2. Ензими.pdf

# Chemical nature and mechanism of enzyme catalysis Enzymes are protein-based biological catalysts that significantly accelerate biochemical reactions within living systems [1](#page=1). ### 1.1 Chemical nature of biological catalysts Every cell continuously carries out hundreds of biochemical reactions with high coordination and speed, a process facilitated by catalysts with specific characteristics known as biological catalysts. These biological catalysts include proteins with catalytic functions called enzymes, as well as certain RNA molecules with catalytic functions termed ribozymes [1](#page=1). Enzymes are substances of protein nature that speed up chemical reactions in living systems. For instance, the hydrolysis of sucrose in distilled water at room temperature can take years, whereas cells accomplish the same reaction rapidly with the aid of the enzyme invertase [1](#page=1). At the tertiary structure level, enzymes are globular proteins. They perform their catalytic action through their active site, also referred to as the catalytic center [1](#page=1). Enzymes can be classified based on their composition: * **Single-component enzymes**: These enzymes are entirely proteinaceous, constructed from one or more polypeptide chains. An example of a single-component enzyme is the digestive enzyme lactase [1](#page=1). * **Two-component enzymes**: In addition to a protein component, these enzymes possess a non-proteinaceous constituent. This non-proteinaceous part integrates into the active site. These non-proteinaceous components bind either firmly or loosely and reversibly to the protein part. Firmly bound non-proteinaceous components are termed prosthetic groups, while those associated with weaker bonds to the protein component are called coenzymes [1](#page=1). ### 1.2 Mechanism of enzyme catalysis Enzymes share properties with non-biological catalysts but are distinguished by important peculiarities: they operate at normal temperatures, are specific towards substances and reaction types, and their activity is influenced by various factors [2](#page=2). #### 1.2.1 General properties of enzymes compared to inorganic catalysts | General Properties of Enzymes with Inorganic Catalysts | Specific Properties of Enzymes | | :----------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------- | | Change the rate of chemical reactions. | Operate at normal temperatures. Their activity decreases at very high or very low temperatures. | [2](#page=2). | Do not change the direction of the reaction. | Act selectively with respect to the substrate and the type of reaction they catalyze – they are specific. | [2](#page=2). | Operate in small quantities and remain unchanged at the end of the reaction. | Their activity is altered by various environmental factors and substances (effectors). | [2](#page=2). | Influence only reactions that occur even without a catalyst. | They are more potent than chemical catalysts. | [2](#page=2). | Overcome the energy barrier by proceeding through an alternative pathway with lower activation energy. | | #### 1.2.2 The role of the active site and substrate The catalytic center of each enzyme contains functional groups that correspond to its substrate – the substance it modifies. Therefore, the mechanism of enzyme catalysis is described as a mechanism of spatial correspondence, often compared to a lock and key, visually represented by complementary shapes [2](#page=2). At the beginning of an enzyme-catalyzed reaction, the starting material, the substrate (S), binds to the enzyme's active site (E), forming an enzyme-substrate complex (ES). Within this complex, covalent bonds in the substrate are broken, and new bonds characteristic of the product are formed. Subsequently, the ES complex transforms into an enzyme-product complex (EP). Finally, the product (P) is released from the enzyme. The enzyme remains unchanged and is then available to bind another substrate molecule [2](#page=2). The enzyme reaction can be summarized as: $$E + S \leftrightarrow ES \rightarrow EP \rightarrow E + P$$ [2](#page=2). > **Tip:** The equation $E + S \leftrightarrow ES \rightarrow EP \rightarrow E + P$ is a fundamental representation of enzyme kinetics and mechanism. Remember that 'E' is the enzyme, 'S' is the substrate, 'ES' is the enzyme-substrate complex, 'EP' is the enzyme-product complex, and 'P' is the product. The reversibility ($ \leftrightarrow $) is indicated for the initial binding step, while the arrow ($ \rightarrow $) signifies the catalytic transformation. #### 1.2.3 Activation energy Life processes are the result of a vast number of chemical reactions. Most of these reactions do not proceed at a noticeable rate at normal temperatures because the starting materials require a certain amount of activation energy to participate in the reaction. While activation energy can be easily provided by heating, this method, common in chemistry, is incompatible with life, as proteins denature at high temperatures [3](#page=3). Catalysts are substances that alter the rate of chemical reactions. Most substances accelerate reactions by "proceeding through an alternative pathway" with lower activation energy [3](#page=3). For any reaction to occur, the reacting substances need energy. For interaction between molecules (breaking or forming chemical bonds), they must reach an energetic state that creates a probability for their encounter, ultimately leading to new molecules. The difference between the average energy of molecules and the energy required for a chemical reaction is called activation energy. With the involvement of enzymes, the reaction proceeds through energetically more economical pathways [3](#page=3). > **Note:** Enzymes are crucial for life because they allow essential biochemical reactions to occur at biologically compatible temperatures by lowering the activation energy. Without them, these reactions would be too slow to sustain life. --- # Factors influencing enzyme activity Enzyme activity is influenced by several factors, including substrate concentration, pH, and temperature, all of which affect the rate of the enzymatic reaction [3](#page=3) [4](#page=4). ### 2.1 Impact of substrate concentration The rate of an enzyme-catalyzed reaction increases with increasing substrate concentration, but this increase is not indefinite. Initially, as substrate concentration rises, the reaction rate increases rapidly. However, the rate eventually plateaus and reaches a maximum velocity ($V_{max}$), after which further increases in substrate concentration do not lead to a significant change in reaction speed [3](#page=3). #### 2.1.1 Saturation of active sites This plateau occurs because at high substrate concentrations, all the enzyme's active sites become saturated with substrate molecules, forming enzyme-substrate complexes. An active site can only bind a new substrate molecule after the product has been released and the site is free again [3](#page=3). ### 2.2 Impact of pH and temperature #### 2.2.1 Optimal conditions Enzyme activity is also significantly influenced by pH and temperature. For each enzyme, there are specific optimal pH and temperature values at which the reaction rate is maximized. These optimal conditions are enzyme-specific and generally fall within relatively narrow ranges [4](#page=4). #### 2.2.2 Effect of temperature In uncatalyzed reactions, reaction rates generally continue to increase with increasing temperature. However, for enzyme-catalyzed reactions, the rate increases with temperature only up to a certain point. Beyond this optimal temperature, the enzyme's activity rapidly declines due to denaturation [4](#page=4). #### 2.2.3 Denaturation Denaturation is a process where the enzyme loses its three-dimensional structure, which is crucial for its function. High temperatures can cause proteins, including enzymes, to denature. This loss of functional structure leads to a loss of enzymatic activity [3](#page=3) [4](#page=4). > **Tip:** Understanding optimal conditions and the point of denaturation is critical for predicting enzyme behavior in biological systems and for various industrial applications. > **Example:** Many human enzymes function optimally around a pH of 7.4 and a body temperature of approximately 37 degrees Celsius. Enzymes in the stomach, like pepsin, have a much lower optimal pH due to the acidic environment. --- # Regulation and control of enzyme activity Enzyme activity within cells is precisely controlled through mechanisms of activation and inhibition to regulate biochemical reactions [5](#page=5). ### 3.1 Enzyme activators and inhibitors Enzyme activity can be modulated by activators and inhibitors. Metal ions such as calcium, manganese, and copper can act as activators. However, the primary focus in cellular regulation is on inhibition, which allows for the control of specific biochemical reactions [5](#page=5). #### 3.1.1 Irreversible inhibition Irreversible inhibition occurs when inhibitors bind permanently to the enzyme. This typically involves heavy metal ions that cause denaturation of the enzyme, rendering it inactive in cellular metabolism [5](#page=5). #### 3.1.2 Reversible inhibition Reversible inhibition involves a temporary binding between the inhibitor and the enzyme. This allows for the potential restoration of enzyme activity once the inhibitor is removed [5](#page=5). ### 3.2 Competitive inhibition Competitive inhibition is a type of reversible inhibition where the substrate and the inhibitor contend for the enzyme's active site [5](#page=5). * **Mechanism:** The inhibitor (I) and the substrate (S) have similar structures and compete to bind to the enzyme's active center [5](#page=5). * **Outcome:** A high concentration of the inhibitor can lead to it binding to the active site, forming an inactive enzyme-inhibitor (EI) complex [5](#page=5). * **Reversibility:** If the concentration of the product of the enzymatic reaction is low, the inhibitor may detach, and the enzyme's activity can be restored [5](#page=5). > **Tip:** Visualizing the competition between the substrate and inhibitor for the active site is key to understanding this mechanism [5](#page=5). ### 3.3 Allosteric regulation Allosteric regulation controls enzyme activity by the binding of molecules to a site distinct from the active site, known as the allosteric site. These molecules are called allosteric effectors [5](#page=5). #### 3.3.1 Allosteric effectors Allosteric effectors induce a change in the native conformation of the enzyme's active site. Depending on the type of change, these effectors can be either allosteric activators or allosteric inhibitors [5](#page=5). #### 3.3.2 Allosteric inhibition In allosteric inhibition, an inhibitor binds to the allosteric site. This binding alters the enzyme's spatial structure, causing the active site to change shape. As a result, the active site can no longer bind to the substrate. The enzyme's activity is restored when the inhibitor detaches, which may occur when the product is needed [5](#page=5). #### 3.3.3 Allosteric activation Some enzymes are only active when an allosteric activator binds to their allosteric site [5](#page=5). > **Tip:** Allosteric regulation allows for finer control of enzyme activity, influencing it through sites other than the direct substrate-binding site [5](#page=5). ### 3.4 Feedback inhibition (retroinhibition) Feedback inhibition, also known as retroinhibition, is a common regulatory mechanism where the end product of a metabolic pathway inhibits an enzyme earlier in that pathway [6](#page=6). * **Mechanism:** When significant amounts of the final product accumulate, it acts as an inhibitor for the first enzyme in the sequence. For example, if product 'D' is the final product, and enzyme 1 catalyzes the first step, high concentrations of 'D' can block enzyme 1 [6](#page=6). * **Self-regulation:** This mechanism enables self-regulation of numerous biochemical reactions within the cell [6](#page=6). * **Broader implications:** Because most metabolic pathways are branched, feedback inhibition allows for the production of various end products [6](#page=6). > **Example:** In a pathway A $\rightarrow$ B $\rightarrow$ C $\rightarrow$ D, if product D builds up, it can inhibit the enzyme that converts A to B, thus controlling the overall production of D and potentially allowing for the accumulation of intermediate products like C or M if alternate pathways exist [6](#page=6). ### 3.5 Enzyme nomenclature and classification Enzymes are typically named with a suffix "-ase" appended to the name of the substrate or the reaction type they catalyze. Exceptions include historically discovered enzymes like pepsin and trypsin [6](#page=6). The International Union of Biochemistry and Molecular Biology (IUBMB) classifies enzymes into six main groups based on their catalytic mechanisms [6](#page=6): 1. **Oxidoreductases:** Catalyze oxidation-reduction reactions [6](#page=6). 2. **Transferases:** Transfer functional groups from one molecule to another [6](#page=6). 3. **Hydrolases:** Catalyze hydrolysis reactions (breaking bonds using water) [6](#page=6). 4. **Lyases:** Catalyze the cleavage of chemical bonds without hydrolysis or oxidation, often forming double bonds [6](#page=6). 5. **Isomerases:** Catalyze isomerization reactions, rearranging atoms within a molecule [6](#page=6). 6. **Ligases (Synthetases):** Catalyze the formation of covalent bonds between two molecules, typically requiring energy input [6](#page=6). --- # Enzyme nomenclature and classification Enzymes are named according to established conventions, typically ending in "-ase", and are classified into six main groups based on their catalytic functions [6](#page=6). ### 4.1 Naming conventions for enzymes Enzymes are generally given names that describe their function and commonly end with the suffix "-ase". However, some early-discovered and well-studied enzymes are exceptions to this rule, such as pepsin and trypsin [6](#page=6). ### 4.2 International classification of enzymes The International Union of Biochemistry and Molecular Biology (IUBMB) has established an internationally accepted classification system for enzymes. This system categorizes enzymes into six primary groups based on the type of catalytic reaction they perform [6](#page=6). #### 4.2.1 The six main enzyme classes The six main classes of enzymes and their primary catalytic functions are as follows [6](#page=6): 1. **Oxidoreductases:** Catalyze oxidation-reduction reactions [6](#page=6). 2. **Transferases:** Catalyze the transfer of functional groups from one molecule to another [6](#page=6). 3. **Hydrolases:** Catalyze hydrolysis reactions, which involve the breaking of chemical bonds using water [6](#page=6). 4. **Lyases:** Catalyze the cleavage of chemical bonds by elimination, leading to the formation of double bonds or rings, or the addition of groups to double bonds [6](#page=6). 5. **Isomerases:** Catalyze intramolecular rearrangements, converting a molecule into one of its isomers [6](#page=6). 6. **Ligases (Synthetases):** Catalyze the formation of covalent bonds between two molecules, usually coupled with the hydrolysis of ATP or another nucleoside triphosphate [6](#page=6). > **Tip:** Understanding these six classes provides a foundational framework for comprehending the vast array of enzymatic reactions occurring in biological systems. When encountering a new enzyme, its classification can often predict its general function [6](#page=6). --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |------|------------| | Biological catalysts | Substances that accelerate biochemical reactions in living systems. Enzymes are the primary biological catalysts, composed of proteins, though some RNA molecules (ribozymes) also exhibit catalytic functions. | | Enzymes | Biological catalysts that are protein in nature and significantly increase the speed of chemical reactions within living organisms. They are essential for life processes, enabling reactions that would otherwise be too slow. | | Ribozymes | RNA molecules possessing catalytic activity, meaning they can speed up biochemical reactions. They represent a class of biological catalysts distinct from protein-based enzymes. | | Active center | A specific region on the enzyme molecule, also known as the catalytic center, where the substrate binds and the chemical reaction is catalyzed. It contains functional groups precisely shaped to interact with the substrate. | | Globular proteins | Proteins that have a compact, roughly spherical shape. Enzymes, at their tertiary structure level, are typically globular proteins, which contributes to their three-dimensional structure and active site formation. | | Unicomponent enzymes | Enzymes that are composed solely of protein. Their catalytic function is entirely dependent on their polypeptide chains. An example is the digestive enzyme lactase. | | Bicomponent enzymes | Enzymes that consist of a protein component and a non-protein component. The non-protein component is crucial for the active site's function and can be tightly bound as a prosthetic group or loosely bound as a coenzyme. | | Prosthetic groups | Non-protein components that are tightly and permanently bound to the protein part of a bicomponent enzyme. They are essential for the enzyme's catalytic activity. | | Coenzymes | Non-protein molecules that are weakly and reversibly bound to the protein component of a bicomponent enzyme. They assist in the catalytic process, often acting as carriers of specific chemical groups. | | Substrate | The molecule upon which an enzyme acts. The substrate binds to the enzyme's active site, and the enzyme facilitates its conversion into a product. | | Enzyme-substrate complex | A temporary complex formed when a substrate molecule binds to the active site of an enzyme. This binding is specific and is a crucial intermediate step in enzyme-catalyzed reactions. | | Enzyme-product complex | A transient complex formed after the substrate has undergone chemical transformation within the active site but before the product is released from the enzyme. | | Activating energy | The minimum amount of energy required for reactant molecules to initiate a chemical reaction. Enzymes lower the activation energy, thereby speeding up reactions without being consumed. | | Denaturation | The process by which the three-dimensional structure of a protein, including enzymes, is disrupted, leading to a loss of its biological function. This can be caused by factors like extreme pH or high temperatures. | | Vmax | The maximum rate of an enzyme-catalyzed reaction. It is reached when the enzyme's active sites are saturated with substrate. Further increases in substrate concentration do not increase the reaction rate. | | Allosteric center | A site on an enzyme, distinct from the active site, where regulatory molecules (allosteric effectors) can bind. This binding can alter the enzyme's conformation and thus its activity. | | Allosteric effectors | Molecules that bind to an allosteric center of an enzyme, modulating its activity. They can act as either activators or inhibitors. | | Competitive inhibition | A type of enzyme inhibition where an inhibitor molecule competes with the substrate for binding to the enzyme's active site. The inhibitor's effect can be overcome by increasing substrate concentration. | | Retroinhibition (Feedback inhibition) | A regulatory mechanism where the end product of a metabolic pathway inhibits an enzyme that catalyzes an earlier step in the same pathway. This prevents the overproduction of the end product. | | Oxidoreductases | A class of enzymes that catalyze oxidation-reduction reactions. They are involved in electron transfer processes within cells. | | Transferases | A class of enzymes that catalyze the transfer of functional groups from one molecule to another. Examples include kinases that transfer phosphate groups. | | Hydrolases | A class of enzymes that catalyze hydrolysis reactions, which involve the breaking of chemical bonds by the addition of water. Digestive enzymes like proteases and lipases are hydrolases. | | Lyases | A class of enzymes that catalyze the cleavage of chemical bonds by means other than hydrolysis or oxidation, often forming double bonds or rings. | |isomerases | A class of enzymes that catalyze intramolecular rearrangements within a single molecule, such as the conversion of one isomer to another. | | Ligases (Synthetases) | A class of enzymes that catalyze the formation of new chemical bonds between two molecules, typically requiring energy in the form of ATP. They are involved in synthesis and joining processes. |