The active site of an Enzyme

Definition

The active site of an enzyme is the region that binds substrate molecules. This is crucial for the enzyme’s catalytic activity. Enzymes are proteins that drastically increase the speed of chemical reactions by lowering their activation energy.

They do this by interacting with chemical reactants – the substrates – in ways that make them more likely to undergo their chemical reaction. This interaction is carried out at the active site, where the enzyme binds the substrates to increase their chances of reacting.

The role of enzymes

Enzymes catalyze countless chemical reactions. For example, stringing together nucleotides and amino acids to make DNA and proteins, breaking down sugar and fat into energy, and breaking down toxins in the liver. Thus, enzymes are some of the most important molecules in biology. Without enzymes, life as we know it could not exist.

Features that Determine Active Site Specificity

Because enzymes – like all proteins – are made of amino acids, there are a wide variety of potential sequences. Therefore, their active sites also have diverse sequences, structures, and physical properties. This is an important feature that allows enzymes to bind specifically to different substrates. Some of the properties that affect substrate binding include:

Size and shape of the active site – Enzyme active sites are shaped such that they will only ‘fit’ with certain substrates.

Polarity or non-polarity – Polar molecules are attracted to other polar molecules, while non-polar molecules prefer other non-polar molecules. In this way, certain amino acids in 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 – for example, two positive charges – will actively repel each other. This is another way in which an enzyme active site can attract substrates or regions of substrates, while repelling others, to create the right fit.

Hydrophobicity or hydrophilicity – In this case, opposites do not attract. Instead, 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. For example, several B vitamins 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.

Active Site Binding Theories

There are two theories about how exactly an enzyme active site binds to substrates. These are the lock and key model and the induced fit model.

The Lock and Key Model

The lock and key model of active site binding postulate that active sites possess the perfect shape to bind their substrates. When they make contact, the substrate can “pop” into place at the active site, similar to a lock and key.

The Induced Fit Model

The induced fit model competes with the lock and key model. It 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 drives the substrate into its new formation. After the reaction is complete and new products form, the product and enzyme are no longer compatible and they separate. The induced fit model is more in line with current scientific evidence and is more widely accepted.

Examples of Enzymes

Some examples of chemical reactions catalyzed by enzymes include the breakdown of starch by maltase, the breakdown of proteins by pepsin, and the synthesis of DNA by DNA polymerase. For each of these reactions, the characteristics of the active site are crucial.

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 is shown below:

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 is important for digestion is pepsin. The cells of the stomach release pepsin, allowing it to catalyze the reaction of proteins with stomach acid. Therefore, pepsin allows your body to break down protein from food into amino acids. Your body can use these amino acids to build new proteins. The reaction occurs as follows:

Protein + Acid → Amino acids

DNA Polymerase

Another essential enzyme is DNA polymerase. It’s DNA polymerase that allows your cells to multiply, by making copies of their DNA to pass on to daughter cells.

DNA polymerase does this by stringing together nucleic acids in the correct sequence. This synthesis reaction is the opposite of the breakdown reactions of maltase and pepsin. The reaction catalyzed by DNA polymerase is as follows:

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

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