Enzymes structure and function

RNA polymerase from Saccharomyces cerevisiae, a species of yeast that has been instrumental in winemaking, baking and brewing since ancient times,

During the third session we continued to study enzymes. We learned that there is movement to the enzyme parts, like certain amino acids, certain functional groups that can create loops, a secondary unit or a whole domain of protein. Enzymes are called by the name of the reaction they catalyze, like Lactase, DNA polymerase, or the name of the substrate, like DNA polymerase, Lactase. We mentioned digestive enzymes in our digestive system like Pepsin, Trypsin, Chymotrypsin, and they are pure proteins.

We mentioned a few groups of enzymes:

Transferases, they transfer methyl or phosphate groups.

Hydrolases, they perform hydrolysis of various bonds.

Lyases, they cleave various bonds NOT by hydrolysis.

Isomerases, they catalyze isomerization changes.

Ligases, they join two molecules with covalent bonds.

Enzymes are globular proteins acting alone or with larger complexes. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme.

Structure determines function. The structure unfolds when exposed to heat or chemical denaturants and those cause loss of biological activity.

However, in hot springs there are microorganisms containing enzymes that are protected from denaturation by the high temperature.

Enzymes are larger than their substrate. Only a small portion of them, 2-4 amino acids is directly involved in the catalysis. The catalytic site and the binding site together are called the active site. The remaining majority of the enzyme structure serves to maintain the precise orientations and dynamics of the active site. In some enzymes no amino acids are directly involved in the catalysis. Enzyme structure may also contain allosteric sites where the binding of a small molecule causes conformational change that increases or decreases its activity.

There is a small number of RNA based biological catalysts called ribosimes. They can act alone or in complex with proteins like the ribosome and catalytic RNA components

Enzymes must bind to their substrate before they can catalyze any chemical reaction. They are very specific to the substrate they bind. Specificity is achieved by binding pockets with complementary shape, charge, and hydrophilic / hydrophobic characteristics to the substrate.

Enzymes can distinguish between similar substrate molecules to be chemo selective, region selective and stereo specific.

Enzymes lower the activation energy required for the reactions to happen and cause the reactions to be performed much faster than it would have happened without the enzymes.

They act according to the "Induced fit model" that many scientists support. We will continue to experiment next session.