Bke2 Biochemistry Exercises
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
- 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.
Introduction to enzymes
Active sites and modes of catalysis
Exercise by Stefan Knight
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