Enzymology and Enzyme Structure

Enzymology

• Enzymology is the study of enzymes
• Enzymes are proteins that catalyze specific chemical reactions in biological systems
• Enzymes increase the rate of reactions, lowering the activation energy required
• Enzymes have a specific active site where the substrate binds

Structure of Enzymes

• Active site: the region of an enzyme surface that binds the substrate, also known as the catalytic site
• Catalytic activity depends on the native protein conformation; the surface of the active site is lined with amino acid residues that bind the substrate and catalyze the chemical transformation
• Enzymes increase the speed of reactions

Enzymes Properties

• High specificity; enzymes bind to only one substrate and catalyze a specific reaction
• Efficiency: proximity creates tension between the substrate and catalytic residues; increase the reaction rate in mild conditions, compatible with life
• Enzymatic reactions occur in specialized pockets called active sites
• Under regulation: Some agents can modulate their activity by modifying the active site

How Do Enzymes Work?

• Enzymes lower the activation energy needed for a chemical reaction to occur
• Enzymes decrease the energy needed to reach the intermediate state between reactants and products, improving reaction rates
• Enzymes form a temporary complex (enzyme-substrate complex) with the substrate
• Steps in an enzymatic reaction:
  • Enzyme-substrate complex formation
  • Transition-complex formation from the enzyme-substrate complex
  • Formation of the enzyme-product complex
  • Release of the product and the enzyme

Enzymatic Kinetics

• Study of the rate of reaction and how it changes in response to changes in experimental parameters
• Rate or velocity of a reaction (V): number of substrate molecules converted to product per unit time

Enzymatic Kinetics (External Factors)

• Factors affecting reaction rate:
  • Enzyme concentration
  • Substrate concentration
  • pH
  • Temperature
  • Maximum velocity (Vmax): Maximum rate of a reaction when the enzyme is saturated with substrate

Metabolic Pathways

• Metabolic pathway: sequence of consecutive enzymatic reactions
• Each pathway consists of several reactions with multiple enzymes.
• Each pathway includes one or more enzymes with a significant effect on the rate (velocity) of the overall process.
• Enzymes with a regulatory function are called regulatory enzymes; they undergo changes in activity through mechanisms like allosteric regulation or covalent modification
• Changes in the rate of a metabolic pathway are caused by changes in the regulatory enzymes present within the specific pathway

Regulators of Enzyme Activity (Allosteric Regulation)

• Allosteric regulation: regulatory enzyme with catalytic activity modulated by non-covalent binding of a specific metabolite at a site different from the active site
• Allosteric inhibitor: modulator that distorts the active site to inhibit enzymatic activity
• Allosteric activator: modulator that distorts the active site to improve enzymatic activity

Regulators of Enzyme Activity (Reversible Covalent Modification)

• Reversible covalent modification: enzyme activity is modulated by covalent modifications (e.g., phosphorylation or dephosphorylation)
• Phosphorylation: addition of a phosphate group to an amino acid residue within the enzyme; often a signal for increased activity
• Dephosphorylation: removal of a phosphate group, typically leading to reduced activity
• Hormonal signals like adrenaline, glucagon, or insulin often control these modifications

Regulators of Enzyme Activity (Phosphorylation Cascade)

• Phosphorylation cascade: series of proteins in a pathway where phosphorylation of one protein activates the next, amplifying the signal
• Active Protein Kinase associates with the receptor and initiates a cascade of interactions between proteins

Coenzymes

• Coenzymes: complex organic or metalloorganic molecules; derive from vitamins (e.g., Coenzyme A, NADH, FADH2) or non-vitamins (e.g., Coenzyme Q, NTP)
• Apoenzyme: protein component of an enzyme
• Prosthetic group: non-protein component essential for enzyme function