1.  Minimal code. What is the minimum number of contiguous bases required to encode 20 amino acids? Explain your answer. ✓ 1

2.  Nearly universal. Why has the code remained nearly invariant through billions of years of evolution, from bacteria to human beings? ✓ 1

3.  Like Pooh and Christopher Robin. Match each term with its description.

4.  A code you can live by. What are the key characteristics of the genetic code? ✓ 1

5.  Degeneracy. Usually degeneracy should be avoided, except perhaps in well-controlled circumstances. However, it is advantageous for the genetic code to be degenerate. What does it mean to say that the code is degenerate, and explain why a degenerate code is valuable? ✓ 1

6.  Odds of getting it right. Calculate the probability of synthesizing an error-free protein of 50 amino acids and one of 300 amino acids when the frequency of inserting an incorrect amino acid is 10⁻². Repeat the calculations with error frequencies of 10⁻⁴ and 10⁻⁶.

7.  Careful, but not too careful. Why is it crucial that protein synthesis has an error frequency of 10⁻⁴?

8.  Going wobbly. Explain how it is possible that some tRNA molecules recognize more than one codon. ✓ 1

9.  Encoded sequences.

(a) Write the sequence of the mRNA molecule synthesized from a DNA template strand having the following sequence. ✓ 1

5′-ATCGTACCGTTA-3′

(b) What amino acid sequence is encoded by the following base sequence of an mRNA molecule? Assume that the reading frame starts at the 5′ end.

5′-UUGCCUAGUGAUUGGAUG-3′

(c) What is the sequence of the polypeptide formed on addition of poly(UUAC) to a cell-free protein-synthesizing system that does not require a start codon?

10.  Deciphering the code, 1. Synthetic RNA molecules of defined sequence were instrumental in deciphering the genetic code. Their synthesis first required the synthesis of DNA molecules to serve as a template. H. Gobind Khorana synthesized, by organic-chemical methods, two complementary deoxyribonucleotides, each with nine residues: d(TAC)₃ and d(GTA)₃. Partly overlapping duplexes that formed on mixing these oligonucleotides then served as templates for the synthesis by DNA polymerase of long, repeating double-helical DNA strands. The next step was to obtain long polyribonucleotide strands with a sequence complementary to only one of the two DNA strands. How did Khorana obtain only poly(UAC)? Only poly(GUA)? ✓ 1

11.  Deciphering the code, 2. The code word GGG cannot be deciphered in the same way as can UUU, CCC, and AAA, because poly(G) does not act as a template for protein synthesis. Poly(G) forms a triple-stranded helical structure. Why is it an ineffective template? ✓ 1

12.  Overlapping or not. In a nonoverlapping triplet code, each group of three bases in a sequence ABCDEF … specifies only one amino acid—ABC specifies the first, DEF the second, and so forth—whereas, in a completely overlapping triplet code, ABC specifies the first amino acid, BCD the second, CDE the third, and so forth. Assume that you can mutate an individual nucleotide of a codon and detect the mutation in the amino acid sequence. Design an experiment that would establish whether the genetic code is overlapping or nonoverlapping. ✓ 1

13.  Triple entendre. The RNA transcript of a region of T4 phage DNA contains the sequence 5′-AAAUGAGGA-3′. In theory, this sequence is capable of encoding three different polypeptides. What are they? ✓ 1

14.  Valuable synonyms. Proteins generally have low contents of Met and Trp, intermediate ones of His and Cys, and high ones of Leu and Ser. What does this observation suggest about the relation between the number of codons of an amino acid and its frequency of occurrence in proteins? What might be the selective advantage of this relation?

15.  A new translation. A transfer RNA with a UGU anticodon is enzymatically conjugated to ¹⁴C-labeled cysteine. The cysteine unit is then chemically modified to alanine. The altered aminoacyl-tRNA is added to a protein-synthesizing system containing normal components except for this tRNA. The mRNA added to this mixture contains the following sequence:

5′-UUUUGCCAUGUUUGUGCU-3′

What is the sequence of the corresponding radiolabeled peptide?

16.  Commonalities. What features are common to all tRNA molecules? ✓ 2

17.  The ol’ two step. What two reaction steps are required for the formation of an aminoacyl-tRNA? ✓ 2

18.  The same but different. Why must tRNA molecules have both unique structural features and common structural features? ✓ 2

19.  Charge it. In the context of protein synthesis, what is meant by an activated amino acid? ✓ 2

20.  1 = 2, for sufficiently large values of 1. The energetic equivalent of two molecules of ATP is used to activate an amino acid, yet only one molecule of ATP is used. Explain.

21.  Sieves. Using threonyl-tRNA synthetase as an example, account for the specificity of threonyl-tRNA formation. ✓ 2

22.  Knowledge rich. Aminoacyl-tRNA synthetases are the only components of gene expression that know the genetic code. Explain. ✓ 2

23.  A tougher strand. RNA is readily hydrolyzed by alkali, whereas DNA is not. Why?

24.  Synthetase mechanism. The formation of isoleucyltRNA proceeds through the reversible formation of an enzyme-bound Ile-AMP intermediate. Predict whether ³²P-labeled ATP is formed from ³²PP_i when each of the following sets of components is incubated with the specific activating enzyme. ✓ 2

(a) ATP and ³²PP_i

(b) tRNA, ATP, and ³²PP_i

(c) Isoleucine, ATP, and ³²PP_i

25.  Finding direction. A series of experiments were performed to establish the direction of chain growth in protein synthesis. Reticulocytes (young red blood cells) that were actively synthesizing hemoglobin were treated with [³H]leucine. In a period of time shorter than that required to synthesize a complete chain, samples of hemoglobin were taken, separated into α and β chains, and analyzed for the distribution of ³H within their sequences. In the earliest samples, only regions near the carboxyl ends contained radioactivity. In later samples, radioactivity was present closer to the amino terminus as well. Explain how these results determine the direction of chain growth in protein synthesis.

26.  Mission possible. Your mission, should you accept it, is to determine the direction in which the mRNA is read during protein synthesis. You are provided with synthetic polynucleotide



as the template in a cell-free protein-synthesizing system, which is also kindly provided to you. The polypeptide product was



What does the nature of this product say about the direction in which the mRNA is read? ✓ 2