lec18

Question 1

chrymotrypsin

Answer 1

Chymotrypsin is a digestive enzyme that breaks down proteins in the small intestine. It is a serine protease that specifically cleaves peptide bonds adjacent to large hydrophobic (nonpolar)/aromatic amino acid residues, such as tryptophan, phenylalanine, and tyrosine.

Question 2

which resiudes does chrymotrypsin recogmzie and cleave

Answer 2

-Trp
-Phe
-Tyr
-Me

Question 3

Hydrolysis by chymotrypsin 2 steps

Answer 3

Chymotrypsin Mechanism Flashcard

1.	Covalent Bond Formation & Peptide Bond Hydrolysis – Ser195 attacks substrate, forming a transient covalent bond. The peptide bond is broken, and the first product (P1) is released quickly.
2.	Second Product Release (Slow Step) – The remaining part of the substrate (P2) stays bound to the enzyme briefly before being released, regenerating the enzyme.

Question 4

Reaction energy Diagram for Enzyme-Catalyzed Hydrolysis

Answer 4

1. The first peak represents the transition state for the formation of the acyl-enzyme intermediate (E-P2).
2. The dip after the first peak corresponds to the acyl-enzyme intermediate (E-P2), which is a relatively stable, lower-energy intermediate.
3. The second peak represents the transition state for the release of the second product (P2). It is higher in energy because this step is slower and requires more energy to proceed.
4. The enzyme (chymotrypsin) lowers the activation energy for both steps, making the reaction proceed faster than it would without the enzyme.

Question 5

what is the first intermediate state in the chymotrypsin reaction

Answer 5

the tetrahedral molec; where ser-O- attacks carbonyl and that double bond goes up and becomes another co-. and rmb that co- is stabilized by backbone amides of gly and ser

Question 6

What happens during hydrolytic deacylation in the chymotrypsin mechanism?

Answer 6

A: Water enters, and His 57 deprotonates it to form OH⁻, which attacks the acyl-enzyme intermediate’s carbonyl carbon, forming a tetrahedral intermediate. This collapses, breaking the bond between Ser 195 and the substrate, releasing a carboxyl product. His 57 donates a proton back to Ser 195, regenerating the enzyme.

Question 7

first vs second tetrahedral intermediate:

Answer 7

First tetrahedral intermediate:
Occurs when Ser 195 attacks the substrate’s carbonyl carbon (after His 57 deprotonates it), forming a tetrahedral intermediate.
The intermediate has Ser 195 covalently bonded to the substrate, with the oxygen of the carbonyl (now part of Ser 195) carrying a negative charge (oxyanion).

Second tetrahedral intermediate:
After water enters, His 57 deprotonates the water, forming OH⁻, which attacks the acyl-enzyme intermediate (the first intermediate).
This results in the formation of the second tetrahedral intermediate, where the OH⁻ is now attacking the carbonyl carbon, and Ser 195 is still attached to the carbonyl carbon of the substrate.
This intermediate is stabilized by the oxyanion hole.

Question 8

If you wanted to improve the catalytic efficiency of an
enzyme, would you mutate amino acid residues to
increase binding affinity for the substrate or increase the
binding of the transition state?

Answer 8

would increase affinity of transition state cuz increasing tighter bonding of subrtate would invcrease ea and trans state would loower it.