Question

Biochemistry

Consider the hypothetical serine protease in the image, which shows the specificity pockets. The S, pocket has a glutamic acid in the bottom, the S, pocket is small and hydrophobic, and the S,' pocket is deep and hydrophobic Suggest a 3-amino acid sequence that this prolcase would cleave and indicate between which sites the peptide bond would be broken. Which sequence would this protease cleave? O Gly-Met-Lys Met-Gly-Lys Lys-Met-Gly O Gly-Lys-- Met Lys-Gly - Met Met-Lys-Gly The peptide bond that is broken is between which sites? OS, and S,' OS, and S. OS, and S, OS, and S, and S, and S,'

multiple choice question related to biochemistry

Answer 1

S2 pocket is small and hydrophobic, so the amino acid which should fit in the pocket must also be small and hydrophobic e.g Glycine, alanine or valine. The S1 pocket has a glutamic acid residue that is negatively charged at physiological pH and so would attract a positively charged amino acid e.g Lysine, Arg or Histidine. The S1' pocket is deep and hydrophobic so it can contain amino acids that are bulky and hydrophobic in nature e.g Leucine, Isoleucine, Met, Trp or phenylalanine. By looking at the possibilities, the only likely answer would be Ala-Arg-Met.

Again in a peptide structure, the sites on the enzyme are labelled S1, S2 and S3 (scissile bonds) on the amino side while S1', S2' and S3' are on the carboxyl side. So cleave must take place between the opposite sides so the answer should be S1 and S1'.

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