Chapter 8. Enzymes: Basic Concepts and Kinetics Flashcards
the energy required to form the transition state from the substrate of a reaction.
Free energy ofactivation
a reaction involving multiple substrates in which one or more products are released before all substrates bind the enzyme. The defining feature of these reactions is the formation of a substituted-enzyme intermediate.
double-displacement (ping-pong)
antibodies generated by using transition-state analogs of a particular reaction as antigens. Such antibodies often function as catalysts for the reaction.
catalytic antibody (abzyme)
A tightly bound cofactor required for a protein's activity
Prosthetic group
a small organic molecule required for the activity of many enzymes; vitamins are often components of coenzymes.
Coenzyme
form of energy capable of doing work under conditions of constant temperature and pressure. Also, a measure of the usable energy generated in a chemical reaction; denoted by the symbol G in thermodynamics. The change in free energy (delta G) of a system undergoing transformation at constant pressure is equal to the change in enthalpy (delta H) minus the product of the absolute temperature (T) and the change in entropy (delta S).
Free energy
the reduction in the rate of enzyme activity observed when the enzyme can bind the substrate and the inhibitor simultaneously. Noncompetitive inhibitors decrease the turnover number for an enzyme but do not diminish the proportion of enzyme molecules bound to the substrate; their effects are not overcome by increasing substrate concentration.
noncompetitive inhibition
A reactant in a chemical reaction. An enzyme catalyzes a single chemical reaction or set of closely related reactions, and the components of those reactions are called substrates
Substrate
the reduction in the rate of enzyme activity observed when the enzyme can bind the substrate or the inhibitor but not both. Many competitive inhibitors resemble the substrate and compete with it for binding to the active site. Relief from inhibition by saturation with substrate is a kinetic hallmark of competitive inhibition.
competitive inhibition
a specific region of an enzyme that binds the substrate and carries out catalysis.
Active site
A bisubstrate reaction in which both substrates must bind to the enzyme before any product is released. Consequently, a ternary complex of the enzyme and both substrates is a reaction intermediate
sequential reaction
Inhibition that results when an enzyme converts a pseudosubstrate into a reactive inhibitor that immediately inactivates its catalytic activity.
mechanism-based (suicide) inhibition
the concentration of substrate at which half the active sites of an enzyme are filled.
KM (the Michaelis constant)
an enzyme that consists of the protein component forming the main body of the enzyme (the apoenzyme) and any necessary, usually small, cofactors.
Holoenzyme
biological macromolecules that act as catalysts for biochemical reactions; while almost all are composed of protein, catalytically active RNA molecules have also recently been discovered.
Enzyme
The modification of the shape of an active site in an enzyme after the substrate is bound.
Induced fit
a means of mapping the active site of an enzyme by using a substrate analog that binds to the active site and forms a covalent bond with a nearby amino acid.
affinity label (reactive substrate analog)
A chemical agent that reacts with the side chain of specific amino acid. Group-specific reagents can be used to probe protein function.
group-specific reagent
Small molecules, such as metals or coenzymes, that many enzymes require for catalytic activity
Cofactor
an equation that expresses the velocity (V) of an enzyme-catalyzed reaction in terms of maximum velocity (Vmax), substrate concentration (S), and the Michaelis-Menten constant (KM). The equation accounts for the hyperbolic kinetics observed when V is plotted as a function of S; the equation is V = Vmax[S]/([S] + KM).
Michaelis-Menten equation
A plot of 1/V0 versus 1/[S] which yields a straight line with a y -intercept of 1/Vmax and a slope of KM/Vmax (Figure 8.12).
Lineweaver-Burk equation (double reciprocal plot)
Measure of catalytic efficiency because it takes into account both the rate of catalysis with a particular substrate and the nature of the enzyme-substrate interaction.
kcat/KM ratio (the specificity constant)
An enzyme without its cofactor.
apoenzyme
Enzyme that consist of multiple subunits and multiple active sites whose activity is regulated by signal molecules binding to distinct regulatory sites. Allosteric enzymes do not obey Michaelis-Menten kinetics.
Allosteric enzyme
the number of substrate molecules converted into product by an enzyme molecule in a unit time when the enzyme is fully saturated with substrate; it is equal to the kinetic constant k2(see Michaelis constant).
Turnover number
a chemical species that has the highest free energy and the lowest concentration of those on the pathway from a substrate to a product.
Transition state
compounds resembling the transition state of a catalyzed reaction. Such compounds are often potent inhibitors of enzyme-catalyzed reactions.
transition-state analog
The highest rate of an enzyme-catalyzed reaction, under conditions of constant enzyme concentration and saturating amounts of substrate.
Vmax (maximal rate)
Substrate-dependent inhibition in which the inhibitor binds only to the enzyme-substrate complex.
Uncompetitive inhibition
