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14: Mechanisms of Catalysis – Serine proteases, Enzyme modification, Ribozymes

. external link: Chymotrypsin - hydrolyzes peptide bonds on the carboxyl side of aromatic amino acid residues.

B. Mechanism, external link: Chymotrypsin mechanism handout

  1. Catalytic triad forms a charge transfer system to facilitate catalysis
  2. Tetrahedryl intermediate stabilized by enzyme structure, including oxyanion hole
  3. Covalent acyl-enzyme intermediate is relatively stable
  4. Entry of water allows formation of second tetrahedryl intermediate that is similarly stabilized by enzyme
  5. Resolution of second tetrahedryl intermediate restores enzyme and produces second hydrolysis product
  6. Reaction accelerated by approximately a factor of 1010

II. Cofactors - non amino acid compounds that aid catalysis

A. Prosthetic groups - tightly bound to enzyme, e. g. heme and other tetrapyrrols

B. Coenzymes - like prosthetic groups, but not tightly bound so they transiently associate with enzymes, e. g. coenzyme A, FAD, NAD, NADP

Most Vitamins are precursors to coenzymes. Animals cannot make them and they must be obtained from plants or microbes in animal food.

C. Metal ions: like the iron in heme.

Enzymes have been found that require: Fe, Cu, Zn, Mn, Mg, Co, Ni, Mo, V, Se. This is the reason for organisms requiring trace minerals in their diets. They must have these ions for specific enzymes to function.

III. Ribozymes- catalytic RNA

  1. Ribonuclease P - a ribonucleoprotein ribonuclease where the RNA component is catalytic
  2. Self-splicing ribosomal RNA - an RNA that can both cleave and ligate RNA (acting on itself)
  3. The ribosome is a ribozyme - peptidyl transferase (linking amino acids) occurs in a region of the ribosome where there is only ribosomal RNA
  4. Hypotheses for the early life - the "RNA world"

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