Enzyme Mechanisms I

What are the main types of enzymatic catalysis? —

Acid-base, covalent, metal ion, electrostatic, proximity/orientation, transition state binding

Q: What is general acid-base catalysis? —

Enzyme donates proton (acid) or accepts proton (base) to stabilize intermediates and lower activation energy

Q: How does acid-base catalysis speed reactions? —

Stabilizes transition state/intermediates → lowers energy barrier

Q: What is mutarotation? —

Interconversion between α-D and β-D glucose via linear form

Q: How is mutarotation catalyzed? —

Acid protonates ring oxygen, base removes proton from C1 OH → ring opens

Q: What happens in absence of acid/base (aprotic solvent)? —

No mutarotation unless weak acid (phenol) + weak base (pyridine) added

Q: What residues commonly perform acid-base catalysis? —

Asp, Glu, His, Cys, Tyr, Lys “

‘A Good Hero Can Teach Lessons’”

Q: How does RNase use acid-base catalysis? —

His12 acts as base, His119 acts as acid → RNA cleavage

Q: What is covalent catalysis? —

Formation of temporary covalent bond between enzyme and substrate

Q: What type of groups act as nucleophiles? —

RO⁻, RS⁻, RNH₂, imidazole

Q: What is a Schiff base? —

Intermediate formed when amine reacts with carbonyl (C=N bond)

Q: What are the steps of covalent catalysis? —

Nucleophile attacks → covalent intermediate forms → eliminated to release product

Q: What determines rate-limiting step? —

Whether nucleophilic or electrophilic step is slower

Q: Which amino acids commonly participate in covelent calyatis? —

Lys (Schiff base), Cys, His, Ser, Thr

Q: Which cofactors are involved in covalent catalysis? —

Thiamine pyrophosphate, pyridoxal phosphate

Q: What fraction of enzymes require metal ions? —

~1/3

Q: What are metalloenzymes? —

Tightly bound metal ions (Fe²⁺, Fe³⁺, Cu²⁺, Zn²⁺, Mn²⁺, Co²⁺)

Q: What are metal-activated enzymes? —

Loosely bound metals (Na⁺, K⁺, Mg²⁺, Ca²⁺)

Q: What are the 3 main roles of metal ions? —

Position substrate, assist redox, stabilize negative charges

Q: Why are metal ions better catalysts than protons? —

Higher charge (>+1) and work at neutral pH

Q: How do metals affect water? —

Increase acidity → form OH⁻ nucleophile

Q: Example of metal ion catalysis enzyme? —

Carbonic anhydrase (Zn²

Why is Mg²⁺ used with phosphate groups? —

Neutralizes negative charge repulsion

What is proximity effect? —

Bringing reactants close increases reaction rate

Q: How much does proximity alone increase rate? —

~4.6×

Q: Why is proximity limited? —

Molecules must already collide; effect mainly increases contact frequency

Q: What is orientation effect? —

Aligning molecules correctly increases reaction rate

Q: How much can orientation increase rate? —

~100×

Q: What happens when motion is restricted? —

Rate increases dramatically (up to 5 × 10⁷)

What is preferential transition state binding? —

Enzyme binds transition state stronger than substrate

Q: What is the RACK mechanism? —

Enzyme strains substrate to resemble transition state

Q: Why does RACK increase rate? —

Stabilizes transition state → lowers activation energy

Q: What is relationship between rate enhancement and binding? —

10⁶ rate increase = 10⁶ stronger TS binding (~34.2 kJ/mol stabilization)

Q: How can hydrogen bonds increase rate? —

2 H-bonds to TS → ~10⁶ increase

What are transition state analogs? —

Molecules that mimic transition state

Q: How do transition state analogs affect enzyme activity?

Bind very tightly → act as competitive inhibitors

Q: Example of transition state analogs? —

Pyrrole-2-carboxylate, Δ¹-pyrroline-2-carboxylate

How strongly do transition state analogs bind compared to the normal substrate?

~160× stronger