This course is part of a series taught by Kevin Ahern at Oregon State University on General Biochemistry. For more information about online courses go to http://ecampus.oregonstate.edu/
1. "Perfect" enzymes are enzymes that have evolved to the point where any additional mutation will reduce their ability to catalyze reactions. They are not common. Perfect enzymes have a very high ratio of Kcat/Km and are such that the only thing that inhibits their ability to function more efficiently is the rate of diffusion of substrate in water.
2. Substrate binding to enzymes is relevant to catalysis that we will consider. The first is the category of Sequential Displacement. It has two subsets.
a. Random binding - the order of binding multiple substrates is not rigidly set.
b. Ordered binding - Simple ordered binding - one substrate binds first followed by another followed by release of product.
3. Note that the models of substrate binding above are all non-covalent.
4. Allosterism is a phenomenon in which a small molecule interacts with a protein and affects the proteins activity. Such an enzyme is an allosteric enzyme. I pointed out the similarity between the kinetics of allosterically acting enzymes and the coopertivity of binding of oxygen by hemoglobin.
5. Lineweaver-Burk plots are alternative plots of V vs S data obtained by taking the inverse of each and plotting it, thus making a 1/V vs 1/[S] plot (also called a double reciprocal plot).
6. On a Lineweaver-Burk plot, the Y intercept is 1/Vmax and the X intercept is -1/Km.
7. Enzymatic reactions can be inhibited by reversible and irreversible processes. Reversible processes involve binding of an inhibitor and its subsequent release. Irreversible processes generally involve covalent attachment of a molecule to an enzyme followed by its inactivation.
a. Competitive Inhibition - This type of reversible inhibition occurs when the inhibitor competes with the substrate for the binding site on an enzyme. The greater the concentration of inhibitor, the greater the inhibition. However, competitive inhibition can be overcome by increasing amounts of substrate. The apparent Vmax of competitive inhibition does not vary from the Vmax of the same reaction when uninhibited. The apparent Km, however, does vary, because it requires more substrate to get the same velocity as the uninhibited reaction.
b. Non-competitive inhibition - This type of reversible inhibition occurs when an inhibitor binds to an enzyme at a site unrelated to the substrate binding site. In this case, the inhibitor's binding to the enzyme is unrelated to the binding of the substrate and the inhibitor does not have to have a structure like that of the substrate. Thus, the inhibitor and substrate don't compete with each other. The inhibitor can kill the enzyme (during its binding) without interference from the substrate. Therefore, increasing substrate concentrations cannot eliminate the effect of the inhibitor. In this case, the Vmax is lowered, but the Km is unchanged.
c. Irreversible inhibition can occur by mechanisms where the inhibitor has a structure similar to the substrate or where there is no relation between the two. In either case, the enzyme is destroyed for catalysis.
8. You should be able to depict or understand graphically (V vs S, Lineweaver-Burk) what occurs in competitive and noncompetitive inhibition.
9. Chemicals, such as DIPF and iodoacetate, covalently (and irreversibly) bind to the side chains of specific amino acids (serine and cysteine, respectively) and if these side chains are essential for the catalytic action of the enzyme, the enzyme will not catalyze reactions after being treated with these chemicals.
10. Penicillin is a substance that resembles the substrate of an enzyme in bacteria that helps make the bacterial cell wall. When it binds to the enzyme, it inactivates the enzyme by covalently bonding to the active site, thus destroying the enzyme (and killing the bacterium containing it). An inhibitor of this type is known as a suicide inhibitor.
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