Enzymes: Your MCAT Guide

What are enzymes?

Wilhelm Kuhne (German physiologist) first used the word ‘enzyme’ in 1877. The term ‘enzyme’ comes from the Greek ‘enzymos’, which means "leavened." An enzyme is a complex molecule that acts as a catalyst and speeds up a chemical process without being consumed. Different biological processes occur for cell maintenance and sustaining life, such as respiration, digestion, excretion, etc. To accelerate these biological processes, enzymes are pivotal. Zymase (enzyme complex) was the first enzyme to be discovered. It naturally appears in yeast and facilitates the fermentation of sugar molecules to produce ethanol and carbon dioxide. Most enzymes are proteins except for some RNA molecules (ribozymes) that also function as enzymes.

Structure of enzymes

A linear amino acid sequence controls the structure of an enzyme's active site and its three-dimensional structure. The catalytic activity of enzymes depends upon the sequence of amino acids. Catalysis takes place only in a restricted portion of the enzyme's structure. The enzyme's active site comprises the binding and functional (catalytic) sites. The binding site is where a substrate (reactant) molecule temporarily binds with an enzyme while the catalytic site catalyzes the biochemical reactions. An active site is a grove or crevice where a substrate can bind to enhance the catalyzed chemical process. When the active site is free, it is often flooded with water. The average size of the enzymes is large, with the 4-Oxalocrotonate tautomerase having 62 amino acid residues and fatty acid synthase having an average of 2500 residues. 

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Classification of enzymes

Based on the reaction catalyzed, enzymes are categorized into six groups. These include

1. oxidoreductases
2. ligases
3. lyases
4. hydrolases
5. transferases
6. isomerases.

Functions of enzymes: biological catalysts

Our body systems utilize enzymes for a variety of purposes. For example, enzyme facilitates the digestive system to break down macromolecules (proteins, carbohydrates, fats) into smaller ones so the body can absorb them. Many enzymes are used in digestion, including amylases, lipases, and proteases.

They assist the body in producing energy. Enzymes transform energy into appropriate molecular forms, then store it in ATP molecules. For instance, ATP synthetase plays this role.

In the cell membrane, some enzymes serve as ion transporters. In active transport systems, they move ions across a plasma membrane against their concentration gradient. These are called ATPases because they hydrolyze the ATP to use energy for ion transport.

Enzymes are capable of taking part in the signal transmission process. They aid in transmitting a chemical or physical signal through the cell and generating a cell response. Protein kinases, which initiate the phosphorylation of proteins, are the most common enzymes used in signal transduction.

Enzymes are also involved in the defense and clearance of various nonnutritive substances inside the cell. So, they initiate the immune response and cleanse the cellular waste. For instance, superoxide dismutase prevents the production of lipid peroxides by eliminating highly reactive superoxide ions.

Enzymes control cellular activities by rearranging the cell's internal structures. For example, they pull cilia to cause cell movement or assist cells in moving mucus up the airway to keep the airway clear, move chromosomes apart when the cells go through mitosis, and transport the package from one area of the cell to another. Enzymes are also crucial in numerous other processes, such as muscle contraction and aging.

Enzyme activity as biological catalysts

Enzymes play a central role as biological catalysts by reducing the activation energy and speeding up the reaction rate. First, they bind the substrate at the active site, creating an enzyme-substrate complex. This complex transforms the reactant into the product by lowering the activation energy. For example, the enzyme sucrase hydrolyzes the substrate ‘sucrose (a disaccharide)’ into two monosaccharides (glucose and fructose). The activation energy is the initial energy the substrate molecule requires to contort the bonds. This energy (for starting the reaction) comes from the thermal energy the reactant molecules absorb from their environment.

The reaction rate is accelerated when the substrate molecules absorb the thermal energy. In turn, this facilitates bond breakage by distorting the molecules of the substrate. With enough energy absorption, the substrate molecules reach an unstable “transition (active) state.” This absorbed energy is released as heat when the products are formed (with new bonds). As a result, the molecules return to their stable state with less power than in their contorted form.

Each enzyme catalyzes a specific reaction and can differentiate between its particular substrate and chemically similar compounds. For example, sucrose is the only disaccharide on which sucrase will act, and it won't bind to other disaccharides like maltose. An enzyme's shape, which comes from its amino acid sequence, determines its specificity. Its shape is not always with the lowest energy, but it assumes shape when the active site binds the substrate molecule. A complementary match between the substrate's shape and an enzyme's active site is also a cause of its specificity.

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Interaction between enzyme’s active site and substrate

Two models explain how enzymes interact with substrates:

Active site model

Weak interactions (hydrogen and ionic bonds) between the substrate and the active site characterize the majority of enzymatic reactions. A few amino acids' R groups located near the active site accelerate the transformation of the substrate into the product. Sometimes, a temporary covalent link is created between the side chain of an enzyme's amino acid and the substrate. Subsequently, the product exits the active region enabling the enzyme to accept a new substrate molecule into its active site. Ultimately, enzymes emerge from the reaction in their original state and function repeatedly.

The substrate's initial concentration affects the substrate's conversion rate into the product. Access to the active sites of the enzyme molecules increases as more substrate molecules become available. All the enzyme molecules' active sites will be occupied and referred to as saturated when the substrate concentration hits a certain threshold. In the saturated condition, the rate of product formation can only be accelerated by adding more enzymes. So, the cell produces more enzymes to speed up the reaction.

Induce fit model

Daniel Koshland proposed the induced-fit model in 1958. According to this model, the substrate can cause the enzyme's active region to reshape and align properly for an ideal fit for catalysis. This change in shape can enhance or inhibit enzyme activity. Induce fit model strengthens the initial weak bonding between the enzyme and substrate.

Factors affecting the enzymatic activity

Enzymes work at an optimum temperature, pH, and concentration. Any change in these environmental variables impacts the 3-D shapes of enzymes and limits enzymes’ ability to function. Temperature and pH are the most crucial factors for an enzyme's activity. With the temperature rise, the rapid movement of molecules causes the substrate to collide with the active site repeatedly, which speeds up the reaction rate. Every enzyme has an optimum temperature where its response rate is highest. Most human enzymes function best at temperatures between 35 and 40 °C (approximately equal to body temperature). Enzymes with an optimal temperature of 70 °C or greater are found in the thermophilic bacteria that inhabit hot springs. However, once the optimum temperature is reached, the speed of the enzymatic process rapidly decreases. As a result, enzymes may lose shape (denature) and cease functioning at extremely high temperatures.

Each enzyme has a preferred pH level, just as it has an optimum temperature. Most enzymes work optimally between pH values of 6 and 8. Some deviations from this limit exist, e.g., pepsin (human digestive enzyme) works best when the pH level is very low. It is evolutionarily adapted to an acidic environment where most enzymes (such as trypsin) get denatured.

Concentrations of enzymes and substrates also influence the rate of biological pathways. If the quantity of the substrate is high, the concentration of the enzymes determines how quickly the reaction will start. However, increased substrate concentration does not impact the reaction rate when all active sites are occupied and enzymes are saturated.

Enzymes’ cofactors and coenzymes

Cofactors are nonprotein helpers that enzymes require for their efficient catalytic activity. These are either bound tightly with the enzymes (as permanent partners) or loosely (and reversibly) attached to the substrates. Some cofactors, like the ionic forms of the metal elements zinc, iron, and copper, are inorganic. Coenzymes are used to describe cofactors that are inorganic in nature. Most vitamins are crucial for nutrient absorption because they serve as coenzymes or the building blocks for coenzymes. In some cases, they can serve as catalysts without enzymes but work less efficiently than when an enzyme is present.

How enzyme activity is regulated

Cell regulates various metabolic pathways by controlling enzyme activity.

Enzyme kinetics

Studying the rates of chemical processes catalyzed by enzymes is known as enzyme kinetics. It is the traditional and still most crucial approach for understanding enzyme mechanism of action. The general catalysis of a reaction involves how an enzyme binds to a substrate; the ES complex is formed and converted into an enzyme product (EP) complex. Therefore, we first draw a general equation to measure the reaction rate:

S → P

where S is a substrate and B is a product, and the rate equation is given as rate = K(S).  

Now enzyme is added to the reaction, and the equation is written as

E+S → ES → E+P

Here, E stands for the enzyme, and P is the product. This indicates a two-step process where ES is formed in the first step and EP in the following step. So, there will be two rates for this two-step reaction:

K1 = (E) (S) and K2 = (ES)

The reaction rate can be accelerated by increasing the enzyme and substrate concentrations. Maximum speed (Vmax​) is achieved when the substrate concentration is high and all enzymes are saturated. This happens when environmental conditions such as pH, temperature, and enzyme concentration are constant.

Michaelis-Menten

It is another kinetics used for examining the interaction of enzymes and substrate. The Michaelis-Menten equation illustrates the relationship between a reaction's substrate concentration and reaction velocity. Most single-substrate enzyme reactions are based on this equation. Its primary function is to indicate the enzymatic rate at various substrate amounts. It assumes that the ES complex's concentration determines the product formation rate. The equation uses the V₀ (initial velocity), Vmax (the maximum reaction rate), and Km (Michaelis constant). The final equation is written as follows: 

Vmax = S / (K_m + S)

In this equation, Vmax is the system's highest reaction rate at substrate concentration saturating conditions. When the reaction rate is half of Vmax, K_m matches the substrate concentration.

Cooperativity

Enzymes show cooperativity when they have more than one binding site. Every substrate binding influences the substrate attachment on the following site. It could be positive cooperativity (which increases enzyme affinity for the next substrate), negative cooperativity (decreases enzyme affinity), or non-cooperative binding (does not affect the enzyme affinity for subsequent substrate).

Feedback regulation of enzymes

The feedback mechanism is a metabolic control method that involves inhibiting an enzyme's activity by its byproduct. For instance, in the amino acid ‘isoleucine’ synthesis pathway, as isoleucine builds up, it inhibits the enzyme responsible for the first stage of the path, slowing down the rate at which it is synthesized. As a result, feedback inhibition stops the cell from producing more isoleucine than is required and preserves the cell’s resources.

Inhibition of enzymes

Certain substances specifically inhibit the working of enzymes. Inhibition is usually irreversible when the inhibitor covalently binds with enzymes. However, the inhibition reverses weak interaction between the enzyme and the inhibitor. Most poisons and toxins act as permanent (irreversible) enzyme inhibitors. For instance, the pesticides DDT and parathion are irreversible inhibitors of vital nervous system enzymes. Similarly, antibiotics work by inhibiting bacterial enzymes. For example, the antibiotic penicillin blocks an enzyme's active site that many bacteria need to assemble their cell walls.

Reversible inhibitors inactivate the enzyme’s active site through noncovalent interactions. A reversible inhibitor can detach from the enzyme, unlike an irreversible one. For example, carbamate pesticides are reversible inhibitors. Some reversible inhibitors are competitive inhibitors that mimic natural substrates and compete with them to bind to the active site. They reduce the enzymes' efficiency by preventing substrates from interacting with the active sites. By raising the substrate concentration, this inhibition can be regulated. As a result, more substrate molecules than inhibitor molecules can connect the active sites.

Another type of reversible inhibitor, noncompetitive inhibitors, do not directly compete with the substrate for binding to the enzyme’s active site. Instead, they bind to another enzyme region and block enzymatic action. This interaction causes a change in enzyme structure, and the active site becomes less effective for binding to the substrate.

Competitive and noncompetitive inhibition combine to result in mixed inhibition. In this inhibition, the inhibitor may still bond to the enzyme whether or not the substrate has already bound. This inhibition can be reduced by increasing substrate concentrations (due to the competitive contribution) but not entirely. Overcome (due to the non-competitive component)

In contrast to the above inhibitors, uncompetitive inhibitors bind only to the enzyme-substrate complex. Therefore, these inhibitors are common in reactions involving two or more substrates and products. Enzyme inhibition is usually abnormal, but cellular metabolism regulation sometimes requires selective inhibition.

The impact of increasing the substrate concentration [S] on the level of inhibition brought on by a specific quantity of inhibitor can also be used to differentiate between these four kinds of inhibition. While the degree of inhibition for noncompetitive (also known as anticompetitive) inhibition remains constant, the degree of inhibition for uncompetitive (also known as anticompetitive) increases with the substrate.

Regulatory enzymes

Any enzyme that regulates the various metabolic processes in the cell by turning them on or off. Both active and inactive regulatory enzymes exist; these include allosteric enzymes, covalently modified enzymes, and zymogen.

Allosteric enzymes

These compounds naturally control enzyme activity in a cell and often exhibit properties similar to reversible noncompetitive inhibitors. Allosteric enzymes bond away from the active site. They change the enzyme’s structure and interfere with the functioning of the active site by conformational changes. In addition, they affect the pathway by reducing the enzyme rate and product concentration.

Covalently modified enzymes

Enzymes can be regulated by covalent modification wherein a molecule (functional group) is transferred from the side chain of the donor amino acid to the acceptor. This will modify enzyme structure, switching the enzyme off or on. Phosphorylation is a common example of covalent modification. Protein kinases transfer a terminal phosphoryl group from ATP onto a residue bearing a hydroxyl group. In this reaction, the substrate molecule receives a phosphate group from the high-energy ATP molecule. Because phosphate groups are negatively charged, they modify the enzyme's charge when they form a covalent bond with the enzyme. This change in charge brings conformational changes in the enzyme, affecting its function. Protein phosphatases can be added to counteract the impacts of protein kinases and phosphorylation.

Zymogen

Zymogens are enzyme precursors that show no catalytic activity. They are also called proenzymes because they can be transformed into enzymes through biochemical change (e.g., hydrolysis). For example, Pepsinogen and trypsinogen are inactive forms (zymogens) secreted by the pancreas. However, pepsinogen converts into pepsin (activated form) when it reacts with stomach acid via hydrolysis, and trypsinogen is activated to trypsin by enterokinase (secreted by the small intestine). Enzymes are fascinating and complex molecules with far-reaching implications in many aspects of our lives.

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