Chapter 6: Enzymes

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Chapter 6 Enzymes

• Dr. Clower
• Chem 4202

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Part 1 Enzymatic Catalysis

• Sections 6.1, 6.2, 6.4
• What is an enzyme?
• What is a catalyst?
• Mechanisms of enzyme catalysis
• Examples

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What is an enzyme?

• Globular proteins acting as the bodys catalysts
• Nomenclature
• Root ase
• Classification
• Oxidoreductases
• Transferases
• Hydrolases
• Lyases
• Isomerases
• Ligases/synthetases
• E.C. Numbers

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What is a catalyst?

• Speed up time for reaction to reach equilibrium
• Lowers activation energy

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Enzymes as Catalysts
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Methods of catalysis

• Provide a reaction surface/suitable environment
• Bring reactants together
• Position reactants correctly for reaction
• Weaken bonds in the reactants

CH2
H
H
H
H
CH2
Metal
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Enzymes as catalysts

• Provide a reaction surface (the active site)
• Provide a suitable environment (hydrophobic)
• Bring reactants together
• Position reactants correctly for reaction
• Weaken bonds in the reactants
• Provide acid / base catalysis
• Provide nucleophiles

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An example reaction

• Reduction of pyruvate to lactate
• Homolactic fermentation
• LDH Lactate dehydrogenase (enzyme)
• NADH reducing agent coenzyme
• Pyruvic acid substrate

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The active site

• Hydrophobic hollow or groove on the enzyme
  surface
• Accepts reactants (substrates and coenzymes)
• Contains amino acids which
• bind reactants (substrates and coenzymes)
• catalyze the reaction

chymotrpysin
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Cofactors/Coenzymes
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Enzyme catalysis

• Binding interactions
• strong enough to hold the substrate sufficiently
  long for the reaction to occur
• weak enough to allow the product to depart
• Drug design
• designing molecules with stronger binding
  interactions results in enzyme inhibitors which
  block the active site

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Substrate binding bonding forces

• Ionic
• H-bonding
• Hydrophobic

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Binding of pyruvic acid in LDH
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Substrate binding induced fit

• Active site is nearly the correct shape for the
  substrate
• Binding alters the shape of the enzyme (induced
  fit)
• Binding will strain bonds in the substrate

Induced fit
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Induced Fit

• Hexokinase

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Induced fit

• Active site alters shape to maximize
  intermolecular attractions

• Intermolecular bonds not optimum length for
  maximum bonding

• Intermolecular bond lengths optimized
• Susceptible bonds in substrate strained
• Susceptible bonds in substrate more easily broken

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Binding of pyruvic acid in LDH
O
H
H3N
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Binding of pyruvic acid in LDH
O
H
H3N
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Enzymes are Stereospecific

• Asymmetrical Synthesis

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Catalysis Mechanisms

• Acid-Base
• Covalent
• Metal Ion
• Electrostatic
• Proximity and Orientation Effects
• Preferential TS Binding

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Acid-Base Catalysis

• Proton-transfer reaction stabilize TS
• Example
• Enzymes as acids/bases

Non-ionized Acts as a basic catalyst (proton
'sink')
Ionized Acts as an acid catalyst (proton source)
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Acid-base Catalysis

• What happens if both acid and base are present?
• Solution
• Enzyme

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Covalent Catalysis

• aka Nucleophilic Catalysis

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Metal Ion Catalysis

• Metalloenzymes
• Metal-activated enzymes
• How do metal ions participate in the catalytic
  process?
• Orient substrates
• Redox
• Facilitate formation of hydroxide ion
• Electrostatic stabilization

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Electrostatic Catalysis

• Exclusion of water from active site
• Increases polarity
• Strong electrostatic interactions
• Stabilize TS
• Ion channel

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Proximity and Orientation Effects

• Reactants must come together with the proper
  spatial relationship for a reaction to occur
• Enzymes
• Bring substrates into contact with catalytic
  groups and/or each other
• Bind substrates in proper orientation for
  reaction
• Restrict rotational motion of substrates so align
  reactive portions of molecules

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Proximity and Orientation Effects

• Compare reactions of imidazole with a carbonyl
• Intermolecular
• Intramolecular

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Preferential TS Binding

• Enzymes stabilize TS
• Increase formation of TS
• Typically bind TS better than either reactant or
  product
• Induced fit can distort bond lengths/angles

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An example Lysozyme

• Bactericidal agent
• Destroy cell walls
• Hydrolyze glycosidic linkages in cell wall
  peptidoglycans
• Alternating NAG and NAM

• Peptidoglycan N-acetylmuramoylhydrolase

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Hen Egg White Lysozyme

• Most widely studied/understood species
• Single polypeptide
• 129 AA residues, 5 a-helices, 1 b-sheet, 4
  disulfide bonds
• Roughly ellipsoidal
• Cleft across one side active binding site

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Substrate

• 6 saccharide residues
• - NAG-NAM-NAG-NAM-NAG-NAM

• D distorts to half-chair to avoid steric strain
  and maximize H-bonding
• D-E b1?4 glycosidic bond cleaves

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Mechanism
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Other examples

• Hexokinase
• Enolase
• Serine proteases (chymotrypsin)
• See your textbook section 6.4

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Coming up next

• Enzyme kinetics and inhibition
• section 6.3
• Enzyme regulation
• section 6.5