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)
