enzyme structure/mechanism Flashcards
what is gibbs free energy change?
free energy change for any transformation
it can predict if a reaction will occur spontaneously
what does a delta G less than 0 mean?
reaction will occur spontaneously
what does a delta G greater than 0 mean?
it will not occur spontaneously
what does a delta G equal to 0 mean?
the system is in equilibrium
how is activation energy related to G
it is NOT related to delta G. the RATE of the reaction is the thing that depends on activation energy
can enzymes change the delta G for a reaction?
no!
can enzymes change the activation energy for a reaction?
yes! they can lower it
what are the two ways enzymes can lower the activation energy of a rxn?
- by direct stabilization of the transition state
2. creation of new reaction pathway
What theory of binding do most enzyme-substrate interactions exhibit?
the induced fit (rather than the lock and key)
with what type of interactions do enzymes bind to substrates?
multiple weak non covalent interactions
electrostratic interactions, H bonds, van der waal forces, hydrophobic effect
does this statement describe a prosthetic group or a cofactor? “more loosely bound and generally come on and off the enzyme”
cofactor
explain what “proximity and orientation effects” regarding chemical strategies in enzymatic catalysis means
reactants come together with proper spatial orientation for reaction to occur
what does general acid catalysis mean?
weak acid on enzyme provides a partial proton transfer during the enzymatic reaction
in acid/bad catalysis, what groups are typically at the enzyme’s active site?
HISTIDINE (because it can be an acid or a base)
aspartate, glutamate
in covalent catalysis, what 4 amino acids and 1 group isnormally involved at the enzyme’s active site?
cysteine, serine, lysine, histidine, prosthetic groups
what occurs in covalent catalysis?
transient formation of a covalent bond between enzyme and substrate (creating new intermediate)
what is occurring in electrostatic catalysis?
charge distribution in active site helps stabilize the transition state
what 5 amino acids and 1 cofactor group is usually seen in electrostatic catalysis?
aspartate, glutamate, arginine, histidine, lysine, metal ions cofactors
how do proteases carry out their chemical reaction?
cleavage of a peptide bond by addition of water across the bond
what are the 4 major classes of proteases?
serine protease
aspartyl protease
thiol protease
Zn+2 protease
what 3 amino acids make up the catalytic triad?
serine
aspartate
histidine
all 3 are hydrogen bonded when substrate is not bound
what four catalysis happen in the 1st step of serine proteases?
Preferential binding for transition state
covalent catalysis
general base catalysis
elecrostatic catalysis
what two catalysis happen in the 2nd step of serine proteases?
general acid/base catalysis
Preferential binding for transition state
what is the rate limiting step in the serine protease reactions
formation of the acyl-enzyme intermediate
on the graph, where is the rate limiting step occur?
in the semi stable dip between the two peaks
how do chymotrypsin, trypsin and elastase differ?
they are all serine proteases (so same mechanism) but they differ in their substrate specificities
how is substrate specificity achieved?
the different serine proteases will have different amino acids/confirmations around the invariant catalytic triad that will determine the specificity. *the catalytic triad itself does NOT provide specificity
what type of inhibitor is penicillin?
a suicide inhibitor
irreversible inhibitor
how do suicide inhibitors work?
they bind to the enzyme because of their resemblance to the substrate and are converted to an irreversible inhibitor by the initial steps of the enzyme’s reaction mechanism
