Enzymology (Lecture 1) Rumeza Hanif

Course Content Introduction and history of enzymes Historical aspects Discovery of enzymes Chemistry of enzymes Function and importance Enzymes in biotechnology Characteristics and properties Catalytic power and specificity Enzymes as catalysts ◦ Enzyme - substrate interactions ◦ Lock & key model ◦ Induced fit model ◦ Transition state model ◦ Quantum tunnelling model ◦ Enzymes as proteins ◦ Non-protein cofactors ◦ Metal ions ◦ Organic cofactors Nomenclature / Classification and Activity Measurements ◦ Oxidoreductase-dehydrogenase ◦ Transferase ◦ Hydrolase ◦ Lyase ◦ Isomerase ◦ Ligase Activity measurements Enzyme Purification and Assay Initial velocity measurements Assay types Enzyme units of activity Turnover number and properties Purification and assessment Methods for measurement Enzyme kinetics ◦ Michaelis-Menten Kinetics ◦ Introduction ◦ Assumptions ◦ Derivation ◦ Description of v o versus [S] ◦ Michaelis constant (K M )

Course Content ◦ Specificity/Substrate constant (SpC) ◦ Graphical Analysis of Kinetic Data, pH and Temp Dependence ◦ Graphical Analysis ◦ Lineweaver-Burk Analysis ◦ Hanes-Woolf Analysis ◦ Eadie-Hofstee Analysis ◦ Direct Linear Plot (Eisenthal/Cornish-Bowden Plot) ◦ Nonlinear Curve Fitting ◦ pH-dependence of Michaelis-Menten Enzymes ◦ Temperature-Dependence of Enzyme Reactions Single Molecule Enzymology ◦ ATP Synthase ◦ ATP Synthase with Tethered Actin ◦ Myosin-V ◦ Kinesin motor attached to a fluorescent bead ◦ Single Molecule Studies of Cholesterol Oxidase ◦ β -galactosidase: a model Michaelis-Menten enzyme? Enzyme inhibition and kinetics Classification of inhibitors ◦ Reversible, Irreversible, Iodoacetamide, DIFP Classification of Reversible Inhibitors ◦ Competitive, Uncompetitive, Noncompetitive, Substrate Multi-substrate Reactions and Substrate Binding Analysis ◦ Substrate Binding Analysis ◦ Single Binding Site Model ◦ Binding Data Plots ◦ Direct Plot ◦ Reciprocal Plot ◦ Scatchard Plot ◦ Determination of Enzyme-Substrate Dissociation Constants ◦ Kinetics ◦ Equilibrium Dialysis ◦ Equilibrium Gel Filtration ◦ Ultracentrifugation ◦ Spectroscopic Methods Mechanism of enzyme catalysis Engineering More Stable Enzymes Incorporation of Non-natural Amino Acids into Enzymes Protein Engineering by Combinatorial Methods DNA Shuffling

Marks distribution Total marks 100 Final exam st OHT 15 2 nd OHT 15 Presentation/Assignments/Project/Practical/ Class evaluation10-20 Quiz 10 (Minimum no of quiz 3) 75% attendance is needed to sit in the final exam

Terminologies Enzyme: Greek enzumouz or en-zume (leaven) any of a group of complex proteins or conjugated prot eins that areproduced by living cells and act as catalyst s in specific biochemicalreactions Catalyst: A substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change. Substrate: A substance or material on which an enzyme act. Active site: A part of an enzyme on which catalysis of a substrate occur. Product: A chemical substance formed as a result of a chemical reaction.

Mechanism of enzyme action Substrate (or substrates) binds to the active site on the enzyme. This binding causes changes in the distribution of electrons in the chemical bonds of the substrate and ultimately causes the reactions that lead to the formation of products. The products are released from the enzyme surface to regenerate the enzyme for another reaction cycle. The active site has a unique geometric shape that is complementary to the geometric shape of a substrate molecule, similar to the fit of puzzle pieces. This means that enzymes specifically react with only one or a very few similar compounds.

Lock and Key Theory First postulated in 1894 by Emil Fischer

Induced fit theory Substrate plays a role in determining the final shape of the enzyme and that the enzyme is partially flexible. This explains why certain compounds can bind to the enzyme but do not react because the enzyme has been distorted too much. Other molecules may be too small to induce the proper alignment and therefore cannot react. Only the proper substrate is capable of inducing the proper alignment of the active site.

Enzyme catalysis An active site directly binds to a substrate and carries a reaction. It contains catalytic groups which are amino acids that promote formation and degradation of bonds. By forming and breaking these bonds, enzyme and substrate interaction promotes the formation of the transition state structure. Enzymes help a reaction by stabilizing the transition state intermediate. This is accomplished by lowering the energy barrier or activation energy- the energy that is required to promote the formation of transition state intermediate. The active site is only a small part of the total enzyme volume. It enhances the enzyme to bind to substrate and catalysis by many different weak interactions because of its nonpolar microenvironment. The weak interactions includes the Van der Waals, hydrogen bonding, and electrostatic interactions. The overall result is the acceleration of the reaction process and increasing the rate of reaction. Furthermore, not only do enzymes contain catalytic abilities, but the active site also carries the recognition of substrate.

Transition state

Enzymatic activity Enzymes are evaluated according to their activity. Example Group A: 10 workers saw 10 cubic meter of wood in one hour Group B: 20 workers saw 10 cubic meter of wood in one hour An enzyme can be more active than another. ‘’A measure of conversion per unit time is the amount of product formed per minute under well-defined, standardised conditions.’’

Optimal conditions for enzymatic activity An optimal supply of substrate is needed by enzyme. Substrate saturate the enzyme. Example: The workers can reach their maximum performance only when there is sufficient wood available to be sawed. Enzyme and substrate must have a constant and unimpaired contact for maximum enzymatic activity. This occurs when the enzyme and substrate are present in dilute aqueous solutions. Insoluble substrate and dry solids are enzymatically inert.

Enzymes work at a constant rate Relative amount As long as the reaction conditions do not change, twice the yield of the product will be generated in twice the time. The conversion rate is reduced when there is insuffcicient substrate available to saturate the enzyme.

pH dependence of enzymatic activity

Temperature dependence of enzyme activity