Enzymology

added in lipidation, these proteins go into the membranes found in vesicles, mitochondria, endoplasmic reticulum, Golgi apparatus, and the plasma membrane. Proteolysis tends to be irreversible. Proteases are enzymes that cleave peptide bonds in post-translational protein modification. There are regulatory processes that make sure that proteolysis doesn’t become uncontrolled.

ENZYMOLOGY

Enzymes are all catalysts for chemical reaction but not all catalysts are enzymes. The catalyst in any reaction will lower the activation energy of a reaction, allowing the reaction to proceed faster. In biological systems, the enzymes are almost always proteins; however, some ribosomal RNA molecules can be enzymes as well. As we have discussed in a previous chapter, enzymes will bind to reactants or substrates in a reaction, holding them in a way such that the chemical process can become the endproduct much more efficiently. Figure 33 shows what enzymes do in order to facilitate a reaction:

Figure 33.

As you remember from the previous chapters, enzymes only change the activation energy. They do not lower the beginning energy level or ending energy level. The reaction must be favorable with a negative free energy level change in order for the reaction to occur. The activation energy or the energy of the transition state is lowered. The transition state is the unstable state that the substrates must go through in order to have the final end-product.

As you can see by figure 33, the enzyme will bind to the reactants or “substrates” in such a way that they are in close proximity to one another. These binding sites are specific to the substrates. While attached to the enzyme, the reaction occurs efficiently, leading to the transition state and finally the products or “end-products” are made and released by the enzymatic binding sites. This binding site is also referred to as the “active site”.

The active site is made from specific amino acids that are designed to attract and bind the substrates. There can be hydrophobic, hydrophilic, acidic, basic, or ionic amino acids that fit specifically to the amino acids of the reaction substrates.

Enzymes are very sensitive molecules and only function under certain conditions. Temperature is perhaps the most important thing to keep in mind with regard to enzymatic function. These enzymes are highly temperature-dependent and will work only with a certain temperature range. High temperatures can denature proteins. This includes enzymes, which denature or “break down” in higher temperatures.

The pH of a system can also affect the enzyme function. There are certain amino acids that have basic or acidic properties. This means that a pH change will affect how the enzyme is able to bind to the substrate. In addition, the concentration of the enzyme and substrate affect how much work the enzyme is able to do.

The fit between an enzyme and substrate isn’t exactly a lock and key model. Instead, researchers refer to the fit of an enzyme and substrate as an “induced fit model”. What this means is that the enzyme will slightly change its conformation as a result of binding to the substrate. This results in a tighter fit with the substrate. It is similar to the sodium-potassium ATPase pump, which is an enzyme system. Binding of sodium onto the pump induces a conformational change that cleaves the ATP molecule and opens the pump so that sodium can pass through.

You should think of the enzymatic process as being temporary. The enzyme changes it conformation, allows for the reaction to occur, releases the end-products and then returns to its original state. This means that enzymes are not consumed in the enzymatic process so that it can participate in another enzymatic reaction.