King Saud University Foundation Block

Enzyme & Coenzyme Lecture 7 + 8

Color Index:

Important ⇒ Red

Explanation ⇒ Orange

Additional ⇒ Purple

Mind Map

that محفز They are biological catalysts - speed up the rate of a reaction without being consumed by the reaction.

- All enzymes are proteins, but not all proteins are enzymes.

Substrate is the substance that enzymes act on, and convert it into products.

Classification of Enzymes

Enzymes are classified into 6 classes according to the reaction catalyzed

Classification Type of Reaction Catalyzed 1 Oxidoreductases Oxidation-Reduction reactions 2 Transferases Transfer of functional groups

3 Hydrolases Hydrolysis reaction 4 Lyases Group elimination to form double bonds

5 Isomerases Isomerization

6 Ligases Bond formation + ATP hydrolysis

Enzyme Nomenclature (Naming)

Enzyme Nomenclature is based on the rules given by EC 3.4.17.1 (Carboxypeptidase) IUBMB (International Union of Biochemistry and EC = Enzyme Commission Molecular Biology. Class.subclass.subsubclass.Enzyme number

Properties of Enzymes

Active Site Regulation Specificity

- The region of - Enzymes can be - Enzymes bind to enzyme that binds activated or their specific with substrate inhibited so that substrates in the the rate of product active site to - Where Catalysis formation convert them to occur responds to the products need of the cell. - All enzymes have - Enzymes are 1 or more active highly specific sites - They interact with only one or few substrates

- Catalyze only one reaction

Enzyme-Substrate Binding

Lock and Key Binding Induces Fit Binding

The enzyme has an active site In this case, after binding to the that fits the exact dimensions of substrate, the enzyme changes its the substrate. shape to fit more perfectly with substrate. From the beginning the active site is complementary to the The active is not complementary to the shape of substrate. substrate, but when binding happens the active site changes its confirmation according to the substrate.

- Some enzymes require non-protein groups to become active. -The inactive form of the enzyme “without its non-protein part” is called Apoenzyme. -The active form of the enzyme “with its non-protein part” is called Holoenzyme.

Apoenzyme (Inactive) Non-protein part Holoenzyme (active) + =

This non-protein part can either be Coenzyme Cofactor If the non - protein part is a small organic or molecule its called Coenzyme. If the non-protein part is a metal ion such as Cu+2, Fe+3, and they are also divided into 2 types Zn+2 its called Cofactor 1-Prosthetic Groups

They are coenzymes hat are permanently attached with an enzyme e.g. FAD

2-Cosubstrates

They are coenzymes that only temporarily associate with an enzyme e.g. NAD

Permanently = All the time

Temporarily = Not all the time

Riboenzymes Isoenzymes Zymogens Enzymes that They are inactive catalyze the same enzyme precursors RNAs with enzyme reaction, but they that require a activity biochemical change have slightly to become active. different structure. Usually, the biochemical change is removing a peptide chain from the active site, so the zymogen becomes active.

Transition State

Enzyme-Substrate Complex

Transition State: it’s a state that reactants pass through, in every chemical reaction, which has greater energy than reactant and products alone. “without enzymes”

Activation Energy (Ea): The deference in energy between the reactants and the transition state + It’s the energy required to

- If the activation energy is available, then the reaction can be proceed forming production.

Free Energy GΔ: The difference in energy between the reactants and the products. ADDITIONAL BUT IMPORTANT TO KNOW. Enzymes decrease the activation energy, but they don’t affect free energy GΔ. “Check the graph” - Enzymes provide alternative transition state with lower activation energy called Enzyme Substrate Complex, thus it speeds up the reaction.

Enzyme Activity or Velocity

It is the rate of a reaction catalyzed by an enzyme.

Measured in millimole of product formed/Minute/mg of enzyme. Factors Affecting Enzyme Activity

Concentration of Enzyme [E] and Temperature dpH Concentration of Substrate [S]

- Every enzyme has an - any effect of pH on the ionizable -Reaction y optimal”perfect” groups in the active site or in the ,initially, increases temperature for catalyzing substrate can affect catalysis. with increasing a reaction. substrate - Every enzyme has an optimal pH for concentration [S] - At first, the enzyme catalyzing but when the reaction increase with enzyme reaches increasing temperature - Most enzymes have highest activity saturation, the between 6 pH and 8 pH addition of - If the temperature is substrate will not very HIGH, enzymes are - Pepsin has highest activity at pH 2 affect enzyme denatured and become because it works in the stomach which velocity inactive. is an acidic medium. - At low substrate - Most human enzymes The bell-shaped curve concentration [S], have an optimal energy of the reaction velocity 37° C. is low.

- If the substrate concentration is higher than enzyme, the rate of an enzyme reaction will be directly proportional to the concentration of enzyme.

Enzyme Kinetics

Michaelis and Menten first proposed the model of enzyme kinetics “Movement

K1 K E = Enzyme E + S ES 2 E + P S = Substrate K-1 P = Product

Pre-steady state kinetics Steady State Kinetics

When an enzyme is mixed with - After initial state, the reaction high [S], there is an initial short of rate and the concentration of period of time (few hundred intermediates change slowly with

microseconds) during which time called steady state reaction. intermediates* build up, that leads to the formation of product - An intermediate is called steady state when its rate of synthesis is equal to its rate of degradation

The Michaelis Menten Equation: Vmax [S]

It describes the relationship of the vo = ------initial rate of an enzyme to the

concentration substrate [S]. It measures Km + [S] the initial velocity (vo) of an enzyme V = maximum velocity reaction. max

K = Michaelis constant m

is the substrate concentration[S] at which the initial rate is one-half of the maximum rate (½ Vmax)

Km value of a substrate depends on its affinity with the enzyme It is the [S] required to saturate half of all of the active sites of an enzyme High Km means Low Km means low affinity with high affinity with enzyme (more enzyme (less substrate needed substrate needed to saturate the to saturate the enzyme) enzyme)

Lineweaver-Burk plot

• Also called the double-reciprocal plot، obtained by taking reciprocals of the Michaelis Menten equation

• It is plotted to calculate the Km and Vmax values and to determine the mechanism of action of enzyme inhibitors

Inhibition a process in which the enzyme activity is

regulated or controlled. To inhibit means to stop the enzyme activity

Inhibitor constant(K ) types i

Competitive Known as Measure of the dissociatio affinity of the n constant inhibitor for the Noncompetitive enzyme

Uncompetitive

Competitive inhibition Noncompetitive inhibition Inhibitor does not have structural Inhibitor & substrate Inhibitor shape similarity to the substrate are Structural analogue

Inhibitor binds to the enzyme at a site away from the substrate Competes with the substrate for binding site (No competition exists Competition binding at the active site of between the inhibitor and the with substrate enzyme substrate).

• E + S ↔ ES à E + P • ES + I ↔ ESI (inactive) Possible (active) • E + I ↔ EI (inactive) equilibria • E + I ↔ EI (inactive)

Unchanged in the presence and Value of V Decreased by the inhibitor max the absence of inhibitor Increased (because substrate K is unchanged (because the and inhibitor compete for m Value of K affinity of S for E is unchanged) m binding at the same site)

Higher concentration of substrate is required to achieve

half-maximal velocity

Characteristi cs n

• Regulatory enzymes usually catalyze the first or an early reaction in a metabolic When the end When the end pathway product of a product of a

• They catalyze a rate metabolic pathway metabolic pathway regulatio of Types limiting reaction that exceeds its is below its controls the overall concentration concentration pathway limit, it inhibits limit, it activates • They may also catalyze a the regulatory the regulatory reaction unique to that enzyme to enzyme to pathway known as normalize the normalize the committed step pathway pathway

Know that: Allosteric enzyme Cooperative binding • The term “allosteric” regulation came from Greek word “allos” meaning “other” Compounds that bind Process by which • E= Enzyme to enzyme other than binding of a ligand to • S= Substrate the catalytic site. a regulatory site affects binding of the Binding of an same or of another allosteric modulator ligand to the enzyme causes a change in the conformation of the enzyme

Modulator Change in the may be binding affinity of enzyme for the substrate Negative decreased Positive: increased E, E, S S affinity(activation) affinity(inhibition)

The subunits are known as Most allosteric enzymes are protomers oligomers (two or more polypeptide chains or subunits)

Allosteric enzyme regulation

Types of interactions occur in allosteric enzymes

Homotropic: Effect of one ligand on the binding of Heterotropic: Effect of one the same ligand (a ligand on the binding of a regulatory enzyme different ligand modulated by its own substrate)

Enzymatic diagnosis and prognosis of diseases

As indicators of enzyme As analytical reagents in activity or conc. in body measuring activity of fluids (serum, urine) in the other enzymes or As therapeutic agents diagnosis/prognosis of compounds in body diseases fluids

Plasma- Serum The most commonly used body fluids for specific markers in measuring enzyme activity are enzymes the diagnosis of diseases There are Serum Plasma • Heart Nonplasma- disease specific • Pancreatic enzymes diseases • Liver diseases