Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2008
Lecture Notes: 10 October	© R. Paselk 2008
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pH Effects on Enzymes (and Proteins)

Papain: inflection at pH 4.2 for cys-25 and at pH 8.2 for his-159.

Note that the two legs represent two pH titration curves (rotate the left leg 90 deg. then flip; rotate the right leg 90 deg. counter clockwise and you can see them), with pK's equal to 4.2 and 8.2 respectively. This is a typical example for an enzyme with titratable groups in the active site. Can also have non-symmetrical curves with only one group. And of course can have curves due to denaturation by titration of charged surface and interior side chains.

Zymogens: define and give examples of trypsin/trypsinogen.

Allosterism and Allosteric Enzymes

• Look at V vs. [S] plots - very mnuch like Hb plot.
  • As with Hb, cooperativity due to binding interactions.
    • Homotropic.
    • Heterotropic.
      • Negative effectors
        • (-) effector affects a V vs. [S] plot for a allosteric system by shifting to higher concentration (shift curve to right and steepens-increases sigmoidicity)
          • Negative effector vs. inhibitor (can be considered a special case).
        • (-) effectors increase cooperativity.
      • Positive effector
        • (+) effector affect a V vs. [S] plot for a allosteric system shifts curve to left and decreases sigmoidicity (approaches non-cooperative curve).
        • (+) effectors increase cooperativity.
• Concerted (symmetry) and Sequential Model for allosteric enzymes - go back to Hb discussion.

Enzyme Catalysis

We will look at catalysis in two types of systems:

• Model systems in organic chemistry to elucidate probable mechanisms of chemical catalysis.
• Example enzymes to demonstrate these mechanisms in enzyme catalysis.

Mechanisms of Chemical Catalysis

Look at some examples of catalysis in model systems (organic chemistry) and how they might operate in enzymes.

Types of Catalysis:

• Acid/Base
• Specific (H⁺ & OH^- in water)
• General (Bronsted acid definition: proton donor/acceptor pairs; buffers.)
• Covalent
• nucleophilic
• electrophilic
• Proximity/orientation
• Stabilization of Transition State Conformation (Strain/distortion; Charge neutralization)
• Metal/Metal ion.

So how does catalysis work? Recall that the slow step of a reaction is reaching the transition state. Thus if we can find a way to stabilize the transition state (lower E_a) then the reaction rate will be enhanced. Generally we will be looking at three ways to increase rates

1. stabilize transition states
2. increase the concentrations of intermediates
3. use a different reaction pathway.

Pathway Diagrams

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Lecture Notes

Last modified 10 October 2008