4.20:
Introduction to Mechanisms of Enzyme Catalysis
Enzymes catalyze reactions using various physical and chemical mechanisms to lower the activation energy.
These mechanisms may increase the reaction rate by positioning the enzyme and substrate appropriately, stabilizing the transition state, and helping to form or break bonds.
Most enzymes adopt an induced fit when they bind their substrates. This conformational change alters the relative positions at the amino acids to increase interactions with the substrate.
In reactions with multiple substrates, enzymes often position the molecules to resemble the transition state to aid their transformation.
Many enzymes require metal ions for catalysis. Metal ions attract oppositely charged groups on substrates and orient them for the reaction. Ions can also change their oxidation state to stabilize charges on reaction intermediates.
In some enzymes, amino acids accept or donate protons to locally change the pH or react directly with the substrate. This can strengthen or weaken bonds to increase reaction rates.
4.20:
Introduction to Mechanisms of Enzyme Catalysis
For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme's structure that confirms an ideal binding arrangement between the enzyme and the substrate's transition state. This ideal binding maximizes the enzyme's ability to catalyze its reaction.
The active sites of enzymes are suited to provide specific environmental conditions and are also subject to local environmental influences. Increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site to influence substrate binding. High temperatures will eventually cause enzymes, like other biological molecules, to denature, changing the substance's natural properties. Likewise, the local environment's pH can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties optimal for catalysis. Enzymes function optimally within a specific pH range, and altering the temperature or acidic or basic nature can affect the catalytic activity.
Many enzymes don't work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe2+) and magnesium (Mg2+). For example, DNA polymerase requires a bound zinc ion (Zn2+) to function. Coenzymes are organic helper molecules with a basic atomic structure comprised of carbon and hydrogen, required for enzyme action. The most common sources of coenzymes are dietary vitamins. Some vitamins are precursors to coenzymes, and others act directly as coenzymes.
This text is adapted from Openstax, Biology 2e, Section 6.5 Enzymes