BIOCHEMISTRY - L. Stryer - 1984

VOLUME 3

ANSWERS TO QUESTIONS AND PROBLEMS

Chapter 24

1. a) TTGATC;

b) GTTCGA;

c) ACGCGT;

d) ATGGTA.

2. a) [T] + [C] = 0.46.

b) [T] = 0.30; [C] = 0.24; [A] + [G] = 0.46.

3. 5.88 • 10³ Base Pairs.

4. After 1.0 generation, half of the molecules will be ¹⁵N — ¹⁵N and the other half will be ¹⁴N — ¹⁴N. After 2.0 generations, one-quarter of all molecules will be ¹⁵N — ¹⁵N, and the remaining three-quarters will be ¹⁴N — ¹⁴N. Hybrid ¹⁴N — ¹⁵N molecules will not be detected under conservative Replication.

5. FAD, CoA, NADP⁺.

6. DNA ligase relaxes supercoiled DNA by catalyzing the Cleavage of a phosphodiester bond in one of the DNA strands. The attacking group is AMP; it becomes attached to the 5'-phosphoryl group at the cleavage site. AMP is required because this reaction represents the Reversal of the final step in joining different DNA fragments (see Fig. 24.32 in Section 24.15).

7. 5'-GGCATAC-3'.

Chapter 25

1. a) DNA polymerase consists of a single polypeptide chain, whereas RNA polymerase has a subunit Structure of α2ββ'σ.

b) The precursors are deoxynucleoside triphosphates rather than ribonucleoside triphosphates.

c) The direction of synthesis for both Enzymes is 5' → 3'.

d) DNA polymerase I possesses 5' → 3' and 3' → 5' exonuclease activities, whereas RNA polymerase possesses neither.

e) DNA polymerase I carries out semi-conservative synthesis, whereas RNA polymerase carries out conservative synthesis.

f) DNA polymerase I requires a primer, whereas RNA polymerase does not.

g) The driving force for both reactions is the Hydrolysis of pyrophosphate.

2. 5'-UAACGGUACGAU-3'

3. The 2'-OH group within RNA acts as an intramolecular catalyst. Alkaline hydrolysis of RNA yields a 2',3'-cyclic intermediate.

4. Cordycepin terminates RNA Synthesis. The RNA chain containing cordycepin lacks a 3'-OH group.

5. a) pGCp, AGUp, ACp, Up, GUp, and C.

б) pGp, CAGp, UACUGp, and UC

в) pGp, САр, Gp, UAp, CUGp, and UC.

г) pGp, CAp, Gp, Up, Ap, CUp, and C.

6. UAGCCUGAAUp.

Chapter 26

1. Leu-Pro-Ser-Asp-Trp-Met-.

2. Poly (Leu-Leu-Thr-Tyr).

3. a) Pro (CCC), Ser (UCC), Leu (CUC), and Phe (UUC). Alternatively, the last base of each of these codons may be U.

б) These C → U Mutations were induced by nitrous acid.

4. а) This would require two base substitutions.

б) Arg, Asn, Gln, Gln, Ile, Met, or Thr.

5. а) No, this sequence arose As a result of the deletion of the first base in the sequence shown below and the insertion of another base at the end.

б) —AGUCCAUCACUUAAU—.

6. They have the following sequences: Lys-stop; -Met-Arg-; -Asn-Gln-.

Chapter 27

1. а) No;

б) no;

в) yes.

2. There will be 4 bands in the gradient: light; heavy; a band corresponding to the hybrid of the light 30S and heavy 50S subunits; and a band corresponding to the hybrid of the heavy 30S and light 50S subunits.

3. Approximately 799 energy-rich phosphate bonds are consumed: 400 for activating 200 Amino Acids, 1 for initiation, and 398 for forming 199 peptide bonds.

4. b), c), and f) - type 1 mechanism;

a), d), and e) - type 2 mechanism.

5. The simplest assumption is that the CCA anticodon of Tryptophan tRNA mutated to a UCA codon complementary to UGA. However, The Study of this modified tRNA yielded an unexpected result. Its anticodon remained unchanged. Instead, an A-to-G substitution occurred at position 24. Thus, a residue located at a considerable distance from the anticodon in the linear sequence can influence the accuracy of codon recognition.

6. One approach is to synthesize a tRNA attached to a reactive amino acid analogue. For instance, bromoacetylphenylalanyl-tRNA serves as an affinity labeling reagent for the P site of E. coli Ribosomes.

7. The GAGGU sequence is complementary to a five-base sequence at the 3' end of 16S rRNA and is located a few bases upstream (in the 5' direction) from the AUG codon. Therefore, this region acts as a signal for the initiation of Protein Synthesis. Substituting G with A would likely weaken the interaction between this mRNA and 16S rRNA, thereby reducing the efficiency of this sequence as an initiation signal. Indeed, this mutation results in a 10-fold decrease in the synthesis rate of the protein encoded by the mRNA.

8. Both cases involve hydrolysis reactions: the 3' → 5' exonuclease activity of DNA polymerase I and the hydrolysis of the erroneous aminoacyl-AMP intermediate by aminoacyl-tRNA synthetase.

Chapter 28

1. a) The i-mutant lacks the lac repressor. Consequently, such a mutant is constitutive for the synthesis of lac Operon Proteins.

б) This mutant is constitutive for the synthesis of trp operon proteins because it lacks the trp repressor.

в) In this mutant, the arabinose operon is not expressed, as the P2 form of the araC protein is required to activate METABOLISM/31.html">Transcription.

г) This mutant exhibits a lytic rather than a lysogenic phenotype because it is unable to synthesize the repressor.

д) This mutant is capable of Lysogeny but is deficient in lytic growth because it cannot synthesize the N protein, a positive regulatory factor for transcription.

2. One possibility is that the i^s mutant produces an altered lac repressor that has almost no affinity for the inducer while retaining normal affinity for the operator. Such a lac repressor will bind to the operator and block transcription even in the presence of the inducer.

3. In this mutant, the lac operator is altered in such a way that it can no longer bind the repressor. Such a mutation is designated as O^c (operator constitutive).

4. In this mutant, the cyclic AMP receptor protein (CRP) apparently either has an altered structure (is defective) or is completely absent.

5. An E. coli Cell carrying the prophage contains repressor molecules, which also block the transcription of very early genes of other incoming phage particles.

6. a) Introduction/27.html">Translation of the P_re transcript occurs 5 to 10 times faster than that of the P_rM transcript because it contains a full-fledged initiation signal for protein synthesis (as discussed in Section 27.14).

б) More efficient translation of the P_re transcript leads to the rapid production of A large number of cI repressor molecules required to establish the lysogenic state.