Enzymes: Structure and Function

• Enzymes are biological catalysts speeding up chemical reactions within living organisms
• Typically proteins, some RNA molecules (ribozymes) can also act as enzymes

Enzyme Structure

• Enzymes possess a complex three-dimensional structure crucial for function
• The active site is a specific enzyme region where substrate binds and catalysis occurs
• The active site's shape and chemical properties are complementary to the substrate
• Some enzymes need non-protein components called cofactors or coenzymes to function
• Cofactors can be metal ions, examples include magnesium, iron, and zinc
• Coenzymes are organic molecules such as vitamins, NAD+, and FAD
• Apoenzyme refers to the protein part of an enzyme without its cofactor
• Holoenzyme denotes the complete, catalytically active enzyme with its cofactor

Enzyme Function

• Enzymes catalyze reactions by reducing the activation energy needed to start a reaction
• Enzymes provide an alternative reaction pathway with a lower activation energy
• Enzymes do not alter reaction equilibrium, only accelerate the rate at which equilibrium is reached
• Enzymes exhibit specificity, typically catalyzing a single reaction or a set of closely related reactions
• The "lock-and-key" model suggests a perfect fit between the enzyme and substrate
• The "induced-fit" model proposes the enzyme's active site changes shape upon substrate binding for optimal fit

Enzyme Kinetics

• Enzyme kinetics studies the rate of enzyme-catalyzed reactions
• The Michaelis-Menten equation relates initial reaction rate (v0), substrate concentration ([S]), and enzyme kinetic parameters: v0 = (Vmax[S]) / (KM + [S])
• Vmax represents the maximum reaction rate when the enzyme is saturated with substrate
• KM (Michaelis constant) is the substrate concentration at which the reaction rate is half of Vmax, indicating the enzyme's substrate affinity
• A low KM signifies high affinity, while a high KM indicates low affinity
• The Lineweaver-Burk plot (double reciprocal plot) is a graphical representation of the Michaelis-Menten equation, determining Vmax and KM
• Catalytic efficiency measures how efficiently an enzyme converts substrate to product: kcat/KM
• kcat (turnover number) is the number of substrate molecules converted to product per enzyme molecule per unit of time when the enzyme is substrate saturated

Enzyme Regulation

• Enzyme activity can be regulated to control metabolic pathways and maintain cellular homeostasis
• Allosteric regulation involves an effector molecule binding to a site separate from the active site, altering the enzyme's conformation and activity
• Positive effectors increase enzyme activity
• Negative effectors decrease enzyme activity
• Feedback inhibition is regulation where a metabolic pathway product inhibits an earlier enzyme in the pathway
• Covalent modification involves adding or removing a chemical group (e.g., phosphorylation, acetylation) to the enzyme, altering its activity
• Proteolytic activation involves activating an enzyme by cleaving a proenzyme (zymogen) to form the active enzyme; an example of this is the activation of digestive enzymes
• Enzyme synthesis and degradation: cells maintain control over the amount of enzyme present by controlling the rate of enzyme synthesis or degradation

Enzyme Inhibitors

• Enzyme inhibitors are molecules that reduce enzyme activity
• Competitive inhibitors bind to the active site, competing with the substrate
• Competitive inhibition raises the apparent KM but doesn't affect Vmax
• Noncompetitive inhibitors bind to a site other than the active site, altering enzyme conformation and reducing its activity
• Noncompetitive inhibition decreases Vmax but doesn't affect KM
• Uncompetitive inhibitors bind only to the enzyme-substrate complex
• Uncompetitive inhibition decreases both Vmax and KM
• Irreversible inhibitors bind permanently to the enzyme, inactivating it
• Transition state analogs are stable molecules resembling the reaction's transition state, binding tightly to the enzyme and acting as potent inhibitors
• Inhibitors are used in drugs, pesticides, and research to study enzyme mechanisms and metabolic pathways