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39 Cards in this Set

  • Front
  • Back
Define catalyst:
A molecule that increases reaction rate but is not consumed in the reaction.
What numerical value is affected by enzymatic action?
Rate Constant - enzymes act to increase the rate constant.
What part of a reaction does an enzyme affect to allow for catalysis?
the Transition State
How do enzymes affect the net delta G in a reaction?
It is unchanged; there is still an equal decrease in energy from reactants vs. products
What are 3 ways to classify enzymes?
-Trivial name (LDH)
-Formal name (Substrate/class/ase)
-4-digit number
What are the 6 major enzyme classes?
What do ligases do?
Joni 2 molecules together via hydrolysis of a high-energy bond.
What do isomerases do?
Change a molecule's geometric or spatial configuration.
What do lyases do?
Cleave other bonds (C-C, CO, or CN) via elimination, leaving double bonds, or addition to double bonds.
What do hydrolases do?
Hydrolyse CO, CN, or CC bonds.
What do oxidoreductases do?
cause simultaneous oxidation and reduction via H-donor substrate.
What do transferases do?
Exchange groups; example:
X-Y + Z -> X + Z-Y
What are the requirements for a general uncatalyzed reaction to be successful?
-Hydration spheres (reactants)
-Encounter complex (needed)
-Suffic. E necess to reach Ea
-Correct collision orientation
How do enzyme-catalyzed reactions differ from uncatalyzd? (4 points)
1. Active site PUTS reactants in correct orientation (not random)
2. Proximity effects - increase the [Reactant] at active site.
3. Possiblity of Rxn increased
4. Enzyme binds transition state tightly.
What exactly is activation energy?
The energy needd for molecules to overcome repulsion of their electron clouds in order for molecular bond rearrangement.
What makes an active site so great?
It favors the functional groups of both the enzyme and its substrate coming into close proximity of each other.
How do enzymes stabilize transition states?
By pulling electrons away from the bond being changed.
What type of kinetics do all enzymes exhibit? Why?
Graphing rate vs. [substrate] for all enzymes (even normally sigmoidal) results in a HYPERBOLIC curve. Because of enzymes specificity.
What is Proximity Effect?
The enhancing of environment near an enzyme's Active Site, so to increase the [substrate] high enough to cause RFG collision.
What are transition state analogs?
Molecules with much higher enzyme affinity than the natural substrate; as a result, potent inhibitors of the rxn that would have taken place.
What is an example of a transition state analog?
Anti-HIV protease inhibitor
What element is commonly used to synthetically make transition state analogs with unstable, transient central Carbons?
Phosphate - naturally accomodates a higher # of electrons so it is not off-kilter, but still binds enzyme w/ high affinity.
What 8 amino acids have reactive fucntional groups?
Glu, Asp (COOH)
Lys, Arg (NH3)
Cys (R-SH)
His (R-imino NH)
Ser (R-OH)
Tyr (R-Phe-OH)
What is a microenvironment?
The area surrounding the RFG within an enzyme.
What are 2 forms of microenvironment conditions?
1. Hydrophobic
2. Charged
What are 2 methods of establishing a hydrophobic microenvironment?
1. Use hydrophobic AA to line the active site (GAVLIMP
2. Substrate binding active site changes its conformation and increases hydrophobicity.
How does a hydrophobic microenvironment increase an enzyme's efficiency?
Solvent is excluded -> hence RFG's are desolvated and free to react.
What establishes charged/polar microenvironments?
Amino acid R-groups in the active site near an RFG.
How do charged/polar microenvironments change an enzyme's efficiency?
-Alter its pKa
-Alter reactivity of RFG
What are 2 examples that exhibit charged/polar microenvironments?
1. Acetoacetate Decarboxylase
2. Carboxypeptidase
What is the nature of Acetoacete decarboxylase's charged/polar microenvironment?
The RFG is Lysine; but the enzyme pKa is 5.9!! (usually 10)
What makes the pKa of Acetoacetate decarboxylase so low?
A Lys adjacent to the RFG Lys; protons repel each other - the nonRFG Lys suppresses RFG Lys protonation, so it deprotonates way earlier (5.9 pH) than it normally would.
Why is it good that the RFG Lys is unprotonated at much lower pH levels than it normally would be?
Because then it can do its job which is to act as a base and stabilize a Schiff base intermediate.
What does carboxypeptidase do?
Cleaves peptide bonds at the C-terminus of proteins.
What are the 2 requirements of all peptide bond hydrolyses?
1. Polarization of the C=O bond to form an oxyanion-like transn state.
2. A Nu: must be within close enough proximity to C=O so it can attack it.
How does Carboxypeptidase satisfy the 1st requirement of peptide bond hydrolysis?
It has a Zn2+ molecule at RFG; Zn is electrophilic and picks electrons from oxygen, pulling them away from C so its bond to N is broken more easily.
What characteristic of Carboxypeptidase satisfies the 2nd requirement of peptide bond hydrolysis?
Glu residue (Nu:) nearby attacks the C=O and allows H2O hydrolysis of the C-N bond.
Overall what are 4 mechanisms of enzyme efficiency?
1. Microenvironment
2. General acid/base catalysis
3. Induced fit mechanism
4. Covalent Catalysis
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