Enzyme Kinetics

General Properties of Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in living organisms. They are highly specific for their substrates and operate under mild physiological conditions.

• Specificity: Enzymes typically act on a single substrate or a group of closely related substrates.

• Efficiency: Enzymes can increase reaction rates by factors of 106 or more.

• Regulation: Enzyme activity can be regulated by various mechanisms, including allosteric control and covalent modification.

• Reusability: Enzymes are not consumed in the reactions they catalyze.

Single Substrate Enzyme Kinetics

Single substrate enzymes follow characteristic kinetic patterns, often described by the Michaelis-Menten model.

• Substrate Binding: The enzyme binds to its substrate to form an enzyme-substrate (ES) complex.

• Product Formation: The ES complex is converted to product, releasing the enzyme for another catalytic cycle.

Transition State Stabilization

Enzymes lower the activation energy of reactions by stabilizing the transition state, the high-energy intermediate between reactants and products.

• Transition State: The configuration of atoms at the maximum energy point along the reaction pathway.

• Stabilization: Enzymes provide an environment that favors the formation of the transition state, often through specific interactions with substrate functional groups.

Michaelis-Menten Equation

The Michaelis-Menten equation describes the rate of enzymatic reactions as a function of substrate concentration:

• Equation:

• v: Initial reaction velocity

• Vmax: Maximum velocity

• [S]: Substrate concentration

• Km: Michaelis constant, substrate concentration at half-maximal velocity

Michaelis-Menten Plot: A hyperbolic curve showing v versus [S].

Lineweaver-Burk Plot: A double reciprocal plot (1/v vs. 1/[S]) used to determine kinetic parameters.

Pre-Steady-State and Steady-State Kinetics

• Pre-Steady-State: The initial phase of the reaction before the ES complex concentration becomes constant.

• Steady-State: The phase where the formation and breakdown of the ES complex are balanced, and the reaction rate is constant.

Enzymatic Kinetic Parameters

• Km (Michaelis Constant): Indicates the affinity of the enzyme for its substrate; lower Km means higher affinity.

• kcat (Turnover Number): Number of substrate molecules converted to product per enzyme molecule per unit time at saturation.

• Vmax (Maximal Velocity): The maximum rate achieved by the system at saturating substrate concentration.

• kcat/Km (Catalytic Efficiency): A measure of enzyme efficiency, combining substrate binding and turnover.

Allosteric Regulation

• Allosteric Activator: A molecule that increases enzyme activity by binding to a site other than the active site.

• Allosteric Inhibitor: A molecule that decreases enzyme activity by binding to a regulatory site.

• Allosteric effects are often observed as sigmoidal (S-shaped) curves in kinetic plots.

Enzyme Mechanisms

Exergonic vs. Endergonic Reactions

Enzyme-catalyzed reactions can be classified based on their free energy changes:

• Exergonic: Reactions that release energy (ΔG < 0); spontaneous.

• Endergonic: Reactions that require energy input (ΔG > 0); non-spontaneous.

Proximity Effect

Enzymes increase reaction rates by bringing substrates into close proximity and proper orientation for the reaction to occur.

Substrate Binding Models

• Lock-and-Key Model: The enzyme's active site is complementary in shape to the substrate.

• Induced-Fit Model: The enzyme changes shape upon substrate binding to better accommodate the substrate.

Transition State Stabilization

Enzymes stabilize the transition state through specific interactions, such as hydrogen bonding, ionic interactions, and van der Waals forces.

Serine Protease Catalysis

• Catalytic Triad: A set of three amino acids (Serine, Histidine, Aspartate) that work together to facilitate peptide bond hydrolysis.

• Substrate Specificity: Determined by the structure of the enzyme's binding pocket.

Chymotrypsin Mechanism

• Chymotrypsin is a serine protease that cleaves peptide bonds adjacent to aromatic amino acids.

• The mechanism involves formation of a covalent acyl-enzyme intermediate and stabilization of the transition state by the oxyanion hole.

Enzyme Inhibition

Types of Inhibition

• Competitive Inhibition: Inhibitor binds to the active site, competing with the substrate. Increases Km, Vmax unchanged.

• Uncompetitive Inhibition: Inhibitor binds only to the ES complex. Decreases both Km and Vmax.

• Noncompetitive Inhibition: Inhibitor binds to both the enzyme and ES complex at a site other than the active site. Vmax decreases, Km unchanged.

Lineweaver-Burk Plots

• Double reciprocal plots used to distinguish types of inhibition by their effects on slope and intercepts.

Mechanism-Based Inhibitors

• Also called suicide inhibitors; these bind irreversibly to the enzyme, often by mimicking the transition state.

• Distinguished by their covalent modification of the enzyme during the normal catalytic process.

Cofactors

Types of Cofactors

• Essential Ions: Metal ions required for enzyme activity (e.g., Mg2+, Zn2+).

• Coenzymes: Organic molecules that assist enzymes; can be further divided into:

  • Cosubstrates: Transiently associated with the enzyme (e.g., NAD+).

  • Prosthetic Groups: Tightly bound to the enzyme (e.g., FAD).

ATP as a Cofactor

• ATP acts as a phosphate group donor in group transfer reactions, providing energy for many cellular processes.

Redox Cofactors

• NAD(P)+/NAD(P)H: Involved in oxidation-reduction reactions, transferring hydride ions.

• FAD/FADH2: Also participates in redox reactions, often as a prosthetic group.

Monosaccharides

Functions of Carbohydrates

• Serve as energy sources (e.g., glucose), structural components (e.g., cellulose), and recognition molecules (e.g., glycoproteins).

Classification of Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides linked (e.g., sucrose, lactose).

• Oligosaccharides: 3–10 monosaccharide units.

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen).

Aldoses vs. Ketoses

• Aldoses: Monosaccharides with an aldehyde group (e.g., glucose).

• Ketoses: Monosaccharides with a ketone group (e.g., fructose).

Fischer Projections and Chirality

• Fischer projections are two-dimensional representations of sugars, showing the configuration of chiral centers.

• Chirality is determined by the arrangement of groups around asymmetric carbons.

Stereochemistry of Monosaccharides

• Stereoisomers: Same molecular formula, different spatial arrangement.

• Enantiomers: Non-superimposable mirror images.

• Diastereomers: Stereoisomers that are not mirror images.

• Epimers: Differ at only one chiral center.

Cyclization of Monosaccharides

• Monosaccharides can cyclize to form ring structures via intramolecular reactions.

• Hemiacetal: Formed when an aldehyde reacts with an alcohol (aldoses).

• Hemiketal: Formed when a ketone reacts with an alcohol (ketoses).

• The new chiral center formed is called the anomeric carbon.

Haworth Projections

• Show the cyclic form of sugars.

• Pyranose: Six-membered ring.

• Furanose: Five-membered ring.

Disaccharides

Glycosidic Bonds

• Disaccharides are formed by linking two monosaccharides via a glycosidic bond, involving the anomeric carbon of one sugar.

• Reducing sugars: Have a free anomeric carbon capable of acting as a reducing agent.

• Non-reducing sugars: Both anomeric carbons are involved in the glycosidic bond.

Examples

• Sucrose: Glucose + Fructose (non-reducing)

• Lactose: Glucose + Galactose (reducing)

Polysaccharides and Glycoproteins

Polysaccharide Structure and Function

• Starch: Storage polysaccharide in plants; composed of amylose and amylopectin.

• Glycogen: Storage polysaccharide in animals; highly branched structure.

Glycoproteins

• Proteins with covalently attached carbohydrate chains.

• O-linked: Carbohydrate attached to the oxygen atom of serine or threonine side chains.

• N-linked: Carbohydrate attached to the nitrogen atom of asparagine side chains.

ABO Blood Classification

• Blood types are determined by specific oligosaccharide structures on glycoproteins and glycolipids of red blood cells.

• Compatibility between donors and recipients depends on these carbohydrate antigens.

Nucleic Acids

Components of Nucleotides

• Nucleobase: Purine (adenine, guanine) or pyrimidine (cytosine, thymine, uracil).

• Sugar: Ribose (RNA) or deoxyribose (DNA).

• Phosphate group: Attached to the 5' carbon of the sugar.

Nucleobases, Nucleosides, and Nucleotides

• Nucleobase: Nitrogenous base only.

• Nucleoside: Nucleobase + sugar.

• Nucleotide: Nucleoside + phosphate group(s).

Structures and Codes

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

• One-letter codes: A, G, C, T, U

Phosphoanhydride and Phosphoester Linkages

• Phosphoester bond: Between phosphate and sugar.

• Phosphoanhydride bond: Between two phosphate groups (as in ATP).

DNA vs. RNA Nucleotides

• DNA contains deoxyribose and thymine; RNA contains ribose and uracil.

DNA and RNA: Structures and Functions

Nucleotide Linkage

• Nucleotides are linked by phosphodiester bonds between the 3' hydroxyl of one sugar and the 5' phosphate of the next.

• Polynucleotide chains have directionality: 5' to 3'.

Base Pairing

• Watson-Crick base pairs: A-T (DNA), A-U (RNA), G-C.

• Base pairs are stabilized by hydrogen bonds: A-T (2 bonds), G-C (3 bonds).

Major Classes of RNA

• mRNA (messenger RNA): Encodes proteins.

• tRNA (transfer RNA): Brings amino acids to the ribosome.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

RNA Secondary Structures

• Hairpins, loops, bulges, and pseudoknots are common secondary structures in RNA.