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probset_6_2009 - Identify(a all the loops and stems by...

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Problem Set 6 BMB 100A Fall, 2009 Name__________________ 1. What are the codons for Trp, Glu, Ile, Leu and Ser? 2. What is the minimum number of tRNAs required to recognize all of the codons for each amino acid in problem 1? What are their corresponding anticodon sequences? 3. How many codons can be deduced using the repeating block copolymer (AGCU)n as mRNA? What are they, and which amino acids do they code for? 4. Reconstruct in a standard chemical structure drawing the structures of the bases, sugars and phosphates, and their molecular interactions depicted in the electron density contour map (i) in your tRNA handout.
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5. Draw a rough schematic of the 3-dimensional structure of tRNA, starting with the "cloverleaf" secondary structure model, and then folding it into the 3-d tertiary structure.
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Unformatted text preview: Identify (a) all the loops and stems by name, (b) the 5' and3' ends, (c) the two longest conserved sequences, (d) the seven crucial tertiary base-base interactions, (e) the anticodon (f) the point of attachment of the amino acid and (g) a π turn. 6. Referring to the tRNA structure on your tRNA handout or in RASMOL, determine which pairs of nucleotides are closer to each other: (a) 5 and 8 vs. 7 and 49 (b) 10 and 14 vs. 15 and 59 (c) 10 and 56 vs. 19 and 57 (d) 5 and 67 vs. 22 and 53 (e) 9 and 46 vs. 10 and 47 7. Which bases in tRNA are not stacked? For each of them, can you explain why? 8. Peptide bond formation is one step in protein synthesis that does not require ATP or GTP. Explain where the energy of peptide bond formation comes from....
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