Chapter 39

  1. Three contiguous bases. Because there are four bases, a code based on a two-base codon could encode only 16 amino acids. A three-base codon would allow 64 different combinations, more than enough to account for the 20 amino acids.

  2. A mutation that altered the reading of mRNA would change the amino acid sequence of most, if not all, proteins synthesized by that particular organism. Many of these changes would undoubtedly be deleterious, and so there would be strong selection against a mutation with such pervasive consequences.

  3. Complete the interactive matching exercise to see answers.

  4. Three nucleotides encode an amino acid; the code is nonoverlapping; the code has no punctuation; the code is degenerate.

  5. Degeneracy of the code means that, for most amino acids, there is more than one codon. This property is valuable because, if the code were not degenerate, 20 codons would encode amino acids and the rest of the codons would lead to chain termination. Most mutations would then likely lead to inactive proteins.

  6. The probability is calculated with the equation p = (1 − ε)n, where p is the probability of synthesizing the error-free protein, ε is the error rate, and n is the number of amino acid residues in the protein.

     

    Probability of synthesizing an error-free protein
     

    Number of amino acid residues

    Frequency of inserting an incorrect amino acid

    50

    500

    10−2

    0.605

    0.0066

    10−4

    0.995

    0.951

    10−6

    0.999

    0.999

  7. An error frequency of 1 incorrect amino acid every 104 incorporations allows for the rapid and accurate synthesis of proteins as large as 1000 amino acids. Higher error rates would result in too many defective proteins. Lower error rates would likely slow the rate of protein synthesis without a significant gain in accuracy.

  8. The first two bases in a codon form Watson–Crick base pairs that are checked for fidelity by bases of the 16S rRNA. The third base is not inspected for accuracy, and so some variation is tolerated.

  9. (a) 5′-UAACGGUACGAU-3′; (b) Leu-Pro-Ser-Asp-Trp-Met; (c) Poly(Leu-Leu-Thr-Tyr)

  10. Incubation with RNA polymerase and only UTP, ATP, and CTP led to the synthesis of only poly(UAC). Only poly(GUA) was formed when GTP was used in place of CTP.

  11. Only single-stranded RNA can serve as a template for protein synthesis.

  12. These alternatives were distinguished by the results of studies of the sequence of amino acids in mutants. Suppose that the base C is mutated to C′. In a nonoverlapping code, only amino acid 1 will be changed. In a completely overlapping code, amino acids 1, 2, and 3 will all be altered by a mutation of C to C′. The results of amino-acid-sequence studies of tobacco mosaic virus mutants and abnormal hemoglobins showed that alterations usually affected only a single amino acid. Hence, the genetic code was concluded to be nonoverlapping.

  13. A peptide terminating with Lys (UGA is a Stop codon), -Asn-Glu-, and -Met-Arg-

  14. Highly abundant amino acid residues have the most codons (e.g., Leu and Ser each have six), whereas the least abundant amino acids have the fewest (Met and Trp each have only one). Degeneracy (1) allows variation in base composition and (2) decreases the likelihood that a substitution for a base will change the encoded amino acid. If the degeneracy were equally distributed, each of the 20 amino acids would have three codons. Both benefits (1 and 2) are maximized by the assignment of more codons to prevalent amino acids than to less frequently used ones.

  15. Phe-Cys-His-Val-Ala-Ala

  16. (1) Each is a single chain. (2) They contain unusual bases. (3) Approximately half of the bases are base-paired to form double helices. (4) The 5′ end is phosphorylated and is usually pG. (5) The amino acid is attached to the hydroxyl group of the A residue of the CCA sequence at the 3′ end of the tRNA. (6) The anticodon is located in a loop near the center of the tRNA sequence.

  17. First is the formation of the aminoacyl adenylate, which then reacts with the tRNA to form the aminoacyl-tRNA. Both steps are catalyzed by aminoacyl-tRNA synthetase.

  18. Unique features are required so that the aminoacyl-tRNA synthetases can distinguish among the tRNAs and attach the correct amino acid to the correct tRNA. Common features are required because all tRNAs must interact with the same protein-synthesizing machinery.

  19. An activated amino acid is one linked to the appropriate tRNA.

  20. The ATP is cleaved to AMP and PPi. Consequently, a second ATP is required to convert AMP into ADP, the substrate for oxidative phosphorylation.

  21. Amino acids larger than the correct amino acid cannot fit into the activation site of the tRNA. Smaller but incorrect amino acids that become attached to the tRNA fit into the editing site and are cleaved from the tRNA.

  22. These enzymes convert nucleic acid information into protein information by interpreting the tRNA and linking it to the correct amino acid.

  23. The 2′-OH group in RNA acts as an intramolecular nucleophile. In the alkaline hydrolysis of RNA, the 2′-OH group forms a 2′-3′ cyclic intermediate.

  24. (a) No; (b) no; (c) yes

  25. This distribution is the one expected if the amino-terminal regions of some chains had already been partly synthesized before the addition of the radioactive amino acid. Thus, protein synthesis begins at the amino terminus and extends toward the carboxyl terminus.

  26. AAA encodes lysine, whereas AAC encodes asparagine. Because asparagine was the carboxyl-terminal residue, we can conclude that the codon AAC was the last to be read.