Proteins › Enzymes

Enzyme Naming Conventions

Notes

Enzyme Naming Conventions

Sections


Overview

ENZYME NOMENCLATURE

  • Derived from substrate or chemical reaction the enzyme catalyzes
  • Most enzyme names have suffix "–ase"

Isozymes (isoenzymes)

  • Enzymes that catalyze same reaction but have different amino acid sequences (different proteins)

ENZYMES REQUIRING COFACTORS

Apoenzyme

  • Enzyme without the cofactor.

Holoenzyme

  • Enzyme and cofactor together

6 classes of enzymes

Oxidoreductases

  • Catalyze electron transfer reactions (oxidation/reduction reactions)
  • A- + B → A + B-

Transferases

  • Catalyze transfer of functional groups to a molecule
  • A-B + PO4 → A-B-PO4

Hydrolases

  • Catalyze breakage of bonds by hydrolysis (addition of water)
  • A-B-C + H2O → A-B + C

Lyases

  • Catalyze bond cleavage reactions that are not oxidation or hydrolysis reactions
  • A-B-C → A-B + C

Isomerases

  • Catalyze rearrangement reactions
  • A-B-C → A-C-B

Ligases

  • Catalyze reactions in which covalent bonds join two molecules
  • A-D + B-C→ A-D-B-C

Full-Length Text

  • Here we will learn about the naming conventions of enzymes: their characteristic activity typically determines their nomenclature and classification.
  • Start a table.
  • Denote that enzyme names are derived from the substrate or the chemical reaction the enzyme catalyzes.
  • Denote that most enzyme names have the suffix "–ase."
  • Denote that isozymes (aka isoenzymes) are enzymes that catalyze the same reaction but have different amino acids sequences (so they are different proteins).
  • Denote that for enzymes requiring cofactors:
    • An apoenzyme is an enzyme without the cofactor.
    • A holoenzyme is the enzyme and cofactor together.

Let's spend the remainder of our time learning the six classes of enzymes that cover every type of enzyme-catalyzed reaction.

  • Denote that they are:
    • Oxidoreductases
    • Transferases
    • Hydrolases
    • Lyases
    • Isomerases
    • Ligases

Let's start with oxidoreductases.

  • Write that oxidoreductases catalyze electron transfer reactions (oxidation or reduction reactions).
  • As an example, create an equation wherein oxidoreductase catalyzes the transfer of electrons from molecule X to molecule Y.
  • List dehydrogenases as a specific type of oxidoreductase.
    • As a clinical correlation, write that alcohol dehydrogenase metabolizes alcohol via oxidation, thus alcohol affects individuals differently based on their level and isoform of alcohol dehydrogenase.
  • Now, write that transferases catalyze the transfer of functional groups to a molecule.
  • To see how, draw an amorphous protein.
  • Then, show draw that protein with a group added to it.
  • Draw reversible arrows with a group above them to represent how transferases add functional groups to a molecule, such as a protein or a lipid.
  • List phosphotransferases as a type of transferase.
  • As a clinical correlation, write that the transferase phosphofructokinase transfers phosphate groups to substrates.
    • Phosphofructokinase deficiency results in a glycogen storage disease (Tauri's disease) wherein exercise causes patients to develop muscle cramps, weakness, and dark urine (from hemolytic anemia).
  • Now, write that hydrolases catalyze the breakage of bonds by hydrolysis (the addition of water).
  • To illustrate this, draw a drop of water breaking the bond between two molecules.
  • Hydrolysis is one of the most common physiological ways of breaking bonds.
    • List nucleases (which cut nucleic acids) and proteases (which cut proteins) as types of hydrolases.
    • As an experimental correlation, write that endonucleases (called restriction enzymes) cut specific sequences of DNA and are used for DNA modification and molecular cloning.
  • Now, write that lyases catalayze bond cleavage reactions that are not oxidation or hydrolysis reactions.
    • Draw a pair of scissors cutting the bond between two molecules to illustrate the action of lyases.
    • List carboxylases and decarboxylases as examples of lyases.
    • As an ecological correlation, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a plant lyase that cleaves a 5-carbon sugar in the first steps of carbon fixation; it is one of the most abundant and important proteins on earth.
  • Next, write that isomerases catalyze rearrangement reactions.
    • As an abstraction, use several shapes to create a cat
  • Then, show that isomerases rearrange those shapes to form a bird, much like they rearrange atoms to turn one molecule into another.
    • As an example, list triose phosphate isomerase, which converts dihydroxyacteone phosphate to D-glyceraldehyde 3-phosphate during glycolysis.
  • Now, write that ligases catalyze reactions in which covalent bonds join two molecules.
    • As another abstraction, draw a large snowball, then a small one.
  • Next, stack to them to show that ligases join two molecules together.
    • As an example, list DNA ligase, which joins two strands of DNA together to catalyze the formation of a phosphodiester bond.