Bke2 Biochemistry Exercises

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Group exercise: Enzyme structure and function

a) Which of the amino acids Asp, Glu, Lys, Ser, or Tyr is most likely to be involved in binding pyruvate to the enzyme pyruvate dehydrogenase? Why?
b) Which of the amino acids Asp, Glu, His, Lys, or Arg is most ideally suited to participate in acid-base catalysis near neutral pH? Why?
Describe each of the four major "modes" of enzymatic catalysis? What is the estimated rate acceleration from each of these modes?
Some enzymes catalyze reactions at rates close to, or even faster than, that expected of free diffusion (10⁸ to 10⁹ M^-1s^-1) of the substrate to the enzyme. Explain how this is possible.
Explain why very tight binding of a substrate to an enzyme is not desirable for enzyme catalysis, whereas tight binding of the transition state is.
Explain why an enzyme increases the rate of a reaction in both the forward and reverse directions.
The proteases chymotrypsin, trypsin and elastase belong to the same family of enzymes. Their amino acid sequences are very similar, and so are their structures. Their active sites have the same catalytic amino acids, but there are differences in their pockets that determine which peptides they will cleave.

a) Describe the common features of the active sites in these enzymes. What are the important catalytic residues, and what type of catalysis do they perform?
b) What kind of kinetic mechanism (sequential ordered, sequential random, ping-pong) is employed by these enzymes?
c) How do the three enzymes achieve their different substrate specificities?

Reading material: Horton, chapters 5-6.

Lectures:
Introduction to enzymes
Active sites and modes of catalysis
Enzyme kinetics

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