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Lecture 15

BIOL 201 Lecture Notes - Lecture 15: Lysine, Ribonuclease, Pancreatic Ribonuclease


Department
Biology
Course Code
BIOL 201
Professor
Robin Young
Lecture
15

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RNAse Enzyme mechanism (continued)
Review
Hydrolysis = cleavage of P-O bond by water
Uncatalyzed reaction: Base as nucleophile (OH-)
Advantages:
- Base is a stronger nucleophile
- Faster first part (substrate to TS)
Disadvantages:
- Worse leaving group (O-)
- Slower second part
- Multiple products possible
Enzyme-Catalyzed Mechanism (Part 2)
Step 2
- Produces a 2’-3’-cyclic intermediate
- Water enters active site on departure of P1
Step 3
-His-119 acts as a base and deprotonates water, creating a
stronger/better nucleophile
- Resulting hydroxide ion (stronger nucleophile) attacks P atom to
form new P-O bond = TS2
-Lys-41 side group (ionized form) neutralizes -ve charge forming on
oxygen atom
Step 4
-His-12 acts as an acid and donates a proton to the 2’-oxygen
atom, leading to a better LG, Product 2 (PS) – a 3’-nucleoside
monophosphate
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Multi-steps mechanisms increase reaction rates.
Bovine RNase A: Enzyme Mechanism
Note: They all have tetrahedral geometry (more stable)
At the end of the catalytic cycle, after the product leaves, enzyme
is recycled to its original form:
- His-119 NH+
- His-12 N:
Enzymes Specificity
Enzymes catalyze reactions involving specific reactants yielding specific products.
- allows cells to control the rates of individual reactions without affecting other cellular processes
In RNAse, specificity is exhibited in:
1. Enzyme-substrate binding
2. Reaction initiation
3. Products formed
1. Enzyme-substrate binding
Geometry of the substrate is important for binding in the active site.
Example: in RNase mechanism
- The pyrimidine binding pocket is geometrically/chemically complementary to pyrimidine
bases but not purine bases
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