lecture 2 – the kinetics of enzyme catalyzed reaction dr. akm shafiqul islam university malaysia...

Lecture 2 – The Kinetics of Enzyme Catalyzed Reaction

Dr. AKM Shafiqul IslamUniversity Malaysia Perlis

01.01.10

Classification of Enzyme

• Enzymes fall into 6 classes based on function

1. Oxidoreductases: which are involved in oxidation, reduction, and electron or proton transfer reactions

2. Transferases : catalysing reactions in which groups are transferred

3. Hydrolases : which cleave various covalent bonds by hydrolysis

4. Lyases : catalyse reactions forming or breaking double bonds

5. Isomerases : catalyse isomerisation reactions

6. Ligases : join substituents together covalently.

Enzyme Reaction

• For design and analysis of a reacting system, we must have a mathematical formula which gives the reaction ratein terms of – composition, – temperature, – and pressure of the reaction mixture.

Enzyme Kinetics

• Enzymes are protein catalysts that, like all catalysts, speed up the rate of a chemical reaction without being used up in the process.

Enzyme Kinetics

• Synthetic catalysts and enzymes use the common technique for modeling reaction kinetics.

• The rate expressions eventually obtained for both types of catalysts are very similar and sometimes of identical forms.

• This is because, in both cases, the reacting molecules form some sort of complex with the catalyst.

Enzyme Kinetics

• Most synthetic catalysts are not specific; i.e. they will catalyze similar reactions involving many different kinds of reactants.

• While some enzymes are not very specific, many will catalyze only one reaction involving only certain substrates.

• Explain why enzyme catalysis are nonspecific but enzyme catalysis are specific?

• Define– Cofactors– Apoenzyme– Holoenzyme – coenzyme

Enzyme Kinetic

• Enzyme is a catalyst which increases the rate of a chemical reaction without undergoing a permanent chemical change.

• While a catalyst influences the rate of a chemical reaction, it does not affect reaction equilibrium.

• Equilibrium concentrations can be calculated using only the thermodynamic properties of the substrates and products.

Enzyme

Enzyme Kinetics

• Both synthetic and biological catalysts can gradually lose activity as they participate in chemical reactions.

• However, enzymes are in general far more fragile. Enzymes contorted shapes in space often endow enzymes with unusual specificity and activity It is relatively easy to disturb the native conformation and destroy the enzyme's catalytic properties.

Enzyme Kinetics

• It is often asserted that enzymes are more active, i.e., allow reactions to go faster, than nonbiological catalysts.

• At the ambient temperatures where enzymes are most active they are able to catalyze reactions faster than the majority of artificial catalysts.

• When the reaction temperature is increased, solid (synthetic) catalysts may become as active as enzymes.

• The enzyme activity does not increase continuously as the temperature is raised. Instead, the enzyme usually loses activity at quite a low temperature, often only slightly above that at which it is typically found.

Enzyme Kinetics

Enzyme reaction rates are determined by several factors.

• Concentration of substrate molecules – The more of them available, the quicker the enzyme molecules

collide and bind with them). – The concentration of substrate is designated [S] and is expressed in

unit of molarity.

• Temperature. – As the temperature rises, molecular motion - and hence collisions

between enzyme and substrate - speed up. – But as enzymes are proteins, there is an upper limit beyond which the

enzyme becomes denatured and ineffective.

Enzymes cont.

• the presence of inhibitors. – competitive inhibitors are molecules that bind to the

same site as the substrate - preventing the substrate from binding as they do so - but are not changed by the enzyme.

– noncompetitive inhibitors are molecules that bind to some other site on the enzyme reducing its catalytic power.

• pH. The conformation of a protein is influenced by pH and as enzyme activity is crucially dependent on its conformation, its activity is likewise affected.

How we determine how fast an enzyme works

• We set up a series of tubes containing graded concentrations of substrate, [S] . At time zero, we add a fixed amount of the enzyme preparation.

• Over the next few minutes, we measure the concentration of product formed. If the product absorbs light, we can easily do this in a spectrophotometer.

• Early in the run, when the amount of substrate is in substantial excess to the amount of enzyme, the rate we observe is the initial velocity of Vi.

THE ENZYME-SUBSTRATE COMPLEX AND ENZYME ACTION

• There is no single theory which accounts for the unusual specificity and activity of enzyme catalysis.

• However, there are a number of plausible ideas supported by experimental evidence for a few specific enzymes.

• Probably, all or some collection of these phenomena acting together combine to give enzymes their special properties.

THE ENZYME-SUBSTRATE COMPLEX AND ENZYME ACTION

• The x-ray crystallography, spectroscopy, and electron-spin resonance showed the existence of a substrate-enzyme complex.

• The substrate binds to a specific region of the enzyme called the active site, where reaction occurs and products are released.

• Binding to create the complex is sometimes due to the type of weak attractive forces.

THE ENZYME-SUBSTRATE COMPLEX AND ENZYME ACTION

• The complex is formed when the substrate key joins with the enzyme lock.

• The hydrogen bonds formed between the substrate and groups widely separated in the amino acid chain of the enzyme.

THE ENZYME-SUBSTRATE COMPLEX AND ENZYME ACTION

• The protein molecule is folded in such a way that a group of reactive amino acid side chains in the enzyme presents a very specific site to the substrate.

• The reactive groups encountered in enzymes include the R group of Asp, Cys, Glu, His, Lys, Met, Ser, Thr, and the end amino and carboxyl functions.

• Since the number of such groups near the substrate is typically 20, only a small fraction of the enzyme is believed to participate directly in the enzyme's active site.

• Large enzymes may have more than one active site.

• Many of the remaining amino acids determine the folding along a chain of amino acids (secondary structure) and the placement of one part of a folded chain next to another (tertiary structure), which help create the active site itself

THE ENZYME-SUBSTRATE COMPLEX AND ENZYME ACTION

• Enzymes can hold substrates so that their reactive regions are close to each other and to the enzyme's catalytic groups.

• This feature, which quite logically can accelerate a chemical reaction, is known as the proximity effect.

• Reaction will occur only when the molecules come together at the proper orientation so that the reactive atoms or groups are in close juxtaposition.

• Enzymes are believed to bind substrates in especially favorable positions, thereby contributing an orientation effect, which accelerates the rate of reaction.

• Also called orbital steering, this phenomenon has qualitative merit as a contributing factor to enzyme catalysis. The quantitative magnitude of its effect, however, is still difficult to assess in general.