Chapter 5: Properties of Enzymes Flashcards
- efficient, selective, biological catalysts
- speed up the rate of forward and reverse reactions but don’t change the equilibrium concentrations
- highly specific for reactants
enzymes
reactants that enzymes act on
substrates
enzymes exhibit _______, meaning they only act on a single stereoisomer of the substrate
stereospecificity
enzymes display _____, meaning they do not form wasteful by-products
reaction specificity
an unstable arrangement of atoms in which chemical bonds are in the process of being broken and made
transition state
how do enzymes affect the transition state?
stabilize transition states by lowering it and decreasing the activation energy
what are the six classes of enzymes?
- oxidoreductases
- transferases
- hydrolases
- lyases
- isomerases
- ligases
- *catalyze oxidation-reduction reactions
- known dehydrogenases
- includes oxidases, peroxidases, oxygenases, or reductases
oxidoreductases
- *catalyze group transfer reactions
- many require the help of a coenzyme
- usually a portion of the substrate is covalently bound to the enzyme or its coenzyme
- includes kinases
transferases
- *catalyze hydrolysis
- a special class of transferases with water serving as the acceptor of the group transferred
hydrolases
**catalyze lysis of a substrate generating of double bond
lyases
**catalyze isomerization reactions
isomerases
- *catalyze ligation, or joining, of two substrates
- these reactions require energy, usually in the form of ATP
- often referred to as synthetases
ligases
- Model that states it is not until the substrate and enzyme come into contact that they fit together
- enzyme undergoes conformational change
induced fit model
what are the 3 ways to increase the rate of a chemical reaction?
- increase the temperature
- increase the concentration of the reactants
- add a catalyst
what happens to the velocity when the substrate is used up?
velocity becomes 0 and the curve is horizontal
what does an enzyme catalyzed reaction involve?
**the reversible formation of an ezyme-substrate complex (ES), which breaks down to form free enzyme (E) and product (P)
**E + S –> ES –> E + P
Is an enzyme catalyzed reaction first or second order?
Pseudo-first order reaction — the rate is affected by the concentration of E but not S, meaning at saturating concentrations of S, there is sufficient S for ever E to react
the rate constant for ES formation
k1
the rate constant for the dissociation of ES back to E + S
k-1
the rate constant for ES to E + P
k2
the rate constant E + P forming ES
k-2
why is k-2 neglected?
- the formation of ES is not always product-forming (reversible)
- there is no product present at the early stages (very low [P]) so k-2 can be ignored
what is the Michaelis-Menten equation and what type of curve is it?
- ***v0 = Vmax[S]/Km + [S]
* **hyperbolic curve
what is the effect of enzyme concentration on reaction velocity?
if the substrate concentration is held constant, the velocity of the reaction is proportional to the enzyme concentration
what is the effect of substrate concentration on reaction velocity?
- at low [S], reaction velocity is first-order with respect to substrate (linear)
- at high [S], reaction is zero-order with respect to substrate (independent of [S])
- at mid [S], the reaction is mixed-order (proportionality is changing)
what are the steady-state conditions?
the rate of appearance of ES = the rate of disappearance of ES
what is the Michaelis constant?
Km = (k-1 + k2)/ k1
What allows us to determine the turnover number of an enzyme?
Vmax
- the number of substrate molecules converted to product by an enzyme in a unit time when the enzyme is fully saturated with substrate
- the efficiency of ES –> E + P
turnover number (turnover number = k2)
what else is k2 called?
kcat
- ratio of combined rate constants
- concentration of substrate needed to reach half maximum velocity
- often equivalent to k-1/k1
Km
what does a low value of Km mean?
the lower the value of Km, the greater the affinity of the enzyme for the enzyme substrate complex (dissociation is rare)
describes E + S –> ES (formation of ES)
catalytic proficiency
how do we figure out catalytic proficiency?
kcat/Km
what do higher values of catalytic proficiency mean?
indicates more efficient catalysis
where is catalytic efficiency important on the graph?
- at the beginning of the graph - near linear portion
- second order reaction
where is the turnover number important on the graph?
- towards the end of the graph - horizontal portion
- first order reaction in respect to [E]
what type of plot is used since it is difficult to determine Km and Vmax from a hyperbolic curve?
Lineweaver-Burk (double reciprocal plot)
what is the Lineweaver-Burk equation?
1/v0 = (Km/Vmax) 1/[S] + 1/Vmax
what are the different types of reactions with multiple substrates?
- ordered
- random
- ping-pong
a product is released before all substrates have bound
ping-pong reaction
there is an obligatory order in which substrates bind and products are released
ordered reaction
- a compound that binds to an enzyme an interferes with its activity
- most bind reversibly
- some bind covalently and are irreversible
enzyme inhibitor
what is the inhibition (dissociation) constant?
Ki = [E][I]/[EI]
what does a high Ki indicate? a low Ki?
- *high Ki = inhibitory effect is weak
* *low Ki = inhibitory effect is strong - inhibitor is bound tightly, so the amount of active enzyme present is low
what are the types of reversible enzyme inhibition?
- classical competitive inhibition
- non-classical competitive inhibition
- uncompetitive inhibition
- noncompetitive inhibition
- competes with substrate for the same site on the enzyme
- raises apparent Km
- Vmax is unchanged (enough [S] will fill the active site with S
competitive enzyme inhibitor
- does not compete with substrate for binding, but alters catalytic effectiveness
- inhibitor can bind to either E or ES
- lowers Vmax
- Km is unchanged (affinity is not changing)
noncompetitive enzyme inhibitor
- binds only to the ES complex and ESI does not go on to give the product
- lowers Vmax AND Km
uncompetitive enzyme inhibitor
- describes cases that do not conform to classic noncompetitive inhibition
- both Vmax and Km are affected (usually because the affinity of the inhibitor for E is different than its affinity for ES)
mixed enzyme inhibition
inhibitors designed to mimic the shape of the transition state of ES –> P
transition state analogs
uses known information about the shape and reactivity of a biological target to design inhibitors
rational drug design
- forms a stable, covalent bond with an enzyme, thus removing active enzyme molecules from the population
- usually occurs through alkylation or acetylation of a side chain
irreversible enzyme inhibitor
- enzyme activated reagents
- disguised inhibitors
suicide inhibitors
enzymes whose activity can be modified in a manner that affects the rate of an enzyme-catalyzed reaction
regulated enzymes
how are regulated enzymes activity modified?
- amount of enzyme controlled by regulating rate of its synthesis or degradation
- enzymes are more active catalysts when its concentration is high
- enzymes become less active when concentration of substrates decrease or when product accumulates
- those whose properties are affected by a change in structure
- change shape between active and inactive shapes as a result of the binding of substrates at the active site and of regulatory molecules at other sites
allosteric enzymes
the active site becomes available to the substrates when a regulatory molecule binds to a different site on the enzyme
allosteric activation
the active site becomes unavailable to the substrates when a regulatory molecule binds to a different site on the enzyme
allosteric deactivation
what is another name for the allosteric site?
regulatory site
what is another name for the allosteric effector?
regulatory molecule
what happens during allosteric inhibition?
- an enzyme is active in the uncomplexed form, which has a high affinity for its substrate
- binding of an allosteric inhibitor stabilizes the enzyme in its low-affinity form, resulting in little or no activity
what happens during allosteric activation?
- an enzyme is inactive in its uncomplexed form, which has a low affinity for its substrate
- binding of an allosteric activator stabilizes the enzyme in its high-affinity form, resulting in enzyme activity
how does an allosteric activator affect the apparent Km?
lower the apparent Km and raise the activity at a given [S]
how does an allosteric inhibitor affect the apparent Km?
raises the apparent Km and lower the activity at a given [S]
addition of S leads to an increase in the concentration of enzyme in the ________.
R conformation
addition of inhibitor increases the proportion in the _____.
T state
activator molecules bind preferentially to the ____, so they increase the ______.
R state; R/T ratio
- all subunits are either T or R state
- one substrate binds each subunit
- substrate can bind either confirmation but binding in T weaker than binding in R
the concerted model
- one subunit can be R while the other is T state
- one substrate binds each subunit
- substrate can bind either conformation but cooperativity leads to a conformational change from T to R upon substrate binding to any subunit
sequential model
how does the regulation of covalent modification work?
- activity of an enzyme can be modulated by the covalent attachment and removal of groups on the polypeptide chain
- phosphorylation is most common
