C1.1 ENZYMES SL

C1.1.1—Enzymes as Catalysts

• Enzymes: Primarily proteins (some are RNA) that function as biological catalysts.

• Catalysts:

  • Speed up the rate of reaction.

  • Effective in small amounts.

  • Remain unchanged at the end of the reaction.

C1.1.2—Role of Enzymes in Metabolism

• Metabolism: A complex network of interdependent chemical reactions occurring in living organisms.

• Enzymes ensure reactions occur fast enough for life processes.

• Molecules involved in metabolism are called metabolites.

• Each enzyme is specific, requiring a wide variety of enzymes to regulate metabolism.

C1.1.3—Anabolic and Catabolic Reactions

• Anabolism: Formation of macromolecules from monomers by condensation reactions.

• Catabolism: Breakdown of larger molecules into simpler molecules by hydrolysis reactions.

C1.1.4—Enzymes as Globular Proteins with an Active Site for Catalysis

• Substrate: The reactant that binds to an enzyme.

• Product: The final molecule after the enzyme-catalyzed reaction.

• Active Site: Region where the substrate binds and the reaction occurs.

• Enzyme-Substrate (ES) Complex: Temporary structure formed when a substrate binds to the active site.

• Active site properties:

  • Only a few amino acids form the active site, but the entire enzyme structure supports its function.

  • Interactions hold the substrate, allowing the reaction to proceed efficiently.

  • Lowers activation energy to facilitate the reaction.

Lock-and-Key Model of Enzyme Catalysis:

• The active site is precisely complementary to the substrate's shape.

• Enzyme = Lock, Substrate = Key → Their shapes must match perfectly

C1.1.5—Induced-Fit Model of Enzyme Binding

• More widely accepted than the Lock-and-Key model.

• Active site adjusts slightly upon substrate binding.

• Helps raise the substrate to its transition state, making the reaction more efficient.

• Other amino acids in the active site may help break or form bonds within the substrate.

• Explains broad enzyme specificity, allowing enzymes to catalyze closely related reactions.

C1.1.6—Molecular Motion and Substrate-Active Site Collisions in Enzyme Catalysis

• Substrate and enzyme must collide for catalysis to occur.

• Higher kinetic energy → Increased collisions → Higher reaction rate.

• Collisions must have the correct orientation and sufficient energy for a reaction to begin.

Immobilized Enzymes

• More stable than free enzymes in solution, enhancing enzyme activity.

• Attached to insoluble materials, which provide support and maintain enzyme function. 

C1.1.7—Active Site Structure, Specificity, and Denaturation

• Denaturation: Occurs when weak intramolecular interactions (hydrogen bonds, ionic bonds, etc.) break.

• This changes the 3D shape of the enzyme, altering the active site.

• As a result, substrates can no longer bind, stopping enzyme function.

C1.1.8—Effects of Temperature, pH, and Substrate Concentration on Enzyme Activity

Effect of Temperature

• Increasing temperature → More kinetic energy → More frequent successful enzyme-substrate collisions.

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• Optimum temperature: The point at which the reaction rate is highest.

• Q10 Temperature Coefficient:

  • Measures the rate of reaction change with a 10°C temperature increase.

  • Most enzymes have Q10 ≈ 2 (reaction rate doubles every 10°C).

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• Above optimum temperature → Enzymes start denaturing → Reaction rate decreases.

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• Different enzymes have different optimum temperatures (e.g., thermophilic enzymes work at higher temperatures).

Effect of pH

• Enzyme shape is maintained by bonds and weak forces.

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• Changes in pH alter these bonds, leading to structural changes in the active site.

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• If pH deviates too far from optimum, the enzyme loses function.

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• Mild pH changes are reversible—the enzyme can regain function if pH returns to normal.

Effect of Substrate Concentration

• At low substrate concentrations:

  • The reaction rate increases proportionally as more substrate molecules collide with active sites.

  • Active sites are available, ensuring maximum efficiency.

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• At high substrate concentrations:

  • Active sites become saturated—all enzymes are occupied, so adding more substrate has no effect.

  • The reaction rate reaches a plateau as substrate molecules must wait for an available enzyme.

C1.1.10—Effect of enzymes on activation energy 

C1.1 ENZYMES AND METABOLISM HL 

Distinguish between intracellular and extracellular enzymes 

Generation of Heat Energy by Metabolism

Exergonic Reactions

• Release free energy (spontaneous reactions).

• Example: Oxidation of glucose (cellular respiration).

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• Chemical potential energy → Heat energy.

• Energy is used for work, but some is lost as heat due to inefficiencies.

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• Warm-blooded animals rely on this heat to maintain body temperature.

Endergonic Reactions

• Absorb energy, resulting in higher energy at the end than at the start.

• Example: Protein synthesis from amino acids.

ATP: The Energy Carrier

• Endergonic reactions are coupled with exergonic reactions to proceed.

• ATP acts as the energy transfer molecule, linking energy-releasing and energy-absorbing reactions.

Cyclic & Linear Metabolic Pathways

• Metabolic pathway: A sequence of enzyme-catalyzed reactions in cells.

Linear Pathway

• Runs in one direction from reactant to product.

• Example: Glycolysis (breakdown of glucose).

Cyclic Pathway

• A continuous loop of enzyme-catalyzed reactions.

• The end product regenerates the starting reactant.

• Examples: Krebs cycle, Calvin cycle.

Enzyme Inhibition

Competitive Inhibition

• Inhibitor resembles the substrate and competes for the active site.

• Slows down or blocks enzyme function.

Non-Competitive Inhibition

• Inhibitor binds to a different site on the enzyme (not the active site).

• Changes enzyme shape, reducing its ability to bind with the substrate.

Statins – example of competitive inhibition   

·       When people have high levels of cholesterol doctors may recommend a group of drugs called statins.  

·       Statins act as competitive inhibitors  

·       They combine with the active site of an enzyme essential in catalysing the biosynthesis of cholesterol within the liver.  

·       Thus preventing the enzyme from binding and causing a reduction in production of cholesterol reducing the risk of cardiovascular disease.  

Allosteric sites and non-competitive inhibition 

·       Allosteric regulators are molecules that change the shape and activity of an enzyme by reversibly binding at a site on the enzyme away from the active site.   

·       Binding of an allosteric activator temporarily stabilizes enzyme shape and makes it an effective catalyst 

·       Binding of allosteric inhibitor changes enzyme shape into an inactive form.  

·       Allosteric regulation is a form of reversible non-competitive inhibition or activation of an enzyme. 

·       Only specific substances known as effectors can bind to an allosteric site which alter active site preventing catalysis.  

Competitive vs. Non-Competitive Inhibition

Competitive Inhibition

·       Example: Statins

• Used to lower cholesterol levels.

• Compete for the active site of an enzyme essential for cholesterol synthesis.

• Prevent enzyme binding, reducing cholesterol production and the risk of cardiovascular disease.

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·       Key Characteristics:

• Inhibitor competes with substrate for the active site.

• Increasing substrate concentration reduces inhibition, as the substrate outcompetes the inhibitor.

• At very high substrate concentrations, enzyme activity is almost normal.

Non-Competitive Inhibition

• Inhibitor binds to an allosteric site (not the active site).

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• Causes a conformational change in the enzyme, reducing its ability to bind with the substrate.

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• Increasing substrate concentration does not reduce inhibition, as the inhibitor affects enzyme shape, not substrate binding.

• A fixed proportion of enzymes are always inhibited, lowering overall enzyme activity.

Allosteric Regulation

• Allosteric regulators bind away from the active site and modify enzyme function.

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• Allosteric Activators: Stabilize enzyme shape, enhancing its catalytic efficiency.

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• Allosteric Inhibitors: Alter the enzyme’s shape, making it inactive.

• This is a reversible form of non-competitive inhibition.

Regulation of Metabolic Pathways

End-Product Inhibition (Negative Feedback Mechanism)

• The final product of a metabolic pathway inhibits the first enzyme in the pathway.

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• Prevents overproduction of the end product.

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• Reversible process: When the product level decreases, enzyme activity resumes.

• Example: ATP inhibits phosphofructokinase in glycolysis, regulating energy production.

Mechanism-Based Inhibition

• Substrate analogues are molecules that mimic the substrate but are unreactive.

• They bind covalently to the enzyme’s active site.

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• The enzyme modifies the substrate analogue, producing a reactive group.

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• This reactive group irreversibly binds to the enzyme, forming a stable inhibitor-enzyme complex that permanently deactivates the enzyme.

How Does Penicillin Kill Bacteria?

• Bacterial cell walls are made of peptidoglycan, a network of polysaccharide chains linked by short peptides.

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• The bacterial enzyme DD-transpeptidase (a penicillin-binding protein) forms cross-links between peptidoglycan strands, strengthening the bacterial cell wall.

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• Penicillin inhibits DD-transpeptidase, preventing cross-linking, making the cell wall weak.

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• Water enters the bacterial cell by osmosis, increasing pressure inside.

• The bacterial membrane bursts, killing the bacteria.

How Does Penicillin Inhibit DD-Transpeptidase?

• Penicillin's structure resembles the growing peptide chain of peptidoglycan.

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• Instead of binding to a peptide chain, DD-transpeptidase binds to penicillin.

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• Penicillin is modified by the enzyme, forming an inactive enzyme-penicillin complex.

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• This irreversible inhibition prevents further cross-linking, stopping bacterial growth.

Antibiotic Resistance & Mutations

• Genetic mutations in bacterial transpeptidase can change the enzyme’s active site.

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• This structural change prevents penicillin from binding effectively.

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• As a result, bacteria become resistant to penicillin, continuing to form cross-links and survive.