What are enzymes?
Proteins that catalyze thousands of chemical reactions.
How do enzymes facilitate reactions?
Enzymes facilitate reactions by increasing the reaction rate.
Is the enzyme regenerated after the reaction is complete?
What does thermodynamics predict?
1. Whether a chemical reaction is feasible 2. Whether the reaction will occur spontaneously with the release of energy.
Delta G = ?
G(product) - G(reactant)
If G(reactant) > G(product), what happens?
Delta G is negative and the reaction proceeds spontaneously, releasing energy.
Do thermodynamics affect the speed of the reaction?
Draw a Gibbs free energy diagram.
How does an enzyme affect the free energy diagram?
The enzyme lowers the activation energy (the energy it takes to convert a substrate to a product through an intermediate transition state). It does NOT lower the overall free energy of the reaction.
What is the active site of an enzyme?
The active site of an enzyme is the specific region of the enzyme that binds the substrate and carries out the catalysis of the reaction.
What is carboxypeptidase A?
A GI enzyme synthesized in the pancreas and delivered to the small intestine lumen, where it degrades peptides by removing amino acids from the C-terminus one by one.
How does the substrate bind to carboxypeptidase A?
It fits into a hydrophobic pocket C-terminus-first. This enzyme prefers large hydrophobic amino acids. In addition, the C-terminus COO- hydrogen bonds with Arginine (+).
Carboxypeptidase A contains a ___ ion, held in place by 2 ___ and 1 ___ via coordinate covalent bonds. ___ is also bound to this ion and will be used to hydrolyze the peptide bond.
Zinc; His; Glu; Water
Draw the mechanism by which carboxypeptidase A cleaves the peptide bond.
What is the induced fit theory?
The induced fit theory states that the binding of the substrate can induce conformational changes on the enzyme.
Define oxidoreductases and give an example.
Oxidoreductases move an electron, hydrogen, or oxygen from one substrate to another.
Example: Alcohol dehydrogenase moves an OH to an aldehyde.
Define transferases and give an example.
Transferases move a chemical group from one molecule to another.
Example: Kinase that moves a phosphate from ATP to a protein
Define hydrolases and give an example.
Hydrolayses use water to make two products from a substrate.
Example: carboxypeptidase A
Lyases cleave C-C, C-N, or C-O bonds. Sometimes they make them (these are called synthases).
Isomerases move a group or double bond within a molecule.
Ligases join atoms together using energy, usually from ATP (also called synthetases).
What is a coenzyme?
A coenzyme is a small, nonpolypeptide molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a covalent bond to the substrate.
What is a cofactor?
A cofactor is an inorganic ion or coenzyme required for an enzyme's activity.
What is a cosubstrate?
A cosubstrate is a cofactor that is modified during the reaction and leaves the active site.
What is a prosthetic group?
A prosthetic group is a tightly bound cofactor that is regenerated after the reaction.
Draw the reaction equation for a single substrate reaction that forms one product and is irreversible.
What are k1, k2, and k3?
Rate constants; they determine the equilibrium dissociation constant (how tightly the substrate binds).
What does the equilibrium dissociation constant measure?
How tightly the substrate binds
If k3 is relatively small compared to k1 and k2...
...it indicates that ES --> E+P is the rate determing step and is thus designated as kcat (catalytic rate constant).
v = ?
v = d[P]/dt