1. Chapter 7 Using the genetic code

2. 7.1 Introduction 7.2 Codon-anticodon recognition involves wobbling 7.3 tRNA contains modified bases that influence its pairing properties 7.4 (There are sporadic alterations of the universal code) 7.5 tRNAs are charged with amino acids by synthetases 7.6 Accuracy depends on proofreading 7.7 Suppressor tRNAs have mutated anticodons that read new codons 7.8 The accuracy of translation 7.9 tRNA may influence the reading frame

3. Stop codons are the three triplets (UAA, UAG, UGA) which terminate protein synthesis. 7.1 Introduction

4. Figure 7.1 All the triplet codons have meaning: 61 represent amino acids, and 3 cause termination (STOP). 7.1 Introduction

5. Figure 7.2 The number of codons for each amino acid does not correlate closely with its frequency of use in proteins. 7.1 Introduction

6. Wobble hypothesis accounts for the ability of a tRNA to recognize more than one codon by unusual (non-G C, non-AT) pairing with the third base of a codon. 7.2 Codon-anticodon recognition involves wobbling

7. Figure 7.3 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. 7.2 Codon-anticodon recognition involves wobbling

8. Figure 7.4 Wobble in base pairing allows G- U pairs to form between the third base of the codon and and the first base of the anticodon. 7.2 Codon-anticodon recognition involves wobbling

9. Figure 7.5 Codon-anticodon pairing involves wobbling at the third position. 7.2 Codon-anticodon recognition involves wobbling

10. Modification of DNA or RNA includes all changes made to the nucleotides after their initial incorporation into the polynucleotide chain. 7.3 tRNA contains modified bases that influence its pairing properties

11. Figure 7.6 All of the four bases in tRNA can be modified. 7.3 tRNA contains modified bases that influence its pairing properties

12. Figure 7.7 Modification to inosine allows pairing with U, C, and A. 7.3 tRNA contains modified bases that influence its pairing properties

13. Figure 7.8 Modification to 2- thiouridine restricts pairing to A alone because only one H- bond can form with G. 7.3 tRNA contains modified bases that influence its pairing properties

14. Figure 7.7 Modification to inosine allows pairing with U, C, and A. 7.3 tRNA contains modified bases that influence its pairing properties

15. Figure 7.9 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 earlyAUA=Met change was reversed in echinoderms. 7.4 There are sporadic alterations of the universal code

16. Figure 7.9 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 earlyAUA=Met change was reversed in echinoderms. 7.4 There are sporadic alterations of the universal code

17. Cognate tRNAs are those recognized by a particular aminoacyl-tRNA synthetase. Isoaccepting tRNAs represent the same amino acid. 7.5 tRNAs are charged with amino acids by synthetases

18. Figure 7.10 An aminoacyl-tRNA synthetase charges tRNA with an amino acid. 7.5 tRNAs are charged with amino acids by synthetases

19. Figure 7.11 An aminoacyl- tRNA synthetase contains three or four regions with different functions. (Only multimeric synthetases possess an oligomerization domain.) 7.5 tRNAs are charged with amino acids by synthetases

20. Figure 7.12 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. Photographs kindly provided by Dino Moras. 7.5 tRNAs are charged with amino acids by synthetases

21. Figure 7.13 A class I tRNA synthetase contacts tRNA at the minor groove of the acceptor stem and at the anticodon. 7.5 tRNAs are charged with amino acids by synthetases

22. Figure 7.14 A class II aminoacyl-tRNA synthetase contacts tRNA at the major groove of the acceptor helix and at the anticodon loop. 7.5 tRNAs are charged with amino acids by synthetases

23. Proofreading refers to any mechanism for correcting errors in protein or nucleic acid synthesis that involves scrutiny of individual units after they have been added to the chain. 7.6 Accuracy depends on proofreading

24. Figure 7.15 Recognition of the correct tRNA by synthetase is controlled at two steps. First, the enzyme has a greater affinity for its cognate tRNA. Second, the aminoacylation of the incorrect tRNA is very slow. 7.6 Accuracy depends on proofreading

25. Figure 7.16 When a synthetase binds the incorrect amino acid, proofreading requires binding of the cognate tRNA. It may take place either by a conformation change that causes hydrolysis of the incorrect aminoacyl-adenylate, or by transfer of the amino acid to RNA, following by hydrolysis. 7.6 Accuracy depends on proofreading

26. Figure 7.17 The accuracy of charging tRNAIle by its synthetase depends on error control at two stages. 7.6 Accuracy depends on proofreading

27. Missense mutations change a single codon and so may cause the replacement of one amino acid by another in a protein sequence. Nonsense codon means a termination codon. Suppressor (extragenic) is usually a gene coding a mutant tRNA that reads the mutated codon either in the sense of the original codon or to give an acceptable substitute for the original meaning. 7.7 Suppressor tRNAs have mutated anticodons that read new codons

28. Figure 7.18 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 protein in which the original Leu residue has been replaced by Tyr. 7.7 Suppressor tRNAs have mutated anticodons that read new codons

29. Figure 7.19 Nonsense suppressor tRNAs are generated by mutations in the anticodon. 7.7 Suppressor tRNAs have mutated anticodons that read new codons

30. Figure 7.20 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 respond to AGA. 7.7 Suppressor tRNAs have mutated anticodons that read new codons

31. Figure 7.21 Nonsense suppressors also read through natural termination codons, synthesizing proteins that are longer than wild-type. 7.7 Suppressor tRNAs have mutated anticodons that read new codons

32. ◆ 控制正确性的直接机制是将由 A 位点的空间化学来决定密码子－反密码 子的识别地区。核糖体的几何学决定密码子－反密码子的结合以这样的方 式进行：通过蛋白质 S12 ， S4 和 S5 的结构接受氨酰－ tRNA 使得正确性或强 或弱。（或者通过它们对 rRNA 结构的影响力） ◆ 正确性是核糖体运动的间接影响。核糖体的速度可以决定 tRNA 识别的 可能性，从而决定此过程的有效性。这个模型解释了改变链延长的动力学 可以影响链霉素。相关参数是核糖体运动速度随时间的变化决定了是结合 还是分开，如果肽链形成的速度增大，在氨酰 -tRNA 逃避之前，在键形成 中不正确的氨酰决定 tRNA 识别的可能性，从而决定此过程的有效性。这个 模型解释了改变链延长的动力学可以影响链霉素。相关参数是核糖体运动 速度随时间的变化决定了是结合还是分开，如果肽链形成的速度增大，在 氨酰－ tRNA 逃避之前，在键形成中不正确的氨酰 tRNA 更容易被诱捕。减 慢蛋白质合成的速度将会给修正。 7.8 The accuracy of translation

33. ◆ 控制正确性的直接机制是将由 A 位点的空间化学来决定密码子－反密码 子的识别地区。核糖体的几何学决定密码子－反密码子的结合以这样的方 式进行：通过蛋白质 S12 ， S4 和 S5 的结构接受氨酰－ tRNA 使得正确性或强 或弱。（或者通过它们对 rRNA 结构的影响力） ◆ 正确性是核糖体运动的间接影响。核糖体的速度可以决定 tRNA 识别的 可能性，从而决定此过程的有效性。这个模型解释了改变链延长的动力学 可以影响链霉素。相关参数是核糖体运动速度随时间的变化决定了是结合 还是分开，如果肽链形成的速度增大，在氨酰 -tRNA 逃避之前，在键形成 中不正确的氨酰决定 tRNA 识别的可能性，从而决定此过程的有效性。这个 模型解释了改变链延长的动力学可以影响链霉素。相关参数是核糖体运动 速度随时间的变化决定了是结合还是分开，如果肽链形成的速度增大，在 氨酰－ tRNA 逃避之前，在键形成中不正确的氨酰 tRNA 更容易被诱捕。减 慢蛋白质合成的速度将会给修正。 7.8 The accuracy of translation

34. Figure 7.22 A +1 frameshift is required for expression of the tyb gene of the yeast Ty element. The shift occurs at a 7 base sequence at which two Leu codon(s) are followed by a scarce Arg codon. 7.9 tRNA may influence the reading frame

35. Figure 7.22 A +1 frameshift is required for expression of the tyb gene of the yeast Ty element. The shift occurs at a 7 base sequence at which two Leu codon(s) are followed by a scarce Arg codon. 7.9 tRNA may influence the reading frame

36. 1. The sequence of mRNA read in triplets 5 3 is related by the genetic code to the amino acid sequence of protein read from N- to C- terminus. 2. Multiple tRNAs may respond to a particular codon. 3. Each amino acid is recognized by a particular aminoacyl-tRNA synthetase, which also recognizes all of the tRNAs coding for that amino acid. 7.10 Summary

37. 4. Aminoacyl-tRNA synthetases vary widely, but fall into two general groups according to the structure of the catalytic domain. 5. Mutations may allow a tRNA to read different codons; the most common form of such mutations occurs in the anticodon itself. 6. Frameshifts of the +1 type may be caused by aberrant tRNAs that read "codons" of 4 bases. 7.10 Summary