Enzyme Substrate Complex Definition

The enzyme substrate complex is a temporary molecule formed when an enzyme comes into perfect contact with its substrate. Without its substrate an enzyme is a slightly different shape. The substrate causes a conformational change, or shape change, when the substrate enters the active site. The active site is the area of the enzyme capable of forming weak bonds with the substrate. This shape change can force two or more substrate molecules together, or split individual molecules into smaller parts. Most reactions that cells use to stay alive require the actions of enzymes to happen fast enough to be useful. These enzymes are directly coded for in the DNA of the organism.

The enzyme substrate complex is extremely important for a number of reasons. First, the enzyme substrate complex is only temporary. This means that once the substrate has changed, it can no longer bind to the enzyme. The products are released and the enzyme is ready for another substrate molecule. A single enzyme can operate repeatedly millions of times, meaning only a small amount of enzyme is needed in each cell.

Enzyme action
Enzyme action

Enzymes are complex molecules, like little machines meant for one purpose. Built out of a chain of amino acids, this long string experiences interactions between the different amino acids and twists and turns into complex structures. These structures can operate like hinges, wedges, and all sorts of other shapes intended to speed certain reactions. Different mutations give rise to slightly different forms of enzyme. In mutations that are beneficial to the organism, the enzyme substrate complex is changed in a way that effects the output of product or the function of the enzyme as a whole. This change in the organism is only beneficial if it somehow helps the organism reproduce more.

Enzymes are usually named after the substrate that they work on, and have the -ase suffix to designate they are enzymes. Each enzyme has a certain specificity for the substrate it works on, which determines which molecules they can bind to. Some molecules that are similar in structure to the substrate may get stuck in the active site, because they cannot undergo the reaction intended by the enzyme. In this warped enzyme substrate complex, the competitive inhibitor binds to the enzyme and inhibits its further action. Other inhibitors do not copy the substrate, but modify the enzyme in other ways so the enzyme substrate complex cannot be formed.

Examples of Enzyme Substrate Complex

Amylase and Amylose

Amylose is a complex sugar produced by plants. In our saliva is an enzyme, amylase, used to break amylose apart. Amylase uses one substrate molecule of amylose and a cofactor of one water molecule to produce an enzyme substrate complex. The complex severely reduces the amount of energy required to start the reaction, which increases the time in which it happens. A typical sugar molecule would take millions of years to break apart, were it not for the actions of enzymes such as amylase.

In fact, enzymes are so important in digesting the foods we eat that our body produces an enzyme for almost every type of food the body is evolutionarily prepared to consume. New foods are poorly processed, because the enzymes have not had time to adjust their efficiency. For instance, the modern diet of processed foods is leading to an obesity epidemic because the process foods are rich in easily accessible nutrients, but only to the pathways that are used to storing fat. As a result, much of the population experiences weight related illnesses. Many nutritionists are pushing for more natural, whole-food, plant based diets that tend to support the enzymes our bodies have naturally developed.

Allosteric Regulation in Enzymes

Although the enzyme substrate complex forming quickly is important for most reactions, in some cases it is important to “turn off” the enzyme to conserve energy or resources. Many enzymes are regulated in this way to provide just the right amount of energy and products. One of the most important places this happens is in the production of adenosine triphosphate (ATP), or the molecule that provides energy to cellular processes. Many of the enzymes in the pathway that creates ATP are inactivated by ATP. In this way, when too much ATP is produced, the enzyme shuts off. This is known as feedback inhibition, or the ability to self-regulate. In the same way, the enzymes can be reactivated by the presence of adenosine diphosphate ADP, an ATP that has used a phosphate group to provide energy to a process or reaction.

Many bodily processes are controlled in this manner, and the enzyme substrate complex in these cases can only be formed with the proper molecules present. Many of the cofactors that activate enzymes are vitamins, minerals, and other inorganic molecules present in the diet.

  • Enzyme – Protein catalysts that lower the activation energy and speed biological reactions.
  • Substrate – The molecule or atom that an enzyme acts on.
  • Activation Energy – The energy required for a reaction to start taking place.
  • Catalyst – Any molecule or substance that lowers the activation energy of a particular reaction.


1. Carbon monoxide is a dangerous molecule to inhale. In your blood stream, carbon monoxide can get into your cells and bond tightly with iron, a cofactor of an important enzyme in the production of ATP. Without this enzyme function ATP cannot be formed. Why can’t the enzyme function?
A. The enzyme substrate complex cannot be formed.
B. The carbon monoxide prevents oxygen from getting into the lungs.
C. It still can, once it causes the carbon monoxide to undergo a reaction.

Answer to Question #1
A is correct. Without the enzyme substrate complex fully forming with the proper substrate, the substrate cannot be transformed. The carbon monoxide binds to the iron cofactor, slightly changing the shape of the enzyme and causing it to no longer accept its substrate, partly because the carbon monoxide molecule is in the way. The enzyme will not be able to work on the molecule, but it will eventually be released.

2. Some enzymes produce a single product from two substrate molecules. In these enzymes, the substrates are loaded into the active site, the enzyme substrate complex is formed, and a single product is released. Can this process happen in reverse, as in, can the product load into the enzyme and be split into two products?
A. Yes
B. No
C. Depends on the enzyme

Answer to Question #2
B is correct. No, the enzyme cannot work in reverse. The enzyme can be thought of like a tool. While you can use an axe to split a log, you cannot use it to put the log back together. In that case you must use a different tool, like a clamp, to put the log back together. In the same way, an enzyme is a specifically designed machine. The forces required to force to molecules together are very different from the forces required to break the same large molecule back apart. As such, the enzymes have very different forms.

3. Which of the following is an enzyme?
A. Lactose
B. Lactase
C. Lactol

Answer to Question #3
B is correct. The suffix -ase tells the reader that the chemical in question in an enzyme. The prefix is usually the molecule being acted on, in this case the sugar lactose. -Ose designates a sugar. Lactol is an alcohol formed from the from sugar lactose, as designated by the -ol suffix.