Discussion Problem Set 4 C483 Spring 2014
Problems from lectures 9-10-11
1. Binding constants may be determined in a number of ways. One way is to
measure the association rate constant (kon, or kassoc) and the dissociation rate
constants (koff, or kdissoc). What do the following values give you? (Hint, consider the
units)
koff/ kon
kon/ koff
2. Consider a protein complex with a Ka of 1010 M-1. If you make the assumption
that this complex from at the rate of diffusion of large molecules (roughly 107M-1S-1)
what is the dissociation rate? What lifetime does this correspond to?
3. It is often the case that complex formation is actually quite a bit slower than the
diffusion rate. If this is so, what would it mean for the lifetime of the complex
described in question 2.
4. The books shows a binding isotherm (Fig 4.29) for the interaction of two proteins.
What assumption needs to be made for this mathematical analysis to be valid? For
which protein-protein association is this assumption never valid? What is the
consequence of this assumption for your understanding of the analysis depicted in
the figure?
5. What is the role of crosslinking in the structure of collagen? What amino acids
are linked?
6. What are the major differences between a 310 helix and an alpha helix? Why is
glycine likely found so often in a 310 helix?
7. Myoglobin and Hemoglobin both have a similar structural unit and an identical
prosthetic group. What advantage does hemoglobin have by virtue of being a higher
order complex?
8. Explain the binding of oxygen to hemoglobin as a function of its biological role.
Explain the shape of the binding isotherm. What is the effect of 2,3-BPG? What
other factors modify oxygen binding to hemoglobin? Why does this make sense?
9. Consider the kinetic scheme shown below.
Please answer the following questions.
a) The production of enzyme-substrate complex is drawn as being reversible.
However, formation of P is drawn as being irreversible. What is the justification for
doing this?
b) In the formalism, formation of the enzyme-substrate complex is shown as
reversible (double arrows). What must be true if this step is truly to be fully
reversible? What consequence would this have for the meaning of Km? What would
Km be equal to under these conditions?
c) In the original derivation of the Michaelis Menten equation, the explicit
assumption of a fully reversible binding step was made. Briggs and Haldane
produced another version of the equation that was mathematically equivalent, but
did not make this assumption. What assumption did they make? Show the equation
that states this assumption.
10. Most drugs are competitive enzyme inhibitors. However, many medicinal
chemists feel that uncompetitive and especially noncompetitive inhibitors may
make better drugs than competitive inhibitors. Explain why this might be so.
11. Enzymes display a remarkable degree of catalytic potency considering the
constraints of the physiological environment in which they function. Explain, using
ester hydrolysis as an example, the basic idea behind how an enzyme can achieve
such catalysis.