Enzymes are proteins that act on substrates, catalyzing chemical reactions within the cell. Enzymes are specific in the sense that each enzyme only reacts with a few closely related substrates. Some enzymes require cofactors (biotin, lipoamide, cobalamin) to function properly. Enzymes can become denatured by changes in temperature or pH. Enzymes are classified as oxidoreductases, transferases, hydrolases, lyases, ligases, and isomerases, based on the type of reaction they catalyze. Enzyme kinetics is the study of enzyme reaction rates, which are determined using the Michaelis-Menten and Lineweaver-Burk equations. These equations can be also used to evaluate how different types of enzyme inhibitors affect the reaction rate. Enzyme deficiencies can result in severe diseases such as Lesch-Nyhan syndrome, Gaucher disease, and phenylketonuria.
- Complex proteins that catalyze chemical reactions
- Act on substrates that can either be cleaved or joined to form a new product (e.g., carbonic anhydrase enzyme → CO2 + H20 ⇄ H2CO3)
- Essential for life; if enzymes did not exist, cellular reactions would not occur fast enough to sustain life.
- Enzyme deficiencies can result in severe diseases (e.g., ).
- Enzyme name is usually based on the reaction catalyzed plus the suffix “-ase”: e.g., for the enzyme that adds hydroxyl groups (OH-) is formed as follows: hydroxyl + -ase → hydroxylase
General characteristics of enzymes
- Active site: binding site for a specific substrate on a specific enzyme
- Rate: enzymes catalyze reactions by a factor of 106–1011
- Enzymes do not affect the energy level of substrates or products (free energy released remains the same).
- Enzymes are able to decrease the energy of activation required to start a reaction.
- The velocity of enzymatic reactions increases with temperature (up to 37o C in humans).
- Each enzyme has a specific pH at which it can achieve maximum velocity (Vmax).
- Alterations in pH can cause denaturation of enzymes (specific to each enzyme).
- Example: Pepsin works best in acidic environment like the stomach (pH ∼1.5–2) and it is inactivated in the duodenum when bicarbonate is release from the pancreas, increasing the pH to > 7.
Energy (∆G) for enzymatic reactions usually comes from the break down of ATP or GTP bonds (hydrolysis). Enzymatic reactions can occur spontaneously or nonspontaneously. The following are relationships between energy and enzymatic activity.
- Exergonic: Energy (∆G) < 0: Reactions can occur spontaneously (often irreversible).
- Endergonic: Energy (∆G) > 0: Reactions require energy to occur (from ATP or GDP).
- Balanced reaction: Energy (∆G) = 0: The reaction is at equilibrium (reversible).
|Overview of enzyme classes|
|Oxidoreductases|| || |
|Transferases|| || |
|Hydrolases|| || || |
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|Isomerases|| || |
|Ligases (sometimes called synthetases)|| |
|Overview of energy carriers|
|Base molecule||Transferred group||Carrier of energy||Released energy||Metabolic site||Molecular structure|
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For more information, see “.”
|Overview of cofactors|
|Thiamine pyrophosphate (TPP)|| |
|Coenzyme A|| |
|S-Adenosylmethionine (SAM)|| || |
|Ascorbic acid|| |
|Tetrahydrobiopterin|| || |
|ATP|| || |
|Overview of rate-limiting enzymes|
|Gluconeogenesis|| || |
|De novo pyrimidine synthesis|| |
|De novo purine synthesis|
|Urea cycle|| |
|Fatty acid synthesis|| |
|Ketogenesis|| || |
Description of an enzymatic reaction
Enzymatic reactions with a hyperbolic curve (most common, e.g., alcohol dehydrogenase in ethanol oxidation): E + S ⇄ ES → E + P
- [E] = enzyme
- [S] = substrate
- [P] = product
- [V] = velocity
- A sigmoid curve indicates cooperativity (e.g., oxygen binding to hemoglobin)
Enzymatic reactions with a sigmoidal kinetic are indicative of cooperative binding (e.g., oxygen to hemoglobin).
- Equation: v = Vmax [S] / (Km + [S])
- Maximum velocity (Vmax)
- Michaelis constant: (Km): the substrate concentration at which half of the active sites of the enzymes are bound to the substrate
Lineweaver-Burk equation and plot
- The Lineweaver-Burk equation is a double reciprocal of the Michaelis-Menten equation, where V = Vmax [S] / Km + [S] (if [E] remains constant), becomes 1 / v = Km / Vmax× 1/[S] + 1 / Vmax.
- Represents enzyme kinetics in a linear graph rather than a hyperbola
- Equation is particularly important to determine the effect of drugs on enzymes
- Intercept with y-axis: 1/Vmax, the further from zero, the lower Vmax
- Intercept with x-axis: 1/-Km : the closer to zero, the lower the affinity and the higher the Km
- Slope: Km/Vmax
For details, see “.”
|Overview of drug-response dynamics|
|Parameter||Uncompetitive inhibitors|| |
Competitive inhibitors (reversible)
Competitive inhibitors (irreversible)
|Similar to the substrate|| || || || |
|Effect of increased [S]|| || || || |
|Binding site|| || || |
|Effect on Km|| || || || |
|Effect on Vmax|| || || || |
|Pharmacodynamic effect|| || || || |
Uncompetitive inhibitors are enzyme inhibitors that bind to the enzyme-substrate complex, decreasing Km and Vmax.
Only Companions meet on the waY: Competitive inhibitors meet on the Y-axis (same Vmax), noncompetitive do not.