Active Site Definition

Enzymes are proteins which drastically increase the speed of chemical reactions by lowering their activation energy. Enzymes do this by interacting with the chemical reactants – called substrates – in ways that make them more likely to react.

Enzymes catalyze countless chemical reactions, including the stringing together of nucleotides and amino acids into DNA and proteins, the breakdown of sugar and fat into energy, and the breakdown of toxins in the liver. Without enzymes, life as we know it could not exist.

The enzyme’s active site is the site at which the enzyme binds to the substrates and increases their chances of reacting.

Types of Active Site

Because enzymes, like all proteins, are made of amino acids, they can create active sites with a wide variety of properties that can bind specifically to different substrates. Properties of amino acids which enzymes can use to bind to substrates include:

  • Size and shape of active site – Can be created specifically to fit around a substrate.
  • Polarity or non-polarity – Polar molecules are attracted to other polar molecules, while non-polar molecules prefer other non-polar molecules. In this way, parts of the active site can attract or repel different parts of the substrate to create a better fit.
  • Positive or negative charge – When it comes to ions, opposites really do attract! Positive charges are attracted to negative charges, and vice versa.
    Similar charges – two positive charges, for example – will actively repel each other instead of attracting.
    This is another way in which an enzyme active site can attract certain parts of substrates, while repelling others to create the right fit.
  • Hydrophobicity or hydrophilicity – Just like with polarity, in this case “like attracts like.” Hydrophobic amino acids attract other hydrophobic molecules, and hydrophilic amino acids attract hydrophilic substrates.
  • Special properties of co-factors – Some vitamins and minerals are important because they are used as co-factors that help enzymes bind to their substrates.

Several B vitamins, for example, are used as co-factors by enzymes involved in producing energy. That’s why many energy “shots” and supplements contain a collection of B vitamins.

Theories about Active Sites

There are two theories about how exactly an enzyme active site binds to substrates. These are:

The Lock-and-Key Model

The lock-and-key model of enzyme active sites postulates that enzyme active sites are perfectly shaped to receive substrates and “pop” them into their new forms.

The Induced Fit Model

Induced Fit Enzyme Catalyst
Induced Fit Enzyme Catalyst

A competing theory, the induced fit model, states that the active site and the substrate are not necessarily an ideal fit for each other in their resting states. Instead, as the substrate draws near to the enzyme, one or both undergo shape changes as a result of interacting with each other.

In this model, it is the continuing interaction of the binding site and the substrate that drive the substrate into its new formation. After the reaction has completed and new products are formed, the product and enzyme are no longer compatible and they separate.

Examples of Active Sites

Some examples of chemical reactions catalyzed by enzymes include:

Maltase and Starch

Maltase is an enzyme found in saliva. It breaks down starches – long chains of sugar molecules that don’t taste sweet – into simpler, sweeter tasting sugars. The reaction catalyzed by maltase looks like:

Starch + Water → Sugars

You can see maltase in action if you chew on a saltine cracker for a few minutes. While the cracker did not initially taste sweet, after a few minutes, you will be able to taste the sugars that the maltase is creating from the starch!

Pepsin and Protein

Another enzyme that’s important for digestion is pepsin, which is found in your stomach. Pepsin catalyzes the reaction of proteins with stomach acid, allowing your body to break down protein from food into amino acids that you can use to build new proteins. That reaction looks like this:

Protein + Acid → Amino acids

DNA Polymerase

Another very important enzyme is DNA polymerase. It’s DNA polymerase that allows your cells to multiply, by making copies of their DNA to give to daughter cells.

It does this by stringing together nucleic acids in the correct sequence – the opposite of what maltase and pepsin do when they take things apart. The reaction catalyzed by DNA polymerase looks like this:

DNA triphosphate molecule + DNA strand → Longer DNA strand + diphosphate molecule

  • Activation energy – The energy required to complete a chemical reaction.
  • Amino acid – The “building blocks” of proteins.
  • Protein – A protein is a structure made of one or more long chains of amino acids.


1. Enzymes need to be constantly replenished because they are used up in their reactions with substrates.
A. True
B. False

Answer to Question #1
False. Enzymes are not changed by the reactions they catalyze. That’s why they are called “catalysts” instead of “reactants.”

Catalysts only lower the activation energy of a reaction by their presence.

Reactants – like water and starch, in the case of maltase – participate in the chemical reaction and are used up in the process.

2. Without enzymes, our cells would not be able to digest food, break down toxins, or create new DNA.
A. True
B. False

Answer to Question #2
True. Enzymes are required for all of these reactions, and many more, to happen at a rate that sustains life!

3. Enzymes and substrates are perfectly shaped to fit together, like a lock and key.
A. True
B. False

Answer to Question #3
Both. This is a trick question! Scientists aren’t sure whether enzymes and substrates are perfectly shaped to fit together, or whether the shape of the enzyme changes to fit the substrate as they interact. It may vary from enzyme to enzyme. So the answer is “we don’t know!”