Enzymes Cheatsheet

Cheatsheet Content

3.1 What are Enzymes? Biological catalysts, mostly proteins, that speed up biochemical reactions without being consumed. Lower the activation energy ($E_a$) of reactions. Highly specific for their substrates. 3.2 Properties & Functions of Enzymes 3.2.1 General Properties Catalytic Power: Increase reaction rates by $10^6$ to $10^{17}$ times. Specificity: Act on specific substrates to produce specific products. Reversibility: Catalyze both forward and reverse reactions, reaching equilibrium faster. Sensitivity: Optimal activity at specific pH and temperature; denature outside these ranges. Regulation: Activity can be increased or decreased by various mechanisms. No Consumption: Are not used up in the reaction. Proteinaceous: Mostly proteins, some RNA molecules (ribozymes) also have catalytic activity. 3.2.2 Functions of Enzymes Digestion of food (e.g., amylase, pepsin, lipase). Energy production (e.g., enzymes in glycolysis, Kreb's cycle). Synthesis of complex molecules (e.g., DNA polymerase, RNA polymerase). Detoxification (e.g., catalase, cytochrome P450). Waste removal. Muscle contraction, nerve impulse transmission. 3.3 Protein Structures Primary Structure: Linear sequence of amino acids linked by peptide bonds. Secondary Structure: Local folding into $\alpha$-helices and $\beta$-sheets, stabilized by hydrogen bonds. Tertiary Structure: Overall 3D shape of a single polypeptide chain, formed by interactions between R-groups (hydrophobic interactions, ionic bonds, disulfide bridges, H-bonds). Quaternary Structure: Arrangement of multiple polypeptide subunits (e.g., hemoglobin). Enzyme activity is highly dependent on its specific 3D tertiary/quaternary structure. 3.4 Enzyme-Substrate Models 3.4.1 Enzyme-Substrate Binding Models Active Site: Region on the enzyme where the substrate binds and catalysis occurs. Lock-and-Key Model (Fischer, 1894): Enzyme active site has a rigid shape, perfectly complementary to the substrate. Like a key fitting into a lock. Explains enzyme specificity but not flexibility. Induced Fit Model (Koshland, 1958): Active site is flexible; its shape changes slightly upon substrate binding. Conformational change optimizes binding and catalytic efficiency. More widely accepted model. 3.4.2 Enzymatic Transition State Transition State: Unstable, high-energy intermediate state between reactants and products. Enzymes stabilize the transition state, effectively lowering the activation energy ($E_a$). Binding to the transition state is stronger than to the substrate or product. 3.5 Enzyme Regulation Allosteric Regulation: Regulator molecules bind to a site other than the active site (allosteric site). Causes a conformational change in the enzyme, affecting active site activity. Activators: Increase enzyme activity. Inhibitors: Decrease enzyme activity. Feedback Inhibition: Product of a metabolic pathway inhibits an enzyme early in the pathway. Covalent Modification: Addition or removal of chemical groups (e.g., phosphorylation, dephosphorylation). Can activate or inactivate an enzyme. Proteolytic Cleavage (Zymogen Activation): Inactive enzyme precursor (zymogen) is activated by irreversible cleavage of a peptide bond. e.g., Pepsinogen $\rightarrow$ Pepsin. Gene Expression: Regulating the amount of enzyme synthesized. 3.6 Types of Enzymes 3.6.1 Enzyme Structural Classification Mostly globular proteins. Can be simple proteins (only amino acids) or conjugated proteins (contain non-protein part called cofactor). Cofactors can be: Metal ions: e.g., $Fe^{2+}$, $Mg^{2+}$, $Zn^{2+}$. Coenzymes: Organic molecules, often derived from vitamins (e.g., NAD+, FAD, Coenzyme A). Prosthetic groups: Tightly bound coenzymes (e.g., heme in catalase). Holoenzyme: Apoenzyme (protein part) + Cofactor. Apoenzyme: Protein part of an enzyme, inactive without its cofactor. 3.6.2 Basic Classification of Enzymes (IUBMB System) Based on the type of reaction catalyzed: Oxidoreductases: Catalyze oxidation-reduction reactions (transfer of electrons/H atoms). e.g., Dehydrogenases, Oxidases, Reductases. Transferases: Catalyze transfer of a functional group (e.g., methyl, phosphate, amino) from one molecule to another. e.g., Kinases, Transaminases. Hydrolases: Catalyze hydrolysis reactions (cleavage of bonds by addition of water). e.g., Lipases, Proteases, Amylases, Nucleases. Lyases: Catalyze cleavage of bonds without hydrolysis or oxidation, often forming double bonds. e.g., Decarboxylases, Aldolases. Isomerases: Catalyze intramolecular rearrangements (isomerization). e.g., Mutases, Racemases, Epimerases. Ligases: Catalyze formation of new bonds coupled with ATP hydrolysis. e.g., Synthetases, Carboxylases. 3.7 Factors Affecting Enzyme Action 3.7.1 Description on Factors Affecting Enzymatic Actions Temperature: Increase in temp $\rightarrow$ increase in kinetic energy $\rightarrow$ increase in reaction rate (up to optimum). Optimum Temperature: Temperature at which enzyme activity is maximal (typically $37^\circ C$ for human enzymes). High temperatures beyond optimum cause denaturation (loss of 3D structure and activity). pH: Each enzyme has an Optimum pH at which its activity is maximal. Extreme pH values alter the ionization state of amino acid residues in the active site, disrupting ionic bonds and H-bonds, leading to denaturation. e.g., Pepsin (stomach) optimum pH $\sim 2$; Trypsin (small intestine) optimum pH $\sim 8$. Substrate Concentration: Initially, reaction rate increases with increasing substrate concentration. At high substrate concentrations, the enzyme becomes saturated (all active sites are occupied). Reaction rate reaches maximum velocity ($V_{max}$) and plateaus. Enzyme Concentration: Assuming abundant substrate, reaction rate is directly proportional to enzyme concentration. More enzyme molecules mean more active sites to bind substrate. Inhibitors: Molecules that decrease enzyme activity. Reversible Inhibition: Competitive: Inhibitor resembles substrate, binds to active site, preventing substrate binding. Can be overcome by increasing substrate concentration. Non-competitive: Inhibitor binds to an allosteric site, altering enzyme conformation and reducing catalytic efficiency. Substrate binding may still occur, but catalysis is impaired. Cannot be overcome by increasing substrate concentration. Uncompetitive: Inhibitor binds only to the enzyme-substrate complex (ES complex), preventing product formation. Irreversible Inhibition: Inhibitor binds permanently (e.g., covalently) to the enzyme, often at the active site, causing permanent inactivation. e.g., many toxins and poisons. Activators: Molecules that increase enzyme activity (e.g., cofactors, allosteric activators). 3.8 Enzyme Kinetics Studies the rates of enzyme-catalyzed reactions. Michaelis-Menten Kinetics: Describes the relationship between reaction rate and substrate concentration. $E + S \rightleftharpoons ES \rightarrow E + P$ Michaelis-Menten Equation: $v = \frac{V_{max}[S]}{K_m + [S]}$ $v$: observed reaction rate. $V_{max}$: maximum reaction rate when enzyme is saturated with substrate. $[S]$: substrate concentration. $K_m$ (Michaelis Constant): Substrate concentration at which the reaction rate is half of $V_{max}$. Significance of $K_m$: Low $K_m$ indicates high affinity of enzyme for substrate. High $K_m$ indicates low affinity of enzyme for substrate. Lineweaver-Burk Plot: A double reciprocal plot ($1/v$ vs. $1/[S]$) used to determine $K_m$ and $V_{max}$ and distinguish between types of inhibition. Y-intercept: $1/V_{max}$ X-intercept: $-1/K_m$ 3.9 Application of Enzymes in Industries & Benefits 3.9.1 Uses of Enzyme Application Food Industry: Baking: Amylases (starch breakdown), proteases (dough conditioning). Brewing: Amylases, glucanases (clarity, fermentation). Dairy: Rennet (cheese making), lactase (lactose-free products). Fruit Juices: Pectinases (clarification). Meat Tenderization: Papain, bromelain. Textile Industry: Amylases (desizing), cellulases (bio-polishing, denim stonewashing). Proteases (wool treatment). Detergent Industry: Proteases (remove protein stains). Amylases (remove starch stains). Lipases (remove fat stains). Cellulases (fabric softening, color brightening). Pharmaceutical Industry: Synthesis of drugs (e.g., penicillin acylase). Diagnostic tools (e.g., glucose oxidase in blood glucose tests). Thrombolytic agents (e.g., streptokinase for dissolving blood clots). Biofuel Production: Cellulases, amylases (ethanol production from biomass). Paper Industry: Amylases, xylanases (pulp bleaching, de-inking). Bioremediation: Enzymes used to degrade pollutants. Molecular Biology: Restriction enzymes, DNA ligase, DNA polymerase (recombinant DNA technology). Benefits: Highly specific, operate under mild conditions (temp, pH), biodegradable, reduce energy consumption, produce fewer by-products.