Enzymes and Their Classifications

Enzyme Definition

• Enzymes are protein catalysts that speed up chemical reactions.

Enzyme Classification

• Oxidoreductases: Transfer of electrons (e.g., dehydrogenases, oxidases).
• Transferases: Group transfer reactions (e.g., transaminase, kinases).
• Hydrolases: Hydrolysis reactions (e.g., estrases, digestive enzymes).
• Lyases: Addition of groups to double bonds or formation of double bonds by removal of groups (e.g., phospho hexose isomerase, fumarase).
• Isomerases: Transfer of groups within molecules to yield isomeric forms (e.g., decarboxylases, aldolases).
• Ligases: Formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to ATP cleavage (e.g., citric acid synthetase).

Enzyme Specificity

• Substrate specificity: An enzyme's ability to react with only one substrate (e.g., lactase, urease, glucokinase).
• Reaction specificity: An enzyme is specific to a particular reaction, catalyzing only one type (e.g., pyruvate can undergo several reactions, each catalyzed by different enzymes).
• Stereo specificity: An enzyme is specific to one isomer (e.g., L-lactate dehydrogenase act on L-lactic acid, not D-lactic acid).

How Enzymes Lower Ea

• Molecules collide with each other, absorbing sufficient energy to overcome activation energy.
• Reactants convert to an activated condition (transition state).
• Reactants are converted into products.
• The rate of reaction increases

Meaning of Ea

• The energy difference between reactants and a high-energy intermediate (transition state).
• The transition state is formed during the conversion of reactant to product

Enzyme Function

• Enzymes provide catalytic groups that enhance the formation of the transition state.
• Enzymes stabilize the transition state and enhance product formation.
• Enzymes provide alternate reaction pathways by lowering activation energy, increasing reaction rate.
• Enzymes do not alter the free energy of reactants or products and do not change the equilibrium of the reaction.
• Enzymes have an active site where the reaction occurs.
• The active site has a binding site for the substrate.
• The substrate binds to the active site, and an enzyme-substrate complex (ES complex) is formed.
• The ES complex undergoes conformational change.
• The enzyme catalyzes the conversion of substrate to products.
• The resulting product is released, and the enzyme returns to its original form.

Lock and Key Model

• The active site of the enzyme has a fixed shape.
• The substrate must be completely complementary to the enzyme's active site shape.

Induced-fit Model

• The enzyme's active site is not initially fully complementary to the substrate's shape.
• The active site is flexible.
• When a substrate binds to the active site, the enzyme's conformation changes, allowing the substrate to fit precisely into the active site.

Properties of Enzyme

• Enzymes are reusable.
• Enzymes exhibit specificity, catalyzing specific reactions.
• Enzymes' catalytic activity can be regulated to control the rate of product formation.
• Enzymes are highly catalytically efficient.

Michaelis-Menten Kinetics

• The Michaelis-Menten equation describes how reaction velocity (V₀) changes with substrate concentration ([S]).
• V₀ = (Vmax [S]) / (Km + [S])
• Assumptions:
  • Substrate concentration is much higher than enzyme concentration.
  • Steady-state assumption: the concentration of enzyme-substrate complex (ES) remains constant over time.
  • Initial velocity (V₀) is used in the analysis of enzyme reactions..

Factors affecting enzyme-catalyzed reactions: Substrate Concentration

• Michaelis-Menten plot is hyperbolic.
• Vmax is the maximum velocity of the reaction.
• Km represents the substrate concentration at which the reaction velocity is half of Vmax, reflecting enzyme affinity for substrate.
• When [S] is much less than Km, the reaction is first order, and velocity is directly proportional to [S].
• When [S] is much greater than Km, the reaction is zero-order, and velocity is independent of [S].
• Increasing enzyme concentration increases Vmax but does not affect Km.

Factors affecting enzyme catalysed reactions: Temperature

• Velocity increases with temperature up to a peak.
• Further increases cause denaturation resulting in decreased velocity.
• Graph is bell-shaped.

Factors affecting enzyme catalysed reactions: pH

• Each enzyme has an optimal pH for maximal activity.
• Extreme pH values can cause denaturation and change in active sites conformation.
• Graph is bell-shaped.

Cofactors

• Inorganic cofactors (metal ions): -Loosely associated (metal-activated enzyme) - Mg, Mn -Tightly associated (metalloenzymes)-Fe, Cu, Zn
• Organic cofactors (coenzymes): -Tightly associated (Riboflavin: FMN, FAD) -Loosely associated (Readily associate and dissociate) - Niacin, NAD, NADP, B5, Coenzyme A

Holoenzyme vs. Apoenzyme

• Holoenzyme: complete, active enzyme with its cofactor.
• Apoenzyme: the protein component of a holoenzyme without its cofactor

Prosthetic Groups vs. Co-substances

• Prosthetic groups: permanently associated with the enzyme.
• Co-substances: temporarily associated with the enzyme.

Coenzymes derived from B Vitamins

• Specific B vitamins serve as coenzymes for various reactions, including those involving the transfer of one-carbon groups, oxidation-reduction reactions, acyl group transfers, and carboxylation reactions.

Enzyme Inhibition

• Competitive inhibition: inhibitor binds to the active site, competing with the substrate.
• Non-competitive inhibition: inhibitor binds to a site other than the active site, changing the enzyme's shape and reducing activity.
• Suicide inhibition: inhibitor is a substrate that is modified by the enzyme to become an irreversible inhibitor.

Antibiotic Sulfanilamide inhibition

• Sulfanilamide is a structural analog of PABA (para-aminobenzoic acid), an intermediate in folic acid synthesis.
• Sulfanilamide competitively inhibits the enzyme that uses PABA, preventing bacterial growth.

Hypercholesterolemia

• Statin drugs inhibit HMG-CoA reductase, lowering cholesterol levels.
• Statins are structural analogs of HMG-CoA, the substrate.
• They compete with HMG-CoA for the active site.

Non-competitive inhibitor

• Non-competitive inhibitors bind to a site other than the active site.
• They change the shape of the enzyme, decreasing activity, with little or no effect on Km.
• The presence of an inhibitor reduces Vmax.

Suicide Inhibitor

• Suicide inhibitors have a structure similar to a substrate.
• The inhibitor is initially bound normally and becomes chemically modified by the enzyme and forms an irreversible inactivator complex.
• Irreversible inhibition.