Chapter 6

Sequence and structure. A comparison of the aligned amino acid sequences of two proteins each consisting of 150 amino acids reveals them to be only \(8 \%\) identical. However, their three-dimensional structures are very similar. Are these two proteins related evolutionarily? Explain.

Overwhelmed by numbers. Suppose that you wish to synthesize a pool of RNA molecules that contain all four bases at each of 40 positions. How much RNA must you have in grams if the pool is to have at least a single molecule of each sequence? The average molecular weight of a nucleotide is \(330 \mathrm{g} \mathrm{mol}^{-1}\).

Form follows function. The three-dimensional structure of biomolecules is more conserved evolutionarily than is sequence. Why?

Assume that the sequence matches are distributed uniformly along each aligned sequence pair. Would you expect protein \(A\) and protein \(C\) to have similar three-dimensional structures? Explain. BLAST away. Using the National Center for Biotechnology Information Web site (www.ncbi.nlm.nih.gov), find the sequence of the enzyme triose phosphate isomerase from \(E .\) coli. Use this sequence as the query for a protein- protein BLAST search. In the output, find the alignment with the sequence of triose phosphate isomerase from human beings (Homo sapiens). How many identities are observed in the alignment?