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 vo versus [S]

◦ Michaelis constant (KM)

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 distributionTotal marks 100Final exam 40-501st OHT 152nd OHT 15Presentation/Assignments/Project/

Practical/Class evaluation10-20Quiz 10 (Minimum no of quiz 3)75% attendance is needed to sit in

the final exam

TerminologiesEnzyme: Greek enzumouz or en-zume

(leaven)any of a group of complex proteins or conjugated proteins that areproduced by living cells and act as catalysts 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 actionSubstrate (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 activityEnzymes are evaluated according to their

activity.ExampleGroup A: 10 workers saw 10 cubic meter of

wood in one hourGroup 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

Rela

tive

am

ount

•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