C2005/F2401 '10 -- Recitation Problems #7 -- Hints & Answers

Hints:

1. A. Will your new RNA be the same as the strand shown? It's complement?

    B. You will find B easier if you rewrite your mRNA in the standard convention, with the 5' end on the left.

    C. Look at the class handout called 'Protein Synthesis.' If you didn't draw a ribosome on it yet, do it now.


2. A. Which strand serves as template, the sense strand or its complement?

    B. What is shown in the code table, and what's in the mRNA -- the codons or the anti-codons?

    C-1. Is it possible to change the DNA and not change the protein?

    C-2 Consider the properties of the two amino acids found in wild type and mutant 2. What effect would you expect if you substitute one for the other? (If you don't remember the properties of the various amino acids, look them up in your text.)

    D-1. Consider the genetic code. Consider both degeneracy & wobble  -- will the new codon specify the same amino acid? Even if the new codon specifies the same amino acid, can the same tRNA be used? If you aren't sure, look up the wobble rules.

    D-2. How is this case different than the previous one?

    D-3. & D-4. Note these questions are not about wobble (how many codons can one tRNA read?) but the reverse -- how many tRNAs can read one codon accurately? Consult the wobble rules and the genetic code.


Answers:

1. A. The mRNA should be 5' AGC AUG CGU UCG CGU 3'. The mRNA is the complement to the strand shown --  anti-parallel  & with U instead of T. The spaces are included to make the answers easy to follow -- the actual RNA has no spaces. The RNA could also be written 3' UGC........CGA 5'

    B. Amino acid sequence should be ser-met-arg-ser-arg. This section is in the middle of a coding sequence, so the start codon is way off to the left. The AUG is not the start codon for this section; it is just a plain old codon for the amino acid met.

    C. P site should hold a tRNA with the anticodon 5'GCU 3's or 3' UCG 5' and A site should hold the tRNA for the amino acid methionine.

Note: The anticodon cannot be 3' UCI 5' -- a tRNA with that anticodon would not be able to discriminate between the ser codons AGU/C and the  arg codon AGA.

Your picture should show an empty, unloaded tRNAser in the P site and tRNAmet with the growing chain in the A site. The next step would be to move the tRNAmet with the growing chain over into the P site, and bump the empty tRNA into the E site.


 


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  anticodons).

    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  is changed, but the protein and its function 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. 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. 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.

    D-2. No. This codon specifies a different amino acid, so you need a different tRNA.

    D-3. 2. Either CUA or CUG can be in the anticodon (both written 3' to 5'). Either A or G can be in the wobble position of the tRNA and pair with U in the wobble position of the mRNA. Adenosine will pair with U only; and G will pair with either U or C (which is compatible with the code).  Inosine won't work in the wobble position of the tRNA -- it will pair with U & C in the wobble position of the mRNA, but also with A  (which is incompatible with the code).

    D-4. 3' CUG 5' is most likely, as it will pair with both codons for asp, and not with the codons for glu. If you use 3' CUA 5', it will pair with GAU, but not with GAC. Therefore you will need a second tRNA to pair with GAC. Since the '2nd tRNA', with anticodon 3' CUG 5' will pair with both asp codons, it alone is sufficient.