Question

We discussed the substrate preference of chymotrypsin several times. Let's imagine that we are comparing the ability of this enzyme to cleave peptide bonds next to phenylalanine vs. next to alanine. As we know, chymotrypsin prefers to cleave next to phenylalanine, as shown by the kcat/Km values. The kcat/Km values also tell us that the enzyme does not prefer to cleave next to alanin Because kcat/Km is a ratio, it is hard to choose one single reason (kcat vs. km) for why the enzyme disfavors cleaving next to alanine based on this ratio. However our later coverage looked at this enzyme in further detail, and so we can make one of the following predictions Based on our coverage, chymotrypsin may have a more difficult time cleaving next to alanine compared with cleaving next to phenylalanine because alanine does not fill the specificity pocket well, and this raises the Km alanine is a poor nucleophile and this raises the Kat Slanine is a poor nucleophile and this lower the Raat alanine does not fill the specificity pocket well, and this lower the Km

Answer 1

Option 1 is the answer

Alanine does not fill the specificity pocket well and this raises the Km

Phenylalanine is an aromatic aminoacid and hence varies in structure to that of alanine to a great extent. This means when alanine is present instead of phenylalanine the enzyme specificity pocket does not fill up well which leads to an increase of Km