Basics of enzymes

Active site

specific site for a substrate to bind, this causes a conformational change

Allosteric enzyme

has both an active site and another site that an effector molecule can bind

Efficiency

highly efficient 10^3 to 10^8 faster, speed?

Specificity

highly specific due to active site

Holoenzymes

the active form of the enzyme (apoenzyme + cofactor)

Apoenzyme

inactive form of the enzyme

Cofactor

a nonprotein activator of the reaction such as zinc, magnesium, or iron

Coenzyme

a small organic molecule such as NAD

Isozyme

enzyme varients, different structure bit simular function

Regulation

enzyme activity can be increased or decreased

Location

 different locations can organize the enzymes and provide the best environment for the enzyme to be active

Oxidoreductase

catalyze oxidation-reduction reactions, utilize NADP or NAD as co-factors

• ex. HMG-CoA reductase, superocide reductase

Transferases

catalyze transfer of a functional group from one molecule to another

• ex. Acyltransferase, peptidyl transferase

Hydrolases

catalyze cleavage of bonds by adding water

• ex. lipases, phosphatases, glycosylases, peptidases

Lysases

catalyze cleavage of C-C, C-S, and certain C-N bonds often forming a double bond or a new ring structure

• ex. Citrate lyase

Isomerases

catalyze structural rearrangement of a molecule

• ex. Alanine racemase

Ligases

catalyze formation of bonds between carbon and O, S, N coupled to hydrolysis of high energy phosphates, such as ATP

• ex. DNA ligase

use of enzymes in the Nucleus

DNA and RNA synthesis

use of enzymes in the Cytosol

• Glycolysis

• Pentose phosphate pathway

• Fatty acid synthesis

use of enzymes in the Mitochondria

• TCA cycle

• Fatty acid oxidation

• Oxidation of pyruvate

use of enzymes in the Lysosome

• Degradation of complex macromolecules

what do enzymes change?

the speed and activation energy, not the equilibrium

• delta G stays the same

How do enzymes lower the activation energy?

• transition state stabilization

  • active site of the enzyme binds the substrate and initiates conversion to the transition state

  • by stabilizing the transition state, the reaction can continue to the final product

• catalysis

  • active site on the enzyme participates in providing the catalytic groups to enhance the probability of the formation of the transition state

list the 3 factors affecting the velocity of a reaction

• substrate concentration

• temperature

• pH

Substrate concentration effecting velocity of reaction

• for a concentration of enzyme, there is a maximal amount of substrate that yields Vmax (maximum velocity)

• most enzymes (besides allosteric enzymes) follow a Michaelis-Menten hyperbolic curve (hump)

Temperature effecting reaction velocity

• increasing temperature will increase the number of substrate molecules with sufficient energy to form product

• increasing temperature further will deactivate enzyme

pH effecting reaction velocity

• different enzymes will have peak velocity at a diff pH depending on the ionized state of he enzyme

• concentration of protons will affect velocity of reaction

• pH can denature enzymes

• pH can activate or inactivate enzyme (ex. stomach acid)