Enzymes II Flashcards
Nucleophilicity is related to
basicitiy
Nucleophilies can
covanteltly bond to electron deficient centers
electrophilic group are.
electron deficient so they love electrons
Some nucleophiles groups are
hydroxyl group, sulfhydryl group, amino group, imidazole group
Some electrophilles groups are
protons, metal ions, carbonyl carbon atom, cationic imine
Partial proton donation is also
general acid catalysis
abstraction is also known as
general base catalysis
What amino acids participate in acid-base catalysis?
Asp, Glu, Lys, Arg, and His
What makes a good catalyst
good leaving groups
for a good catalyst, reverasibily
of the bond fromed is key
A good catalyst correlates with
polarizability and how mobile electrons are
highly polarized equals
highly breakables
Step 1 in RNase A for His 12
abstracts proton from 2’-OH
His 12 causes
a nucleophillic attack on P
His 119 step 1
protonates a leaving group causing bond breaking
Step 2 for RNase A His 119
deprives H+ from H2O which results in OH- attacking P
Step 2 His 12
donates its proton → 2’,3’ cyclic intermediate is broken.
Covalent catalysis is via
transient formation of covalent ES intermediate
covalent catalysis is usually
a nuucleophile attacjs abn electrophile and forms covalent bond with it
What are the 2 classes of metal ion catalysis
metalloenzymes and metal-activated enzymes
Decarboxylation of acetoacetate is by
primary amine (via Schiff bond)
What is the first step Decarboxylation of acetoacetate
Nucleophilic attack by amine
formation of covalent bond
What is step 2 of the Decarboxylation of acetoacetate
Catalyst becomes electron-
deficient e - from reaction cente
Metal ion catalysis acts in 3 ways
- Bind to substrates (orient properly for reaction).
- Transiently change redox state (mediate redox reaction).
- Stabilize/shield negative charges.
Metalloenzymes are
tightly bound and usually transition metals
Examples of matelloenzymes
Fe 2+ , Fe 3+ , Cu 2+ , Zn 2+ , Mn 2+ , Co 2+
Metal activated enzymes
loosely bound metal from solution, alkaline
Zn2+ is coordinated
by the imidazole of 3 His and a water
Binding to E forces
substrate in a orient way which is rotational, translational motions cease and actives groups face each other
Proximity and orientation effects comes at the expense of
lost of entropy and is compensated by the binding energy of E to S
theres a preferential binding to the
ES -transition state
the transition state binds
the enzyme’s active site tighthly and acts a potent inhibtor
The transition state analog helps
confirming the structure of the natural transition state
