BSCI Lecture 5: Enzymes and Catalysis
Urea Denaturation (TopHat Question)
TopHat question: In the lab, urea (structure below) is often added to solutions of proteins to denature them. Why would a high concentration of urea cause a protein to unfold?
Brief answer (from the concept): High concentrations of urea disrupt noncovalent interactions that stabilize folded proteins (such as hydrogen bonds and hydrophobic interactions), increasing solvation of the unfolded state and destabilizing the folded conformation. This shifts the balance toward unfolding.
Semaglutide and receptor activation (Zhang et al., Cell Reports overview)
Semaglutide is the active ingredient in Ozempic.
Mechanism: Semaglutide binds to a receptor that is embedded in the plasma membrane of target cells.
Consequence: Binding to its receptor activates another type of protein: enzymes, which are proteins that catalyze reactions.
Conceptual flow: Semaglutide binding → receptor activation → enzyme activation → downstream Semaglutide effects.
Enzymes and catalysis: overview
Enzymes are proteins that catalyze reactions, making them proceed faster than in the absence of a catalyst.
Key idea: They work by lowering the barrier to reaction, not by altering the thermodynamics of the overall reaction.
Reactions: basics and Gibbs free energy
Biological reactions rearrange atoms, break bonds (require energy) and form bonds (release energy).
Exergonic vs. endergonic:
Exergonic: \Delta G < 0 (energy released)
Endergonic: \Delta G > 0 (energy required)
Spontaneity (in this context): refers to the energy requirement not to a need for external energy input from another reaction; it does not guarantee a rapid reaction or that a catalyst isn’t needed.
Example: ATP + H2O → ADP + Pi is exergonic; Pi + ADP → ATP is endergonic.
ATP hydrolysis example: \mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi}, \, \Delta G^{\circ} < 0
Synthesis of ATP from ADP and Pi is endergonic: \mathrm{ADP} + \mathrm{P_i} \rightarrow \mathrm{ATP}, \, \Delta G^{\circ} > 0
Activation energy (EA): the difference between the energy of reactants and the energy of the transition state, i.e.,
Most biological reactions have EA that is too large to be overcome by random thermal motion alone, so catalysts (enzymes) are essential.
How enzymes affect energy profiles
Enzymes lower the activation energy for a reaction, thus increasing the rate.
Energy profile concepts (conceptual):
Uncatalyzed pathway: higher peak (larger Ea).
Enzyme-catalyzed pathway: lower peak (lower Ea).
Result: Enzyme-catalyzed reactions proceed faster at the same substrate concentration.
Substrates, binding, and kinetics
Enzymes bind to the reactants with high specificity; reactants are called substrates.
Binding affinity is described by the dissociation constant Kd, determined by noncovalent interactions between enzyme and substrate.
Example: Lysozyme (enzyme) bound to its substrate (a polysaccharide).
Key implication: Specific binding governs catalytic efficiency and selectivity.
Predictive question (concept check)
Prompt: What might an enzyme do to substrates to make the reaction go faster?
Expected gist: Position substrates in proper orientation at the active site to facilitate bond formation/breakage and stabilize the transition state.
Catalytic mechanisms illustrated by lysozyme
Lysozyme demonstrates several catalytic mechanisms:
1) Substrate binds in a strained conformation, which brings it closer to the transition state.
2) An amino acid side chain in the active site acts as an acid, donating a proton (H+).
3) An amino acid side chain in the active site acts as a base, accepting a proton (H+).
4) An amino acid side chain in the active site transiently forms a covalent bond with the substrate (covalent catalysis).
Additional catalytic mechanisms (two more common themes)
Mechanism 5: Substrate positioning — the enzyme binds two substrate molecules and orients them precisely to facilitate a reaction between them.
Mechanism 6: Reaction coupling — an exergonic reaction can drive an endergonic reaction by coupling them, so the overall reaction becomes favorable.
Example provided: Fructose-6-phosphate + Pi → Fructose-1,6-bisphosphate, ΔG = +14 kJ/mol
ATP hydrolysis: ATP → ADP + Pi, ΔG = -30 kJ/mol
Enzyme phosphofructokinase couples these reactions so that energy from the exergonic step makes the endergonic step possible.
Overall coupling:
Temperature and enzyme activity (TopHat concept)
Every enzyme has an optimal temperature for activity.
Mechanistic reasons:
At lower temperatures: reduced molecular motion leads to fewer productive collisions/orientations between enzyme and substrate.
At higher temperatures: proteins may unfold or lose active-site geometry, reducing activity.
The relational trend is a peak of relative activity at the optimum temperature, with activity decreasing as you move away from that optimum in either direction.
Enzyme naming and common classes (Table 4-1)
Enzyme names typically end in -ase, though with exceptions (e.g., pepsin, trypsin, thrombin, lysozyme).
General principle: the name usually reflects the reaction catalyzed.
Common classes and functions:
Hydrolase: general term for enzymes that catalyze hydrolytic cleavage reactions.
Nuclease: hydrolyzes bonds in nucleic acids by hydrolyzing bonds between nucleotides.
Protease: hydrolyzes peptide bonds in proteins.
Ligase: joins two molecules together; e.g., DNA ligase.
Isomerase: catalyzes rearrangements within a molecule (structural isomers).
Polymerase: catalyzes polymerization (DNA and RNA synthesis).
Kinase: adds phosphate groups to molecules; many kinases phosphorylate proteins; protein kinases are a major group of kinases.
Phosphatase: removes phosphate groups from molecules.
Oxido-reductase: enzymes that catalyze oxidation-reduction reactions; often called oxidases, reductases, or dehydrogenases.
ATPase: hydrolyzes ATP to drive processes; many motor proteins (e.g., myosin) and membrane pumps (e.g., Na+/K+ ATPase) rely on ATPase activity.
Practical note: The enzyme found in a given pathway is often named by the reaction it catalyzes.
Allosteric regulation of enzymes
Allosteric sites are distinct from the active site and regulate activity by binding small molecules.
Allosteric inhibitors reduce reaction rate when bound at allosteric sites (e.g., ATP as an allosteric inhibitor of PFK in glycolysis).
Precursors or products can act as allosteric regulators:
Allosteric activators increase enzyme activity (e.g., ADP activating an enzyme step in glycolysis).
Allosteric activators or inhibitors adjust flux through pathways depending on cellular needs.
Metabolic pathway regulation and pharmacology
Acetyl-CoA → cholesterol synthesis context:
Numerous drugs act as enzyme inhibitors in cholesterol synthesis.
Lovastatin inhibits an initial, rate-limiting enzyme in cholesterol synthesis.
Natural sources: lovastatin-like compounds have been associated with oyster mushrooms in discussions of statin-like activity (illustrative example in the transcript).
Check Yourself: learning objectives (summary of goals)
Explain a reaction diagram and distinguish exergonic vs. endergonic reactions.
Define and explain activation energy and its relation to the transition state.
Explain what enzymes do and draw reaction diagrams with and without enzymes (as shown in the slides).
Define Kd and explain what determines Kd.
Describe six common mechanisms by which enzymes catalyze reactions (the four shown for lysozyme plus the two additional mechanisms).
Explain reaction coupling and allosteric activation/inhibition.
Given a reaction pathway, predict whether a molecule would act as an activator or inhibitor for an enzyme in the pathway.
Announcements (class logistics snippets)
Office hours and tutoring options are listed; use available resources to review TopHat questions and practice quizzes; plan for Quiz 1 timing.