Lesson Explainer: Enzymes Biology

In this explainer, we will learn how to describe the action of enzymes in catalyzing biological reactions.

Proteins are biological molecules that take a wide variety of forms. In the human body, proteins can form hormones that help regulate biological processes or structural components that are responsible for holding cellular structures in place or contracting our muscles. The enzymes in our bodies are also examples of proteins.

Definition: Enzyme

An enzyme is a biological catalyst that speeds up the rate of reactions without being used up.

You may often see enzymes referred to as biological catalysts. They are biological as they are composed of biological material—proteins—and the term catalyst refers to a substance that increases the rate of a reaction without being used up or significantly changed in the reaction itself.

Definition: Catalyst

A catalyst is a substance that lowers the activation energy required for a chemical reaction to occur without being used up itself, so the overall reaction occurs at a faster rate.

Enzymes are crucial for keeping us alive, as many essential reactions occurring within our cells are simply too slow to occur by themselves. For example, if the enzymes involved in cellular respiration did not function properly, the breakdown of glucose to release energy would not occur as frequently. With less energy being released in our cells, we would lack the energy to move, digest our food, and eventually, breathe. In short, if large amounts of enzymes in our bodies were not present or not functioning, we would not be able to survive!

An example of a human disorder caused by the absence of an enzyme is phenylketonuria (PKU). Maybe you have noticed a warning on the packaging of food containing the artificial sweetener aspartame. This is because aspartame is made of phenylalanine, but people affected with PKU do not have the enzyme that breaks down this amino acid, causing it to accumulate in the body at toxic levels, in particular, in the brain.

Example 1: Defining an Enzyme as a Catalyst

Enzymes act as catalysts. What does a catalyst do?

  1. A catalyst speeds up the rate of a reaction.
  2. A catalyst increases the number of reactants in a reaction.
  3. A catalyst always maintains a constant rate of reaction.
  4. A catalyst ensures a reaction never ends.
  5. A catalyst slows down the rate of a reaction.

Answer

Enzymes are examples of proteins that can be found in the human body. Enzymes are incredibly important to carry out many of our biological reactions; without enzymes, these reactions would take place at such a slow rate that our bodies may cease to function normally!

In chemistry, a catalyst is something that increases the rate of a reaction but is not a reactant itself. Because they are biological molecules that speed up reactions without being used up or changed in the process, enzymes are often called “biological catalysts.”

Therefore, our correct answer is A: a catalyst speeds up the rate of a reaction.

Enzymes are typically globular proteins—this means “round shaped”—formed from the interaction of multiple polypeptide chains. Enzymes have distinct structures related to their function. Alpha amylase is an example of an enzyme found in the human body, and an image of its molecular structure is provided in Figure 1. We can see that the structure of this enzyme is fairly complex, with lots of interacting chains.

Alpha-Amylase

Figure1:Acomputer-generatedimageofthemolecularstructureofalphaamylase.Alphaamylaseisanenzymefoundinthehumanbodythatbreaksdownlargecarbohydratemoleculesintosmallermolecules.

Enzymes have a specific region within this structure called the active site. Enzymes will react with other molecules called substrates, and the active site is where the substrate (or substrates) of an enzyme will bind. As illustrated in Figure 2, the shape of the active site is adapted to fit the shape of the substrate—we call this a complementary fit. Active sites are usually located in a groove or a pocket formed by the 3D structure (or conformation) of the protein so that only a specific substrate can be exactly positioned there. Some enzymes have several active sites, catalyzing different reactions.

Definition: Active Site

The active site is the region on the surface of an enzyme molecule to which a specific substrate will bind and undergo a chemical reaction.

Definition: Substrate

The substrate is the molecule, or combination of molecules, that are specific and complementary in shape for a particular enzyme’s active site.

Key Term: Complementary Shape/Fit

The complementary shape of an enzyme’s active site to a specific substrate molecule means that only that substrate will be able to fit with that enzyme so that it only catalyzes one specific reaction.

The complementary fit between an enzyme and its substrate molecules means that enzymes will only catalyze a specific chemical reaction. For instance, amylase (shown in Figure 1) will only catalyze the breakdown of starch into its component sugars. It will not be able to catalyze the breakdown of other food molecules, such as proteins into amino acids or fats into fatty acids and glycerol. We refer to this as “enzyme specificity.”

Some enzymes catalyze reversible reactions. This means that the enzyme may catalyze the reaction that breaks a molecule down into its simpler components, and then catalyze the reaction that reforms the molecule from those components! These enzymes will increase the rate of reaction until it reaches equilibrium (i.e., until the amount of product is equal to the number of substrates).

An example of an enzyme catalyzing a reversible reaction is the enzyme carbonic anhydrase. When we breathe, we take in oxygen, which is used for cellular respiration in our cells. A product of cellular respiration is carbon dioxide, which is a waste product and must be removed from the body. Carbonic anhydrase firstly converts this carbon dioxide into a substance called carbonic acid and bicarbonate ions, and these are transported by the blood to the lungs. Once the blood reaches the lungs, the bicarbonate ions are converted back into carbon dioxide, which can be breathed out. Figure 3 gives a simple outline of the mechanism of an enzyme that catalyzes a reversible reaction.

Example 2: Identifying Enzymes and Substrates That Have Complementary Fits

A diagram of an enzyme and some substrates is shown. Which substrate will the enzyme bind to?

Answer

Enzymes are typically globular proteins that have unique shapes. Enzymes act as biological catalysts, speeding up the rate of chemical reactions. To do this, enzymes must be able to bind to a substrate or multiple substrates.

On an enzyme, there will be a distinct region called the active site—this is where the enzyme binds to the substrate (or substrates). The enzyme’s active site and the substrate (or substrates) will have a complementary fit. This means that their shapes will not be the same, but they will complement each other. It may help to think about this like a lock and key; the key does not have the same shape as the lock, but it has a complementary one, so a particular key fits into a particular lock perfectly to open a door!

Let’s have a look at the shape of our enzyme.

We can see that the active site has a rounded shape, so we are looking for the substrate that would comfortably fit into this site.

Substrate V is the same shape as the enzyme. Remember that a complementary fit does not mean the enzymes and substrate are the same shape. So, we can exclude substrate V.

Substrate Y and Z are made up of rectangular shapes. We are looking for a rounded shape to fit in the active site. So, we can also exclude substrates Y and Z.

Substrate X has a rounded shape and looks like it could fit into the active site well. Let’s put the shapes together to double check this.

Therefore, the substrate that the enzyme will bind to must be substrate X.

Enzymes are not always found in an active state—some will exist as precursors (sometimes called proenzymes or zymogens) and will need certain substances or conditions available to activate them. Let’s have a look at an example.

Pepsin is a protein-digesting enzyme (a protease) that is found in the stomach of humans. The stomach is an extremely acidic environment—the presence of hydrochloric acid means that the gastric juice secreted by the stomach has a pH of 1.5 to 3.5!

However, the stomach cells do not secrete pepsin in its active enzyme form, because they need to prevent the enzyme from digesting the proteins they themselves contain. Instead, the cells in the stomach secrete an inactive form of the enzyme called pepsinogen. The presence of HCl in the stomach initiates a reaction that converts pepsinogen to the active pepsin. It does this by causing the pepsinogen to cleave—or “chop off”—a portion of itself to be activated. Pepsin is now ready to catalyze reactions in the stomach that break down proteins in the food one has ingested! A simple outline of this is demonstrated in Figure 4.

Example 3: Recalling the Conditions Needed for the Production of the Enzyme Pepsin

Pepsin is a protease enzyme that breaks down protein molecules in the stomach. Pepsin is formed from the activation of its precursor, pepsinogen. What condition must be present for pepsin to be produced?

  1. A low pH
  2. A high temperature
  3. A lack of oxygen
  4. A high salinity

Answer

Enzymes are commonly referred to as biological catalysts, as they are biological molecules that speed up the rate of chemical reactions without being used up or changed in the process. Lots of enzymes in the human body are found in their active form, but some need to be “activated” from a precursor (sometimes called a proenzyme or zymogen). This is often the case with digestive enzymes, which cells produce in an inactive precursor to prevent the digestion of their own sugars or proteins. Pepsin is an example of this.

To form the active enzyme pepsin, the proenzyme pepsinogen must undergo some structural changes. When pepsinogen is exposed to the very acidic conditions of the stomach, a part of the molecule is “cleaved” (broken off). This cleavage converts the inactive pepsinogen into the active pepsin enzyme. A simple diagram to summarize this is given below.

To help us answer this question, it may be useful to remember the natural conditions of the stomach. The cells of the stomach secrete stomach acid, which is actually primarily made up of hydrochloric acid. Hydrochloric acid is a very strong acid and results in the stomach having a very low pH of around 1.5–3.5. The secretion of this acid is not only useful in breaking down food molecules but also in acting as a defense mechanism to infection and destroying pathogens that may enter the stomach.

Let’s have a look through the answer options to identify the correct choice.

High salinity indicates that a region is very salty, or has very low water content relative to salt concentration. The stomach is not significantly more salty—and does not contain significantly less water—than the other parts of the human body, so we can exclude this answer.

A high temperature and a lack of oxygen would be very detrimental to the human body. The core temperature of the body is around 37C, and any large increases above this temperature could end up disrupting the molecule structure of enzymes and their precursors, among other damaging effects! A lack of oxygen within the body would prevent cells from carrying out aerobic respiration, so this would need to be avoided.

But as we have seen, the stomach has a very low pH due to the presence of hydrochloric acid, and it is this low pH that instigates the conversion of pepsinogen to pepsin.

Therefore, our correct answer option must be A: a low pH.

What about other conditions that can affect the function of enzymes?

For enzymes to react with their complementary substrates, they must collide. This means they must physically meet in a certain way so the substrate successfully binds to the enzyme’s active site.

If we increase the kinetic energy—the energy associated with movement—of the enzyme and substrate molecules, there is a higher likelihood of enzymes colliding with the substrates. Energy can be transferred from one form to another, so if we increase the temperature at which a reaction is happening, this heat energy can be converted into kinetic energy.

A higher temperature generally means a faster rate of reaction due to the increase in the kinetic energy of the molecules. This can be seen in the graph displayed in Figure 5—as the temperature increases from 0 to around 35C37C, the rate of reaction also increases.

As you may have noticed from Figure 5, an increase in temperature increases the rate of reaction up to a point. If the temperature increases too much, the enzyme can denature. Denaturing occurs when the conditions are so unfavorable for an enzyme that their protein structure is changed, often irreversibly.

This means that the shape of the active site changes. If this occurs, the complementary substrate can no longer bind to the enzyme, and the enzyme-controlled reaction cannot proceed.

Definition: Denaturation

Denaturation occurs when an enzyme’s active site changes shape so that it no longer has a complementary shape to its specific substrate molecule.

We can see a similar trend when we compare the rate of enzyme-controlled reactions to pH. Enzymes have an optimum pH or an optimum pH range, which is the pH (or pHs) at which they work best. Figure 6 shows how the rate of an enzyme-controlled reaction changes with pH.

As we can see in Figure 6, the rate of reaction reaches its maximum around pH 2. This indicates that this enzyme works best in acidic environments. When the pH becomes higher, and so the environment becomes more alkaline, the rate of reaction significantly drops in response to the enzyme denaturing.

The rate of enzyme-controlled reactions can also be affected by changes in either the substrate concentration or the enzyme concentration. If we increase the concentration of enzymes in a reaction, this means that there are more active sites available for substrates to bind to. If there is more binding of substrates to enzymes, more products will form in a shorter period of time, and the rate of reaction increases. However, this only applies up to a point. Eventually, all the substrates will have been used up. To continue to increase the rate of reaction past this point, more substrates will need to be added. The same pattern is seen with an increase in substrate concentration; eventually, all active sites will be filled, and the only way to increase the rate of reaction will be to add more enzymes.

Figure 7 outlines how adding more enzymes or more substrates will initially increase the rate of a reaction, but eventually, a different factor will need to be changed.

Example 4: Applying Knowledge of Enzyme-Controlled Reactions to Example Experiments

A student is completing an experiment studying the rate at which trypsin, an enzyme found in the human body, breaks down proteins in a beaker of milk. They are running the experiment at 20C, with a pH buffer of pH 9.

What change in conditions would most likely speed up the rate of reaction?

  1. Increasing the pH to 14
  2. Decreasing the concentration of trypsin
  3. Reducing the amount of light the reaction is exposed to
  4. Increasing the temperature to 37C

Answer

Enzymes are biological catalysts, which speed up the rate of chemical reactions without being used up in the process. Here, we are told that trypsin breaks down the proteins found in milk and is an enzyme found naturally in the human body. It is also important to note the initial experimental conditions: a pH of 9 and a temperature of 20C.

Let’s have a look at each of the options in turn to establish whether they will increase the rate of reaction.

Increasing the pH to 14 is a substantial change in pH. pH 14 is generally considered the highest pH on the pH scale and would be highly alkaline compared to the current pH of the experiment (9). As enzymes are proteins, a substantial change in pH can disrupt their molecule structure and significantly change their shape, meaning they can no longer work. So, this change is highly unlikely to increase the rate of reaction and could in fact stop the reaction completely.

Decreasing the amount of trypsin would be more likely to decrease the rate of reaction. If there are fewer trypsin enzymes available, this means that there will be less protein broken down. Below is an image to help demonstrate this.

With high trypsin concentrations, more substrates are able to bind to enzymes and be broken down into their products, increasing the rate of reaction. With low trypsin, there are fewer available active sites for the substrates to bind to. Therefore, less product is formed and the rate of reaction is slower.

As we know, trypsin is active within the human body. The internal organs and tissues of the human body are not exposed to light, so reducing the light exposure of this reaction will not significantly affect the rate of reaction.

The typical core body temperature of a human is around 37C. If we were to increase the temperature of the reaction outlined in the question from 20C to 37C, we would expect to see an increase in the rate of reaction. This is because as the temperature of an enzyme-controlled reaction is increased, the kinetic (movement) energy of the enzymes and substrates increases. If the kinetic energy of these molecules increases, the chance of them colliding and binding also increases. This means more reactions are likely to happen in a given period of time, and more products will be formed. Let’s have a look at a graph that demonstrates this.

As the temperature increases from 0C to around 37C, we can see that the rate of reaction also increases. This only happens to a point as an extreme increase in temperature, much like a substantial change in pH, can disrupt the structure of an enzyme and stop it from working.

Therefore, we can see that our correct answer is D: increasing the temperature to 37C is most likely to increase the rate of this reaction.

Let’s recap some of the key points we have covered in this explainer.

Key Points

  • Enzymes are examples of globular proteins.
  • Enzymes are biological catalysts, which speed up the rate of chemical reactions without being used up in the process.
  • An enzyme has an active site that has a specific shape and is complementary to a specific substrate.
  • Some enzymes need to be “activated.” For example, the enzyme pepsin is formed from the activation of its precursor pepsinogen due to the presence of HCl in the stomach.
  • A higher temperature means a faster rate of enzyme-controlled reaction, up to the point of the enzyme being denatured.
  • The rate of enzyme-controlled reactions can also be affected by changes in pH, substrate concentrations, and enzyme concentrations.

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