Chapter 40

  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. The reading frame is a set of contiguous, nonoverlapping three-nucleotide codons that encode the amino acid sequence of the protein. The reading frame begins with a Start codon and ends with a Stop codon.

  3. Complete the interactive matching exercise to see answers.

  4. 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.

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

  6. Two hundred molecules of ATP are converted into 200 AMP + 400 Pi 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. The translation of an mRNA molecule can be blocked by an RNA molecule with the complementary sequence. Such RNAs are called antisense RNAs. 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 the RNA-induced silencing complex. 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.

  12. (a) A5 ; (b) A5 > A4 > A3 > A2 ; (c) synthesis is from the amino terminus to the carboxyl terminus.

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

  14.  

    Bacterium

    Eukaryote

    Ribosome size

    70S

    80S

    mRNA

    Polycistronic

    Not polycistronic

    Initiation

    Shine–Dalgarno is required

    First AUG is used

    Protein factors

    Required

    Many more required

    Relation to transcription

    Translation can start before transcription is completed

    Transcription and translation are spatially separated

    First amino acid

    fMet

    Met

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

  16. The signal-recognition particle (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.

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

  18. 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.

  19. The addition of an IRE to the 5′ end of the mRNA would be expected to block translation in the absence of iron. The addition of an IRE to the 3′ end of the mRNA would not be expected to block translation, but it would make the mRNA more susceptible to degradation.

  20. The sequences of all of the mRNAs would be searched for sequences that are fully or nearly complementary to the sequence of the miRNA. These sequences would be candidates for regulation by this miRNA.

  21. 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.

  22. The α subunits of G proteins are inhibited by a similar mechanism in cholera and whooping cough.

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

  24. 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.

    1. Factor 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.

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

    3. Half-maximal activity was achieved at 0.11 mM of eIF-4H. Therefore, maximal stimulation would be achieved at a ratio of 1:1.

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

    5. The results in graph C suggest that it increases the processivity.

    1. The three peaks represent, from left to right, the 40S ribosomal subunit, the 60S ribosomal subunit, and the 80S ribosome.

    2. 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.

    3. The treatment significantly inhibited the number of polysomes, whereas it increased the number of free ribosomal subunits. This outcome could be due to inhibited protein-synthesis initiation or inhibited transcription.

  27. 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.

  28. Glu-tRNAGln is formed by misacylation. The activated glutamate is subsequently amidated to form Gln-tRNAGln. Ways in which glutamine is formed from glutamate were discussed in Section 31.2. In regard to H. pylori, a specific enzyme, Glu-tRNAGln amidotransferase, catalyzes the following reaction:

    Gln + Glu-tRNAGln + ATP → Gln-tRNAGln + Glu + ADP + Pi

    Glu-tRNAGlu is not a substrate for the enzyme; so the transferase must also recognize aspects of the structure of tRNAGln.

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