly-Gly-Gln at its tip. This region appears to bind a water molecule, which may be brought into the peptidyl transferase center. There it can participate in the cleavage of the peptidyl-tRNA ester bond, with the aid of the glutamine residue and the ribosomal catalytic apparatus. 

In addition to the variety of modifications found on the heterocyclic base discussed above, many nucleosides are also methylated at the 2 -hydroxyl of the ribose moiety and make up approximately 8 % of existing tRNA modifications. One interesting example of the 2 - 0-ribose modification was studied in S. cerevisiae, where the yeast tRNA molecules corresponding to His, Pro, and Gly(G-C-C) contain a 2 -0-methylated nucleoside at position 4 in the acceptor stem. A methylated cytosine is found in tRNA ° and tRNA, and the modified Am nucleoside is found in tRNA . Modifications in a duplex region of tRNA are very rare, yet modification at this position ( 4) is conserved in eukaryotes. A yeast knock-out strain of the gene trmlS was produced, and it was determined by HPLC and primer extension analysis that tRNAs purified from this organism did not exhibit the 2 - 0-methyl modification at position 4. 

Can exposure of E. coli to nitrous acid (HNOj) lead to mutation of a tRNA " to an amber suppressor The Gly codons are GGX (where X = any nucleotide) and the amber codon is UAG. 

Polypeptide synthesis proceeds at peptidyl iP) and aminoacyl (.4) sites in the ribosome (Fig. 21-11). The synthesis in Fig. 21-11 shows initiation followed by sequential addition of Gly and lie. The 5 end of mRNA, located in the smaller subunit of the ribosome, is prepared to receive the tRNAs for Met and Gly (by matching of codon of mRNA and anticodon of tRNA). The tRNAs for Met and Gly pick up Met and Gly from the cytosol, enter the ribosome, and line up at the P and A sites, respectively, by base pairing of codons of mRNA and anticodons of tRNA (Fig. 21-1 la). The enzyme peptidyl transferase, contained in the large subunit of the ribosome, catalyzes the transfer and... 

Beginning with DNA, describe specifically the coding and synthesis of the following tetrapeptide that represents the first four amino acid residues of the hormone oxytocin Gly-Leu-Pro-Cys. Be sure to include processes such as formation of mRNA (use correct codons, etc.), attachment of mRNA to a ribosome, attachment of tRNA to mRNA-ribosome complex, and so on. 

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