enzyme mech and catalysis II Flashcards
enzymes accelerate reaction rates by …
lowering the activation energy barrier, but do not affect reaction equilibria
what is the relationship between k and delta G?
k is larger when delta G is smaller
nucleophile (Nu:)
electron-rich functional group (nucleus loving) that donates (shares) an electron pair with an electrophile to form a bond
electrophile (E)
electron deficient functional group (electron loving) that accepts (shares) an electron pair from a nucleophile to form a bond
transition-state stabilization
lowers energy of transition state making it easier to form
orientation
arranges atoms for optimal activity
desolvation
binding removes interactions with solvent (water)
induced fit
substrate binding changes conformation of enzyme
acid-base catalysis
push or pull a proton
covalent catalysis
adducts or intermediates
metal ion catalysis
lewis acids and redox agents
why and how can substrates be aligned?
by binding to an enzyme so that nucleophiles are positions for reaction
what does substrate binding to an enzyme active site generally exclude or reduce?
the concentration of water in the active site
what does a lower dielectric environment do? (desolvation)
increase the strength of electrostatic interactions
An AA residue can function …
both as a general acid and general base, depending on whether residue is a protonated-conjugate-acid or a deprotonated-conjugate-base
specific acid
H+ really H30+
specific base
-OH
general acid
proton donor
general base
proton acceptor
how can a transient covalent bond form?
between enzyme and substrate
what does metal ion catalysis depend on?
ability of metal ion to serve as a template, a lewis acid, or a redox reactant
what do metal ions do?
bind and orient substrates; shield/stabilize negative charge formed in Transition state; increase acidity of bound water or alcohols; mediate redox reactions
chymotrypsin
protease that catalyzes hydrolysis of a aromatic AA peptide bond at C-terminal side
steps in each phase (I and II)
- positioning
- His57 is General Base
- Nucleophilic Attack
- Covalent Intermediate
- His57 is General Acid
what should you know about chymotrypsin?
THE REACTION CYCLE
what forms the catalytic triad in chymotrypsin?
Asp-102, His-57, and Ser-195
what is step 1 of phase 1 of chymotrypsin reaction?
the catalytic triad forms and asp102 makes his57 a better general base in the first step
what is step 2 of phase 1 of chymotrypsin reaction?
his57 acts as a general base to deprotonate the hydroxyl group of ser195 and make it a better nucleophile; ser195 acts as a nucleophile and attacks the carbonyl group forming a covalent bond with the carbonyl carbon=covalent catalysis
what is step 3 of phase 1 of chymotrypsin reaction?
in the short-lived intermediate: protonated his57 now acts as a general acid to protonate the amine leaving group; next, the peptide bond is broken and the C-terminal end of polypeptide chain leaves; the acyl enzyme is formed completing the 1st phase of the reaction
what is step 4 of phase 2 of chymotrypsin reaction?
water enters the enzyme active site, where the C-terminal end of polypeptide used to be located
what is step 5 of phase 2 of chymotrypsin reaction?
his57 acts as a general base to deprotonate water and make it more nucleophilic and water acts as a nucleophile and attacks the carbonyl carbon
what is step 6 of phase 2 of chymotrypsin reaction?
protonated his57 acts as a general acid to protonate ser195 leaving group; ser195 cleaves from N-terminal end of polypeptide (to regenerate the enzyme)
what is step 7 of phase 2 of chymotrypsin reaction?
final (second) product (N-terminal end of original polypeptide) leaves; enzyme is now returned to its original form
what does hexokinase do?
catalyzes the phosphorylation of glucose in a reversible reaction, involving Mg ion, ADP, and ATP
what induces a conformation shift in the enzyme structure (induced fit) at the binding site? (hexokinase catalytic reaction)
D-glucose binding
