Enzymes and Coenzymes PDF

## Enzymes et Coenzymes ### E chapitre - **Un catalyseur** - A substance that, in small quantities, allows for the acceleration of a thermodynamically possible reaction. - The catalyst is recovered in the same state it was at the start of the reaction (intact). - Catalysts do not change t...

## Enzymes et Coenzymes ### E chapitre - **Un catalyseur** - A substance that, in small quantities, allows for the acceleration of a thermodynamically possible reaction. - The catalyst is recovered in the same state it was at the start of the reaction (intact). - Catalysts do not change the equilibrium of the reaction. - **Enzymes** - Catalysts of the living world (the human organism). ### I. Properties générales - **Structure** - The majority of enzymes in the biological world are of a protein nature. - All properties of proteins apply to enzymes. - **Catalysis** - Enzymes accelerate the rate of thermodynamically possible reactions by a factor greater than 10^6. - **Energy of activation** - Enzymes, as catalysts, lower the energy of activation in a reaction. - To predict whether a reaction will occur, it is necessary to know the energy level of the reactant (substrate) and the energy level of the product. - **If the substrate's energy level is higher than that of the product, the reaction will be possible.** - **How does an enzyme lower the energy of activation?** - **Active site** - The enzyme has a catalytic site, which allows it to interact with the substrate and stabilise it. - The amino acids of the active site aren't close together in the protein sequence (primary structure), but they are close in space (tertiary structure). - **Groups** - **Group 1:** Responsible for substrate fixation. - **Group 2:** Responsible for catalysis. - **If there are two substrates:** - In the absence of a catalyst, the probability of two substrates A and B coming into direct contact is very low. - In the presence of an enzyme, the enzyme attracts the substrates and brings them in the right position for catalysis (in a reactive position), therefore increasing the probability of reaction. ### 3. Specificity Enzymatic - **Specificity of action:** An enzyme can only catalyze one specific type of chemical reaction. - Types of reactions: 1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases - **Specificity of substrate:** An enzyme catalyzes a reaction on a certain type of chemical substrate. - **Group and stereochemical specificity** play a role in this process. - **Examples of specificity:** 1. **Oxidoreductase** - A reduced + B oxidized -> A oxidized + B reduced 2. **Transferase** - A-B + C -> A + B-C 3. **Hydrolase** - A-B + H₂O -> A-H + B-OH 4. **Lyase** - A-B -> A + B 5. **Isomerase** - A-B -> iso-A-B 6. **Ligase** - A-B + molecule (ATP) -> A-B + XDP (energy) - **Can the same enzyme catalyze both hydrolysis and isomerization reactions?** - No. This is limited by the specificity of action. - **Can the same enzyme catalyze the hydrolysis of an ester bond and of a peptide bond?** - No. This is limited by the specificity of substrate. ### II. Activité Enzymatic - Definition: Enzyme activity or velocity is the amount of substrate that disappears (or product that appears) per unit of time. - **Formulas:** - V = -d[S]/dt - V = d[P]/dt - V = UI (unit) - V = Kat (unit) - **A graph of enzyme activity over time shows:** - **Values are null initially:** As there is no substrate. - **Values rise to a maximum:** As there is substrate present. - **Values return to zero:** Once all the substrate has been consumed. - **Scenario:** What happens when there are three isoenzymes? - **Isoenzymes** - These have similar activity and substrate specificities, but they show slight differences in structure. - The best way to compare their actions is to perform the comparison under identical conditions. ### III. Influence of Different Parameters - **Influence of pH:** - Enzyme activity is optimal at a specific pH value. - Deviation from this optimum results in a decrease in enzyme activity. - This decrease in activity is due to enzyme denaturation (changes in the 3D structure). - The human organism must maintain a stable pH to ensure proper enzyme function. - **Influence of Temperature:** - Enzyme activity is optimal at a specific temperature. - An asymmetric curve represents the relationship between temperature and activity, showing an increase in activity with a rise in temperature up to an optimal point. - Beyond the optimal temperature, enzyme activity drops, showing that the enzyme is being denatured. - **Influence of Enzyme Concentration:** - Enzyme activity increases with enzyme concentration. - There is a point of saturation where further increases in enzyme concentration do not increase the reaction rate and all the active sites are occupied. - **Influence of Substrate Concentration:** - Increasing substrate concentration generally leads to an increase in enzyme activity. - Two cases are observed: 1. **Hyperbola shape:** The reaction rate increases proportionally to substrate concentration until the active sites are saturated. - In this case, the maximum reaction velocity is reached. - The equation for this branch of the hyperbola is: **V = V_max[S] / K_m + [S]** 2. **Sigmoidal shape:** In this case, the active sites are cooperative, meaning binding of a substrate molecule to one site affects the binding affinity of other sites. - Increased substrate concentration leads to an initial slow increase in activity, followed by a steeper increase and finally, a plateau, reaching the maximum velocity. - **K_m:** Is the Michaelis-Menten constant, representing the substrate concentration at half the maximum velocity. - It is interpreted as a measure of how much substrate is needed to saturate the enzyme. - **A lower K_m means higher affinity**. ### IV. Enzymes and Metabolic Regulation - **How can you modulate enzyme activity?** - **Changing the amount of enzyme:** - **Increase enzyme levels:** By increasing synthesis or decreasing degradation. - **Decrease enzyme levels:** By decreasing synthesis or increasing degradation. - **Changing the amount of substrate:** - **Regulating the catalytic activity:** - Allosteric effect: When the effector binds to the enzyme at a site other than the active site, it affects enzyme activity. - The effector can be an activator or an inhibitor. - Covalent modification: When a molecule binds to the enzyme via a covalent bond, modifying its activity. - This is typically done by phosphorylation (adding a phosphate group), often catalyzed by a Kinase. ### V. Activation Proteolytic - This is a type of activation where a portion of the enzyme is removed via a proteolytic effect, thereby exposing the active site, allowing the substrate to bind more easily, and increasing enzyme activity. ### I. Inhibition Enzymatic - **Reversible inhibition:** When the inhibitor binds reversibly to the enzyme, partially or completely inhibiting it. - **Irreversible inhibition:** When the inhibitor binds irreversibly to the enzyme, resulting in permanent inactivation. - **Types of reversible inhibition:** - **Competitive:** The inhibitor competes with the substrate for binding to the active site. - **Effect:** It increases K_m, reducing enzyme affinity for the substrate. - **Mechanism:** By competing with the substrate for the active site, the competitive inhibitor reduces the proportion of enzyme molecules bound to the substrate. - **Noncompetitive:** The inhibitor binds to the enzyme at a site other than the active site, altering its conformation and reducing its activity. - **Effect:** It decreases V_max, reducing the maximum velocity of the reaction. ### VI. Coenzymes - **Functions as cofactors:** - Non-protein components needed for enzyme activity. - They can be inorganic ions or organic molecules. - **Types:** - **Cosubstrates:** Loosely bound to the enzyme and modified during a reaction, then released. - **Prosthetic group:** Tightly bound to the enzyme, often permanently attached. - **Cosubstrates:** - They act as carriers of functional groups or electrons in metabolic reactions. - **Examples:** NAD, FAD, NADP, B3, PP - **Characteristics:** - They can be modified and released from the enzyme after the reaction. - They are not permanently bound to the enzyme. - **Prosthetic groups:** - They are tightly bound to the enzyme often as the prosthetic group. - They may be modified during a reaction but remain bound to the enzyme. - **Examples:** The heme group in haemoglobin, riboflavin in some enzymes. ### VII. Coopérativité - **Allosteric regulation:** - This refers to the regulation of enzyme activity by the binding of an effector molecule to a site other than the active site. - The binding of the effector can either activate or inhibit the enzyme. - **Cooperative binding:** - Occurs when the binding of one substrate molecule to an enzyme affects the binding affinity of other substrate molecules to the enzyme. - This can lead to a sigmoidal-shaped curve for the enzyme's activity versus substrate concentration. - **Characteristics:** - **Sigmoidal kinetics:** The enzyme's activity does not increase linearly with substrate concentration, but rather shows a sigmoidal shape. - **Cooperative binding:** The binding of one substrate molecule to the enzyme affects the binding affinity of other substrate molecules. - **Allosteric regulation:** The enzyme's activity can be regulated by the binding of effector molecules at sites other than the active site. - **Examples of cooperative enzymes:** - **Hemoglobin:** The binding of oxygen to one heme group increases the affinity of the other heme groups for oxygen. - **Aspartate transcarbamoylase:** This enzyme is involved in the synthesis of pyrimidine nucleotides. It is regulated by the binding of CTP (a product of the pathway) and ATP (a substrate of the pathway). - **Importance of cooperative binding:** - Allows enzymes to respond to changes in substrate concentration more efficiently. - Enables the enzyme to be regulated more precisely by allosteric effectors. - **Applications of cooperative binding:** - In metabolic pathways, cooperative binding can help to ensure that the pathway is regulated in a coordinated and efficient manner. - In cellular signaling pathways, cooperative binding can help to amplify and fine-tune the response to a signal. - **In general:** - Enzymes that exhibit cooperative binding display a more complex and sophisticated regulation of their activity, allowing for greater fine-tuning and responsiveness to changes in the cellular environment.