Enzyme Kinetics and Regulation; Metabolism

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RobbyG
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283031
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Enzyme Kinetics and Regulation; Metabolism
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2014-09-16 21:51:54
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2014-8-19
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  1. Km
    Km=[S] 

    (at 1/2 Vmax)
  2. phosphofructo-kinase-1
    (PFK-1)
    • -rate limiting step in glycolysis
    • -activated by high levels of fructose-2,6-bisphosphate (high insulin levels)
    • -activated by high AMP
    • -Inhibited by ATP + Citrate and low levels of Fructose-2,6-bisphosphate (high glucagon levels)
  3. Isocitrate Dehydrogenase
    Isocitrate -->alpha-ketoglutarate

    • Inhibited by: ATP and NADH
    • Activated by: ADP and Ca2+

    Rate limited Step of TCA
  4. Pyruvate Dehydrogenase Complex
    • Pyruvate --> acetyl CoA
    • takes place in mitochondria
    • requires thiamine and niacin
    • releases CO2 and NADPH
    • Activated by (dephosphorylated): Ca2+ in muscle; and pyruvate
    • Inhibited by (phosphorylated): ATP; Acetyl CoA; NADH

    (inhibitors and activators work through PDH kinase/phosphatase i.e. pyruvate inhibits PDH kinase)
  5. Pyruvate Kinase
    • PEP -->  Pyruvate
    • in liver: fee forward activation by fructose-1,6-bisphosphate (likes kinase activity to PFK-1)
    • inactivation by phosphorylation due to glucagon signaling (shunts PEP from glycolysis to gluconeogenesis pathway)
  6. fructose-2,6-phosphatase
    • active when insulin/glucagon ratio is low
    • active when phosphorylated
    • converts fructose-2,6-bisphosphate (activator of PFK-1) to fructose-6-phosphate (gluconeogesis pathway)
  7. PFK-2
    • active with high insulin/glucagon ratio
    • active when not phosphorylated
    • converst fructose-6-phosphate to fructose-2,6-bisphosphate (activator of PFK-1)
  8. glucokinase
    • glucose --> glucose-6-phosphate
    • only in liver
    • Inhibition: sequestered by GKRP in presence of fructose-6-phosphate (isomer of glucose-6-phosphate and substrate for PFK-1); additionally inhibited by low blood glucose
  9. hexokinase
    • glucose --> glucose-6-phosphate
    • in most tissues
    • inhibited by: glucose-6-phosphate
  10. Valine
    • Val; V
    • hydrophobic
  11. Tyrosine
    • Tyr; Y
    • hyrdophobic (with slight polar at -OH)
    • aromatic with -OH group
    • can be phosphorylated
  12. phenylalanine
    • Phe; F
    • hyrdophobic
  13. tryptophan
    • Trp; W
    • hyrdrophobic
    • aromatic with >NH group
  14. Methionine
    • Met; M
    • hydrophobic
    • contains sulfur
    • start amino acid (N-term)
  15. isoleucine
    • Ile; I
    • hydrophobic
  16. Leucine
    • Leu; L
    • hydrophobic
  17. glycine
    • Gly; G
    • special amino acid
    • no R-group
    • allows for flexibility
    • found in loops between secondary structure
  18. proline
    • Pro; P
    • special amino acid
    • disrupts secondary structure by causing conformational constraints
  19. glutamic acid
    • Glu; E
    • charged
    • deprotonated (- charged) carboxyl group
  20. aspartic acid
    • Asp; D
    • charged
    • deprotonated (- charged) carboxyl group
  21. arginine
    • Arg; R
    • charged
    • =NH2+ group
  22. lysine
    • Lys; K
    • charged
    • -NH3+ group
  23. histidine
    • His; H
    • charged
    • numidazol ring with >NH pKa=6:
  24. glutamine
    • Gln; Q
    • polar
    • -NH2 group
  25. asparagine
    • Asn; N
    • polar
    • -NH2 group
  26. serine
    • Ser; S
    • polar
    • -OH group
    • can be phosphorylated
  27. cysteine
    • Cys; C
    • polar
    • -SH group
    • disulfide bonds under oxidizing conditions
  28. threonine
    • Thr; T
    • polar
    • -OH
    • can be phosphorylated
  29. first order rxn
    A -->P
  30. second order rxn
    • 2A --> P
    • A + B --> P
  31. reaction order
    refers to the number of molecules that need to interact
  32. steady-state
    • reaction is at saturation
    • [ES] does not change
  33. Michaelis-Menton Equation
    V0= (Vmax[S])/(Km+[S])

    V0=initial velocity at these conditions

    assumes [S]>[E] and steady state conditions
  34. kcat
    • catalytic constand or turnover # for an enzyme. 
    • Number of rxns that an enzyme performs per second
  35. Catalytic Efficiency
    • kcat/Km
    • a measure of the catalytic efficiency
    • limited to the diffusion rate of an enzyme
    • 108-109 is the theoretical maximum
  36. Lineweaver-Burke Plot
  37. Eadie-Hofstee Plot
  38. Competitive Inhibition
    • this occurs when an inhibitor binds reversibly to the same site as the substrate
    • reduces the effective enzyme concentration
    • apparent Km is reduced and Vmax remains unchanged
  39. Mixed (noncompetitive) Inhibition
    • occurs when the inhibitor can bind the enzyme or ES complex
    • neither situation gives a product
    • reduces the activity of an enzyme
    • causes a decrease in Vmax
    • Enzyme affinity for the substrate is not affected so Km remains unchainged
  40. Sequential reaction
    occurs when both substrates first bind to E and then the products are released
  41. Sequential Ordered rxn
    must bind substrate A then B and then product is released
  42. sequential random
    enxyme does not care which (of two) enzymes it binds first.  After simultaneously binding both it releases a product
  43. ping-pong reactions
    enzyme binds substrate and releases product P and the enzyme ismodified.  It then binds second substrate and releases product Q and returns to its original state. 
  44. Oligomeric Allosteric Enzymes
    • do not obey Michealis-Menton Kinetics
    • show sigmoidal curve ([S] v. Velocity]
    • multimeric allosteric enzymes
  45. feedback inhibition
    where the product of a pathway acts to slow down an intial step, often through allosteric effects
  46. covalent modification
    directly affects the affinity of an enzyme for a substrate
  47. binding of ligand
    signaling molecule that often affects the quaternery structure of the enzyme
  48. What amino acids can be phosphorylated?
    serine, threonine, and tyrosine
  49. Ligand binding (Ca2+ and calmodulin) 
    • Calmodulin is a long helical structure that is broken in the middle when bound by Ca2+
    • this new flexibility allows it to wrap around a target protein
    • this can block an inhibitor bound to an enzyme such as in the case of phosphoylase kinase
  50. cAMP
    • Glucagon binds receptor
    • Internally-the heterotrimeric complex falls off
    • alpha unit is released and exchanges GDP for GTP
    • alpha unit stimulates cAMP synthesis before being hydrolized back to GDP form
    • cAMP causes a phosphorylation cascade signaling low blood glucose
  51. Futile cycle
    Unregulated catabolism and biosynthesis which leads to heat production and no life
  52. ATP set point
    • 3%AMP
    • 12%ADP
    • 85%ATP
  53. NAD+/NADH
    • participates in redox rxns
    • can reduce molecules by taking H:
    • NAD+/NADH is in 100:1 ratio (favors oxidized form;  creates a oxidizing environment for catabolism)
  54. NADP+/NADPH
    • maintained at a lower total conc. than NADH
    • used as a reducing agent for biosynthesis
    • NADP+/NADPH is in 1:100 ratio (favors reduced form; creates a reducing environment for biosynthesis)
  55. Roles of Carbohydrates in our bodies
    • 1: structural (attached to proteins and lipids)
    • 2: catabolic (fuel)
    • 3: Biosynthetic (precursor to nucleic acids)
    • 4: storage (as glycogen or converted to fat)
  56. pyruvate carboxylase
    • mitochondrial enzyme that generates OAA from pyruvate 
    • Inhibited by: ADP (OAA is needed for gluconeogenesis; shunts pyruvate down catabolic pathway)
    • Activated by: acetyl CoA (if this builds up TCA is not working fast enough)
  57. PEP carboxykinase (PEPCK)
    • In liver cytosol: converts OAA to PEP for gluconeogenesis
    • Rate limiting step 
    • Inhibited by: ADP; Insulin
    • Activated by: Glucagon (low blood glucose promotes gluconeosynthesis in liver)
  58. Fructose-1,6-bisphosphatase
    • reciprocal of PFK1 in glycolysis
    • used in gluconeogenesis to convert fructose-1,6-bisphosphate to fructose-6-phosphate
    • inhibited by: AMP; fructose-2,6-biphosphate (high insulin levels; PFK2 is unphosphorylated and convers more fructose-6-phosphate to fructose-2,6-bisphosphate)
    • Activated by: citrate (high citrate means that there is lots of substrates in TCA and a backup in catabolism)
  59. Glucose-6-phosphatase
    • removes phosphate to make free glucose to be exported into blood
    • active with high internal cAMP levels (high glucogan)
    • part of gluconeogenesis in liver cells
  60. glycogen synthase
    • starting with 4 glucose primer, makes glycogen from UDP Glucose (found in quasi equilibrium with G6P)
    • makes straight chain
    • branching requires additional enzyme
    • active when insulin is high (dephosphorylated)
  61. glycogen phosphorylase
    • removes glucose from glycogen chain
    • activated by high glucagon levels (phosphorylated)
    • Ca2+ in muscle during contraction signals increased need for energy and activates phosphorylase through calmodulin binding
    • Ca2+ in liver is triggered by epinephrine 'fight or flight' and activates phosphorylase through calmodulin binding

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