Enzymes: Catalysis and Factors Affecting Activity

Molecular Components of Living Organisms: Enzymes

Learning Outcomes

This section covers the mechanisms of enzyme action, factors affecting enzyme activity, enzyme assays, kinetic parameters of enzymes and inhibitors, and the characteristics of allosteric enzymes.

Chemical Reactions

A chemical reaction is a process that converts reactants into products. Living organisms rely on these reactions (e.g., digestion, cellular respiration, photosynthesis) to maintain life. Many chemical reactions occur slowly; enzymes are essential to speed up these reactions.

Enzymes

  • Enzymes are proteins, specifically globular proteins, that act as biological catalysts.

  • Enzyme names typically end in "-ase."

  • Enzymes accelerate chemical reactions by lowering the activation energy.

  • Enzymes exhibit specificity, working on specific substrates or related substrates with similar chemical properties.

  • Enzymes speed up reactions, are not consumed in the reaction, and can be used repeatedly.

Activation Energy

Activation energy (E_a) is the energy required to initiate a chemical reaction. Enzymes lower the activation energy, thus increasing the reaction rate. Enzymes do not alter the amount of product formed.

Thermodynamics of Chemical Reactions

The activation energy must be overcome before products are formed. The heat of reaction is the difference between the energy of reactants and products.

  • Exothermic Reaction: Energy of reactants > energy of products, releasing heat.

  • Endothermic Reaction: Energy of products > energy of reactants, absorbing heat.

  • Reactions with low activation energy proceed faster.

  • Catalysts lower activation energy, accelerating the reaction without affecting the energy of products or reactants.

Catalase Enzyme

Catalase converts harmful hydrogen peroxide (H2O2) into water (H2O) and oxygen (O2). This prevents damage to cells and tissues.

Catalytic Efficiency

Enzymes reduce activation energy needed for reactions. For example, the decomposition of hydrogen peroxide:

2H2O2 \rightarrow 2H2O + O2

  • Uncatalyzed reaction: E_a = 18 kcal/mol

  • Catalyzed reaction (with catalase): E_a = 5 kcal/mol

Without an enzyme, this conversion takes 115 days. With catalase, it takes 1 second.

Calculation of rate increase:

  • 1 minute = 60 seconds

  • 1 hour = 60 minutes x 60 seconds = 3600 seconds

  • 1 day = 24 hours x 3600 seconds = 86,400 seconds

  • 115 days x 86,400 seconds = 9,936,000 seconds

  • Speed increase = 9,936,000 / 1 = 1 \times 10^7 times faster with catalase.

Enzyme Mechanisms

Enzymes bind to reactant molecules, facilitating bond-breaking and bond-forming processes. Enzymes bind to one or more reactant molecules called substrates. The active site is where the substrate binds and the catalytic action occurs.

Enzyme Active Site

The active site includes:

  1. Binding site: Amino acids that form temporary bonds with the substrate.

  2. Catalytic site: Site where the substrate reaction occurs.

Some enzymes require non-protein components called cofactors (metal ions or coenzymes). An enzyme-cofactor complex is called a holoenzyme. Without the cofactor, the remaining protein is an apoenzyme, which is catalytically inactive.

Enzyme Specificity

Enzyme specificity is determined by the arrangement of amino acids in the active site and the structure of the substrates.

  • Absolute specificity: Enzyme reacts with only one substrate.

  • Group specificity: Enzyme acts on a group of similar substrates.

  • Linkage specificity: Enzyme acts on a specific bond type.

Steps in a Reaction

  1. Enzyme (E) + Substrate (S) \rightarrow Enzyme-Substrate complex (ES)

  2. Chemical change of substrate \rightarrow Enzyme-Product complex (EP)

  3. Enzyme (E) + Product (P) dissociate, regenerating the enzyme

Example

Sucrose is hydrolyzed by sucrase into glucose and fructose.

  • Substrate: Sucrose

  • Products: Glucose + Fructose

  • Enzyme: Sucrase

Models of Enzyme Activity

Lock and Key Model

Proposed by Emil Fischer in 1894, this early model suggests a rigid substrate binds to a rigid enzyme, like a key fitting into a lock. It assumes no change in enzyme shape during the reaction.

Induced Fit Model

Proposed by Daniel Koshland in 1958, this model suggests a flexible active site that changes shape as the substrate binds and is correctly oriented. Hexokinase and glucose forming an enzyme-substrate complex is a good example.

How Enzymes Increase Reaction Rates

  1. Proximity: Enzymes bring reactants closer, increasing the likelihood of a reaction.

  2. Orientation: Enzymes bind substrates in the correct orientation for a reaction, positioning reactive groups appropriately.

  3. Strain: Enzymes weaken substrate bonds, lowering the activation energy.

  4. Catalytic Functional Groups: Amino acids in the active site facilitate catalysis through covalent catalysis (transient covalent bonds) and acid-base catalysis (proton donors and acceptors).

Naming Enzymes

Enzyme names usually end in "-ase" (e.g., sucrase acts on sucrose). Some enzymes have common names (e.g., pepsin, trypsin). The name often identifies the reacting substance or describes the enzyme's function (e.g., oxidases catalyze oxidation reactions).

Enzyme Classification

The Enzyme Commission classification system assigns a systematic name and a unique four-digit number to each enzyme. Enzymes are classified into six groups based on the type of reaction they catalyze:

  1. Oxidoreductases: Catalyze oxidation-reduction reactions.

  2. Transferases: Transfer functional groups.

  3. Hydrolases: Catalyze hydrolysis reactions (break down bonds using H2O).

  4. Lyases: Add or remove atoms to form a double bond.

  5. Isomerases: Rearrange atoms (isomerization).

  6. Ligases: Form bonds and synthesize larger molecules.

Factors Affecting Enzyme Activity

  • pH

  • Temperature

  • Substrate concentration

  • Enzyme concentration

  • Inhibitors

  • Water activity

Temperature and Enzyme Activity

Enzymes have an optimum temperature at which they are most active. In humans, this is around 37°C. Activity increases with temperature up to the optimum, then declines. Enzymes can become denatured at high temperatures, ceasing activity.

pH and Enzyme Activity

Each enzyme has an optimum pH at which it performs best. Activity decreases on either side of this optimum pH. Extremes of pH can denature the enzyme or affect the charge of critical amino acids in the active site. The physiological pH in the human body is around 7.4, but some organs have enzymes that operate at different pH values.

Enzyme Concentration and Enzyme Activity

Generally, reaction rate increases with enzyme concentration. At a constant substrate concentration, the reaction rate is proportional to the amount of enzyme. Higher enzyme concentration increases the likelihood of enzyme-substrate collisions, speeding up the reaction.

Substrate Concentration and Enzyme Activity

At a constant enzyme concentration, the reaction rate increases with substrate concentration until the enzyme is saturated, and maximum activity is achieved.