Lecture 18

Question 1

nucleoplilic

Answer 1

a atom or molecule who is electron rich and wants to donate electrons

Question 2

electrophilic

Answer 2

a atom or molecule that is electron poor and wants to donate electrons.

Question 3

electropositive

Answer 3

is what happens to an atom becomes electron deficient (the nucleophiles goal)

Question 4

electronegative

Answer 4

is what happens to an atom that becomes electron rich (the electrophile’s goal)

Question 5

Electron pushing

Answer 5

the direction on the nucleophilic attack. the electrons on the electronegative nucleophile with attack the electropositive electrophile

Question 6

Base catalysis

Answer 6

When the histidine takes a proton from a serine and water making them now act like nucleophililes

Question 7

Covalent catalysis

Answer 7

when serine get deprotonated (nucleophiles) it attacks electron deficient (electrophiles) atoms so they can form covalent intermediates

Question 8

which comes first, base catalysis or covalent catalysis

Answer 8

Base catalyst comes first as they histide takes away a proton from the serine so it becomes deprotroned and electronegative. Its now a nucleophile so it attacks the electron deficient atoms to form covalent intermediates

Question 9

What are serine proteases?

Answer 9

They are enzymes that cleave peptide bond in proteins

Question 10

Chymotrypsin

Answer 10

a type of serine protease that cleaves peptide bonds at C and N terminus by having a protein specificity for tryptophan, methionine, phenylalanine, tyrosine

Question 11

Substrate specificity pocket

Answer 11

Where the enzyme detects specific amino acid to know where to cut the peptide bond

Question 12

active site of the serine process

Answer 12

is where catalytic triad of ser195, his157 and asp102 reside

Question 13

What is Serine195’ job?

Answer 13

Covalent Catalysis- after being deprotonated it now acts as a nucleophile and must create a covalent intermediate with the substate (polypeptide)

Question 14

What is Histidine57 job?

Answer 14

Base Catalysis - must deprotonate Ser195 so it can act like a nucleophile

Question 15

What is Asp102 job?

Answer 15

it must stabilizes His57 anytime it becomes protonated.

Question 16

Explain the chymotrypsin reaction mechanism process

Answer 16

1) a polypeptide will go through substrate specificity pocket until the desired peptide is detected
2) Base catalysis of Ser195 from His57 and covalent catalysis of the carbonyl carbon of the polypeptide by the nucleophilic Ser195
3) The His57 gives the proton to the N terminus of the animo acid (substrate) causing the bond between the tetrahedral Carbonyl carbon to break as nitrogen is the best leaving group, now product 1 is free
4) The serine is now bonded to the other half of the substrate with the specific amino group forming an acyl-enzyme intermediate.
5) Water comes and the his57 again takes a proton from it causing it to become a nucleophile. It attacks the carbonyl of the acyl enzyme intermediate
6) His57 returns proton to Ser195 allowing it to cleave from the substrate and the second product is formed.
Enzyme is now reset and ready to do it again

Question 17

Oxyanion hole

Answer 17

a place of positive dipole so negative charge can be stabilized while the breaking of bonds

Question 18

scissile bond

Answer 18

the peptide bond that is cleaved to make first product

Question 19

where is the polypeptide cleaved?

Answer 19

in between the c and n terminus after the specific animo acid is detected.