Enzymes: What is it? & How Does it Work?

At all times, without any conscious thought from you, the trillions of cells in your body are undergoing an enormous number of chemical reactions that keep you alive and in balance. While these reactions might happen on their own given enough time, this rate would not be nearly fast enough for the requirements of the human body.

As a result, almost all biochemical reactions are assisted by specialized proteins called enzymes, which are biological catalysts that can make reactions over a million times faster.

The tailoring of enzymes is very high; most of the hundreds of known enzymes can catalyze only one reaction, and most reactions can only be catalyzed by one specific enzyme.

What Are Enzymes, Exactly?

Although the nucleic acid molecule RNA (ribonucleic acid) can sometimes act as a non-enzyme catalyst, true enzymes are proteins, meaning that they consist of long chains of amino acids that are folded into a particular shape. There are 20 amino acids in nature, all of which your body requires in some amount.

Your body can make about half of these, whereas the others must be ingested in the diet. The ones you have to eat are called essential amino acids.

Amino acids all have a central carbon atom joined to a carboxylic acid (-COOH) group, an amino (-NH2) group, and a side chain, usually designated "-R" in chemical diagrams.

The side chain determines the unique behavior of the amino acid. The order of amino acids in a protein is called its primary structure. A string of amino acids is called a polypeptide; usually when a molecule is referred to as such, it is not a complete, functional protein, but a piece of one.

Amino acid strings can arrange themselves into either spiral-like or sheet-like formations; this is referred to as a protein's secondary structure. How the molecule ultimately arranges itself in three dimensions, largely as a result of electric interactions between amino acids in different parts of the molecule, is called the tertiary structure.

As with so many things in the natural world, form fits function; that is, the shape of an enzyme determines its precise behavior, including how strongly it "seeks" a particular substrate (that is, the molecule on which an enzyme acts).

How Do Enzymes Work?

How do enzymes carry out catalytic activity? This question can be separated into two related inquiries.

One: how, in terms of the basic moving around of atoms, do enzymes speed up reactions? And two: what special features about the structure of enzymes allows this to happen?

The way an enzyme speeds up a reaction rate is by smoothing out the path between the start and the end of the reaction. In these kinds of reactions, the products (the molecules left after the reaction is over) have a lower total energy than the reactants (the molecules that are changed into products during the reaction).

To get the reaction rolling, however, the products must overcome an energy "hump," called the activation energy (Ea).

Imagine being on a bicycle a half mile from your house, a point that is 100 vertical feet above your driveway. If the road first climbs 50 feet before quickly dropping 150 feet to get to the driveway, you obviously have to pedal for a while before you can start coasting. But if the stretch of road simply consists of a uniform gentle half-mile-long downgrade, you can coast the whole way.

An enzyme, in effect, transforms the first scenario into the second; the elevation difference is still 100 feet, but the overall layout is not the same.

The Lock and Key Model

At the level of molecular cooperation, the enzyme-substrate complex is often described in terms of a "lock and key" relationship: The part of the enzyme molecule that binds to the substrate, called the active site, is shaped so that it almost perfectly fits into the substrate molecule.

Just as sliding a key into a lock and turning it causes changes to the lock (such as the movement of a deadbolt), a catalyst achieves enzymatic activity by causing the substrate molecule to change shape.

These changes can result in a weakening of chemical bonds in the substrate through mechanical distortion, giving the molecule just enough of a "push" or a "twist" to move toward the shape of the eventual product.

Often, the product-to-be exists in a transition state in the meantime, which looks somewhat like the reactant and somewhat like the product.

A related model is the induced fit concept. In this scenario, the enzyme and substrate do not initially make a perfect lock-and-key fit, but the very fact of their coming into contact causes changes in the shape of the substrate that optimizes the physical enzyme-substrate interaction.

The change to the substrate makes it more closely resemble a transition-state molecule, which is then changed into the end product as the reaction moves forward.

What Affects Enzyme Function?

Though they are powerful, enzymes, like all biological molecules, are not invincible. Many of the same conditions that damage or destroy other molecules, as well as whole cells and tissues, can slow enzyme activity or stop them from working altogether.

As you probably know, your body temperature must remain in a narrow range (usually about 97.5 to 98.8 degrees Fahrenheit) for you to remain healthy. One reason for this is that enzymes stop working properly if body temperature rises above this level – what you perceive as a fever.

Also, highly acidic conditions can disrupt the chemical bonds of the enzyme. Such temperature- and pH-related damage is called denaturing of the enzyme.

In addition, as you might expect, an increase in the amount of enzyme tends to speed up a reaction even more, while a decrease in enzyme concentration slows it down.

Similarly, adding more substrate while keeping the amount of enzyme the same speeds up a reaction until the enzyme is "maxed out" and cannot attend to all of the substrate present.

What Are Coenzymes and Cofactors?

Say you go on a cross-country fundraising bike trip and are supported along the way by friends giving you drinks and fresh clothes from a van.

Your friends will need support of their own during the journey, such as gas for the vehicle and food for the crew.

If your trip can be thought of as a "reaction" and the van crew is the "enzyme" that "catalyzes" your journey, then food stores on the route can be thought of as coenzymes – in biochemistry, substances that are not enzymes, but are needed for enzymes to best carry out their work.

Like substrates, coenzymes bind to the active site of enzymes, where the substrate binds, but they are not considered substrates themselves.

Coenzymes often function as electron carriers, or temporary docking locations for atoms or functional groups that are transferred between molecules in the overall reaction. Cofactors are inorganic molecules such as zinc that help enzymes in living organisms, but unlike coenzymes, they do not bind to the active site of an enzyme.

Examples of common coenzymes include:

  • coenzyme A, or CoA, which binds to acetate to form acetyl CoA, important in cellular respiration, which generates energy for cells from the sugar glucose;
  • nicotinamide adenine dinucelotide (NAD) and flavin adenine dinucelotide (FAD), which are high-energy electron carriers that also contribute to cellular respiration; 
  • pyridoxal phosphate, or vitamin B6, which moves amino groups between molecules.

References

About the Author

Kevin Beck holds a bachelor's degree in physics with minors in math and chemistry from the University of Vermont. Formerly with ScienceBlogs.com and the editor of "Run Strong," he has written for Runner's World, Men's Fitness, Competitor, and a variety of other publications. More about Kevin and links to his professional work can be found at www.kemibe.com.

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