lecture eight - enzyme catalysis Flashcards
proximity and orientation effects
enzymes bind substrates so a reaction can occur without need for random collision between reactants
reduces the entropy of reactants, so ligation or addition reactions are more favorable
two reactants become a single product, reducing the overall loss of entropy
general acid-base catalysis
enzyme can act as an acid or base; substitution of enzyme functional groups for [H+] and [OH-] permits rapid enzyme catalysis at neutral pH
often involves histidine imidazole group
covalent catalysis
substrate forms a transient covalent bond with amino acid R-group, in active site of an enzyme
speeds up the rate of reaction by forming a covalent intermediate that can substitute for the nucleophilic attack by a hydroxyl group – this reduces the energy of later transition sites of the reaction
non-protein acid cofactors are sometimes utilized to form covalent intermediates with reactant molecules (PLP or TPP)
entropy loss
reducing the disorder in a system
binding to the enzyme reduces random tumbling/stretching of the substrate, so it favors reaction of the ES complex
desolvation
substrates often have water tightly bound to their surface, binding to the enzyme can release this water and make the enzyme more reactive
this raises the energy of the ES complex
electrostatic effects
if repulsive charges occur between substrate and enzyme, and these repulsive forces can be relieved during the reaction, the reaction rate may be accelerated forward
covalent catalysis reduces …
energy level of transition states of the reaction by adding an additional covalent intermediate, also lowers the energy of activation
how do the effects of proximity and orientation speed up the rate of reaction
by aligning reactive chemical groups and holding them close together
how can an enzyme function in acid-base catalysis in a way that cannot be accomplished in a non-enzymatic chemical reaction?
the enzyme can function as an acid and base so it can simultaneously provide hydrogen and hydroxyl groups
enhances the rate of reaction bc they provide both groups at the exact place they are needed to facilitate so there is no movement necessary
what amino acid R-group(s) are often involved in acid-base catalysis?
R group imidazole from histidine is involved bc its pK is close to neutral pH so it can accept and donate protons
how does covalent catalysis speed up rate of reaction
by forming a covalent intermediate that can substitute for the nucleophilic attack by a hydroxyl group
what example of covalent catalysis involving enzymes or cofactors are cited in your lectures
proteolytic enzymes: chymotrypsin and trypsin, where acyl-enzyme intermediate is formed
how does entropy loss change the energy level during the course of an enzyme reaction?
reduces the disorder in a system; favors the reaction of the ES complex which lowers energy level during the enzyme reaction
how does desolvation relate to enzyme catalysis
when water is released from substrate, the substrate becomes more reactive, speeding up catalysis
what is electrostatic destabilization and how could such affects contribute to catalysis?
it is the repulsive charge occurring between a substrate and enzyme; can be relieved during reaction, and the reaction rate accelerates forward (faster catalysis)
what would happen to catalysis and the energy of activation if the association between enzyme and substrate were extremely strong?
too tight of binding would place ES complex in an energy well which would make energy of activation higher than for the uncatalyzed reaction
what does it mean that chymotrypsin is a proteolytic enzyme?
it means that chymotrypsin preferentially cleaves peptide bonds on the carboxyl side of tyrosine, tryptophan, and phenylalanine (aromatics)
the active site serine residue briefly becomes covalently bonded to the substrate, forming an acyl-enzyme intermediate
how does the R-group of an active site serine act as a nucleophile in the mechanism of chymotrypsin?
R-group of serine acts as a nucleophile by donating a pair of electrons and forming a brief covalent bond and enzyme-substrate intermediate
distinguish between tetrahedral and acyl-enzyme intermediates in chymotrypsin reaction
tetrahedral intermediate = unstable because of its ionic character, formed before acyl-enzyme.
anionic, stabilized by charged groups in the “anionic hole” of the enzyme’s active site.
the stabilization lowers the energy of activation and speeds the rate of reaction
acyl-enzyme is more stable than other anionic intermediates. under certain conditions, serine proteases can be isolated
the R-groups that function in the catalytic triad of chymotrypsin
histidine, asparagine, serine
which R group has direct contact with active site serine in the chymotrypsin triad?
histidine R-group
where are the three R groups located in the catalytic triad of chymotrypsin?
asparagine is on the leftmost side of the particle, histidine is on the inside, and serine is on the rightmost side
what product of the chymotrypsin reaction is the first to be released, and which remains covalently attached as part of the acyl-enzyme intermediate
amine product is first to be released
carboxylic acid part of substrate is still covalently attached as part of the acyl-enzyme intermediate
what does it mean that there are many evolutionarily related serine proteases that have homologous structures?
means that there are many serine proteases that have similarities in amino acid sequence and have the same catalytic triad and oxyanion hole
what does it mean that there are serine proteases that share a common mechanism, but are not homologous proteins and do not share a common evolutionary precursor protein?
this means that they have the same mechanism, but they aren’t similar in amino acid sequence or have the same catalytic triad or oxyanion hole
what is the catalytic role of carbonic anhydrase and what is the function of the zinc ion in the active site of this enzyme?
catalytic role of carbonic anhydrase is to catalyze the reaction of interconverting carbon dioxide and carbonic acid
zinc aids in transport of carbon dioxide throughout the blood
how does zinc facilitate the formation of hydroxyl ions, and how does this function in the production of bicarbonate ions?
zinc is necessary for catalytic activity; it is bound to the imidazole rings of three histidine residues
water binds to the zinc at the active site; zinc lowers the pK of water to about 7 which results in rapid production of hydroxyl ions. the hydroxyl ion that is formed can act as a nucleophile, it attacks carbon dioxide and converts it to a bicarbonate ion
