You are currently viewing CHAPTER TWO: ENZYMES
Pepsinogen. Molecular model of pepsinogen, the inactive precursor to the digestive enzyme pepsin. Credit: Getty images


In chapter one, we highlighted the chemical basis of human physiology and the basic understanding of the hierarchical organization of the human body from cells to organ systems. We briefly looked at the different nutrients and their structural units, energy, and thermodynamics. Let’s expand our knowledge by summarizing what you should know about the chemical reactions in the body and how enzymes help us live.

A catalyst is any substance that increases the rate of a chemical reaction without undergoing any permanent chemical change. Enzymes are biological catalysts that are proteins in nature.

The human body has more than 1000 enzymes that catalyze millions of chemical reactions.

Any chemical reaction has both reactants and products. The reactants become substrates if enzymes are involved. A substrate is any chemical substance (molecule) that can bind to an enzyme to undergo a series of chemical reactions to form products.

The site where the substrate binds to an enzyme is called the active site. The region is formed as the various protein molecules fold to form three-dimensional shapes that constitute enzymatic structures.

When substrates bind to the active sites of enzymes, they undergo chemical changes that involve bond cleavage using lower energy than that required for spontaneous reactions. The chemical reactions are also faster.

In most cases, the active site is a small region on the binding site of an enzyme. In other scenarios, the active site may be adjacent to the binding site – an allosteric site. It may enhance or depress the enzymatic activity at the binding site.

Enzymes are specific in nature. They catalyze specific reactions. Enzymes like glucokinase catalyze ony one reaction – the addition of an inorganic phosphate to glucose to form glucose-6-phosphate. Others are specific for a certain group of compounds, peptidases for all peptide bonds.

When an enzyme binds a substrate, an enzyme-substrate complex is formed. The interaction leads to the formation of products. This occurs at the enzyme’s active site.

Enzymes ensure specificity by interacting with substrates in one of two ways: lock and key or induced fit.

For the ‘lock and key’ model, the enzyme’s active site has a complimentary fit to the substrate that the latter fits into the site like how a key fits into the lock. However, the substrate has be an exact match. This theory perhaps explains the extreme specificity of enzymes like glucokinase described above.

Induced fit describes a more liberal model. The enzyme’s active site doesn’t necessarily need to have a complimentary fit with the substrate. Rather, it undergoes conformational changes as the substrate binds to it. Through this mechanism, enzymes are able to have more than one substrate from the same class of compounds.

Enzymes models of substrate binding
Credit: Liubov Poshyvailo-Strube

Metabolic pathways are created and maintained by enzymes. Biochemical pathways are sequences of chemical reactions undergone by a compound or class of compounds in the body, often enzymatically mediated. They create and use energy.

Metabolic pathways use enzymes to create and use energy.
Credit: Biology LibreTexts

One way of controlling metabolic pathways is allosteric or end-product inhibition. At the end of the pathway, the end-products often accumulate. They then bind to the enzymes at the initial step in the pathway, often at an allosteric site to depress its activity. The reduced enzyme activity dampens the metabolic pathway thereby regulating the amount of end-products that are synthesized. However, the end-product concentration falls below a critical value, its inhibitory effect is lost and the dampened enzyme becomes active again. The cycle is repeated.

end-product inhibition controls the activity of enzymes in a metabolic pathway.
end-product inhibition controls the activity of enzymes in a metabolic pathway.
Credit: The A level Biologist

How do we name enzymes?

Enzymes end with ‘-ase’ unless otherwise specified. The name indicates the enzyme’s function: hydrolases add water to molecules during biochemical reactions. Isomerases rearrange atoms within a compound. Anhydrases remove water from compounds. Lipases digest lipids, kinases add inorganic phosphates to compounds, and so on.

There are a few enzymes that do not follow this rule: for example, trypsin, pepsin, and renin.

Are all enzymes synthesized in an active form?

No! not all enzymes are synthesized in an active form. In other words, such enzymes are inactive and only become active after a series of chemical changes that may involve proteolysis (protein cleavage) using cofactors and coenzymes.

Proteolysis involves the shortening of a polypeptide chain by preexisting enzymes or solutions. For example, the polypeptide chain of pepsinogen is cleaved in the presence of hydrochloric acid to form an active enzyme, pepsin. The inactive proteins often assume a name that ends in -ogen: pepsinogen, trypsinogen, angiotensinogen, et cetera.

Pepsinogen. Molecular model of pepsinogen, the inactive precursor to the digestive enzyme pepsin.
Credit: Getty images

We often confuse cofactors with coenzymes, but they are different.

Coenzymes are organic molecules, typically vitamin derivatives, that enzymes need to become active. They often accept electrons during an enzymatic reaction and transfer them to another chain of reactions. The electron chain transport system uses such compounds, as nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD).

Cofactors, on the other hand, are inorganic molecules that enzymes require to bind substrates at the active sites. They are often metal ions – manganese, magnesium, zinc, copper, calcium, iron(II), and iron(III) ions. Zinc and iron are the most abundant cofactors in the human body. Enzymes that require cofactors assume specific names. They are apoenzymes when inactive and holoenzymes when active.

Cofactors and coenzymes are often provided by the foods we eat. For instance, eggs, lean meat, milk, and broccoli are good sources of riboflavin, the precursor of FAD. Whole grains, leafy green vegetables, and meat provide niacin, the precursor of NAD and NADP. All these foods provide pantothenic acid, the precursor of coenzyme A.

Factors that affect how enzymes work.

Various factors affect how enzymes work: these conditions provide an optimal environment for maximal enzymatic activity, without which the chemical reactions catalyzed may slow down. Such factors include temperature and pH, among others.

  • Temperature

By convention, enzymes work optimally at a body temperature of 370C (97.60F). At extremes of temperatures, their work slows down. When temperatures are low, enzymatic activity is slow. Extremely high temperatures denature enzymes. Denaturation may be temporary or permanent.

  • pH

Optimal pH is a prerequisite for maximal enzyme activity. Each enzyme has its own. Enzymes in the mouth (ptyalin) work best in an alkaline pH. Those in the stomach (pepsin) do so in an acidic pH. The enzymes from the mouth cease to work once they reach the stomach with food after swallowing.

  • Enzyme inhibitors

Enzymes have inhibitors. They bind to the active sites or anywhere on the enzyme structures to render them inactive. The nature of inhibition may be competitive or non-competitive.

Competitive inhibitors bind to the same active site as the substrate, hence blocking the breakdown of the substrate since it won’t occupy the active site. The inhibitor may or may not be broken down. This principle is utilized in many clinical settings. For example, methanol and ethylene glycol are often grave causes of poisoning among people. One of the treatments involves using administering ethanol to the affected people. It is because both of these compounds are broken down by the same enzyme that breaks down ethanol during normal metabolism. All three compounds compete for the same active site on this enzyme – alcohol dehydrogenase.



During methanol poisoning, commonly seen among people who consume locally brewed alcohols in remote villages, methanol binds to alcohol dehydrogenase. The enzyme breaks it down to formaldehyde. Formaldehyde then spontaneously dissociates to formic acid.

Formic acid is highly toxic to the body – it reduces blood pH to cause acidosis. It also irreversibly binds to molecules in the optic nerve to cause blindness. Affected persons receive ethanol as one of the treatment modalities.

In the presence of ethanol, alcohol dehydrogenase preferentially binds ethanol. This reduces the amount of formic acid that is being generated to allow methanol excretion before it affects body organs.

Non-competitive inhibition occurs when an inhibitor binds to a site on the enzyme other than the active site. It causes conformational changes at the active site that render it unable to catalyze its substrates.

Enzyme inhibition may be reversible as in competitive inhibition or irreversible, especially in non-competitive inhibition.

  • Enzyme modulators

Enzyme modulators do not activate or inactivate their respective enzymes but increase or decrease their activity. They accomplish this by altering the configuration of the enzyme structures. They do so via bond formation – covalent or ionic bonds. Calcium and inorganic phosphates are the two most potent enzyme modulators.

How do we determine rates of reaction?

Substrate consumption and product synthesis are the markers of enzyme-catalyzed reaction rates.

The reaction rate is directly proportional to the concentration of both the substrate and enzyme.

Rates of reactions reach a maximal point when the enzyme becomes saturated with the substrate.

Equilibrium and the Law of Mass Action

All reversible reactions behave in a format whereby the products can dissociate to become substrates and vice versa. They constitute the forward and backward reactions. The point at which the forward and reverse reaction rates are equal is called the equilibrium point.

Adding or removing a substrate or product increases the forward reaction, respectively. When reaction products accumulate, they favor the backward reaction. This principle underlies the law of mass action.

The law of mass action states that the rate of any chemical reaction is proportional to the product of the masses of the reacting substances. It implies that the direction of any reversible reaction will be determined by the number of substrates or products present. The aim is to establish an equilibrium when the ratio of substrates to products is equivalent. Any deviation prompts adjustments to restore the equilibrium state. One of the most relevant reversible reactions in the body is shown below. It determines the pH of the blood, and it is catalyzed by an enzyme – carbonic anhydrase.

pH regulation requires multiple enzymes and one of them catalyzes this reaction
Carbonic anhydrase catalyzes the conversion of carbon dioxide and water to hydrogen and bicarbonate ions and vice versa.

Any increase in the concentration of hydrogen ions will drive the reaction to the left to form more carbon dioxide consuming more bicarbonate ions. Any increase in the concentration of carbon dioxide will lead to the formation of more hydrogen ions, a shift to the right of the equation.

The reversibility of reactions in the body is an area of constant regulation. It dictates the order and rate of metabolism. As noted, the rates of these reactions are determined by both the concentration of the enzymes and their substrates. However, metabolism rates are principally controlled at one-way reactions, i.e., irreversible reactions. It allows specific organs to control the utilization of compounds in these processes. It also facilitates dependence. For instance, skeletal muscles rely on the liver to provide glucose because they cannot synthesize the compound. The liver and kidney cells have an enzyme, glucose-6-phosphatase, that catalyzes the final step in the de novo synthesis of glucose during times of starvation. It cleaves an inorganic phosphate from glucose-6-phosphate to form glucose that diffuses out of the cells (liver and kidney) and enters blood to reach other organs for utilization as a source of energy.

Without enzymes, the body’s metabolic processes would be too slow to facilitate survival for even 5 minutes! Cherish them.


MBChB (MUK), Graduate Fellow, Department of Physiology, Makerere University Founder and Content Creator Peer reviewer, Associate Editor

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