Enzymes-1

Study Notes

Enzymes-1

Enzymes are proteins that act as catalysts, increasing the rate of chemical reactions. A literal definition relates them to yeast.
Enzymes are proteins, and some are ribonucleic acids.
Enzymes are highly efficient, producing 10³ to 10⁸ products per second and operating at 37°C. They are not consumed or changed during a chemical reaction.
Enzymes exhibit specificity.
- Substrate specificity: enzymes only attach to one particular substrate (e.g., urease for urea). If the substrate is an isomer (D or L), the enzyme only works on one isomer.
- Group specificity: enzymes target groups of similar compounds (e.g., L-amino acid oxidase only attacks L-amino acids, not D-amino acids).
- Low/relative specificity: enzymes bind to specific types of bonds (e.g. peptidase binds to peptide bonds in different peptide proteins).
- Reaction specificity: enzymes catalyze specific pathways (e.g., glucose oxidase only catalyzes gluconic acid synthesis, not sorbitol synthesis).
Most enzyme names end in "-ase".
Active site (often a cleft): the substrate binding site of an enzyme.
Substrate: the molecule on which an enzyme acts (e.g., starch for amylase, lipids for lipase).
Holoenzyme (active enzyme) = Apoenzyme (protein part of the enzyme) + Coenzyme or cofactor (non-protein part of the enzyme).
Not all enzymes require coenzymes. Coenzymes are complex, non-protein organic molecules that function as group transfer reagents and are categorized into two groups.
Prosthetic group: a cofactor that binds strongly to an apoenzyme (e.g., heme in hemoglobin).
Cofactors: cofactors weakly bind and easily dissociate from apenzymes (e.g., NAD in liver alcohol dehydrogenase).
Not all enzymes are synthesized in their active form; some are synthesized as zymogens (e.g., pepsinogen, trypsinogen, and chymotrypsinogen).
Most polar amino acids participate in catalysis within one or more enzymes.
Enzyme-catalyzed reaction have three steps (Michaelis-Menten equation):
- Binding of substrate: E + S <=> ES
- Conversion of substrate to product: ES <=> EP
- Release of product : EP → E + P
  - S = substrate; E= enzyme; ES= enzyme-substrate complex; P = product
  - k₁, k_-1, and k₂ are rate constants.
The graph of substrate over time shows a decrease in substrate concentration with corresponding increase in product.
Active enzyme = protein part + non-protein part
Holo enzyme = (apoenzyme) + (cofactor)
Protein part features an active site (like a pocket or cleft).
Role of active site: substrate binding, determining enzyme specificity, and participating catalytically.
E + S <=> ES <=> EP <=> E + P

Enzyme Nomenclature

Trivial names: common names (e.g., pepsin, trypsin).
Systematic names: include substrate name and "ase" (e.g., lipase, amylase, protease). This can also include type of reaction (e.g., lactate dehydrogenase).