Enzymes and Catalysis Quiz

Introduction to Enzymes

• Enzymes are protein catalysts that increase the rate of reactions without being altered in the process.
• All enzymes are proteins, with a notable exception being ribozymes, which are catalytic RNA molecules involved in RNA processing.

Learning Objectives

• Explain how substrates are enzymatically transformed into products, including transition states and activation energy. Use energy diagrams to illustrate the process.
• Compare and contrast the lock-and-key and induced-fit models of enzyme-substrate interactions.
• Differentiate between cofactors, coenzymes, and isozymes.
• Describe how functional groups, amino acid side chains, coenzymes, and metal ions contribute to enzymatic reactions.
• Describe how factors like pH, temperature, and enzyme/substrate concentrations affect reaction rates.
• Compare and contrast Michaelis-Menten and Lineweaver-Burk plots, including the roles of Vmax and Km in enzyme inhibition.
• Explain how different factors impact enzyme activity. Explain KD vs. Km comparisons. Compare different methods of enzyme regulation
• Explain the importance of regulatory enzymes, including various methods for regulation (feedback inhibition, allosteric regulation, covalent modification, and hormonal regulation), in metabolic pathways.
• Compare the catalytic mechanisms of allosteric and Michaelis-Menten enzymes.

Enzyme Substrates and Transition States

• The combination of an enzyme and its substrate forms an enzyme-substrate complex.
• The rate of an enzyme-catalyzed reaction is directly proportional to the amount of enzyme-substrate complex.
• The transition state is a highly unstable intermediate between substrate and product.
• Enzymes stabilize transition states, lowering activation energy, and thus increasing the reaction rate.

Catalytic Efficiency

• Uncatalyzed reactions are slow, requiring high activation energy.
• Enzymes lower the free energy of activation, increasing the reaction rate.
• Enzymes do not alter the free energy of reactants/products.
• Enzymes are not altered during the reaction.

Free Energy of Activation

• The free energy of activation is the difference in free energy between the transition state and the reactants.
• Enzymes increase the rate of exergonic reactions by lowering the activation energy.

Types of Enzyme-Substrate Interactions

• "Lock and Key" model: substrate fits precisely into the active site.
• "Induced Fit" model: enzyme active site changes shape to fit the substrate.

Factors for Enzyme Catalysis

• Active sites: pockets on the enzyme with specific shapes and chemical properties.
• Cofactors: non-protein molecules. Can be metal ions or coenzymes.
• Coenzymes: organic molecules derived from vitamins.
• Prosthetic groups: tightly bound coenzymes.
• Compartmentalization: enzymes are localized in specific organelles, isolating reaction substrates.
• Specificity: enzymes are highly specific for their substrates and reactions.

Reaction in the Active Site

• Enzymes contain an active site where substrates bind and reactions occur.
• The active site is specific for the substrate, creating a three-dimensional structure matching the substrate.
• Amino acids in the active site form weak bonds with the substrate, which helps catalyze the reaction.
• A transition complex (intermediate between substrate and product) is created.
• Products are released, and the enzyme returns to its original state.

Cofactors

• Inorganic cofactors: include metal ions (e.g., Mg2+, Fe2+, Zn2+).
• Organic cofactors (coenzymes): derived from vitamins (e.g., NAD+, FAD, Coenzyme A).
• Prosthetic groups: tightly bound to the enzyme.
• Co-substrates: temporarily bind to the enzyme.

Enzyme Kinetics

• Kinetics measures the speed of a reaction.
• The rate of an enzyme-catalyzed reaction is affected by pH, temperature, enzyme concentration, and substrate concentration.
• Michaelis-Menten equation describes the relationship between reaction rates and substrate concentration. Vmax and Km are important constants.

KM and KD

• KM: Michaelis-Menten constant; numerically equivalent to substrate concentration when reaction velocity equals half Vmax; measures the impact of substrate concentration on reaction speeds, and can be used as an indirect measure of affinity
• KD: Dissociation constant: thermodynamic constant, measures the affinity of ligand to binding site; concentration at which 50% ligand dissociates from the enzyme; doesn't reflect reaction speed.

Important Information from Michaelis-Menten Kinetics

• Comparison of Isoenzymes (e.g., hexokinase and glucokinase)
• The role of the enzymes in transferring a phosphate from ATP to glucose

Hexokinase

• Found in all cells, but little in the liver
• Has broad specificity (glucose or fructose)
• High affinity, so low substrate concentration (e.g., low blood glucose) is enough to get a reaction.

Glucokinase

• Found primarily in liver and pancreatic cells.
• Only acts on glucose
• Low affinity, requiring higher substrate concentrations to activate.
• Essential to remove excess glucose from the bloodstream after eating (high blood glucose).

Enzyme Regulation

• Regulation by other molecules that either promote or inhibit activity.
• Activators, inhibitors. Diverse pathways and molecules that block, promote, or otherwise affect enzyme function.
• Examples:
  • Substrate availability: The velocity of reaction changes with substrate availability.
  • Product inhibition: Product inhibition can impact Vmax and/or Km
  • Allosteric control: allosteric effectors (or activators/inhibitors) binds at a site other than the active site; these effectors can change the enzyme's conformation
  • Covalent modification: another enzyme adds a phosphate group (or otherwise covalently alters the enzyme); e.g., phosphorylating/dephosphorylating a protein
  • Induction/repression: alters the amount of an enzyme, typically via changes to gene expression to produce an enzyme

Regulatory Enzymes

• Catalyze irreversible reactions and are at committed steps in metabolic pathways
• Important for precisely controlling metabolic flux.
• Examples: Phosphofructokinase (a key enzyme in glycolysis)

Enzyme Inhibition

• Types of inhibition include:
  • Competitive: inhibitor resembles substrate, binding reversibly at the active site.
  • Noncompetitive: inhibitor binds to an enzyme site different from the active site (changing the conformation), altering Vmax, but not Km.
  • Uncompetitive: inhibitor binds only to the enzyme-substrate complex, altering both Km and Vmax.
  • Irreversible: inhibitor binds covalently to the enzyme (often at the active site). The inhibitor permanently inactivates the enzyme

Irreversible (Suicide) Inhibitors

• Bind covalently to the enzyme, permanently inactivating it
• Useful in new drugs and therapies

Enzyme Examples

• Use of inhibitors (for example lovastatin, aspirin, and penicillin)
• Regulation of enzymes such as HMG-CoA reductase, cyclooxygenase(COX), dihydrofolate reductase (DHFR)

Nutrition and Enzymes

• Endogenous enzymes (produced by the body) include those for digestion (proteases, lipases, amylases), and autolytic enzymes.
• Exogenous enzymes (from other sources) are often inactivated by high temperatures (e.g., cooked foods vs. raw foods), and are found in raw food sources.

Study Questions

• Clinical scenarios and examples of how drugs affect enzyme functioning

Test your knowledge on the specificity, function, and characteristics of enzymes through a series of challenging questions. This quiz covers topics such as enzyme activity, transition states, proenzymes, and the impact of pH and temperature on enzyme function.