Enzymes – The Molecular Miracles

Everybody knows that the food we eat is broken down into small usable molecules for the body to absorb from the intestine. But not many know the significance of thousands of small molecules called enzymes breaking down food during digestion. Enzymes are biological catalysts, which increase the velocity of biological reactions without undergoing any changes themselves. Enzymes are mostly proteins and like all proteins are made up of chains of amino acids. Once they are activated, they can bind reversibly to a substrate and convert it to a product which is important for cell function. Enzymes are very specific for the type of reaction that they catalyse and work in a very controlled manner.

 Enzyme reaction


Enzyme PropertiesFor a chemical reaction to occur, the molecule should possess a certain amount of energy called activation energy. Enzymes can accelerate biological reactions by drastically reducing the activation energy of the molecule. Enzymes lower the activation energy of reactions by bringing reactants closer to each other on the active site, rather than relying on collisions between them to produce the product. Chemically, it would take a very strong acid such as hydrochloric acid or sulphuric acid a few days to break down protein when kept at 100° C. However, we break down the same protein in our digestive system within a few hours, and that too at body temperature using enzymes.



The word ‘Enzyme’ was coined by Kuhne after studying the fermentation of sugars to alcohol by the enzyme Zymase. Enzymes are named according to the kind of reaction they catalyse. For example, lactase breaks down the sugar lactose and protease breaks down proteins. But this is not the same for all enzymes as some of them are named pepsin, trypsin, chymotrypsin and rennin which are more arbitrarily named by their discoverers.



Enzymes are huge protein molecules and are usually many times larger than the substrate itself. On this enormous molecule, the actual portion of the enzyme that is involved in catalysis is a very small region called the active site, which binds with the substrate and facilitates the reaction. Being proteins, they are made up of amino acids(forming a polypeptide chain) strung together like pearls on a necklace.

active site

Active site of an enzyme. The Substrate fits into the active site of the enzyme where the reaction takes place.

This chain is then folded due to chemical attraction between different amino acids in the chain creating a 3 dimensional structure. This folded structure creates pockets and crevices where the substrates can bind and the chemical reaction basically occurs here. These protein structures are very sensitive to extreme conditions like high temperatures or pH which can unfold or denature them, resulting in losing the 3D structure required for catalytic activity.


Sometimes, a number of these folded polypeptides come together and form multimeric enzyme complexes. The proteinaceous enzymes are found closely associated with non protein molecules such as metal ions (Mg 2+, Mn2+, Zn 2+, Fe2+, Fe3+) and Vitamins (B complex). These molecules are critical for enzyme activity as they form part of the active site.



Digestion would be impossible without the help of enzymes, which break down the complex molecules that are eaten, to the nutrients that the body requires. Digestion begins the moment the food hits the mouth, when the amylase and lipase break down starches and lipids respectively. Another enzyme lysozyme destroys the bacteria and viruses by dissolving their protein based membranes. In the stomach, gastric enzymes are secreted and are activated by the hydrochloric acid present here. The stomach is the headquarter of protein digestion, where the protein digesting enzyme, Pepsin is present. This enzyme works well in spite of the presence of Hydrochloric acid in the stomach.


The next step is in the small intestine or ileum, where the pancreas pours in a cocktail of enzymes, to continue the process of digestion.


Later in the ileum or small intestine, a number of other enzymes are secreted to extract the maximum nutrition from the food. This is the headquarters of sugar digestion.


Sometimes, disease or injury to the pancreas may affect their ability to secrete important enzymes for digestion, leading to malabsorption and malnutrition. This can be corrected with over the counter digestive enzyme supplements to help the digestive system. Bromelein is a protelytic (proteo= protein, lytic=break) enzyme obtained from pineapple. Papain is another such proteolytic enzyme in raw papaya. These two natural and easily available enzymes can be used to tenderise meat by breaking down some of the tough protein structures, making meat succulent and easy to digest.



DNA codes for a large number of protein products, which includes enzymes. A mutation in some genes can cause a faulty enzyme to be produced or sometimes even no enzyme is produced. A single mutation leading to a single change in the amino acid sequence in the enzyme can drastically influence its structure. This leads to an inactivation of the mutant protein produced, as it no longer structurally resembles the actual enzyme (wild type). Many metabolic disorders are due to enzyme defects and require enzyme supplements and in some cases even gene therapy to correct the enzyme at a DNA level.


  • Lactose intolerance: This disorder is characterised by insufficient levels of Lactase enzyme, which breaks down the milk sugar called lactose. This enzyme has evolved in mammals to help digest milk when they are infants. Most human beings have developed the ability to produce adequate levels of lactase, even after the individual has been weaned off the mother’s milk. Some populations, like the Ashkenazi Jews, and Northern Europeans are unable to digest lactose beyond infancy and experience stomach cramps, bloating, nausea, diarrhoea and flatulence when they consume milk products. The lactose is broken down and fermented in the colon by the bacteria present there, leading to production of gas and abdominal pain.
  • Sucrose intolerance: Individuals with this disorder are unable to produce the enzyme sucrase to break down sucrose or table sugar to glucose and fructose. This deficiency leads to low levels of glucose in the blood. People with sucrose intolerance suffer from mental disorders, schizophrenia and mood disorders.
  • alkaptoneuria-urine-sampleAlkaptonuria or maple syrup urine disease is due to the faulty breakdown of amino acids called Phenylalanine and Tyrosine, caused due to the absence of the enzyme homogentisate 1,2-dioxygenase enzyme. The unmetabolised product is excreted in urine, which assumes a dark maple syrup consistency on standing.
  • Lesch Nyhan Syndrome: This is a disorder caused due to a deficiency in the enzyme called Hypoxanthine guanine phosphoribosyl transferase, leading to an accumulation of uric acid. This uric acid can easily crystallize in joints and kidneys causing gout and kidney stones. All this uric acid floating around the body, especially in the brain causes behavioural problems, mainly self mutilating intentions.
  • Severe Combined Immuno Deficiency Syndrome (SCID): This disorder is the result of a deficiency in an enzyme Adenosine deaminase (ADA), which is involved in the breakdown of DNA. Immune cells called B and T lymphocytes are most affected, as they fail to develop healthily. Sufferers are especially prone to infections as they have virtually no immune cells to protect them.



Many enzymes are produced on a large scale in microorganisms like E.coli, or purified from other sources to treat diseases and enzyme deficiencies.

  • Thrombolytic enzymes such as streptokinase and urokinase dissolve dangerous blood clots in people suffering from strokes and heart attacks.
  • Pulmozyme is an inhalable DNAse, which breaks the DNA in the thick mucus of cystic fibrosis patients, giving them some relief.
  • L- Asperginase is used to starve cancer cells by breaking down an amino acid called Aspergine, which is essential for their rapid growth.
  • Lysozyme is used as an antibacterial agent as it specifically dissolves bacterial cell walls.
  • Chitinase is an antifungal which dissolves chitin in the cell walls of fungi.

Inhibition of certain overactive or unregulated enzymes can be beneficial in some cases and this inhibition can be achieved using small molecule enzyme inhibitors.

  • Sildenafil or Viagra is a potent cGMP phosphodiesterase inhibitor, increasing blood flow to the corpus cavernosum. This drug is used to treat erectile dysfunction and also cardio vascular disease.
  • Methotrexate is an inhibitor of Dihydrofolate reductase, which is essential for rapid cancer cell division.
  • Uncontrolled Tyrosine kinase activity drives rapid cell division in cancer cells. A number of small molecules such as Imatinib, Gefitinib and Afatinib are being used as cancer chemotherapy by inhibiting this enzyme.
  • Enzymes are also used to diagnose and quantify diseases such as heart attacks, liver disorders and diabetes mellitus .
  • Amylase is used to break down starch to produce high fructose corn syrup.
  • Cellulase and pectinase are used to clarify fruit juices. The enzymes break down fruit pulp giving it a clear look.
  • Proteases, amylases and lipases in detergents break down stains from proteins, starches and greases.
  • Proteases like papain are used to break down protein accumulation on contact lenses and are regularly added to contact lens cleaning solutions.
  • Rennin from the stomach of young calves is used to curdle milk in cheese production.