⚗️Chemical Kinetics Unit 8 – Catalysis and Enzyme Kinetics

Key Concepts and Definitions

• Catalysis involves the use of a substance called a catalyst to increase the rate of a chemical reaction without being consumed in the process
• Catalysts work by lowering the activation energy ($E_a$) required for a reaction to occur, allowing it to proceed more quickly and efficiently
• Catalysts provide an alternative reaction pathway with a lower energy barrier, enabling reactants to more easily overcome the energy hurdle and form products
• Catalytic efficiency is a measure of how effectively a catalyst accelerates a reaction and is influenced by factors such as temperature, pressure, and catalyst concentration
• Turnover number (TON) represents the number of moles of substrate that a mole of catalyst can convert before becoming inactivated
  • TON is calculated as the moles of product formed divided by the moles of catalyst used
• Catalytic selectivity refers to a catalyst's ability to preferentially accelerate a specific reaction or produce a desired product when multiple reaction pathways are possible
• Active sites are specific regions on a catalyst's surface where the catalytic reaction takes place, often involving the adsorption and interaction of reactants
• Catalytic cycles describe the series of steps involved in a catalytic reaction, including the binding of reactants, the formation of intermediates, and the release of products

Types of Catalysts

• Homogeneous catalysts are in the same phase as the reactants and products, typically dissolved in a liquid medium (enzymes, organometallic complexes)
  • Advantages include high selectivity, easy mixing, and the ability to operate under milder conditions
  • Disadvantages include difficulty in separating the catalyst from the reaction mixture and potential catalyst instability
• Heterogeneous catalysts are in a different phase than the reactants, often as a solid interacting with liquid or gaseous reactants (supported metal nanoparticles, zeolites)
  • Advantages include easy separation, recyclability, and high thermal stability
  • Disadvantages include lower selectivity and the need for harsher reaction conditions
• Biocatalysts are enzymes or whole cells that catalyze biochemical reactions, offering high specificity and efficiency under mild conditions (lipases, cellulases)
• Organocatalysts are small organic molecules that catalyze reactions through non-covalent interactions (proline, thiourea derivatives)
• Photocatalysts harness light energy to drive chemical reactions, often involving the generation of reactive species (titanium dioxide, ruthenium complexes)
• Electrocatalysts facilitate electrochemical reactions by lowering the overpotential required for electron transfer (platinum, palladium)
• Nanocatalysts leverage the unique properties of nanoscale materials to enhance catalytic performance (gold nanoparticles, carbon nanotubes)

Catalytic Mechanisms

• Catalytic mechanisms describe the detailed steps involved in how a catalyst interacts with reactants to form products
• Adsorption is the process by which reactants bind to the surface of a heterogeneous catalyst, often involving weak van der Waals forces or stronger chemisorption
• Langmuir-Hinshelwood mechanism involves the adsorption of both reactants onto the catalyst surface, followed by their interaction and the formation of products
  • The rate-determining step is often the surface reaction between adsorbed species
• Eley-Rideal mechanism involves the adsorption of only one reactant onto the catalyst surface, which then reacts with a second reactant from the gas or liquid phase
  • The rate-determining step is typically the reaction between the adsorbed species and the non-adsorbed reactant
• Mars-van Krevelen mechanism is common in oxidation reactions and involves the transfer of oxygen from the catalyst to the reactant, followed by the replenishment of oxygen from the gas phase
• Bifunctional catalysis occurs when a catalyst possesses two distinct types of active sites that work cooperatively to facilitate a reaction (metallic and acidic sites in hydrocracking catalysts)
• Catalyst deactivation can occur through various mechanisms, such as poisoning (strong adsorption of impurities), fouling (physical blockage of active sites), and sintering (loss of surface area due to particle growth)

Enzyme Structure and Function

• Enzymes are biological catalysts that are highly specific and efficient, accelerating biochemical reactions under mild conditions
• Enzyme structure consists of amino acid chains folded into a three-dimensional shape, with the active site responsible for catalytic activity
  • The primary structure is the linear sequence of amino acids
  • The secondary structure involves local folding patterns (α-helices and β-sheets)
  • The tertiary structure is the overall three-dimensional shape of a single polypeptide chain
  • The quaternary structure arises from the association of multiple polypeptide subunits
• The active site is a specific region of an enzyme where the substrate binds and the catalytic reaction takes place
  • It is composed of amino acid residues that interact with the substrate through various non-covalent interactions (hydrogen bonding, electrostatic interactions, van der Waals forces)
• Substrate specificity refers to an enzyme's ability to recognize and bind to a specific substrate, determined by the complementary shape and chemical properties of the active site
• Cofactors are non-protein molecules that are required for enzyme function, often serving as electron donors or acceptors (metal ions, coenzymes)
• Enzyme activity is influenced by factors such as temperature, pH, and the concentration of substrates, products, and inhibitors
• Enzyme immobilization involves the attachment of enzymes to solid supports, enhancing their stability and facilitating their recovery and reuse

Michaelis-Menten Kinetics

• Michaelis-Menten kinetics describes the relationship between enzyme concentration, substrate concentration, and reaction rate for many enzymes

• The Michaelis-Menten equation relates the initial reaction velocity ($v_0$) to the maximum velocity ($V_\text{max}$) and the Michaelis constant ($K_\text{M}$):

  $v_0 = \frac{V_\text{max}[S]}{K_\text{M} + [S]}$

  • $[S]$ is the substrate concentration

• $V_\text{max}$ represents the maximum reaction rate achieved when the enzyme is fully saturated with substrate

  • It is directly proportional to the enzyme concentration and the catalytic constant ($k_\text{cat}$)

• $K_\text{M}$ is the substrate concentration at which the reaction rate is half of $V_\text{max}$

  • It is an inverse measure of the enzyme's affinity for the substrate
  • A lower $K_\text{M}$ indicates a higher affinity, as less substrate is required to reach half of the maximum velocity

• The Lineweaver-Burk plot (double-reciprocal plot) is a linear transformation of the Michaelis-Menten equation, allowing for the determination of $V_\text{max}$ and $K_\text{M}$ from experimental data

• Enzyme efficiency is often expressed as the specificity constant ($k_\text{cat}/K_\text{M}$), which measures the catalytic efficiency of an enzyme

• Michaelis-Menten kinetics assumes steady-state conditions, where the concentration of the enzyme-substrate complex remains constant over time

Inhibition and Activation

• Enzyme inhibitors are molecules that decrease the activity of an enzyme by binding to the enzyme and interfering with its function
• Competitive inhibition occurs when an inhibitor binds to the active site of an enzyme, preventing substrate binding
  • The inhibitor competes with the substrate for the active site
  • Increasing substrate concentration can overcome competitive inhibition
• Non-competitive inhibition involves an inhibitor binding to a site other than the active site, causing a conformational change that reduces the enzyme's activity
  • The inhibitor binds equally well to the enzyme and the enzyme-substrate complex
  • Increasing substrate concentration does not reverse non-competitive inhibition
• Uncompetitive inhibition occurs when an inhibitor binds only to the enzyme-substrate complex, not to the free enzyme
  • This type of inhibition is rare and results in a decrease in both $V_\text{max}$ and $K_\text{M}$
• Mixed inhibition is a combination of competitive and non-competitive inhibition, where the inhibitor binds to both the enzyme and the enzyme-substrate complex with different affinities
• Allosteric regulation involves the binding of molecules (activators or inhibitors) to sites other than the active site, causing conformational changes that affect enzyme activity
  • Allosteric activators increase enzyme activity, while allosteric inhibitors decrease it
• Feedback inhibition is a regulatory mechanism in which the end product of a metabolic pathway inhibits the activity of an enzyme earlier in the pathway, controlling the flux of metabolites

Experimental Techniques

• Enzyme assays are used to measure the activity of an enzyme by monitoring the rate of product formation or substrate depletion
  • Spectrophotometric assays measure changes in absorbance due to the formation or consumption of a chromogenic substrate or product
  • Fluorometric assays detect changes in fluorescence intensity resulting from the enzymatic reaction
  • Coupled assays indirectly measure enzyme activity by linking the reaction of interest to a secondary reaction that produces a detectable signal
• Enzyme kinetics experiments involve measuring the initial reaction rates at different substrate concentrations to determine kinetic parameters such as $V_\text{max}$ and $K_\text{M}$
• Enzyme inhibition studies are conducted by measuring enzyme activity in the presence of various concentrations of an inhibitor to determine the type and potency of inhibition
• Site-directed mutagenesis is a technique used to introduce specific mutations into the gene encoding an enzyme, allowing for the study of structure-function relationships
• X-ray crystallography is used to determine the three-dimensional structure of enzymes at atomic resolution, providing insights into the active site and catalytic mechanism
• Isothermal titration calorimetry (ITC) measures the heat released or absorbed during the binding of ligands (substrates, inhibitors) to enzymes, providing thermodynamic information about the interaction
• Stopped-flow techniques enable the rapid mixing of enzymes and substrates, allowing for the study of fast kinetic events and the detection of reaction intermediates

Real-World Applications

• Industrial biocatalysis uses enzymes to catalyze reactions in the production of chemicals, pharmaceuticals, and food ingredients (high-fructose corn syrup, semi-synthetic penicillins)
  • Enzymes offer advantages such as high specificity, mild reaction conditions, and reduced environmental impact compared to traditional chemical processes
• Metabolic engineering involves the modification of enzyme pathways in microorganisms to optimize the production of desired compounds (biofuels, amino acids)
• Enzyme replacement therapy is a medical treatment that involves the administration of functional enzymes to patients with genetic deficiencies (Gaucher disease, Fabry disease)
• Biosensors are analytical devices that use enzymes to detect the presence of specific analytes (glucose, lactate)
  • Enzyme-based biosensors rely on the specific interaction between the enzyme and the target analyte, generating a measurable signal
• Bioremediation employs microorganisms and their enzymes to degrade environmental pollutants (oil spills, pesticides)
• Enzyme immobilization is used in various applications, such as the development of reusable biocatalysts, the design of continuous-flow reactors, and the creation of enzyme-based medical devices
• Directed evolution is a technique used to engineer enzymes with improved properties (stability, activity, specificity) through iterative rounds of mutagenesis and selection
• Enzymes are used in the development of novel biomaterials, such as self-healing polymers and biocompatible scaffolds for tissue engineering