Enzyme Structure, Function, and Environmental Effects

How enzymes work

Chemical reactions need a push to get started. Even a reaction that releases energy overall, an exergonic reaction, first needs reactants to reach an unstable, high-energy state. The energy needed to get there is the activation energy ($E_A$).

An enzyme is a biological catalyst, almost always a protein. It lowers the activation energy, so many more molecules can react per second at body temperature.

• The reactant an enzyme acts on is the substrate.

• The substrate binds to a small pocket on the enzyme called the active site.

• The active site fits the substrate through induced fit: the enzyme changes shape slightly as the substrate binds, which strains bonds and helps the reaction happen.

• The substrate is converted to products, which are released. The enzyme is unchanged and ready for another substrate.

Notice what the enzyme does not change: the energy of the reactants, the energy of the products, and therefore $\Delta G$. It only lowers the hill in the middle.

Temperature and pH

An enzyme works because of its three-dimensional shape, which is held together by hydrogen bonds, ionic bonds, and other weak interactions. Anything that disrupts those interactions changes the shape of the active site.

Temperature. As temperature rises, molecules move faster and collide more often, so the rate goes up. Past the optimum temperature, the enzyme's bonds break, the protein unfolds, and the active site loses its shape. This is denaturation. A denatured enzyme no longer binds its substrate, so the rate drops sharply, usually for good.

pH. Changing pH changes the charges on amino acid R groups. Ionic bonds and hydrogen bonds that hold the folded protein together are disrupted, and the active site changes shape. Each enzyme has an optimum pH. Pepsin in the stomach works best near pH 2, while trypsin in the small intestine works best near pH 8.

Substrate concentration

Suppose you have a fixed amount of enzyme and keep adding substrate.

• Low substrate: many active sites are empty. Each added substrate molecule finds an enzyme quickly, so the rate rises almost in a straight line.

• High substrate: nearly every active site is occupied at every moment. The enzyme is saturated, and the rate levels off at a maximum, $V_{max}$.

Adding more substrate cannot raise the rate above $V_{max}$. To raise $V_{max}$, you need more enzyme, because more enzyme means more active sites. Doubling the enzyme roughly doubles $V_{max}$.

Inhibitors

An inhibitor is a molecule that slows an enzyme.

Think of it like a parking spot. A competitive inhibitor is a car parked in the spot, but it can leave if a better-fitting car arrives. A noncompetitive inhibitor is like a flat tire on the spot's owner: the spot is there, but the car cannot use it.

What an enzyme changes and does not change

An enzyme lowers $E_A$ and speeds up how fast equilibrium is reached. It does not change $\Delta G$, the equilibrium position, or the equilibrium constant, because the energies of reactants and products stay the same. For an exergonic reaction with $\Delta G = -20$ kJ/mol, the products are lower in energy than the reactants with or without the enzyme. The forward and reverse reactions are both sped up equally.

Designing an enzyme experiment

Experimental design. Say you test how temperature affects amylase, which breaks down starch. Iodine solution turns blue-black with starch, so loss of color shows starch is gone.

• Independent variable: temperature (for example 10, 25, 37, 50, 70 °C).

• Dependent variable: time for the blue-black color to disappear, or the color intensity after a set time.

• Controlled variables: amount and concentration of amylase and starch, pH, volume, and time.

• Control: boiled (denatured) amylase with starch. It should show no starch breakdown, which proves that the active enzyme caused the change.

Predicted results: starch disappears fastest near the optimum (about 37 °C for human amylase), more slowly at low temperatures, and not at all at high temperatures where the enzyme is denatured.

Back to the start: your body digests pizza because amylase lowers the activation energy for breaking down starch at 37 °C. A high fever is dangerous because heat can disrupt the shape of enzymes, and without the right shape the active sites stop working.

Summary

• Enzymes are protein catalysts. They bind substrates at the active site (induced fit) and lower activation energy. They are not used up and do not change $\Delta G$.

• Enzyme function depends on shape. Heat or extreme pH denatures the enzyme and the rate falls.

• Rate increases with substrate until the enzyme is saturated at $V_{max}$. More enzyme raises $V_{max}$.

• Competitive inhibitors bind the active site and can be overcome with more substrate. Noncompetitive (allosteric) inhibitors bind elsewhere and lower $V_{max}$.

• A good enzyme experiment changes one variable, keeps the others constant, and includes a control such as boiled enzyme.