Enzymes

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Enzymes

• BL4010 10.26.06

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Objectives

• What is an enzyme?
• How do enzymes work?
• energetics
• underlying general mechanism
• components (prosthetic groups, coenzymes)
• specific mechanisms

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What is an enzyme?

• Macromolecular biological catalyst
• Can be protein or RNA

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What is an enzyme?

• Macromolecular biological catalyst
• What is a catalyst?
• is not altered by reaction
• participates but emerges unchanged
• increases the rate at which substrates and
  products reach equilibrium
• does not alter equilibrium

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Why enzymes?

• Why invest energy and resources into creating a
  large catalyst?
• Enzymes endow cells with the remarkable capacity
  to exert kinetic control over thermodynamic
  potentiality
• Fine tune selectivity (substrate binding
  specificity)
• Fine tune catalytic rate
• Additional regulatory control (e.g. allostery,
  signalling networks)

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Enzymes are good catalysts

• Enzymes can accelerate reactions as much as 1016
  over uncatalyzed rates!
• Urease is a good example
• Catalyzed rate 3x104/sec
• Uncatalyzed rate 3x10 -10/sec
• Ratio is 1x1014 !

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Enzymes are selective catalysts

• Enzymes selectively recognize proper substrates
  over other molecules
• Enzymes produce products in very high yields -
  often much greater than 95
• Specificity is controlled by structure - the
  unique fit of substrate with enzyme controls the
  selectivity for substrate and the product yield

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How do enzymes work?

• How do catalysts in general work?

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The transition state

• Understand the difference between ?G and ?G
• The overall free energy change for a reaction is
  related to the equilibrium constant
• The free energy of activation for a reaction is
  related to the rate constant
• It is extremely important to appreciate this
  distinction!

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How do enzymes work?

• Enzymes accelerate reactions by lowering the free
  energy of activation
• HOW?

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Four contributing factors to enzyme catalysisNO
ONE MECHANISM ACCOUNTS FOR CATALYSIS ALONE!

• Specific substrate binding
• local concentration of reactants
• productive orientation of reactants
• binding energy used to offset loss of entropy
• Control over solvent interactions
• desolvation (binding energy offsets)
• ordered solvent in binding pocket
• Induction of strain on reactants
• Alternate reactive pathway
• transient involvement of enzyme functional groups

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How do enzymes work?

• Enzymes accelerate reactions by lowering the free
  energy of activation
• Enzymes do this by binding the transition state
  of the reaction better than the substrate

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Protein Databank

• http//www.rcsb.org
• Extensive source of protein structural data
• Whenever a structure paper is published, the data
  must be made pubically available!

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Enzyme mechanisms

• Objectives
• Understand the major mechanisms of enzymes
• Know the specific mechanisms of a few
  well-studied enzymes in detail

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General enzyme catalysis
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Transition states and analogs
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Classification of enzymesIUPAC (International
Union of Pure and Applied Chemistry)IUBMB
(International Union of Biochemistry and
Molecular Biology)

• Oxidoreductases (electron transfer)
• donor (e.g. 1.1 CH-OH)
• acceptor (e.g. 1.1.1 NAD)
• Transferases (group transfer)
• group (e.g. 2.4 glyco-)
• Hydrolases (transfer to water)
• Lyases (double bonds - addition or elimination)
• Isomerases (transfer within molecule)
• Ligases (condensation coupled to ATP hydrolysis)

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Examplehttp//www.chem.qmul.ac.uk/iubmb/enzyme/

• common name trypsin
• IUPAC/IUBMB designation EC 3.4.21.4
• EC 3 (hydrolases)
• EC 3.4 (peptide hydrolases - peptidases)
• EC 3.4.21 (serine endopeptidases)
• EC 2.4.1.40 glycoprotein-fucosylgalactoside
  ?-N-acetylgalactosaminyltransferase