1. Chapter 9
Using the Genetic Code

2. 9.1 Introduction
The sequence of a coding strand of DNA is read in the direction from 5′ to 3′.
This corresponds to the amino acid sequence of a polypeptide read from N-terminus to C-terminus.

3. 9.2 Related Codons Represent Related Amino Acids
Sixty-one of the sixty-four possible triplets code for twenty amino acids.
Three codons do not represent amino acids and cause termination of translation.
Figure 9.01: The genetic code is triplet.

4. 9.2 Related Codons Represent Related Amino Acids
The genetic code was frozen at an early stage of evolution and is universal.
Most amino acids are represented by more than one codon.
The multiple codons for an amino acid are usually related.
Related amino acids often have related codons, minimizing the effects of mutation.

5. Figure 9.02: The number of codons for each amino acid does not correlate closely with its frequency of use in proteins.

6. 9.3 Codon–Anticodon Recognition Involves Wobbling
Multiple codons that represent the same amino acid most often differ at the third base position.

7. 9.3 Codon–Anticodon Recognition Involves Wobbling
The wobble in pairing between the first base of the anticodon and the third base of the codon results from the structure of the anticodon loop.
Figure 9.04: G-U pairs form at the third codon base.

8. 9.3 Codon–Anticodon Recognition Involves Wobbling
Figure 9.5 Codon-anticodon pairing involves wobbling at third position.

9. 9.4 tRNA Contains Modified Bases
tRNAs contain >50 modified bases.
Modification usually involves direct alteration of the primary bases in tRNA.
There are some exceptions in which a base is removed and replaced by another base.

10. 9.4 tRNA Contains Modified Bases
Figure 9.06: Base modifications in tRNA vary in complexity.

11. 9.5 Modified Bases Affect Anticodon–Codon Pairing
Modifications in the anticodon affect the pattern of wobble pairing.
They are important in determining tRNA specificity.

12. 9.5 Modified Bases Affect Anticodon–Codon Pairing
Figure 9.07: Inosine pairs with three bases.

13. 9.5 Modified Bases Affect Anticodon–Codon Pairing
Figure 9.8: Modification to 2-thiouracil restricts paring to A alone because only one H-bond can form with G.

14. 9.6 There Are Sporadic Alterations of the Universal Code
Changes in the universal genetic code have occurred in some species.
These changes are more common in mitochondrial genomes, where a phylogenetic tree can be constructed for the changes.
In nuclear genomes, the changes are sporadic and usually affect only termination codons.

15. 9.6 There Are Sporadic Alterations of the Universal Code

16. 9.6 There Are Sporadic Alterations of the Universal Code
Figure 9.10: Mitochondria have changes in the genetic code.

17. 9.7 Novel Amino Acids Can Be Inserted at Certain Stop Codons
Changes in the reading of specific codons can occur in individual genes.
The insertion of seleno-Cys-tRNA at certain UGA codons requires several proteins to modify the Cys-tRNA and insert it into the ribosome.
Pyrrolysine can be inserted at certain UAG codons.

18. 9.7 Novel Amino Acids Can Be Inserted at Certain Stop Codons
SelB is an elongation factor specific for Seleno-Cys-tRNA.

19. 9.8 tRNAs Are Charged with Amino Acids by Synthetases
Aminoacyl-tRNA synthetases are enzymes that charge tRNA with an amino acid to generate aminoacyl-tRNA in a two-stage reaction that uses energy from ATP.
There are twenty aminoacyl-tRNA synthetases in each cell. Each charges all the tRNAs that represent a particular amino acid.
Recognition of a tRNA is based on a small number of points of contact in the tRNA sequence.

20. 9.8 tRNAs Are Charged with Amino Acids by Synthetases
Figure 9.12: The charging reaction uses ATP.

21. 9.9 Aminoacyl-tRNA Synthetases Fall into Two Groups
Aminoacyl-tRNA synthetases are divided into the class I and class II groups by sequence and structural similarities.

22. 9.9 Aminoacyl-tRNA Synthetases Fall into Two Groups
Figure 9.13: Class I (Glu-tRNA synthetase) and Class II (Asp-tRNA synthetase).
Photo courtesy of Dino Moras, Institute of Genetics and Molecular and Cellular Biology

23. 9.10 Synthetases Use Proofreading to Improve Accuracy
Specificity of recognition of both amino acid and tRNA is controlled by aminoacyl-tRNA synthetases.
They function through proofreading reactions that reverse the catalytic reaction if the wrong component has been incorporated.

24. 9.10 Synthetases Use Proofreading to Improve
Figure 9.16: Synthetases use chemical proofreading.

25. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
A suppressor tRNA typically has a mutation in the anticodon that changes the codons to which it responds.
Each type of nonsense codon is suppressed by tRNAs with mutant anticodons.

26. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
When the new anticodon corresponds to a termination codon, an amino acid is inserted and the polypeptide chain is extended beyond the termination codon.
This results in:
nonsense suppression at a site of nonsense mutation, or
readthrough at a natural termination codon

27. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons

28. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
Figure 9.20: Nonsense suppression causes readthrough.

29. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
Suppressor tRNAs compete with wild type tRNAs that have the same anticodon to read the corresponding codon(s).
Efficient suppression is deleterious because it results in readthrough past normal termination codons.

30. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
Missense suppression occurs when the tRNA recognizes a different codon from usual, so that one amino acid is substituted for another.

31. 9.11 Suppressor tRNAs Have Mutated Anticodons That Read New Codons
Figure 9.21: Missense suppressors compete with wild type.

32. 9.12 Recoding Changes Codon Meanings
Changes in codon meaning can be caused by mutant tRNAs or by tRNAs with special properties.

33. 9.12 Recoding Changes Codon Meanings
Figure 9.22: Special or mutant tRNAs change meaning.

34. 9.12 Recoding Changes Codon Meanings
The reading frame can be changed by frameshifting or bypassing, both of which depend on properties of the mRNA.
Figure 9.23: Frameshifts can suppress termination.

35. 9.12 Recoding Changes Codon Meanings
Figure 9.24: Bypassing skips between identical codons.

36. 9.13 Frameshifting Occurs at Slippery Sequences
The reading frame may be influenced by the sequence of mRNA and the ribosomal environment.
Slippery sequences allow a tRNA to shift by one base after it has paired with its anticodon, thereby changing the reading frame.
Translation of some genes depends upon the regular occurrence of programmed frameshifting.
Some mutant tRNA suppressors recognize a four base codon instead of normal three bases.

37. 9.13 Frameshifting Occurs at Slippery Sequences

38. 9.14 Bypassing Involves Ribosome Movement
A ribosome encounters a GGA codon adjacent to a stop codon in a specific stem-loop structure.
It moves directly to a specific GGA downstream without adding amino acids to the polypeptide.
Figure 9.26: A ribosome can bypass a sequence of mRNA.