Enzymes

Enzymes are protein catalyst that increase the rate of reaction without changing itself in the end of the process.

Classification of Enzymes

Enzymes are classified according to International Union of Biochemistry and Molecular Biology (IUBMB). There are classified into 6 major classes:

Oxidoreductases

Oxidareductases catalyst the oxidation and reduction reactions. For example: lactate dehydrogenase.

Hydrolases

Hydrolases catalysts the cleavage of bonds by adding in water.

Transfereases

Transfereases catalyst the transfer of group from one to another.

Lyases

Lyases catalysts the breakdown of substances.

Ligases

Ligases catalyst the joining of substances by forming new products.

Isomerases

Isomerases catalyst the racemization of geometric isomers.

Action of Enzymes

Enzymes have active sites which create the 3D surface complementary to substrates. Enzymes are specific to substrates. Substrate binds to enzyme forming enzyme-substrate complex (ES). After the reaction, the product is released from enzyme (Figure 1). Example of Ubiquitin-activating enzyme binds with substrate ubiquitin as shown in Figure 2.

Most enzyme-catalyzed reactions are highly efficient by increasing the reactions 103 to 108 faster compared uncatalyzed reactions.

Enzyme mechanism
Figure 1: Action of Enzyme
Enzymes
Figure 2: Ubiquitin-activating enzyme bound to Ubiquitin
Enzymes, free activation of energy
Figure 3: How Enzyme Works

Basically, all the chemical reactions have the energy barrier separating the reactants and products as shown in Figure 3. This energy barrier is called free activation of energy. Reactants have to overcome this barrier then only the products will be formed. The higher the free activation of energy, the slower the chemical reaction to form products. Enzymes increase the rate of reactions by providing an alternative reaction pathway with lower free energy of activation. The enzymes do not change the energy of reactants and products (Figure 3).

Michaelis-Menten Equation

Leonor Michaelis and Maude Menten proposed a enzyme reaction model where the enzyme combines reversibly to substrate to form enzyme-substrate complex and subsequently form product and free enzyme (Figure 4).

Michaelis Menten, Enzymes
Figure 4: Michaelis Menten Model

Michaelis-Menten equation describes how the reaction velocity is affected by concentration as shown in Figure 5 and Figure 6.

Michaelis Menten Equation, Enzymes
Figure 5:Michaelis Menten Equation

V max is the maximal velocity of an enzyme activity.

Km is the concentration of substrate from half of Vmax.

 

Enzymes, Velocity, Substrate
Figure 6: Effects of Substrate Concentration against Velocity

Three assumptions of Michaelis-Menten equation:

  1. The concentration of substrate is greater than concentration of enzymes.
  2. Concentration of enzyme-substrate complex does not change the time.
  3. The enzyme reaction is analyzed based on initial velocity.

The conclusions of Michaelis-Menten equation:

  1. Small Km means higher affinity between enzyme with substrate. The low concentration of substrate is needed to achieve the 1/2 Vmax.
  2. Larger Km means lower affinity between enzyme with substrate. The large concentration of substrate is needed to achieve the 1/2 Vmax.
  3. The rate of reaction is directly proportional to enzyme concentration at all concentration of substrates.

Inhibition of Enzyme Activity

Inhibitor is substrate that can reduce the enzyme catalyzed reaction. Two types of inhibitions:

  1. Competitive enzyme inhibition
  2. Noncompetitive enzyme inhibition

Competitive Enzyme Inhibition

Inhibitors bind reversible to active site of enzymes. Inhibitors compete with substrates for the active site.

The reaction with inhibitors show the same Vmax with reaction without inhibitors. Sufficient amount concentration of substrates will reach the Vmax same with reaction without inhibitors. Competitive inhibitors increase the Km where more substrates are necessary to achieve the same 1/2 Vmax.

Michaelis-Menten plot competitive inhibition
Figure 7: Michaelis-Menten Plot Competitive Inhibition (1- Enzyme reaction without inhibitors, 2- Enzyme reaction with inhibitors)

Noncompetitive Enzyme Activity

Michaelis-Menten plot non-competitive inhibition
Figure 8: Michaelis-Menten Plot Noncompetitive Inhibition (1- Enzyme reaction without inhibitors, 2- Enzyme reaction with inhibitors)

Noncompetitive inhibitors bind everywhere of enzyme except active site. They do not compete with substrate.

The Vmax cannot be overcome by increasing the concentration of substrate. Thus, The Vmax decreases. The noncompetitive inhibitors do not compete with substrate for active sites, so the Km is remain the same.

Reference:

  1. Champe, PC, Harvey, RA. 2007. Biochemistry. Lippincott’s Illustrated Review. 4th Edition. Lippincott Williams & Wilkins.

Comments

comments

%d bloggers like this:
Visit Us On TwitterVisit Us On FacebookVisit Us On PinterestVisit Us On Google PlusCheck Our Feed