T A C T C A T C G A 3’ ..… Promotor; transcription right to left.

D. AAU; UGA. In the beginning of peptide synthesis, the AUG start codon (for met) goes in the P site and the next codon, the one for the second amino acid (AAU for asn in this case) is the first codon that goes in the A site. The special initiator met-tRNA lines up met in the P site and the asn-tRNA lines up asn in the A site to get peptide synthesis started. At the end of peptide synthesis, the CGA codon, the one before the stop codon, is the last codon to be translated, but not the last codon to fit in the A site. Peptide synthesis stops when the CGA codon is in the P site and the stop codon is in the A site because there is no tRNA that can match the stop codon.

2. A. Sense strand is the bottom (= strand that matches mRNA). Top strand is transcribed. Any one gene is always transcribed from the same strand, in the same direction.
Note: It is customary to write the sense strand 5' to 3' and the transcribed strand in the other orientation. (It is also common to just write the sense strand and omit the "other" or transcribed strand.)

B. Mutant 1 mRNA is GAA; amino acid for wild type and mutant 1 is glu. See the code table for the rest. Note that the triplets listed in the table are the codons -- the triplets in the mRNA, not the ones in the tRNA. (The triplets in the tRNA are anti codons).

C-1. In this case, the mutation has simply changed the DNA and mRNA from one codon for glu to a different codon for the same amino acid. The DNA (genotype) is changed, but the protein and its function should be unaltered. So the appearance and properties of the organism (phenotype) should be unaltered. This is an example of the "degeneracy" of the code -- there is more than one codon for many amino acids.

C-2. Yes. Both codons specify the same amino acid (that's degeneracy), so it would be reasonable for the same tRNA to read both codons. The same tRNA can read them both because of wobble. The same base in the 'wobble'position' of the tRNA anticodon (the 5' end or first base of the anticodon) can pair with either G or A in the 'wobble position' of the mRNA codon (the 3' end or last base of the codon).
Note that wobble is not the same thing as degeneracy -- not all degenerate codons can be read by the same tRNA. Consult your handout or texts to see why the "wobble" base in the tRNA must be U, and how it pairs with both G and A.

C-3. No. This codon specifies a different amino acid, so you need a different tRNA.

C-4. Asp and glu are very similar, so changing one for the other usually doesn't have a big effect on the shape or function of a protein.

D. 1. Glu and val are quite different, so changing one for the other is more likely to have an effect on shape and/or function than the change of glu to asp. (This is the mutation responsible for sickle cell disease. (See text or lecture #5 notes.)

E-1. This sort of mutation causes a stop codon where a codon for an amino acid is supposed to be. A stop in the middle of a gene makes no sense; it is usually much more disruptive than a change of one amino acid to another, which merely changes the "sense." The effect of a change in "sense" can be mild or severe, depending on the actual amino acid change. (Compare mutants 2 & 3.)The effect of a change from sense to nonsense is almost always drastic (see below).

E-2. A misplaced stop leads to production of a shorter protein that almost never works at all. (The shorter protein only works in a few rare cases where the mutation is very close to the 3' end of the translated part of the mRNA, so only a short part of the COOH end of the protein is missing.) A change of one amino acid to another often leads to an abnormal protein that works somewhat, if not as well as the original.

E-3. None. No new loaded tRNA's can be added, because there is no tRNA with an anticodon to match the stop codons. There is one "loaded" tRNA on the ribosome already -- the one with the growing chain (in the P site), but you can't add any more.

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