Mechanisms of Catalysis

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Questions and Answers

What is a role of active-site histidine in enzymatic reactions?

  • It can only act as a proton donor.
  • It serves solely as a stabilizing agent.
  • It can function as a metal ion catalyst.
  • It can be deprotonated to act as a base. (correct)

Which amino acids are suggested as candidates for facilitating proton transfer in enzymes?

  • Ser and Thr
  • Leu and Val
  • Glu and Asp (correct)
  • Pro and Gly

What is the primary function of metal ions in catalysis?

  • To act purely as a buffer for pH regulation.
  • To provide structural stability without interaction.
  • To increase the electronegativity of nearby atoms.
  • To stabilize charge and assist in forming strong nucleophilic species. (correct)

Which statement about secondary roles of amino acids in active sites is true?

<p>They can raise or lower catalytic residue pKa values. (D)</p> Signup and view all the answers

What are Low-Barrier Hydrogen Bonds (LBHBs) characterized by?

<p>An O-O separation typically less than 0.28 nm. (C)</p> Signup and view all the answers

What is the primary purpose of bringing substrates into proximity in enzyme action?

<p>To facilitate higher frequency collisions (B)</p> Signup and view all the answers

What characterizes a near-attack complex (NAC)?

<p>Atoms are within 3.2 Å and at a ±15° angle to the transition state bond (A)</p> Signup and view all the answers

In covalent catalysis, the enzyme forms a temporary bond with the substrate. What happens at the end of the reaction?

<p>The temporary bond is broken, regenerating the enzyme (C)</p> Signup and view all the answers

Which of the following processes is a key feature of general acid-base catalysis?

<p>Proton transfer in the transition state (A)</p> Signup and view all the answers

What is a double displacement mechanism in enzyme action?

<p>Two substrates bind and react separately in a ping pong manner (D)</p> Signup and view all the answers

What role do protein motions play in enzyme catalysis?

<p>They assist in binding and facilitate catalytic actions (C)</p> Signup and view all the answers

What common characteristic is observed in NACs regarding their atomic arrangement?

<p>Atoms must be very close and at a specific angular orientation (C)</p> Signup and view all the answers

What is a significant consequence of covalent catalysis mechanism?

<p>Facilitation of electron transfer during the reaction (C)</p> Signup and view all the answers

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Study Notes

Mechanisms of Catalysis

  • Enzymes speed up reactions by increasing the rate of collisions between substrates within the active site.
  • Enzyme active sites are pre-organized to form near-attack complexes (NACs) where reacting atoms are in Van der Waals contact at an angle resembling the bond to be formed in the transition state.
  • The presence of an enzyme increases the substrate collision rate from 0.0001% to 1-70%.
  • NACs are characterized by reacting atoms within 3.2 Å and an approach angle of ±15° of the bonding angle in the transition state.
  • Protein Motions Are Essential to Enzyme Catalysis
    • Proteins are constantly moving: bonds vibrate, side chains bend and rotate, backbone loops wiggle and sway, and whole domains move as a unit.
    • Active site conformation changes:
      • assist substrate binding
      • bring catalytic groups into position
      • induce formation of NACs
      • assist in bond making and bond breaking
      • facilitate conversion of substrate to product

Covalent Catalysis

  • Active site residues form a temporary covalent bond with the substrate.
  • At the end of the reaction, the covalent bond is broken to regenerate the enzyme.
  • Often occurs due to nucleophilic attack by amino acid side chains on electrophilic groups on substrates.
  • Can also involve prosthetic groups.
  • Facilitates electron transfer.
  • Double Displacement
    • Two substrates bind and react separately in a ping pong manner.
    • The product of the enzyme's reaction with the first substrate is released prior to the reaction with the second substrate, e.g., Enzyme-substrate Intermediates.

General Acid-Base Catalysis

  • Proton transfer in the transition state.
  • Transferring an H+ can:
    • Activate nucleophiles
    • Stabilize charged groups
    • Improve electrostatic interactions that stabilize the transition state
  • Facilitates proton transfer
  • Specific Acid-Base Catalysis
    • H+ or OH- that has diffused into the active site.
  • Candidate amino acids are Glu, Asp, or His.
    • Histidine can be deprotonated by another group and then act as a base accepting a proton from the substrate.
  • Water often plays a role as an acid or base at the active site through proton transfer with an assisting active-site residue.

Metal Ion Catalysis

  • Common metal ions involved in catalysis include zinc, magnesium, and iron.
  • Metal atoms lose electrons easily and exist as cations.
  • Positive charge allows them to:
    • Stabilize transient and intermediate structures.
    • Assist in forming strong nucleophilic species.
    • Hold the substrate inside the active site.
    • Stabilize charge.

Low-Barrier Hydrogen Bonds (LBHBs)

  • Typical H-bond strength is 10-30 kJ/mol, and the O-O separation is typically 0.28 nm.
  • As the distance between heteroatoms becomes smaller, the H-bond becomes stronger, and the barrier to proton transfer decreases.
    • The lower the barrier, the stronger the bond.

Secondary Roles of Amino Acids

  • About half of the amino acids engage directly in catalytic effects in enzyme active sites.
  • Other residues may function in secondary roles in the active site:
    • Raising or lowering catalytic residue pKa values.
    • Orientation of catalytic residues.
    • Charge stabilization.
    • Proton transfers via hydrogen tunneling.

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