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III. Molecular Genetics
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11. Gene Expression: Translation
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Exercises and Problems
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PROBLEM 1: What is the energy requirement of protein
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P R O B L E M S
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to the A and P sites differs in prokaryotes and eukaryotes.In prokaryotes, the Shine-Dalgarno sequence allows the 16S ribosomal RNA and the messenger RNA to form hydrogen bonds, locating the beginning of the messenger RNA at the ribosome.In eukaryotes,the 5 cap is usually recognized by the ribosome, and the ribosome then proceeds to scan the messenger RNA for the initiation codon.
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PROBLEM 3: What amino acids could replace methio-
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biosynthesis Answer: The cost of adding one amino acid to a growing polypeptide is four or ve high-energy bonds:two from an ATP during the charging of the transfer RNA, and two or three from the hydrolysis of GTPs during transfer RNA binding to the A site of the ribosome and during translocation.Thus, for an average protein of three hundred amino acids, there is a cost of 1,200 to 1,500 high-energy bonds.
PROBLEM 2: What are the start and stop signals of trans-
lation Answer: Once a messenger RNA is attached at the ribosome, the start signal is the methionine initiation codon (usually AUG), whereas the stop signal is one of the three nonsense codons (UAA, UAG, and UGA). Binding to the ribosome in order to position the messenger RNA in relation
nine if a one-base mutation occurred Answer: The codon for methionine (internal as well as initiation) is AUG. If the A is replaced, we would get UUG (Leu), CUG (Leu), or GUG (Val); if the U is replaced, we would get AAG (Lys),ACG (Thr), or AGG (Arg); and if the G is replaced, we would get AUA (Ile),AUU (Ile), or AUC (Ile). Hence, a one-base change in the codon for methionine could result in any of six different amino acids.
E X E R C I S E S
INFORMATION TRANSFER
A N D
P R O B L E M S*
1. Given the following end part of a gene, which will be transcribed and then translated into a pentapeptide, provide the base sequence for its messenger RNA. Give the anticodons on the transfer RNAs by making use of wobble rules. What amino acids are incorporated Draw the actual structure of the pentapeptide. 3 -TACAATGGCCCTTTTATC-5 5 -ATGTTACCGGGAAAATAG-3 2. Give an alternative translation mechanism that would require only one transfer RNA site on the ribosome. 3. Draw the details of a moment in time at the ribosome during the translation of the messenger RNA produced in problem 1. Include in the diagram the ribosomal sites, the transfer RNAs, and the various nonribosomal proteins involved. 4. How do prokaryotic and eukaryotic ribosomes recognize the 5 end of messenger RNAs Could eukaryotic messenger RNAs be polycistronic 5. How many aminoacyl-tRNA synthetases are there What do they use for recognition signals 6. What are the similarities and differences among the three nonsense codons Using the wobble rules, what are their theoretical anticodons
*Answers to selected exercises and problems are on page A-12.
7. Describe an experiment that demonstrates that the transfer RNA, and not its amino acid, is recognized at the ribosome during translation. 8. Other than the antibiotics named in the chapter, suggest ve theoretical antibiotics that could interfere with the prokaryotic translation process. 9. How many single-base deletions are required to restore the reading frame of a messenger RNA Give an example. 10. A nonsense mutation is one in which a codon for an amino acid changes to one for chain termination. Give an example.What are its consequences 11. The reverse situation to problem 10 is a mutation from a nonsense codon to a codon for an amino acid. Give an example.What are its consequences 12. What are the consequences when an internal methionine codon recognizes a prokaryotic initiation transfer RNA 13. What role does EF-Ts play in elongation EF-Tu What are their eukaryotic equivalents 14. What roles do RF1 and RF2 play in chain termination What are their eukaryotic equivalents 15. What is a signal peptide What role does it play in eukaryotes What is its fate 16. Why doesn t puromycin disrupt eukaryotic translation
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