biochem lecture 8 - enzyme mech

enzyme mechanisms, nucleic acids

degradome

complete repertoire of proteases expressed by organism

serine, cysteine, aspartyl, metallo-

4 classes of proteases

polyprotein

a large protein precursor translated from a single messenger RNA (mRNA) strand and later cut into smaller, functional proteins

protease inhibitors

drugs used to treat HIV usually involve ….

protease inhibitor; tightly; irreversible

________ inhibitors forms NON-COVALENT but ________ associated interactions that make them considered ________

transition-state analogs

protease inhibitors are "________-________ ________”

transition-state analog

resembles the TS more than the GS of the substrate

benzyl; OH

protease inhibitors used to treat HIV have ____ groups that fit in the binding pocket and ____ that mimix the O in the tetrahedral intermediate

attacks carbonyl between Phe and Pro residues in substrate

role of water in the 1st step of HIV protease mechanism

primes water for attack by deprotonating it

role of the right Asp25 in the 1st of HIV protease mechanism

stabilizes the tetrahedral intermediate through h-bond

role of left Asp25 during second step of HIV-protease mech

tetrahedral intermediate

what forms after water nucleophilic attack in the 1st step of HIV-protease mech?

right Asp25

HIV-protease:

after tetrahedral intermediate collapses, Pro residue LG deprotonates ______

fungi (Penicillium notatum)

penciliin was first isolated from _____

same environment; same resources

fungi first produced penicillin as it competes with bacteria in the ______ ______ and for ______ ______

transpeptidase

penicillin blocks _________

transpeptidase; peptidoglycan

cell-wall synthesizing enzyme: __________; specifically synthesizes _______

polysaccharides; crossed-linked peptides

peptidoglycan consists of ______ and ____-____ _________

beta-lactamase

enzyme that cleaves Beta-lactam antibiotics (ex: penicillin)

D-Ala

amino acids found in peptidoglycan chains

Ser-OH

residue in transpeptidase that attacks peptidoglycan in the 1st step (include functional group)

amino

the ____ group of Gly5 in a neighboring polypeptide chain attacks the transpeptidase-peptidoglycan intermediate

attack from nearby peptidoglycan chain

what releases transpeptidase from peptidoglycan

cross-linked peptidoglycan

what is the product of the transpeptidase mechanism

substrate; inhibitor

penicililn is a ____ not a ____ for beta-lactamse

D form

pencillin is similar to peptidoglycan in that it is also in the ________ _______

Ser-OH; carbonyl

transpeptidase ____-_____ also attacks _____ of penicillin

inactive transpeptidase

the mechanism of transpeptidase and penicillin produces a ___________ _________

clavulanic acid

inactivates beta-lactamse

chymotrypsin

serine protease produced by your digestive system that cleaves aromatic residues

chymotrypsinogen

inactive precursor of chymotrypsin

His57, Asp102, Ser195

catalytic triad of chymotrypsin

enzyme-substrate

1st step of chymotrypsin mechanism forms a _____ _____ complex

deprotonates Ser-OH for attack onto substrate

what does His57 do in the 1st of chymotrypsin mechanism?

1st tetrahedral intermediate

what does 1st step of chymotrypsin mechanism form?

Ser195; hydrogen bonding

backbone of _______ stabilizes the substrate through _______ in the oxyanion hole

oxyanion hole

part of chymotrypsin enzyme in which backbone of ser195 stabilizes the substrate

acylation

step that involves the collapse of the first tetrahedral intermediate in chymotrypsin mechanism

Gly193; Ser195

backbone of ______ and ____ stabilize the 1st tetrahedral intermediate

protonated; substrate

in the acylation step of chymotrypsin mechanism, His57 is now _____ and stabilizes the backbone of the _____

acylation; product 1

in the __________ step of chymotrypsin mechanism, the 1st tetrahedral intermediate collapse releasing __________ __

deprotonates His57

in step 2 of chymotrypsin mech, when the 1st tetrahedral intermediate collapses, the amino leaving group _______ ________

acyl-enzyme intermediate

following the release of product 1, the ____-_____ ________ forms

Ser195

backbone of _____ stabilizes the acyl-enzyme intermediate in step 3

water; 2nd tetrahedral intermediate

_____ nucleophilic attack forms the ____ _________ _________

His57

______ deprotonates H2O (general base catalysis) in step 4

carbonyl

-OH attack on _____ of substrate forms 2nd tetrahedral ilntermediate

2nd tetrahedral intermediate; deacylation

the collapse of the ____ _________ ________ occurs in the ______ step

Ser195

the collapse of the 2nd tetrahedral intermediate kicks out _____

His57+

O-Ser195 deprotonates ____

Gly193; Ser195

Backbone of ________ and ________ stabilizes the substrate in Oxyanion Hole