Enzymes as biological catalysts, activation energy, the active site, and environmental effects on enzyme activity.

Introduction

As a kid, I wore glasses and desperately wanted a pair of contact lenses. When I was finally allowed to get contacts, part of the deal was that I had to take very, very good care of them, which meant washing them with cleaner every day, storing them in a sterile solution, and, once a week, adding a few drops of something called “enzymatic cleaner.” I didn’t know exactly what “enzymatic cleaner” meant, but I did learn that if you forgot you’d added it and accidentally put your contacts in your eyes without washing them, you were going to have burning eyes for a good fifteen minutes.
As I would later learn, all that “enzymatic” meant was that the cleaner contained one or more enzymes, proteins that catalyzed particular chemical reactions – in this case, reactions that broke down the film of eye goo that accumulated on my contacts after a week of use. (Presumably, the reason it stung when I got it in my eyes was that the enzymes would also happily break down eye goo in an intact eye.) In this article, we’ll look in greater depth at what an enzyme is and how it catalyzes a particular chemical reaction.

Enzymes and activation energy

A substance that speeds up a chemical reaction—without being a reactant—is called a catalyst. The catalysts for biochemical reactions that happen in living organisms are called enzymes. Enzymes are usually proteins, though some ribonucleic acid (RNA) molecules act as enzymes too.
Enzymes perform the critical task of lowering a reaction's activation energy—that is, the amount of energy that must be put in for the reaction to begin. Enzymes work by binding to reactant molecules and holding them in such a way that the chemical bond-breaking and bond-forming processes take place more readily.
Reaction coordinate diagram showing the course of a reaction with and without a catalyst. With the catalyst, the activation energy is lower than without. However, the catalyst does not change the ∆G for the reaction.
Image modified from "Potential, kinetic, free, and activation energy: Figure 5," by OpenStax College, Biology, CC BY 3.0.
To clarify one important point, enzymes don’t change a reaction’s G value. That is, they don’t change whether a reaction is energy-releasing or energy-absorbing overall. That's because enzymes don’t affect the free energy of the reactants or products.
Instead, enzymes lower the energy of the transition state, an unstable state that products must pass through in order to become reactants. The transition state is at the top of the energy "hill" in the diagram above.

Active sites and substrate specificity

To catalyze a reaction, an enzyme will grab on (bind) to one or more reactant molecules. These molecules are the enzyme's substrates.
In some reactions, one substrate is broken down into multiple products. In others, two substrates come together to create one larger molecule or to swap pieces. In fact, whatever type of biological reaction you can think of, there is probably an enzyme to speed it up!
The part of the enzyme where the substrate binds is called the active site (since that’s where the catalytic “action” happens).
A substrate enters the active site of the enzyme. This forms the enzyme-substrate complex.The reaction then occurs, converting the substrate into products and forming an enzyme products complex. The products then leave the active site of the enzyme.
Image modified from "Enzymes: Figure 2," by OpenStax College, Biology, CC BY 3.0.
Proteins are made of units called amino acids, and in enzymes that are proteins, the active site gets its properties from the amino acids it's built out of. These amino acids may have side chains that are large or small, acidic or basic, hydrophilic or hydrophobic.
The set of amino acids found in the active site, along with their positions in 3D space, give the active site a very specific size, shape, and chemical behavior. Thanks to these amino acids, an enzyme's active site is uniquely suited to bind to a particular target—the enzyme's substrate or substrates—and help them undergo a chemical reaction.
Different types of enzymes have different degrees of specificity, or "pickiness" about which molecules can be used as substrates. Some enzymes accept only one particular substrate and will not catalyze a reaction even for a very closely related molecule. Other enzymes can act on a range of target molecules, provided that these target molecules contain the type of bond or chemical group that the enzyme targets.start superscript, 1, end superscript

Environmental effects on enzyme function

Because active sites are finely tuned to help a chemical reaction happen, they can be very sensitive to changes in the enzyme’s environment. Factors that may affect the active site and enzyme function include:
  • Temperature. A higher temperature generally makes for higher rates of reaction, enzyme-catalyzed or otherwise. However, either increasing or decreasing the temperature outside of a tolerable range can affect chemical bonds in the active site, making them less well-suited to bind substrates. Very high temperatures (for animal enzymes, above 40 degree, C or 104 degree, F) may cause an enzyme to denature, losing its shape and activity.start superscript, 2, end superscript
  • pH. pH can also affect enzyme function. Active site amino acid residues often have acidic or basic properties that are important for catalysis. Changes in pH can affect these residues and make it hard for substrates to bind. Enzymes work best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) can make enzymes denature.

Induced fit

The matching between an enzyme's active site and the substrate isn’t just like two puzzle pieces fitting together (though scientists once thought it was, in an old model called the “lock-and-key” model).
Instead, an enzyme changes shape slightly when it binds its substrate, resulting in an even tighter fit. This adjustment of the enzyme to snugly fit the substrate is called induced fit.
Illustration of the induced fit model of enzyme catalysis. As a substrate binds to the active site, the active site changes shape a little, grasping the substrate more tightly and preparing to catalyze the reaction. After the reaction takes place, the products are released from the active site and diffuse away.
Image modified from "Enzymes: Figure 2," by OpenStax College, Biology, CC BY 3.0.
When an enzyme binds to its substrate, we know it lowers the activation energy of the reaction, allowing it to happen more quickly. But, you may wonder, what does the enzyme actually do to the substrate to make the activation energy lower?
The answer depends on the enzyme. Some enzymes speed up chemical reactions by bringing two substrates together in the right orientation. Others create an environment inside the active site that's favorable to the reaction (for instance, one that's slightly acidic or non-polar). The enzyme-substrate complex can also lower activation energy by bending substrate molecules in a way that facilitates bond-breaking, helping to reach the transition state.
Finally, some enzymes lower activation energies by taking part in the chemical reaction themselves. That is, active site residues may form temporary covalent bonds with substrate molecules as part of the reaction process.
An important word here is "temporary." In all cases, the enzyme will return to its original state at the end of the reaction—it won't stay bound to the reacting molecules. In fact, a hallmark property of enzymes is that they aren't altered by the reactions they catalyze. When an enzyme is done catalyzing a reaction, it just releases the product (or products) and is ready for the next cycle of catalysis.

Attribution:

This article is a modified derivative of “Enzymes,” by OpenStax Biology (CC BY 3.0). Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@9.85:32/Biology.
The modified article is licensed under a CC BY-NC-SA 4.0 license.

Works cited:

  1. Worthington Biochemical Corporation. (2015). Specificity of enzymes. In Introduction to enzymes. Retrieved from http://www.worthington-biochem.com/introbiochem/specificity.html.
  2. Worthington Biochemical Corporation. (2015). Temperature effects. In Introduction to enzymes. Retrieved from http://www.worthington-biochem.com/introbiochem/tempEffects.html.

References:

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Enzymes speed up metabolic reactions by lowering energy barriers. In Campbell biology (10th ed., pp. 151-157). San Francisco, CA: Pearson.
Purves, W. K., Sadava, D. E., Orians, G. H., and Heller, H.C. (2003). Enzymes are affected by their environment. In Life: The science of biology (7th ed., pp. 122-123 ). Sunderland, MA: Sinauer Associates.
Purves, W. K., Sadava, D. E., Orians, G. H., and Heller, H.C. (2003). What are the chemical event at active sites of enzymes? In Life: The science of biology (7th ed., pp. 115-116). Sunderland, MA: Sinauer Associates.
Worthington Biochemical Corporation. (2015). Specificity of enzymes. In Introduction to enzymes. Retrieved from http://www.worthington-biochem.com/introbiochem/specificity.html.
Worthington Biochemical Corporation. (2015). Temperature effects. In Introduction to enzymes. Retrieved from http://www.worthington-biochem.com/introbiochem/tempEffects.html.