Biochemistry Lo: Enzyme Mechanisms

Front 1

Define the active site of enzymes

Back 1

The active site is the "binding site" and is a specific region on an enzyme where the substrates are bound.

Properties:

--Takes up a relatively small part of the total volume of the enzyme

--3D entity formed by groups from different parts of the linear amino acid sequence

--It is a cleft or crevice

--Bound to substrates via multiple weak, reversible attractions such as hydrophobic interactions, ionic interactions, and hydrogen bond.

--Displays specificity of binding, which depends on the precisely defined arrangement of atoms in the active site.

Front 2

Outline the induced-fit model of enzyme-substrate interaction

Back 2

In a reaction, the enzyme active site and substrate have a similar structure. During the reactions, the binding of the substrate induces changes at the active site that allow the active site to become complimentary to the substrate. This is accomplished by the rearrangement of the chemical groups and the enzyme becomes complimentary to the transition state. When the substrate binds to the enzyme, the multiple weak interactions release a large amount of energy that offsets the activation energy for the reaction to occur.

Front 3

Identify the three catalytic mechanisms: acid-base, metal ion, and covalent catalysis

Back 3

--Acid-base: a proton can be transferred to help stabilize an unstable intermediate to promote the production of products and not reform the reactants.

--Metal ion: ionic interaction between an enzyme-bound metal and a substrate can help orient the substrate for reaction of stabilize charged reaction transition states. Metals can also mediate oxidation-reduction reactions by reversible changes in the metal ion's oxidation state.

--Covalent catalysis: a transient covalent bond is formed between enzyme and the substrate. The functional groups of some enzyme cofactors can serve as nucleophiles in the formation of covalent bonds with substrates, which can activate a substrate for farther reaction.

Front 4

Outline the catalytic mechanism of the serene protease chymotrypsin

Back 4

Chymotrypsin uses a combination of acid-base catalysis and covalent catalysis. Chymotrypsin is a protease that specifically cleaves the peptide bond between bulky hydrophobic amino acid residues (Phe, Trp, Tyr, and others) and the next residue. At active sites: histamine, Asp, and Ser =catalytic triad. Most active at pH 8 (pH of GI tract). Chymotrypsin catalysis involves a covalent intermediate.

When substrate binds, the side chain of the residue adjacent to the peptide bond to be cleaved nestles in a hydrophobic pocket on the enzyme, positioning the peptide bond for attack. The oxyanion hole is + and attracts the negative charge of the carbonyl oxygen, stabilizing it with H-bonding. The oxyanion hole is formed by Gly and Ser. Cleavage of peptide bond releases half the product. The other half is (transiently) covalently bound to enzyme. A water molecule is deprotonated by base catalysis. Collapse of the tetrahedral intermediate forms the second product, a carboxylate anion, and displaces Ser. Dissociation of the second product from the active site regenerates free enzyme.