The active Site of an enzyme

complementary weak forces

complementary functional groups to establish H-bonds charge-charge interactions, hydrophobic groups, pr van der waals fitting.

H2O catalytic reaction

excluded from the active site but can participate in the reaction by providing needed hydrogens or hydroxyl groups for the reaction.

Geometric specificity

highly selective binding and interacting with specific chemical/functional groups of a substrate. This also uses weak forces for substrate binding (Complementary shapes, Complementary weak forces)

stereospecificity

highly specific binding of chiral substrates. Enzyme binding site only recognizes one stereoisomer of a chiral molecule. (L or D-AA). thus substrate binding can be described as asymmetic. since only one isomer fits in the binding site.

The substrate binding site

the forces involved are weak forces and we want them to be reversible. ( Hydrogen bonds, electrostatic, Van der waals, hydrophobic) which can be easily formed and easily broken.

hydrophobic

the spacial positioning and association of complementary hydrophobic groups helps to stabilize substrate binding.

electrostatic

the spacial positioning or pairing of complementary positive and negative charges helps to establish charge-charge interactions, stabilizing effect.

Hydrogen bonds

the substrate can provide the proton or the electronegative atom with the enzyme providing the complementary proton/electronegative atom to thus form the hydrogen bond and stabilize substrate binding.

Catalyic functions of ionizable side groups.

Anion/cation binders (+/-) charged AAs Proton transfer (ionizable R groups) cavalent linkage (acyl groups to OH/SH)

Critical AA for catalysis

Charged side chains, ionizable side groups, polar side groups. the AAs used for catalysis are specifically positioned on the surface of the active site where they can interact with specific atoms/functional groups of the substrate and help specifically position them to match up with their catalytic AAs.

Active site

On the enzyme the site that binds the substrate is known as the substrate binding site or the active or catalytic site. Note that the substrate binding and catalysis are two separate events which can use two different AAs therefore it is possible to alter specific amino acids within the enzyme pocket and disrupt substrate binding or substrate catalysis without affecting the other.

Coenzymes

Small organic molecules that are either weakly bound (cosubstrates) or tightly bound (Prosthetic groups) to the enzyme. functioning as transfer agents.

complementary shapes

Substrate shape must fit into the enzyme active site

Substrate specificity

recognize a specific substrate structure.

The enzyme catalytic site

the active site possesses amino acid residues that participate in the catalytic reaction of the enzyme. The AA can be the same or different from the ones used in substrate binding. Site-directed mutagenesis to disrupt catalysis but not substrate binding. Amino acid mutation in the active site does not affect catalytic activity but substrate binding.