enzyme mech and catalysis Flashcards
why are enzymes central to all biochemical processes?
enzymes show greater substrate specificity, have optimal arrangement of catalytic groups, and increase reaction rates
Although most enzymes are proteins, what can also catalyze reactions?
RNA molecules
how are enzymes named?
adding “ase” to substrate or words describing reaction
ex) DNA polymerase catalyzes the polymerization of nucleotides to form DNA
what chemically reactive groups do enzymes contain that help catalyze reactions?
amino acid side-chains and N-terminal -NH2 and C-terminal -COOH
what do enzyme cofactors do?
do chemistry impossible with usual functional groups
what can cofactors be?
metal ions or organic molecules
what do enzymes catalyze the conversion of?
substrates to products
in the simple enzymatic reaction, what are transient complexes(reaction intermediates)?
ES and EP
what does the equilibrium between S and P reflect?
the difference in the free energies of their ground states
because the ground state of P is lower than S, hence delta G for the reaction is…
negative and favors P
enzymes accelerate reaction rates by lowering the activation energy barrier, but do not affect…
reaction equlibria
what is the equilibrium constant, Keq?
describes relative amounts of substrates and products present at equilibrium in a biochemical reaction
what is the rate constant, k?
measure of how fast (velocity) a reaction can occur
what happens to delta G when k is larger?
it is smaller (inverse exponential relationship)
what does an enzyme’s tertiary structure create?
unique microenvironment for ES-intermediate substrate binding
what is the interaction between substrate and enzyme mediated by?
the same non-covalent forces that stabilize protein structure
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
binding energy
energy derived from ES interaction
what do enzymes use binding energy for?
to achieve substrate specificity and to stabilize the transition states through non-covalent interactions
what do the non-covalent interactions allow the enzyme to do?
bind substrates, bind and stabilize the transition-state
what is important to remember about the mechanism of enzyme binding?
NOT A LOCK-AND-KEY
what do enzymes bind with a greater affinity to?
bind the transition state over either substrates or products
important corollary about binding
good substrates don’t necessarily bind extremely tightly to enzyme; do not want to get stuck in an ES complex
what are good inhibitors of enzymes
transition state analogs (rational basis for drug design)
