Enzyme Biology Quiz

Enzymes

• Enzymes are biocatalysts synthesized by living cells.
• They are proteins, colloidal, and thermolabile.
• Enzymes are specific in their actions.
• A catalyst increases the velocity or rate of a chemical reaction without being changed itself.
• Friedrich Wilhelm Kuhne (1878) coined the term "enzyme" (En = in; Zyme = yeast).
• James B. Sumner (1926) isolated and crystallized urease from jack beans, identifying it as a protein.

Enzyme Nomenclature and Classification

• Substrate acted upon: Enzymes are named by adding "-ase" to the substrate they act on.

  • Carbohydrates — carbohydrases
  • Proteins — proteinases
  • Lipids — lipases
  • Nucleic acids — nucleases

• Type of reaction catalyzed: Enzymes are named based on the reaction they catalyze

  • Hydrolases - catalyzing hydrolysis
  • Isomerases - isomerization
  • Oxidases - catalyzing oxidation
  • Dehydrogenases - catalyzing dehydrogenation
  • Transaminases - catalyzing transamination
  • Phosphorylases - catalyzing phosphorylation

• Substrate and reaction: Some enzymes are named to indicate both the substrate and the reaction type.

  • Succinic dehydrogenase - catalyzes dehydrogenation of succinic acid
  • L-glutamic dehydrogenase - catalyzes dehydrogenation of L-glutamic acid

• Substance synthesized: A few enzymes are named based on the substance they synthesize.

  • Rhodonase - forms rhodonate from hydrocyanic acid and sodium thiosulphate
  • Fumarase - forms fumarate from L-malate

Endoenzymes and Exoenzymes

• Endoenzymes: Enzymes that act inside the cells where they are produced. Examples include plant enzymes and metabolic enzymes.
• Exoenzymes: Enzymes released by living cells that catalyze reactions outside the cell—in their environment. Examples include bacterial enzymes, fungal enzymes, and digestive tract enzymes.

International Union of Biochemistry (IUB) Nomenclature and Classification

• The chemical reaction catalyzed is the key to enzyme classification.
• In 1961, IUB classified enzymes into 6 major classes.
• Each major class is further divided into subclasses (4 to 13).

Enzyme Classes (IUB)

• 1. Oxidoreductases: Enzymes that catalyze oxidation-reduction reactions between two substrates.

  • Substrates often contain CH—OH, C=O, CH-CH, CH-NH2 and CH=NH groups.
  • Examples: alcohol dehydrogenase, acyl-CoA dehydrogenase, cytochrome oxidase.

• 2. Transferases: Enzymes moving a group (other than hydrogen) between two substrates.

  • These enzymes catalyze the transfer of one-carbon groups, aldehydic or ketonic residues, and acyl, glycosyl, alkyl, phosphorus, or sulfur-containing groups.
  • Examples: acyltransferases, glycosyltransferases, hexokinase.

• 3. Hydrolases: Enzymes that promote hydrolysis of substrates by adding water across the bond to be split.

  • Substrates include esters, glycosyl, ether, peptide, acid-anhydride, C-C, halide, and P-N bonds.
  • Examples: glucose-6-phosphatase, pepsin, trypsin, esterases, glycoside hydrolases.

• 4. Lyases (Desmolases): Enzymes that remove groups from substrates to create double bonds.

  • They act on C-C, C-O, C-N, C-S, and C-halide bonds.
  • Examples: aldolase, fumarase, histidase.

• 5. Isomerases: Enzymes converting one isomer to another through intramolecular rearrangements.

  • Examples: alanine racemase, retinene isomerase, glucosephosphate isomerase.

• 6. Ligases (Synthetases): Enzymes attaching two compounds by utilizing the energy from a pyrophosphate bond in ATP or similar compounds.

  • They catalyze reactions forming C-O, C-S, C-N, and C-C bonds.
  • Examples: acetyl-CoA synthetase, glutamine synthetase.

Chemical Nature of Enzymes

• Simple enzymes: Contain only proteins. Examples include urease, amylase, and papain.
• Complex enzymes: Include proteins (apoenzyme) and non-protein components (prosthetic group). The combination forms the holoenzyme.
• Coenzymes: Organic, low molecular weight, and dialysable components associated with enzyme function. Often regarded as a second substrates or cofactors. Examples include B-complex vitamins.

Cofactors

• Cofactors: Inorganic, low molecular weight, and dialysable components associated with enzyme function. Most are metal ions.
  • Often associated with the protein (metalloenzymes).
  • Examples: ATPase (Mg2+ and Ca2+), Enolase (Mg2+), Alcohol dehydrogenase, carbonic anhydrase, Alkaline phosphatase, carboxypeptidase, and aldolase (contain zinc).

Active Site

• The active site is a small region where substrate binds and catalyses.

• It exists due to the tertiary structure of the protein and consists of amino acids far apart in the linear sequence.

• Active sites are pockets or crevices and are flexible to promote substrate binding.

• Active site has binding site and catalytic site, and many enzymes use coenzymes or cofactors here

• Common amino acids in active sites include serine, aspartate, histidine, cysteine, lysine, arginine, glutamate, and tyrosine.

• Substrate binds to the enzyme to form an enzyme-substrate complex (ES), catalysis happens, and the product is released.

Mode of Enzyme Action

• Lock-and-key model: Enzyme active site is rigid and pre-shaped, allowing only a specific substrate to bind. This model is outdated.
• Induced-fit model: Enzyme active site changes shape after substrate binding to form stronger substrate binding, which facilitates catalysis. Supported by evidence like X-ray diffraction and understanding allosteric modulators and competitive inhibition.