Part 5

• Cellular metabolism

  1. Enzymes work together in sequential pathways

  2. Each reaction catalyzed by a different enzyme

  3. Reaction product of one enzyme becomes substrate of next
• Functional compartmentalization of cellular chemistry

  • Accelerates individual reactions
  • Provides opportunities for precise regulation of all cellular processes
• Regulatory enzymes


  • Have a greater effect on the rate of the overall sequence
  • Catalytic activity increases or decreases in response to certain signals
• Adjustments in the rate of reaction catalyzed by regulatory enzymes

  Allows the cell to meet changing needs for energy and biomolecules required in growth and repair
• Allosteric enzymes

  Function through reversible, noncovalent binding of regulatory compounds called allosteric modulators or allosteric effectors
• Covalent modifications

  Reversible modifications of amino acid residues in the enzyme molecule
• Allosteric enzymes and covalent modifications tend to be multisubunit proteins, and in some cases the regulatory sites and the active site are on separate subunits
• Regulatory proteins


  Enzymes are stimulated or inhibited when bound to separate regulatory proteins
• Proteolytic cleavage


  Enzymes are activated when peptide segments are removed, which is irreversible
• Regulatory protein and proteolytic cleavage are found in physiological processes such as digestion, blood clotting, hormone action, and vision
• Cell growth and survival depend on efficient use of resources, and this efficiency is made possible by regulatory enzymes
• No single rule governs which of the various types of regulation occur in different systems, several types may occur in a single regulatory enzyme
• Allosteric proteins


  Proteins having different shapes or conformations induced by the binding of modulators
• Homotropic regulation

  Regulation in which the substrate and modulator are identical
• Heterotropic regulation


  Regulation in which the modulator is a molecule other than the substrate
• Allosteric enzymes

  • Have active sites and regulatory/allosteric sites
  • Typically larger and more complex than nonallosteric enzymes, with two or more subunits
• Aspartate transcarbamoylase (ATCase)


  • Catalyzes an early step in pyrimidine nucleotide biosynthesis
  • Has 12 polypeptide chains organized into 6 catalytic and 6 regulatory subunits
  • Exhibits allosteric behavior with cooperative catalytic subunits
  • Regulated by ATP and CTP as positive and negative modulators respectively
• Sigmoid kinetic behavior


  Reflects cooperative interactions between multiple protein subunits, changes in one subunit are translated into changes in adjacent subunits
• Small changes in modulator concentration

  Can cause large changes in enzyme activity in the steep part of the sigmoid curve
• Heterotropic allosteric regulation


  An activator may cause the curve to become more hyperbolic, a negative modulator may produce a more sigmoid curve
• Covalent modification of enzymes

  Over 500 different types, including phosphoryl, acetyl, ubiquitin, SUMO, ADP-ribosyl groups
• Phosphorylation


  The most common type of regulatory modification, about one-third of all proteins in a eukaryotic cell are phosphorylated
• Phosphorylation of enzymes

  1. Catalyzed by protein kinases

  2. Gamma-phosphoryl group from ATP is transferred to specific amino acid residues
• Nitrogen reductase


  Enzyme that catalyzes the important process of biological nitrogen fixation
• Diphtheria and cholera toxin

  Enzymes that catalyze the ADP ribosylation (and inactivation) of key cellular enzymes or other proteins
• Types of regulatory modification

  • Phosphorylation
• About one-third of all proteins in a eukaryotic cell are phosphorylated, and one or often many phosphorylation events are part of virtually every regulatory process
• Some proteins have only one phosphorylated residue, while others have several, and a few have dozens of sites for phosphorylation
• Phosphoryl Groups Affect the Structure and Catalytic Activity of Enzymes
• Protein kinases

  Enzymes that catalyze the attachment of phosphoryl groups to specific amino acid residues of a protein
• More than 500 genes encoding these critical enzymes are found in the human genome
• Protein phosphorylation

  1. Substrate binding

  2. Transition state facilitation

  3. Catalysis

  4. Release
• Phosphoprotein phosphatases

  Enzymes that catalyze the removal of phosphoryl groups from proteins
• Glycogen phosphorylase

  Enzyme that catalyzes the reaction (Glucose)_n + Pi (glucose)_n-1 + glucose 1-phosphate
• Glycogen phosphorylase

  • It adds a phosphate to the substrate, but is not itself a kinase as it does not utilize ATP or any other nucleotide triphosphate as a phosphoryl donor
  • It is the substrate for a protein kinase that phosphorylates it
• Phosphorylase a


  The more active form of glycogen phosphorylase
• Phosphorylase b

  The less active form of glycogen phosphorylase
• Conversion of phosphorylase b to phosphorylase a

  2 ATP + phosphorylase b 2 ADP + phosphorylase a
• Conversion of phosphorylase a to phosphorylase b


  Phosphorylase a + 2H2O phosphorylase b + 2Pi
• The phosphoryl groups of phosphorylase a are hydrolytically removed by a separate enzyme called phosphoprotein phosphatase 1 (PP1)