Chapter 15

Assume that the number of different types of bases in RNA is four. What would be the minimum codon size (number of nucleotides) required if the number of different types of amino acids in proteins were: (a) 2, (b) 8, (c) 17, (d) 45, (e) 75?

(a) 1; (b) 2; (c) 3; (d) 3; (e) 4.

A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair. a. 5′-GGC-3′ b. 5′-AAG-3′ c. 5′-IAA-3′ d. 5′-UGG-3′ e. 5′-CAG-3′

(a) 3′-CCG-5′ or 3′-UCG-5′; (b) 3′-UUC-5′; (c) 3′-AUU-5′ or 3′-UUU-5′ or 3′-CUU-5′; (d) 3′-ACC-5′ or 3′-GCC-5′; (e) 3′-GUC-5′.

Using the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences, and indicate the amino and carboxyl ends of the polypeptide produced. a. 5′-AUGUUUAAAUUUAAAUUUUGA-3′ b. 5′-AUGUAUAUAUAUAUAUGA-3′ c. 5′-AUGGAUGAAAGAUUUCUCGCUUGA-3′ d. 5′-AUGGGUUAGGGGACAUCAUUUUGA-3′

(a) amino-fMet-Phe-Lys-Phe-Lys-Phe-carboxyl (b) amino-fMet-Tyr-Ile-Tyr-Ile-carboxyl (c) amino-fMet-Asp-Glu-Arg-Phe-Leu-Ala-carboxyl (d) amino-fMet-Gly-carboxyl (The stop codon UAG follows the codon for glycine.)

A synthetic mRNA added to a cell-free proteinsynthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. a. Initiation factor 1 b. Initiation factor 2 c. Elongation factor Tu d. Elongation factor G e. Release factors RF 1, RF2, and RF3 f. ATP g. GTP

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Explain how some antibiotics work by affecting the process of protein synthesis

A number of antibiotics bind the ribosome and inhibit protein synthesis at different steps in translation. Some antibiotics, such as streptomycin, bind to the small subunit and inhibit the initiation of translation. Other antibiotics, such as chloramphenicol, bind to the large subunit and block the elongation of the peptide by preventing peptide-bond formation. Antibiotics such as tetracycline and neomycin bind the ribosome near the A site yet have different effects. Tetracyclines block the entry of charged tRNAs to the A site, whereas neomycin induces translational errors. Finally, some antibiotics, such as erythromycin, block the translocation of the ribosome along the mRNA

How are tRNAs linked to their corresponding amino acids?

For each of the 20 different amino acids commonly found in proteins, a corresponding aminoacyl-tRNA synthetase covalently links the amino acid to the correct tRNA molecule.

What is the significance of the fact that many synonymous codons differ only in the third nucleotide position?

In synonymous codons that differ only at the third nucleotide position, the "wobble" and nonstandard base-pairing with the anticodons will likely result in the correct amino acid being inserted in the protein.

What different methods were used to help break the genetic code? What did each method reveal and what were the advantages and disadvantages of each one?

Nirenberg and Matthaei used homopolymer and copolymer methods. Advantages: Using a cell-free protein synthesizing system, they were able to determine the amino acid encoded by each homopolymer and thus the amino acids specifi ed by the codons UUU, AAA, CCC, and GGG. Disadvantages: The homopolymer method yielded the specifi cities of only four codons. The copolymer method depended on the random incorporation of the nucleotides, which did not always happen. A further problem was that the base sequence of the codon could not be determined; only the bases contained within the codon could be determined. The redundancy of the code created diffi culties because several different codons specifi ed the same amino acid. Nirenberg and Leder mixed ribosomes bound to short RNAs of known sequences with charged tRNAs. The mixture was passed through a nitrocellulose fi lter to which the tRNAs paired to ribosome-RNA complexes adhered. They next determined the amino acids attached to the bound tRNAs.

Several experiments were conducted to obtain information about how the eukaryotic ribosome recognizes the AUG start codon. In one experiment, the gene that encodes methionine initiator tRNA (tRNAiMet) was located and changed. The nucleotides that specify the anticodon on tRNA i Met were mutated so that the anticodon in the tRNA was 5′-CCA-3′ instead of 5′-CAU-3′. When this mutated gene was placed in a eukaryotic cell, protein synthesis took place but the proteins produced were abnormal. Some of the proteins produced contained extra amino acids, and others contained fewer amino acids than normal. If the same experiment had been conducted on bacterial cells, what results would you expect?

The initiation of translation in bacteria requires the 16S RNA of the small ribosomal subunit to interact with the Shine-Dalgarno sequence. This interaction serves to line up the ribosome over the start codon. If the anticodon has been changed such that the start codon cannot be recognized, then protein synthesis is not likely to take place.

Several experiments were conducted to obtain information about how the eukaryotic ribosome recognizes the AUG start codon. In one experiment, the gene that encodes methionine initiator tRNA (tRNAiMet) was located and changed. The nucleotides that specify the anticodon on tRNA i Met were mutated so that the anticodon in the tRNA was 5′-CCA-3′ instead of 5′-CAU-3′. When this mutated gene was placed in a eukaryotic cell, protein synthesis took place but the proteins produced were abnormal. Some of the proteins produced contained extra amino acids, and others contained fewer amino acids than normal. a. What do these results indicate about how the ribosome recognizes the starting point for translation in eukaryotic cells? Explain your reasoning

The results suggest that, to initiate translation, the ribosome is scanned to fi nd the appropriate start sequence.

The following amino acid sequence is found in a tripeptide: Met-Trp-His. Give all possible nucleotide sequences on the mRNA, on the template strand of DNA, and on the nontemplate strand of DNA that can encode this tripeptide

There are two possible sequences: mRNA: 5′-AUGUGGCAU-3′ DNA template: 3′-TACACCGTA-5′ DNA nontemplate: 5′-ATGTGGCAT-3′ mRNA: 5′-AUGUGGCAC-3′ DNA template: 3′-TACACCGTG-5′ DNA nontemplate: 5′-AT GTGGCAC-3′

Give the elongation factors used in bacterial translation and explain the role played by each factor in translation

Three elongation factors have been identifi ed in bacteria: EF-Tu, EF-Ts, and EF-G. EF-Tu joins GTP, which in turn joins a tRNA charged with an amino acid. The charged tRNA is delivered to the ribosome at the A site. In the process of delivery, the GTP joined to EF-Tu is cleaved to form a EF-Tu-GDP complex. EF-Ts regenerates EF-Tu-GTP. The elongation factor EF-G binds GTP and is necessary for the translocation, or movement, of the ribosome along the mRNA during translation.

Define the following terms as they apply to the genetic code: Sense codon

a group of three nucleotides that encode an amino acid. Sixty-one sense codons encode the 20 amino acids commonly found in proteins.

Define the following terms as they apply to the genetic code: Overlapping code

a single nucleotide is included in more than one codon. The result for a sequence of nucleotides is that more than one type of polypeptide can be encoded within that sequence.

Define the following terms as they apply to the genetic code: Nonoverlapping code

a single nucleotide is part of only one codon, which results in the production of a single type of polypeptide from one polynucleotide sequence.

Define the following terms as they apply to the genetic code: Universal code

each codon specifi es the same amino acid in all organisms. The genetic code is nearly universal but note completely. Most of the exceptions are in mitochondrial genes.

Define the following terms as they apply to the genetic code: Initiation codon

establishes the appropriate reading frame and specifi es the fi rst amino acid of the protein chain. Typically, the initiation codon is AUG; however, GUG and UUG also can serve as initiation codons.

Define the following terms as they apply to the genetic code: Reading frame

refers to how the nucleotides in a nucleic acid molecule are grouped into codons, with each codon containing three nucleotides. Any sequence of nucleotides has three potential reading frames that have completely different sets of codons.

Define the following terms as they apply to the genetic code: Nonsense codon

signals the end of translation. Nonsense codons do not encode amino acids.

Define the following terms as they apply to the genetic code: Termination codon

signals the termination, or end, of translation and the end of the protein molecule. The three types of termination codons—UAA, UAG, and UGA—are also referred to as stop codons or nonsense codons. These codons do not encode amino acids.

Define the following terms as they apply to the genetic code: Nonuniversal Codons

they specify the same amino acids in almost all organisms, there are exceptions in which a codon has different meanings in different organisms.