Understanding Enzyme Mechanism and Structure Flashcards
delta G
- g products minus G reactants
- can predict whether a reaction can occur spontaneously
- neg=spon
- 0=equil
- pos=not spon
- related to overall change in entropy and enthalpy of a system
- deltaG=deltaH-TdeltaS
- DOESNT PREDICT rate of reaction-independent of mechanism
prediction of reaction rate
- activation energy
- catalysts lower Ea
enzymes
- lower the activation energy
- can’t change deltaG
- direct stabilization of TS or creation of new reaction pathways
enzyme catalysis must lower Ea
- need to reduce energy at the transition state by”
1. directly stabilizing the transition state complex with the enzyme
2. creating a new pathway for the reaction
3. or combination of both!
enzyme active sites
- used to think it was lock and key
- probably more likely to be induced fit
common features of an active site
- occupy a small part of total volume of most enzymes
- 3D structure
- bind substrates through multiple weak, non covalent interactions
- water is excluded unless it is a reagent-active sites are in the clefts of proteins
- highly specific binding of substrate
- can include non-protein prosthetic groups and cofactors-increase repertoires
prosthetic groups
-tightly and stably integrated into enzymes, often covalently bound
co factors
loosely bound, generally come on and off the enzyme
chemical strategies in enzymatic catalysis
- direct stabilization of TS-preferential binding of the TS, proximity and orientation effects
- chemical assistance-acid/base catalysis, covalent catalysis, metal ion catalysis, electrostatic catalysis
preferential binding of the TS
- direct stabilization, lowers Ea
- enzyme binds TS structure with greater affinity than substrate or products (does it’s work on TS, not on substrate)
- usually implies that enzyme fits the TS state better than the substrate and can form additional bonds to TS
- important factor in catalytic activity of almost all enzymes
proximity and orientation effects
- reactants must come together with the proper spatial orientation for reaction to occur
- enzymes immobilize substrates by binding, and the active site is designed to orient them for optimal reactivity
acid base catalysis
- general acid-enzyme is weak acid and gives proton
- general base-enzyme is weak base and accepts proton
- concerted-both acid and base groups on enzyme participate
- his
covalent catalysis
- transient formation of covalent bond between enzyme and substrate (new intermediate)
- groups are usually cys, ser, lys, his, prosthetic groups
meal ion catalysis
-metal ions participate
electrostatic catalysis
- charge distribution in active site helps stabilize the TS
- asp, glu, arg, his, lys, metal ion cofactos
proteolysis
- cleavage of a peptide bond by addition of water across bond
- specificity is critical
- breakage of peptide bond is spontaneous
- Ea very high
classes of proteases
- serine
- aspartyl
- thiol
- Zn2+
- each class uses a different set of catalytic strategies
- members of the same class use the same strategy but have different substrate specificity
serine proteases
- catalytic triad-serine, his, asp
- serine does covalent catalysis-forms a TS that decomposes to acyl enzyme intermediate
- his does acid/base
- asp stabilizes acceptance of H+
- two steps
1. nucleophilic attack, TS, covalent catalysis (acyl intermediate), general base catalysis, electrostatic catalysis, and enzyme binding to TS are utilized
2. general base catalysis, general acid catalysis used. amino group half of peptide leaves and water comes in to nucleophilic attack, forms second TS. His donates H+, c terminus formed and released
preferential stabilization by serine protease
- TS of substrate makes new bonds to serine and glycine of enzyme (not in acitve site)
- not available to substrate
- makes E-TS more favorable
rate determining step
- formation of intermediate in this reaction
- E thru TS 1 and intermediate is bigger than TS2 and product
chymotrypsin
- cleaves after large non polar side chain, large non polar pocket on enzyme
- Phe, Try
trypsin
-cleaves after basic (+) aa, neg charged asp in pocket of enzyme
elastase
- cleaves after small uncharged side chain
- bulky aa on enzyme block pocket
- val, thr
suicide inhibitors
- irreversible
- bind to enzyme because of resemblance to the substrate and are converted to an irreversible inhibitor by the initial steps of the enzymes reaction mechanism
penicillin
- inhibitor of glycopeptide transpeptidase-needed for cell wall
- mechanism of transpeptidase is similar to serine protease
- penicillin looks like substrate, but has a 4 membered ring including the peptide bone
- initial step=cleavage, transpeptidase forms intermediate, but N terminus can’t leave
acetylcholinesterase
- breaks down ach in synapses
- similar mech to chymotrypsin
- nerve gases are irreversible inhibs-inactivate active site- can’t breakdown ach-pulm spasms and loss of neuromuscular and cardiac function and death
- reversible inhibitors are AD drugs-aricept and cognex-improve cog function- can’t stop but slow down. competitive or non competitive- boost ach to improve memory and cognition