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 (for the key, I have selected among actual student answers)

1. One way to think about the genetic code is to compare it to the International Morse Code, a system of dots, dashes, and spaces used to send messages by telegraph and shortwave radio. In the Morse code, each letter of the alphabet is represented by a unique combination of two, three, or four dots and dashes. For example, dot-dash represents the letter A, dash-dot-dot-dot represents the letter B, dot-dash-dot represents the letter C, and so forth. Based on this information and your knowledge of the genetic code, explain each of the following terms as it relates to coding, and indicate with an M if it is true of the Morse code, with a G if it is true of the genetic code, and with both letters if it is true for both.

a) degenerate (G): any of several codons can specify a single amino acid

b) unambiguous (G,M): for both the genetic code and morse code, one codon or set of dots and dashes specifies only one amino acid or letter--it does not have multiple meanings

c) triplet (G): A codon consists of three nucleotides in sequence. All amino acids (and start and stop commands) are coded by three nucleotides. Letters in the Morse code can be triplets of dots and dashes, but are not limited to sets of three--they can also be sets of two or four.

d) universal (G,M): Morse code is an internationally recognized and understood form of communication. Likewise, the genetic code is used by all species and the same codons [almost] always specify the same amino acids.

NOTE: you could argue that neither the Morse code nor the genetic code is truly "universal." If you made a clear and sound argument, you got full credit.

e) nonoverlapping (G,M): The triplets of nucleotides in a sequence do not overlap; a nucleotide in one codon is not part of the next codon. This is the same for Morse code. No dot or dash encoding one letter in a word is carried over and re-used in the next letter.

2. A portion of a polypeptide produced by bacteriophage T4 was found to have the following sequence of amino acids:

Deletion of a single nucleotide in one location on the T4 DNA template strand with subsequent insertion of a different nucleotide nearby changed the sequence to

a) what was the nucleotide sequence of the segment of the mRNA that encoded this portion of the original polypeptide?

AAPu AGU CCA UCA CUU AAU GCX (Pu = A or G; X = A, G, C, or U)

b) What was the nucleotide sequence of the mRNA encoding this portion of the mutant polypeptide?

AAPu GUC CAU CAC UUA AUG GCX

c) Can you determine which nucleotide was deleted and which was inserted? Explain your answer.

Deleted: one of the first four nucleotides. Inserted: one of the two "G"s that are 3 and 4 nt's from the 3' end of the mutant sequence.

3. In a cell-free protein synthesis system from E. coli, the polyribonucleotide AUGUUUUUUUUUUUU directs the synthesis of the oligopeptide met-phe-phe-phe-phe. In the presence of Rambomycin, a new antibiotic just developed by Macho Pharmaceuticals, only the dipeptide met-phe is made.

Which step in polypeptide synthesis does Rambomycin inhibit? Explain your answer.

(2 pts): Translocation. The movement of the ribosome along the mRNA, freeing the A site for the binding of the third tRNA. (Or release of the uncharged Met tRNA from the P or E site.)

(1.5 pt): Elongation. (Not specific enough...most of elongation is OK)

(1 pt): Synthesis of sufficient phenylalanine (which is already present in the cell-free extract).

(1 pt): Changes the "bonding" site of Phe so it cannot bind to itself. (This seems unlikely, but is conceivable IF what you mean is that the carboxyl terminus of Phe has been altered so that is a protein "chain terminator," in a sense. This was not specified, however.)

(1 pt): Prevents synthesis of Phe-Phe peptide bonds. (Again, seems unlikely, since peptide bonds do not involve the amino acid's side chain.)

(1 pt): Inhibits another tRNA from moving into the A site. (Then why was the Phe tRNA able to move into the A site?)

4. To enable it to be transmitted intact from one cell generation to the next, the linear DNA molecule of a eukaryotic chromosome must have appropriate nucleotide sequences making up three special kinds of regions: origins of replication (at least one), a centromere, and two telomeres. What would happen if such a chromosomal DNA molecule somehow lost

a) all of its origins of replication? The chromosome would not be replicated. When the cell divides (if it divides at all), only one of the two cells will get a copy of this chromosome.

b) all of the DNA constituting its centromere? Proper segregation of daughter chromatids during cell division will not occur, because the spindle fibers will have no attachment point. Indeed, the sister chromatids may not even be attached to each other.

5. Carefully inspect the double-stranded DNA molecule shown here, and notice that it has twofold rotational symmetry:

Label each of the following statements as T if true or F if false.

a) There is no way to distinguish the right end of the double helix from the left end. T

b) If a solution of these molecules were heated to denature them, every single-stranded molecule in the solution would be capable of hybridizing with every other molecule. T

c) If the molecule were cut at its midpoint into two halves, it would be possible to distinguish the left half from the right half. F

d) If the two single strands were separated from each other, it would not be possible to distinguish one strand from the other. T

e) In a single strand from this molecule, it would be impossible to determine which is the 3' end and which is the 5' end. F

On the CD-ROM, in the Q&A for chapter 4, question #6 is miskeyed.

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