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2013-12-06 12:00:43
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  1. What are the general catalytic strategies with a description?
    • Acid/Base general: AA acts as H+ donor/acceptor
    • Acid/Base specific: water acts as H+ donor/acceptor
    • Covalent: covalent bond formed between enzyme and substrate
    • Metal ion (1): binds to substrate or H2O forming coordination complex (exchange of electrons)
    • Metal ion (2): gain/lose electrons in redox
  2. What is chymotrypsin's catalytic strategy? function?  Describe the important structures and their function.
    • Covalent strategy
    • Cleaves the C side of Y, W, F (aromatics)
    • Hydrophobic pocket: Hydrophobic AAs form pocket and surround aromatic ring of substrate
    • f(x) Gives substrate specificity
    • f(x) Put substrate in correct position
    • Oxyanion hole: Ser195, Gly193
    • f(x) stabilizes tetrahedral intermediates (twice)
    • Catalytic triad: Ser195, His57, Asp102
    • f(x) Acic/base catalysis
    • f(x) covalent catalysis
  3. Give examples of irreversible enzymes
    • COX (cyclooxygenase) is an enzymes which makes prostaglandins (cause pain) and thromboxanes (blood clotting)
    • Aspirin: irreversibly alters COX (cyclooxygenase) active site
    • Thrombocytes do not have organelles and no more COX can be made! (clotting problem)
  4. Give an overview of the initiation/completion of release of glucose from glycogen
    • 1. Epinephrine or glucagon activates adenylate cyclase
    • 2. Adenylate cyclase catalyzes ATP ---> cAMP + PPi
    • 3. cAMP (+ modulator for PKA) increases PKA (protein kinase A) activity
    • 4. PKA phosphorylates glycogen phosphorylase kinase (activated)
    • 5. Glycogen phosphorylase kinase phosphorylates glycogen phosphorylase
    • 6. Glycogen phosphorylase cleaves one glucose-1-P from glycogen
  5. How is glycogen synthesis and breakdown regulated?
    • Glycogen synthase is inactive when phosphorylated (quantity not on/off)
    • Increase in cAMP activates PKA (protein kinase A) which phosphorylates (inactivates) glycogen synthase
    • PP1 (phosphoprotein phosphatase 1) removes P from glycogen synthase (activating)
    • PP1 removes P from phosphorylase kinase (inactivates)
    • PP1 removes P from glycogen phosphorylase (inactivates)
    • PPI (inhibitor) is phosphorylated (activated) by PKA! This binds to PP1 to inactivate!!
  6. Define zymogen, proprotein, and proenzyme
    • Zymogen: proteases that are inactive precursor proteins
    • Proproteins: precursor proteins that get cleaved into proteins (eg procollagen -> collagen)
    • Proenzymes: inactive precursor proteins activated by proteolytic cleave (NOT proteases)
  7. What are the important monomers w/ structure?
    • D-glucose: "anomeric, down, up, down"
    • D-mannose: C-2 epimer of glucose
    • D-galactose: C-4 epimer of glucose
    • D-fructose: ketose, see paper
  8. Describe the maillard rxn
    • aldehyde (aldose) reacts with primary amine (protein) to produce AGEs (age-related glycation endproducts)
    • Causes heart disease, atherosclerosis, kidney disease, blindness, neuropathy
  9. Describe the important disaccharides and give their linkages and relevant enzymes
    • Sucrose: circulating energy in plants (no maillard)
    • glc(α1<->β2)fru
    • Sucrase
    • Trehalose: circulating energy in insects and fungi (no maillard)
    • glc(α1<->α1)glc
    • Trehalase
    • Maltose: breakdown product of starch
    • glc(α1->4)glc
    • amylase
    • Lactose: milk sugar
    • gal(β1<->4)glc
    • lactase
  10. Why store glucose as a polymer?
    • 1. Eliminate free reducing ends (AGEs)
    • 2. Eliminate osmotic pressure ([solute]
    • 3. Reduce hydration shell (increase entropy of bulk water)
    • 4. Increased flow of extracellular glucose
  11. Describe energy storage in plants and animals (w/ linkages)
    • All are glucose homopolymer
    • PLANTS - Starch
    • amylose: α(1->4)
    • amylopectin: α(1->4) with α(1->6) branching
    • ANIMALS: glycogen
    • α(1->4) with extensive α(1->6) branching
  12. Describe large polymers with relevant info (w/ linkages, shape, and enzymes)
    • Cellulose: homopolymer of glucose (#1 in biosphere)
    • β(1->4) ∴ extended structure
    • Not H2O soluble (water barrier)
    • Limited cellulase in nature (protists in ruminids and wood-rot fungi)
    • Starch: homopolymer of glucose
    • α(1->4) ∴ coiled structure
    • amylase, glycogen phosphorylase widely available
    • Chitin: homopolymer of N-acetyl glucosamine (#2 in biosphere)
    • β(1->4) ∴ extended structure
    • Not H2O soluble (water barrier)
    • exoskeleton of arthropods and cell wall of fungi
  13. Describe the glucosaminoglycans (w/ linkage) in detail with function.
    • Hyaluronan: 50,000 monomers (25,000 repeating dimers)
    • GlcA(β1-3)GlcNAc
    • Viscous, clear
    • Synnovial fluid and vitreous humor
    • Chondroitin Sulfate: 20-60 monomers (10-30 repeating dimers)
    • GlcA(β1-3)GalNAc4S
    • Neg charges on same side, forms extended rods that interact +/- sides (cartilage)
    • Keratan: ~25 monomers
    • Gal(β1-4)GalNAc6S
    • Cornea, cartilage, bone, hair, skin, nails
  14. Describe the proteoglycans (w/ linkage) in detail with function
    • Heparin sulfate: 15-90 monomers
    • IdoA2S(α1->4)GlcNS3S6S
    • Most negatively charged biolmolecule on the planet (5- per dimer)
    • Binds antithrombin,preventing clotting
  15. Describe the glycoproteins
    • Proteins with an oligosaccharide
    • ~20 different monomers
    • ~6 different linkages
    • branching
    • eg membrane proteins w/ an oligosaccharide attached
    • present on TSH (thyrotropin) and LH (Luteinizing hormone)
    • Lectin on hepatocyte recognizes the oligosaccharide on TSH and LH, binds them, and pulls them in for degredation
  16. 3 types of inhibition
    • competitive: increase Km, Vmax unchanged
    • Binds E
    • graph shows all intercepting @ y axis (1/Vmax)
    • uncompetitive: decrease Km, decrease Vmax
    • Binds ES
    • graph shows straight lines side by side
    • mixed: increase Km, decrease Vmax
    • Binds E and ES
    • graph shows all lines intercepting not at y-int