1. Chapter 23
Using the Genetic Code

2. Figure : All the triplet codons have meaning: 61 represent amino acids and 3 cause termination (stop codons).

3. Figure : Some correlation of the frequency of amino acid use in proteins with the number of codons specifying the amino acid is observed. An exception is found for amino acids specified by two codons, which occur with a wide variety of frequencies.

4. Figure 23. 3: Third bases have the least influence on codon meanings
Figure : Third bases have the least influence on codon meanings. Boxes indicate groups of codons within which third-base degeneracy ensures that the meaning is the same.

5. Table 23.0.1: Codon–anticodon pairing involves wobbling at the third position.

6. Figure : Wobble in base pairing allows G-U pairs to form between the third base of the codon and the first base of the anticodon.

7. Figure : The tRNA 3ʹ end is generated by cutting (endonucleolytic) and trimming (exonucleolytic) reactions, followed by addition of CCA when this sequence is not encoded; the 5ʹ end is generated by a precise endonucleolytic cleavage.

8. Figure 23.0.6: All four bases in tRNA can be modified.

9. Figure 23.0.7: Inosine can pair with U, C, or A.

10. Figure : Modification to 2-thiouridine restricts pairing to A alone because only one H-bond can form with G.

11. Figure : Changes in the genetic code in bacterial or eukaryotic nuclear genomes usually assign amino acids to stop codons or change a codon so that it no longer specifies an amino acid. A change in meaning from one amino acid to another is unusual.

12. Figure : Changes in the genetic code in mitochondria can be traced in phylogeny. The minimum number of independent changes is generated by supposing that the AUA = Met and the AAA = Asn changes each occurred independently twice and that the early AUA = Met change was reversed in echinoderms.

13. Figure : SelB is an elongation factor that specifically binds tRNASec to a UGA codon that is followed by a stem-loop structure in mRNA.

14. Figure 23.0.12: An aminoacyl-tRNA synthetase charges tRNA with an amino acid.

15. Table : Separation of tRNA synthetases into two classes possessing mutually exclusive sets of sequence motifs and active-site structural domains. The quaternary structure of the enzyme is noted. Multiple designations indicate that the quaternary structure differs in different organisms. The quaternary structure of PylRS has not been clearly established.

16. Figure : Mechanisms for the synthesis of Gln-tRNAGln and Asn-tRNAAsn. The top route in each case indicates the one-step pathway catalyzed by the conventional tRNA synthetase. The bottom, two-step pathways are found in most organisms. They consist of a nondiscriminating tRNA synthetase followed by the action of a tRNA-dependent amidotransferase (AdT).

17. Figure : Crystal structures show that class I and class II aminoacyl-tRNA synthetases bind the opposite faces of their tRNA substrates. The tRNA is shown in red and the protein in blue.
Photo courtesy of Dino Moras, Institute of Genetics and Molecular and Cellular Biology.

18. Figure : Aminoacylation of cognate tRNAs by synthetase is based, in part, on greater affinities for these types, coupled with weak affinities for noncognate types. In addition, noncognate tRNAs are unable to fully undergo the induced-fit conformational changes required for the later catalytic steps.

19. Figure : Proofreading by aminoacyl-tRNA synthetases may take place at the stage prior to aminoacylation (pretransfer editing), in which the noncognate aminoacyl adenylate is hydrolyzed. Alternatively or additionally, hydrolysis of incorrectly formed aminoacyl-tRNA may occur after its synthesis (posttransfer editing).

20. Figure 23. 17: Isoleucyl-tRNA synthetase has two active sites
Figure : Isoleucyl-tRNA synthetase has two active sites. Amino acids larger than Ile cannot be activated because they do not fit in the synthetic site. Amino acids smaller than Ile are removed because they are able to enter the editing site.

21. Figure : Nonsense mutations can be suppressed by a tRNA with a mutant anticodon, which inserts an amino acid at the mutant codon, producing a full-length polypeptide in which the original Leu residue has been replaced by Tyr.

22. Figure : Missense suppression occurs when the anticodon of tRNA is mutated so that it responds to the wrong codon. The suppression is only partial because both the wild-type tRNA and the suppressor tRNA can recognize AGA.

23. Table 23.0.3: Nonsense suppressor tRNAs are generated by mutations in the anticodon.

24. Figure : Nonsense suppressors also read through natural termination codons, synthesizing polypeptides that are longer than the wild type.

25. Figure : Any aminoacyl-tRNA can be placed in the A site (by EF-Tu), but only one that pairs with the anticodon can make stabilizing contacts with rRNA. In the absence of these contacts, the aminoacyl-tRNA diffuses out of the A site.

26. Figure : A tRNA that slips one base in pairing with codon causes a frameshift that can suppress termination. The efficiency is usually about 5%.

27. Figure : A +1 frameshift is required for expression of the tyb gene of the yeast Ty element. The shift occurs at a seven-base sequence at which two Leu codon(s) are followed by a scarce Arg codon.

28. Figure : Bypassing occurs when the ribosome moves along mRNA so that the peptidyl-tRNA in the P site is released from pairing with its codon and then repairs with another codon farther along.

29. Figure : In bypass mode, a ribosome with its P site occupied can stop translation. It slides along mRNA to a site where peptidyl-tRNA pairs with a new codon in the P site. Then translation is resumed.