🔬Biological Chemistry I Unit 5 – Enzymes – Kinetics and Regulation

What Are Enzymes?

• Enzymes are biological catalysts that speed up chemical reactions in living organisms
• Composed of proteins folded into specific three-dimensional structures
• Catalyze reactions by lowering the activation energy required for the reaction to occur
• Highly specific, each enzyme catalyzes a particular reaction or set of related reactions
• Essential for life, involved in processes such as digestion, metabolism, and DNA replication
• Operate under mild conditions (physiological temperature and pH) unlike many industrial catalysts
• Capable of catalyzing reactions at rates up to 10^17 times faster than uncatalyzed reactions
• Produced by living cells and can be isolated and used in various applications (food processing, medicine, biotechnology)

Enzyme Structure and Function

• Enzymes are primarily composed of amino acids linked together by peptide bonds
• Amino acid sequence determines the unique three-dimensional structure of each enzyme
• Active site is the region where the substrate binds and the catalytic reaction occurs
  • Shaped to fit the specific substrate, often described as a "lock and key" or "induced fit" model
  • Contains amino acid residues that interact with the substrate and facilitate the reaction
• Cofactors are non-protein molecules that some enzymes require for catalytic activity
  • Can be inorganic (metal ions like Fe^2+, Mg^2+, Zn^2+) or organic (coenzymes such as vitamins)
• Enzymes are not consumed during the reaction and can catalyze multiple rounds of the same reaction
• Enzyme activity can be affected by factors such as temperature, pH, and the presence of inhibitors or activators
• Some enzymes have regulatory sites distinct from the active site that modulate their activity

Enzyme Kinetics Basics

• Enzyme kinetics is the study of the rates of enzyme-catalyzed reactions
• Reaction rate depends on the concentration of enzyme, substrate, and any cofactors or inhibitors
• Initial reaction rate ($v_0$) is measured when the substrate concentration is much higher than the enzyme concentration
• Michaelis-Menten kinetics describes the relationship between substrate concentration and reaction rate for many enzymes
  • Assumes a simple two-step reaction: E + S ⇌ ES → E + P
  • $K_m$ (Michaelis constant) is the substrate concentration at which the reaction rate is half of the maximum rate ($V_max$)
• Lineweaver-Burk plot (double reciprocal plot) is used to determine $V_max$ and $K_m$ from experimental data
• Turnover number ($k_cat$) represents the maximum number of substrate molecules converted to product per enzyme molecule per unit time
• Catalytic efficiency ($k_cat/K_m$) is a measure of how efficiently an enzyme converts substrate to product

Michaelis-Menten Equation

• The Michaelis-Menten equation describes the kinetics of many enzyme-catalyzed reactions:
  • $v = \frac{V_max[S]}{K_m + [S]}$
  • $v$ is the reaction rate, $V_max$ is the maximum rate, $[S]$ is the substrate concentration, and $K_m$ is the Michaelis constant
• Assumes a simple two-step reaction mechanism: E + S ⇌ ES → E + P
  • E is the enzyme, S is the substrate, ES is the enzyme-substrate complex, and P is the product
• At low substrate concentrations, the reaction rate is approximately proportional to the substrate concentration (first-order kinetics)
• At high substrate concentrations, the reaction rate approaches $V_max$ and is independent of substrate concentration (zero-order kinetics)
• The Michaelis constant $K_m$ is equal to the substrate concentration at which the reaction rate is half of $V_max$
  • A lower $K_m$ indicates a higher affinity of the enzyme for the substrate
• The turnover number $k_cat$ is related to $V_max$ by the equation: $V_max = k_cat[E]_T$, where $[E]_T$ is the total enzyme concentration

Factors Affecting Enzyme Activity

• Temperature influences enzyme activity by affecting the kinetic energy of molecules and the stability of the enzyme structure
  • Optimal temperature is the temperature at which the enzyme exhibits maximum activity
  • Higher temperatures can denature enzymes, causing a loss of activity
• pH affects enzyme activity by altering the ionization state of amino acid residues in the active site and the enzyme structure
  • Optimal pH is the pH at which the enzyme exhibits maximum activity
  • Extreme pH values can denature enzymes or alter the ionization of key residues
• Ionic strength and the presence of salts can affect enzyme activity by influencing the solubility and stability of the enzyme and substrate
• Substrate concentration affects the reaction rate, as described by the Michaelis-Menten equation
• Product concentration can influence the reaction rate through product inhibition or by shifting the equilibrium of reversible reactions
• Enzyme concentration directly affects the reaction rate, with higher concentrations leading to faster rates until the substrate becomes limiting
• Presence of inhibitors or activators can modulate enzyme activity by binding to the enzyme and altering its structure or function

Enzyme Inhibition and Activation

• Enzyme inhibitors are molecules that decrease enzyme activity by binding to the enzyme
• Competitive inhibitors bind to the active site, competing with the substrate
  • Increase the apparent $K_m$ without affecting $V_max$
  • Can be overcome by increasing the substrate concentration
• Non-competitive inhibitors bind to a site other than the active site, altering the enzyme's structure and function
  • Decrease $V_max$ without affecting $K_m$
  • Cannot be overcome by increasing the substrate concentration
• Uncompetitive inhibitors bind only to the enzyme-substrate complex, not to the free enzyme
  • Decrease both $V_max$ and $K_m$
• Mixed inhibitors can bind to both the free enzyme and the enzyme-substrate complex
  • Affect both $V_max$ and $K_m$, depending on the relative affinities for the free enzyme and the complex
• Enzyme activators are molecules that increase enzyme activity by binding to the enzyme
  • Allosteric activators bind to a site other than the active site, inducing a conformational change that enhances activity
  • Some activators are required for enzyme function, such as certain metal ions or coenzymes

Enzyme Regulation in Cells

• Enzyme activity is tightly regulated in cells to maintain homeostasis and respond to changing conditions
• Allosteric regulation involves the binding of effector molecules to sites other than the active site, modulating enzyme activity
  • Allosteric enzymes often have multiple subunits and exhibit cooperative binding of substrates or effectors
  • Positive cooperativity occurs when the binding of one substrate molecule enhances the binding of subsequent molecules
  • Negative cooperativity occurs when the binding of one substrate molecule reduces the affinity for subsequent molecules
• Covalent modification, such as phosphorylation or acetylation, can regulate enzyme activity by altering the enzyme's structure or function
• Feedback inhibition is a common regulatory mechanism in metabolic pathways
  • The end product of a pathway inhibits the activity of an earlier enzyme in the pathway, preventing excessive production
• Compartmentalization of enzymes within the cell can control their access to substrates and regulate their activity
• Gene expression can be regulated to control the amount of enzyme produced in response to cellular needs
  • Induction is the increased expression of an enzyme in response to the presence of its substrate or other signals
  • Repression is the decreased expression of an enzyme when its activity is not needed

Real-World Applications

• Industrial biocatalysis uses enzymes to catalyze reactions in the production of chemicals, pharmaceuticals, and food ingredients
  • Enzymes offer high specificity, mild reaction conditions, and reduced environmental impact compared to traditional chemical processes
  • Examples include the use of lipases in detergents, proteases in leather processing, and glucose isomerase in high-fructose corn syrup production
• Medical applications of enzymes include diagnostic tests, enzyme replacement therapies, and targeted drug delivery
  • Diagnostic tests measure the activity of specific enzymes to detect diseases (liver function tests, cardiac markers)
  • Enzyme replacement therapies provide functional enzymes to treat genetic disorders (Gaucher disease, Fabry disease)
  • Enzymes can be conjugated to drugs or antibodies for targeted delivery to specific tissues or cells
• Biotechnology and genetic engineering use enzymes for DNA manipulation, protein production, and metabolic engineering
  • Restriction enzymes are used to cut DNA at specific sequences for cloning and gene manipulation
  • DNA polymerases are used in polymerase chain reaction (PCR) to amplify DNA fragments
  • Engineered enzymes can be produced in recombinant organisms for various applications (biofuels, bioremediation)
• Enzymes in agriculture and food processing improve crop yields, food quality, and shelf life
  • Cellulases and amylases are used in animal feed to improve nutrient availability and digestion
  • Pectinases and other enzymes are used in fruit juice clarification and wine production
  • Transglutaminases are used to modify the texture and stability of dairy products and processed meats