1. The Oxford English Dictionary defines translation as the action or process of turning from one language into another. Protein synthesis converts nucleic acid sequence information into amino acid sequence information.

2. 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.

3. (i) Each is a single chain. (ii) They contain unusual bases. (iii) Approximately half of the bases are base-paired to form double helices. (iv) The 5′ end is phosphorylated and is usually pG. (v) The amino acid is attached to the hydroxyl group of the A residue of the CCA sequence at the 3′ end of the tRNA. (vi) The anticodon is located in a loop near the center of the tRNA sequence. (vii) The molecules are l-shaped.

4. 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.

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

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

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

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

9. Amino acids larger than the correct amino acid cannot fit into the active 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.

10. Recognition sites on both faces of the tRNAs may be required to uniquely identify the 20 different tRNAs.

11. 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.

12. Four bands: light, heavy, a hybrid of light 30S and heavy 50S, and a hybrid of heavy 30S and light 50S.

13. Two hundred molecules of ATP are converted into 200 AMP + 400 P_i to activate the 200 amino acids, which is equivalent to 400 molecules of ATP. One molecule of GTP is required for initiation, and 398 molecules of GTP are needed to form 199 peptide bonds.

14. The reading frame is a set of contiguous, nonoverlapping three-nucleotide codons that begins with a start codon and ends with a stop codon.

15. A mutation caused by the insertion of an extra base can be suppressed by a tRNA that contains a fourth base in its anticodon. For example, UUUC rather than UUU is read as the codon for phenylalanine by a tRNA that contains 3′-AAAG-5′ as its anticodon.

16. One approach is to synthesize a tRNA that is acylated with a reactive amino acid analog. For example, bromoacetyl-phenylalanyl-tRNA is an affinity-labeling reagent for the P site of E. coli ribosomes.

17. The sequence GAGGU is complementary to a sequence of five bases at the 3′ end of 16S rRNA and is located several bases upstream of an AUG start codon. Hence, this region is a start signal for protein synthesis. The replacement of G by A would be expected to weaken the interaction of this mRNA with the 16S rRNA and thereby diminish its effectiveness as an initiation signal. In fact, this mutation results in a 10-fold decrease in the rate of synthesis of the protein specified by this mRNA.

18. The peptide would be Phe-Cys-His-Val-Ala-Ala. The codons UGC and UGU encode cysteine but, because the cysteine was modified to alanine, alanine is incorporated in place of cysteine.

19. Proteins are synthesized from the amino to the carboxyl end on ribosomes, whereas they are synthesized in the reverse direction in the solid-phase method. The activated intermediate in ribosomal synthesis is an aminoacyl-tRNA; in the solid-phase method, it is the adduct of the amino acid and dicyclohexylcarbodiimide.

20. GTP is not hydrolyzed until aminoacyl-tRNA is delivered to the A site of the ribosome. An earlier hydrolysis of GTP would be wasteful because EF-Tu–GDP has little affinity for aminoacyl-tRNA.

21. The translation of an mRNA molecule can be blocked by antisense RNA, an RNA molecule with the complementary sequence. The antisense–sense RNA duplex cannot serve as a template for translation; single-stranded mRNA is required. Furthermore, the antisense–sense duplex is degraded by nucleases. Antisense RNA added to the external medium is spontaneously taken up by many cells. A precise quantity can be delivered by microinjection. Alternatively, a plasmid encoding the antisense RNA can be introduced into target cells.

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22. (a) A₅. (b) A₅ > A₄ > A₃ > A₂. (c) Synthesis is from the amino terminus to the carboxyl terminus.

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

24. The rate would fall because the elongation step requires that the GTP be hydrolyzed before any further elongation can take place.

25. Protein factors modulate the initiation of protein synthesis. The role of IF1 and IF3 is to prevent premature binding of the 30S and 50S ribosomal subunits, whereas IF2 delivers Met-tRNA_f to the ribosome. Protein factors are also required for elongation (EF-G and EF-Tu), for termination (release factors, RFs), and for ribosome dissociation (ribosome release factors, RRFs).

26. The signal sequence, signal-recognition particle (SRP), the SRP receptor, and the translocon.

27. The formation of peptide bonds, which in turn are powered by the hydrolysis of the aminoacyl-tRNAs.

28. The Shine–Dalgarno sequence of the mRNA base-pairs with a part of the 16S rRNA of the 30S subunit, which positions the subunit so that the initiator AUG is recognized.

29.

30. The SRP binds to the signal sequence and inhibits further translation. The SRP ushers the inhibited ribosome to the ER, where it interacts with the SRP receptor (SR). The SRP–SR complex binds the translocon and simultaneously hydrolyzes GTP. On GTP hydrolysis, SRP and SR dissociate from each other and from the ribosome. Protein synthesis resumes and the nascent protein is channeled through the translocon.

31. The alternative would be to have a single ribosome translating a single mRNA molecule. The use of polysomes allows more protein synthesis per mRNA molecule in a given period of time and thus the production of more protein.

32. (a) 1, 2, 3, 5, 6, 10; (b) 1, 2, 7, 8; (c) 1, 4, 8, 9.

33. Transfer RNAs have roles in several recognition processes. A tRNA must be recognized by the appropriate aminoacyl-tRNA synthetase, and the tRNA must interact with the ribosome and, in particular, with the peptidyl transferase.

34. The aminoacyl-tRNA can be initially synthesized. However, the side-chain amino group attacks the ester linkage to form a six-membered amide, releasing the tRNA.

35. (a, d, and e) Type 2; (b, c, and f ) Type 1.

36. The error rates of DNA, RNA, and protein synthesis are of the order of 10⁻¹⁰, 10⁻⁵, and 10⁻⁴, respectively, per nucleotide (or amino acid) incorporated. The fidelity of all three processes depends on the precision of base-pairing to the DNA or mRNA template. Few errors are corrected in RNA synthesis. In contrast, the fidelity of DNA synthesis is markedly increased by the 3′ → 5′ proofreading nuclease activity and by postreplicative repair. In protein synthesis, the mischarging of some tRNAs is corrected by the hydrolytic action of aminoacyl-tRNA synthetase. Proofreading also takes place when aminoacyl-tRNA occupies the A site on the ribosome; the GTPase activity of EF-Tu sets the pace of this final stage of editing.

37. EF-Ts catalyzes the exchange of GTP for GDP bound to EF-Tu. In G-protein cascades, an activated 7TM receptor catalyzes GTP–GDP exchange in a G protein.

38. The α subunits of G proteins are inhibited by a similar mechanism in cholera and whooping cough (Section 14.5).

39. Glu-tRNA^Gln is formed by misacylation. The activated glutamate is subsequently amidated to form Gln-tRNA^Gln. Ways in which glutamine is formed from glutamate were discussed in Section 24.2. In regard to H. pylori, a specific enzyme, Glu-tRNA^Gln amidotransferase, catalyzes the following reaction:

Glu-tRNA^Glu is not a substrate for the enzyme; so the transferase must also recognize aspects of the structure of tRNA^Gln.

40. The primary structure determines the three-dimensional structure of the protein. Thus, the final phase of information transfer from DNA to RNA to protein synthesis is the folding of the protein into its functional state.

41. (a) eIF-4H has two effects: (1) the extent of unwinding is increased and (2) the rate of unwinding is increased, as indicated by the increased rise in activity at early reaction times.

(b) To firmly establish that the effect of eIF-H4 was not due to any inherent helicase activity.

(c) Half-maximal activity was achieved at 0.11 µM of eIF-4H. Therefore, maximal stimulation would be achieved at a ratio of 1:1.

(d) eIF-4H enhances the rate of unwinding of all helices, but the effect is greater as the helices increase in stability.

(e) The results in graph C suggest that eIF-4H increases the processivity.

42. (a) The three peaks represent, from left to right, the 40S ribosomal subunit, the 60S ribosomal subunit, and the 80S ribosome.

(b) Not only are ribosomal subunits and the 80S ribosome present, but polysomes of various lengths also are apparent. The individual peaks in the polysome region represent polysomes of discrete length.

(c) The treatment significantly inhibited the number of polysomes while increasing the number of free ribosomal subunits. This outcome could be due to inhibited protein-synthesis initiation or inhibited transcription.