Metabolic

Enzymes are catalysts that accelerate biochemical reactions within cells. They are vital to all metabolic processes, from energy production to DNA replication

Enzymes

• Definition: Biological catalysts that speed up chemical reactions in living organisms. They are proteins with specific three-dimensional structures that enable them to bind to reactants (substrates) and facilitate the conversion of substrates into products
• Importance: Enzymes are essential for life because they allow biochemical reactions to occur at a rate fast enough to sustain life. Without enzymes, many of these reactions would occur too slowly or not at all
• Key Concepts
  • Catalysis: Enzymes lower the activation energy of reactions, increasing the reaction rate without being consumed themselves
  • Specificity: Enzymes are highly specific for their substrates and the reactions they catalyze
  • Regulation: Enzyme activity can be regulated by various factors, including substrate concentration, pH, temperature, inhibitors, and activators

Structure

• Apoenzyme: The protein component of an enzyme. It is inactive without its cofactor
• Cofactor: A non-protein chemical compound that is bound to the apoenzyme and is required for its biological activity. Cofactors can be inorganic ions (e.g., Mg2+, Zn2+) or organic molecules (coenzymes)
• Coenzyme: An organic cofactor. Many coenzymes are derived from vitamins (e.g., NAD+ from niacin, FAD from riboflavin, coenzyme A from pantothenic acid)
• Holoenzyme: The catalytically active enzyme complex, consisting of the apoenzyme and its cofactor

Enzyme-Substrate Interaction

• Active Site: A specific region of the enzyme where the substrate binds and catalysis occurs. The active site is a three-dimensional pocket or cleft formed by amino acid residues
• Binding
  • Enzymes bind to substrates through non-covalent interactions (e.g., hydrogen bonds, hydrophobic interactions, ionic bonds)
  • The enzyme-substrate complex (ES complex) is formed when the substrate binds to the active site
• Models
  • Lock-and-Key Model: The enzyme’s active site is perfectly complementary to the substrate
  • Induced-Fit Model: The enzyme’s active site is flexible and changes shape upon substrate binding to achieve a better fit

Mechanism of Action

• Activation Energy: Enzymes lower the activation energy (Ea) of a reaction, which is the energy required to reach the transition state
• Steps
  1. Substrate Binding: The enzyme binds to the substrate to form the ES complex
  2. Transition State Formation: The enzyme stabilizes the transition state, reducing its energy and facilitating the reaction
  3. Product Formation: The reaction occurs, and the substrate is converted into products
  4. Product Release: The products are released from the enzyme, and the enzyme returns to its original state
• Catalytic Strategies
  • Acid-Base Catalysis: Enzymes use acidic or basic amino acid residues to transfer protons and stabilize intermediates
  • Covalent Catalysis: Enzymes form a temporary covalent bond with the substrate
  • Metal Ion Catalysis: Enzymes use metal ions to stabilize charged intermediates or facilitate redox reactions
  • Proximity and Orientation Effects: Enzymes bring substrates into close proximity and proper orientation for the reaction to occur

Factors Affecting Enzyme Activity

• Substrate Concentration
  • Increasing substrate concentration increases the reaction rate until the enzyme is saturated (all active sites are occupied)
  • Michaelis-Menten Kinetics: Describes the relationship between reaction rate and substrate concentration
    • Vmax: The maximum reaction rate when the enzyme is saturated with substrate
    • Km: The Michaelis constant, representing the substrate concentration at which the reaction rate is half of Vmax
• Enzyme Concentration
  • Increasing enzyme concentration increases the reaction rate (if substrate is not limiting)
• Temperature
  • Enzyme activity increases with temperature up to an optimal temperature
  • Above the optimal temperature, the enzyme denatures and activity decreases
• pH
  • Enzymes have an optimal pH range for activity
  • Extreme pH values can denature the enzyme and abolish activity
• Inhibitors
  • Substances that decrease enzyme activity
  • Reversible Inhibitors: Bind to the enzyme through non-covalent interactions and can be removed
    • Competitive Inhibitors: Bind to the active site and compete with the substrate
    • Noncompetitive Inhibitors: Bind to a site distinct from the active site and reduce enzyme activity
    • Uncompetitive Inhibitors: Bind only to the ES complex
  • Irreversible Inhibitors: Form a stable covalent bond with the enzyme, permanently inactivating it
• Activators
  • Substances that increase enzyme activity
  • Bind to the enzyme and change its conformation, making it more active

Regulation of Enzyme Activity

• Allosteric Regulation: Enzymes have regulatory sites (allosteric sites) where modulators (activators or inhibitors) bind, changing the enzyme’s conformation and activity
• Covalent Modification: Enzymes can be regulated by covalent addition or removal of chemical groups (e.g., phosphorylation, acetylation)
• Proteolytic Activation: Some enzymes are synthesized as inactive precursors (zymogens) that are activated by proteolytic cleavage (e.g., digestive enzymes)
• Gene Expression: The amount of enzyme present in the cell can be regulated by controlling the rate of gene transcription and translation

Enzymes in Metabolic Pathways

• Role: Enzymes catalyze each step in metabolic pathways, ensuring that reactions occur efficiently and in a coordinated manner
• Examples
  • Glycolysis: Enzymes such as hexokinase, phosphofructokinase, and pyruvate kinase regulate glucose breakdown
  • Krebs Cycle: Enzymes such as citrate synthase, isocitrate dehydrogenase, and alpha-ketoglutarate dehydrogenase regulate the Krebs cycle
  • Fatty Acid Synthesis: Enzymes such as acetyl-CoA carboxylase and fatty acid synthase regulate fatty acid synthesis
  • DNA Replication: Enzymes such as DNA polymerase, helicase, and ligase are essential for DNA replication

Key Terms

• Enzyme: A biological catalyst that speeds up chemical reactions
• Substrate: The reactant that an enzyme acts on
• Active Site: The specific region of the enzyme where the substrate binds and catalysis occurs
• Cofactor: A non-protein chemical compound required for enzyme activity
• Coenzyme: An organic cofactor
• Holoenzyme: The catalytically active enzyme complex
• Activation Energy: The energy required to reach the transition state
• Vmax: The maximum reaction rate
• Km: The Michaelis constant, representing the substrate concentration at which the reaction rate is half of Vmax
• Inhibitor: A substance that decreases enzyme activity
• Activator: A substance that increases enzyme activity
• Allosteric Regulation: Regulation of enzyme activity by binding of modulators to allosteric sites
• Covalent Modification: Regulation of enzyme activity by covalent addition or removal of chemical groups
• Zymogen: An inactive precursor of an enzyme
• Metabolic Pathway: A series of interconnected biochemical reactions catalyzed by enzymes
• Kinase: An enzyme that transfers phosphate groups to a molecule (phosphorylates). Most kinases act on hydroxyl groups of serine, threonine, and tyrosine residues of proteins
• Phosphatase: An enzyme that removes a phosphate group from a molecule (dephosphorylates)
• Decarboxylase: An enzyme that removes a carboxyl group from a molecule