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1 Previous lecture: The energy requiring step from substrate to transition state is an energy barrier called the free energy of activation G Transition state is the unstable (10-13 seconds) highest energy species on the reaction coordinate Enzymes lower the energy of activation barrier by lowering the energy of the transition state (stabilization) to allow for transformation to occur The active site of enzymes are thought to be structurally similar and bind tighter to the transition state compared with the ground state substrate Today: Acid-base catalysis Electrophilic catalysis Covalent catalysis
2 Principles of Catalysis Uncatalyzed reactions, even when thermodynamically favorable (spontaneous), often are extremely slow. They are slow because of the height of the activation energy needed to reach the transition state Activation energy is high because the formation of the transition state is unfavorable due to the presence of unstable + and - charges that develop. Stabilization of these charges will lower the activation energy and accelerate the rate of the reaction (active site pit)
3 Principles of Enzyme Catalysis Uncatalyzed reactions are too slow due to energetic transition states (very large G ) Analogous reactions found in organic chemistry are observed in Enzymology Acid Base Catalysis - Donation or abstraction of protons Covalent Catalysis - Covalent enzyme-substrate intermediate Metal Ion Catalysis- Substrates and metals positioned for reaction Electrostatic Considerations- Compliment of charges with transition state Proximity and Orientation - Substrates aligned for reaction
4 Types of Enzyme Catalysis Acid Base Catalysis - Donation or abstraction of protons Covalent Catalysis - Covalent enzyme-substrate intermediate Metal Ion Catalysis (Electrostatic)- Substrates and metals positioned for reaction
5 Acid-Base Catalysis General acids transfer protons General bases abstract protons Specific acid or base catalysis is when the proton or hydroxide ion is the catalyst (organic)
6 Acid-Base Catalysis R C O R C - O R C OH CH 2 H CH 2 H + CH 2 Ketone Transition state Enol Uncatalyzed reaction occurs very slowly due to unfavorable carbanion
7 Acid-Base Catalysis R C O HA R C O - R H + A - C OH + HA CH 2 H CH 2 H +.. B CH 2 Ketone Transition state Enol
8 Acid-Base Catalysis Amino Acid side chains that can act as acid-base catalysts: Asp, Glu, His, Lys, Cys, Tyr Acid - base reactions are governed by sidechain pka s Catalysis often sensitive to ph changes (pka-e.g.) ph - rate profiles can distinguish between acid-base catalysis and lead to the identification of participating catalytic residues (mutagenesis)
9 Electrostatic Catalysis When a charged transition state cannot be stabilized by an acid-base catalyst (e.g. no ionization) the charge can be neutralized by an oppositely charged group from the catalyst (active site of enzyme) Amino Acid side chains that participate in electrostatic catalysis: Asp, Glu, His, Lys, Arg In an enzyme s active site several electrostatic interactions (also known as ion-pairs or salt bridges) can collectively attract the substrate into the active site pocket (sometimes followed by Ground state destabilization) and stabilize the transition state contributing to reduction in activation barrier.
10 Orotidine 5 -monophosphate decarboxylase And Ground State Destabilization Wu, Ning et al. (2000) Proc. Natl. Acad. Sci. USA 97,
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13 Orotidine 5 -monophosphate decarboxylase
14 Orotidine 5 -monophosphate decarboxylase And Ground State Destabilization Wu, Ning et al. (2000) Proc. Natl. Acad. Sci. USA 97,
15 Metal Ion Catalysis A specific type of electrostatic catalysis Employs the positively charged metal ion to stabilize negative charges for increased catalysis (also called Electrophilic catalysis) Coordination of the cobalt complex increases the ability of a nucleophile to catalyze the hydrolysis of glycine ester two million fold
16 Metal Ion Catalysis Another common role for metal catalysis is the interaction of the metal ion with the side chain groups of the enzyme to promote the reactivity of the enzyme s groups through electrostatic effects Examples include metalloenzymes (urease)-important for maintaining proper structure of protein and active site residues Also enzymes that accept co-factors in metal form (kinases) MgATP (allows ATP to bind as neutral molecule)
17 Covalent Catalysis A covalent bond is formed between the enzyme and its substrate during the formation of the transition state Covalent bond is initiated by an electron rich group in the active site Covalent catalysis involves a two part reaction process containing two energy barriers in the reaction coordinate diagram G reactant Transition states intermediate Somewhat stable (isolate) Reaction coordinate product
18 Nucleophilic groups in enzymes Nucleophilic group OH SH NH2 imidazole OH Amino Acid serine cysteine aspartic acid lysine histidine tyrosine Intermediate formed acyl or phosphoryl enzyme COOacyl or phosphoryl enzyme acyl enzyme Schiff base acyl enzyme phosphoryl enzyme In their deprotonated forms they attack electron deficient centres to form covalent intermediates (ph dependent) Many of the same groups that make good nucleophilic catalysts are good acid-base catalysts because they contain unshared electron pairs
19 Acid-Nucleophilic Catalysis Acid- -glucosidase 2 nd messenger Mutations in enzyme cause Gaucher disease, a lysosomal storage disease (congested lysosomes) (defective spleens, liver, neurological output)
20 Acid-Nucleophilic Catalysis
21 Acid-Nucleophilic Catalysis
22 Acid-Nucleophilic Catalysis
23 Metal ions as Covalent Catalysts- Carbonic anydrase CO 2 + H HCO - 2 O 3 + H +
24 Metal ion covalent catalysis- Carbonic anydrase CO 2 + H HCO - 2 O 3 + H +
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26 Next Nucleophilic catalysis Microscopic reversibility and kinetic equivalence
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Nucleophilic Substitution and Elimination What does the term "nucleophilic substitution" imply? A nucleophile is an the electron rich species that will react with an electron poor species A substitution
Hydrogen Bonds The electrostatic nature of hydrogen bonds
Hydrogen Bonds Hydrogen bonds have played an incredibly important role in the history of structural biology. Both the structure of DNA and of protein a-helices and b-sheets were predicted based largely