Enzymes: Specificity and Structure

• Enzymes are biological molecules accelerating chemical reactions within cells
• Enzymes are vital for life, aiding digestion and metabolism
• Typically proteins, some are catalytic RNA molecules

Enzyme Specificity

• Enzymes bind to specific substrates, catalyzing single or related reactions
• Specificity arises from the unique 3D structure of the active site
• The active site's shape and chemistry allow binding to certain substrates
• Correct reactions are catalyzed, preventing unwanted side reactions
• Enzyme specificity is essential for proper biological function

Enzyme Structure

• Enzymes are globular proteins varying in size
• Amino acid sequence and structure determine enzyme specificity
• Denaturation or dissociation into subunits can cause enzyme activity loss
• Some enzymes need no additional components for full activity
• Others require cofactors (inorganic or organic) or coenzymes (organic, from vitamins)
• Prosthetic groups are tightly bound coenzymes
• Holoenzymes form when enzymes covalently bind a coenzyme to the protein
• Apoenzymes lack a required cofactor or coenzyme

Mechanism of Action

• Enzymes lower the activation energy of reactions
• Activation energy is the energy required for a reaction to start
• Enzymes bind to substrates, forming enzyme-substrate complexes
• The enzyme-substrate complex is more stable, lowering activation energy
• Enzymes provide a specific environment for reactions
• The active site is a pocket shaped to bind the substrate
• Active sites might contain amino acid side chains (catalytic groups)
• Enzymes release products after the reaction, ready for another reaction

Factors Affecting Enzyme Activity

• Enzyme activity is influenced by Temperature, pH, substrate concentration, enzyme concentration, inhibitors, and activators
• Temperature
  • Each enzyme has an optimal temperature.
  • Reaction rate increases with temperature, up to a point.
  • High temperatures denature enzymes
• pH
  • Enzymes function best at an optimal pH
  • pH changes affect the ionization of active site amino acids
• Substrate Concentration
  • Reaction rate increases with substrate concentration until enzyme saturation
• Enzyme concentration
  • Reaction rate increases with enzyme concentration, given sufficient substrate
• Inhibitors
  • Inhibitors decrease enzyme activity
  • Competitive inhibitors bind to the active site, preventing substrate binding
  • Noncompetitive inhibitors bind elsewhere, changing the active site's shape
  • Uncompetitive inhibitors bind to the enzyme-substrate complex
• Activators
  • Activators increase enzyme activity
  • Activators facilitate substrate binding or change the active site's shape

Enzyme Regulation

• Enzyme regulation controls enzyme activity
• Regulation maintains homeostasis and coordinates metabolic pathways
• Mechanisms include allosteric regulation, covalent modification, proteolytic cleavage, enzyme synthesis and degradation, and compartmentalization
• Allosteric regulation
  • A molecule binds to an enzyme, changing its shape and activity (can be activators or inhibitors)
• convalent modification
  • Adding/removing a chemical group changes enzyme activity
  • Common modifications: phosphorylation, acetylation, methylation
• Proteolytic cleavage
  • Protein cleavage activates/inactivates enzymes
• Enzyme synthesis and degradation
  • Regulating synthesis and degradation controls enzyme availability
• Compartmentalization
  • Localizing enzymes to specific organelles regulates activity
  • Controls access to substrates and cofactors