Pchem Exam 3
List 3 general strategies employed by enzymes to increase reaction rates.
1. Concentrating reactants at the active site. 2. Reducing electrostatic repulsion between reactant molecules. 3. Transition-state binding.
Name the four methods for studying rapid chemical reactions
1. Continuous flow 2. Stopped-flow 3. Relaxation techniques 4. Quenching methods
Time-resolved Spectroscopy for Kinetics
1. Energy transfer, molecular vibrations and conversion from one mode of motion into another- require pulses in the range of 1 fs to 1 ps. 2. Lasers can produce pulses as brief as 1 fs (10^ -15 s) 3. Light-activated, ultrafast chemical reactions can be studied by time-resolved spectroscopy
Name two models of protein folding
1. Framework model 2. Nucleation model
Protein Folding Model (2)
1. Framework model 2. Nucleation model
The majority of drugs used clinically exert their functions in one of two ways:
1. Interfering with a component in the body (receptor antagonist) 2. interfering with an enzyme of the body or pathogens including bacteria/virus, fungi and parasites.
Transition-state binding
1. Non covalent interactions between proteins and ligands can exhibit highly favorable free energy changes. However, in general, high affinity enzyme substrate binding is counterproductive- stabilizing the ES complex and increasing the hight of the activation energy barrier. 2. Instead, enzymes have evolved so that binding interactions between E and S are maximized when the substrate geometry is distorted to resemble the transition state.
Reducing electrostatic repulsion-between reactant molecules
1. Placement of charged side-chains or ions at active site 2. Reacting with one substrate and releasing one product before the second substrate binds (ping-pong mechanisms)
There are 2 strategies employed by enzymes catalyzing bimolecular reactions to reduce electrostatic repulsion between charged substrates. What are they?
1. Placement of charged side-chains or ions at the active site. 2. Reacting with one substrate and releasing one product before the second substrate binds.
Two general approximations are frequently used when analyzing multi-step reactions. What are they?
1. Prior-equilibrium (pre-equilibrium) 2. Steady-state approximation
Consecutive (complex, multi-step) reactions
1. Reactions often involve a series of elementary reaction 2. This sequence of reactions is referred to as the reaction mechanism 3. Although the rate law does not predict the chemical mechanism, the mechanism does predict the rate law
Analysis of complex mechanisms
1. Sequential reactions 2. Ping-pong reactions
Catalytic Efficiency
1. The catalytic constant (a.k.a the turnover frequency or turnover number), symbolized kcat, is the number of catalytic cycles preformed by an enzyme active site in a given interval (usually 1 second) divided by the duration of the interval. a. kcat has the units of a first-order rate constant (typically s^-1). b. kcat is numerically equivalent to kb, the rate constant for product release in the Michaelis-Menten treatment. c.From the definition for vmax, it follows that kcat = vmax/[E]o
Collision Theory continued:
1. The criterion for a successful collision is that the molecules have some minimum kinetic energy along their line of approach 2. The fraction of productive collision is dependent on the kinetic energy, which is dependent on temperature. At higher temperatures, a larger fraction of molecules will have the minimum requisite energy. 3. The fraction, f, of collision that occur with the minimum kinetic energy Ea is given by a Boltzmann distribution: f= e^(-Ea/RT)
Strategic orientation of chemical groups
1. have previously alluded to charge neutralization. 2. proton donors and acceptors. 3. nucleophiles
What are the two general strategies for determining the rate law for a reaction?
1. isolation method and pseudo order reactions 2. the method of initial rates
A reaction has a rate law of the form k[A]^2[B] What are the units of the rate constant if the reaction rate is expressed as mol/dm^3s (M/s)
1/ M^2s L^2/Mol^2s dm^6/Mol^2s
For the second-order conversion of 2A -> A2 products, a plot of ______ will be linear with time.
1/ [A]
The rate law was reported as v=k[A][B][C] where the rate has units of M/s What are the units of k?
1/M^sS
Lineweaver-Burk equation
1/v = 1/vmax + (Km/vmax) * 1/[S]o A plot of 1/v vs 1/[S]o (double-reciprocal plot) should be linear with a slope of Km/vmax, a y-intercept of 1/vmax, and an x-intercept of -1/Km v=vmax [S]o/Km + [S]o = vmax/ (1 + Km/[S]o)
Second-order Reactions
2A -> A(subscript)2 A plot of 1/[A] vs. time will be linear for a type I second-order reaction, with a slope of k
Which reaction responds more strongly to changes in temperature, one with an activation energy of 52 kJ/mol or one with an activation energy of 25 kJ/mol?
52 kJ/mol The larger the activation energy, the more sensitive the reaction rate is to temperature.
Zeroth-order reaction
A -> B The concentration of A decreased linearly with time until it is zero Units would be M/S
First-order Reactions
A -> B The concentration of A decreases exponentially with time This, a plot of ln[A] vs t will be linear for a first-order reaction, with a slope of -k
Equilibrium and Temperature
A. For exothermic (△H<0), Ea,r must be greater that Ea,f. B. So when temperature is raised, the reverse rate constant will be accelerated to a greater extent than the forward rate constant. C. Hence, the equilibrium constant -i.e., the ratio of the rate constants- will decrease
What does A and Ea stand for?
A= pre exponential factor, it has the same units as kr Ea= activation energy, the larger the activation energy the more sensitive the reaction rate is to temperature
When describing reaction dynamics, ______ theory adequately describes the behavior of gas-phase reaction molecules, and _______ theory is applicable to a wider range of reaction environments.
Collision Transition state
Stopped-flow
Continuous flow requires large reactant volumes. In the stopped-flow techniques, a small volume of the reaction mixture is expelled from the driving syringes, through a rapid-mixing device, into capillary tubing. Progress of the reaction is monitored continuously by an optical detector positioned adjacent to the mixing chamber. Reactions can be monitored on the ms timescale.
Approximate Reaction Models
Determination of a complex reaction mechanism is complicated by the potentially large number of rate constants and chemical species 1. Prior- equilibrium (pre-equilibrium) approximation 2. Steady-state approximation
For a single-substrate enzyme-catalyzed reaction the Michaelis constant is a composite constant that includes the rate constants for _______________, _________________, and _______________.
ES formation ES dissociation ES conversion to products
The potential-energy difference between the reactants and the transition state is equal to the
Ea (Activation Energy)
The slope of the linear form of the Arrhenius equation is proportional to
Ea (Activation Energy)
Michaelis-Menten Equation
Experimental studies of enzyme kinetics are typically conducted by monitoring the initial rate of product formation, with the substrate concentration vastly exceeding the enzyme concentration. In 1913, Michaelis and Menten derived a rate equation that was consistent with the general properties of enzymatic reactions. They employed a pre-equilibrium model to treat formation of the ES complex. In 1925, Briggs and Haldane applied the steady-state approximation to get the same equation.
True or False? "A catalyst lowers the activation energy for a reaction by altering the potential energy difference between the reactants and products."
False A catalyst lowers the activation energy for a reaction by altering the activation energy. It does not change the potential energy difference between the reactants and products.
Rate-limiting step (RDS) notes
For a stepwise reaction shown on the left: a. The first step is RDS (highest Ea) b. Once over the initial barrier, the intermediates cascade into products. Note: A RDS may also stem from the low concentration of crucial reactant or catalyst and need not correspond to the step with the highest activation energy
Kinetics vs. Thermodynamic Control graph
For two competing irreversible reactions, the relative amounts of the two products formed is independent of their thermodynamic stabilities, dependent only on the relative rate constants. For a reversible reaction, at long times, the ratio [P2] / [P1] approaches the equilibrium value.
Equilibrium Constant and Rate Constant
If reversible: all forward reactions are accompanied by their reverse reactions
Half-life for a second-order reaction
In contrast to a a first order reaction, t(1/2) for a second order reaction depends on the initial reactant concentration although the initial decrease in reactant concentration can be more rapid for a type I second- order reaction than for a first-order reaction, in the latter stages of the reaction, the rate of decay is slower
Uncompetitive Inhibition
In this scenario, the inhibitor binds only to the ES complex, to a site distinct from the substrate-binding site. 1. ⍺ = 1. Thus the slope of the L-B plot is unchanged. ⍺ ' > 1. Thus the y-intercept is increased. 2. Uncompetitive inhibition (at several concentrations of inhibitor) produces a set of parallel lines. 3. Because the substrate and inhibitor bind to different forms of the enzyme, an infinitely high [S] cannot compete away the effect of I.
Enzyme inhibition
Inhibitors decrease the rate of product formation by binding to the enzyme and/or the ES complex. The lower the values of KI and KI', the more effective the inhibitor.
Consider a two-substrate enzyme-catalyzed reaction. When the initial rate is studied as a function of one of the substrates at several fixed levels of the other substrate, the resulting L-B plot consists of a set of parallel lines. What can you conclude about the mechanisms of the reaction?
It is a ping pong mechanism
Short reaction times favor _____ control.
Kinetic
The slope of a Lineweaver-Burk plot is equal to
Km/Vmax
Michaelis-Menten Equation continued Mechanism
Mechanism: E + S -> ES v=ka[E][S] ES -> E + S v=ka[ES] ES -> E + P v=kb[ES]
Sequestration
The active side isolates reactants from the solvent. 1. In general, substrates must be dehydrates (i.e., stripped of bound water molecules) to be bound at the active site. 2. The reactivity of weak nucleophiles (e.g. carboxylate groups) can be markedly enhanced by immobilization in a hydrophobic active site.
Continuous flow
The reactants are expelled from motor-driven syringes through a mixing chamber into capillary tubing. An optical detector is placed at some position along the tubing. The reaction time monitored by the detector depends on the rate of flow and the distance of the detector from the mixing chamber.
Quenching Method
The reaction after it has been allowed to proceed for a certain time and the composition is analyzed at leisure. In a chemical quench flow, the reaction is quenched by another reagent. Spectroscopic fingerprints are not needed in order to measure the concentration of reactants and products- can be examined by "slow" techniques, such as gel electrophoresis. Freeze it, change pH, separate them
Fixed-time assays
The reaction is allowed to run for a defined period of time, then quenched and analyzed
Relaxation Kinetics
The return to equilibrium will always be exponential with time. always exponential decay
High reaction temperatures favor ______ control
Thermodynamic
Low activation-energy barriers favor _____ control
Thermodynamic
Why is it permissible to replace the free substrate concentration, [S], by [S]o, the total substate concentration, in the Michaelis-Menten equation?
[E] << [S], so [ES] is approximately 0. [E] is approximately equal to [E]o, [S] is approximately equal to [S]o. Also, we're looking at initial rates, so [P] is approximately equal to zero.
The ratio of products is determined by the magnitudes of k1 and k2
[P]/[Q] = k1/k2
Average reaction rate is given by
_ v= ⎮△ [J] ⎮ ------------ △t
Prior- equilibrium (pre-equilibrium) approximation
a. Assumes that the rates of formation an intermediate and its decomposition back to reactants is rapid relative to its conversion to products. b. The approximation requires that k2<< k1 =~ k1
Ping-pong reactions
a. In a ping-pong reaction, products are released prior to addition of all of the substrates to the active site. c. It is called a ping-pong reaction because the enzyme ping-pongs between two different forms, E and E*. E* is generally a covalently modified form of the enzyme.
Sequential reactions
a. In a sequential reaction, all substrates are bound in the active site before there is any conversion to products b. Substrate binding can either be ordered or random. 1. Ordered addition of substrates/ release of products 2. Random addition of substrates/release of products
Thermodynamic control is favored by
a. Long reaction times b. High reaction temperatures c. Reversible reactions (low activation energy barriers)
Kinetic control is favored by
a. Short reaction times b. Lower reaction temperatures c. Irreversible reactions (large activation energies)
Rate-determining step (RDS) notes
a. The rate-determining step is the slowest step of a reaction and acts as a bottleneck b. If a faster reaction can also lead to products, then the slowest step is irrelevant because the slow reaction can then be sidestepped.
Steady-state approximation
a. Under this scenario, the intermediate is highly reactive, so that its concentration remains low (and essentially constant) throughout the reaction. b. In contrast to the pre-equilibrium scenario, the formation of the intermediate is generally considered to be slow relative to its decomposition
In accord with experimental observation:
a. When [S](subscript o) >> Km, the reaction rate reaches its maximum, Vmax v= vmax = kb [E]o b. When [S](subscript o) << Km, the reaction rate is proportional to [S]o v= kb/Km [E]o[S]o = Vmax/Km [S]o Km has same units as substrate
The method of initial rates
a.) the instantaneous rate is measured at the beginning of the reaction before there has been any significant change in reactant concentrations. b.) the initial concentration of a reactant is varied, and the impact on the initial rate is measured. E.g., assume the concentration of A is varied, with the concentration of B held constant: alog[A] (subscript 0) -plot of log v(subscript 0)vs. log[A](subscript 0) wil have a slope= a
An enzyme, or any catalyst for that matter, acts by lowering the activation energy by providing
an alternative reaction pathway or by lowering the energy of the transition state
Rate law
an empirical relationship between reactant concentration and reaction rate v= k[A]^ ⍺[B]^ℬ... k= the rate constant, the value of which depends on T and P ⍺= the reaction order with respect to [A] ℬ= the reaction order with respect to [B]
Elementary reactions
are those that occur in a single step
For chemical reaction at equilibrium, the forward-and reverse reactions must occur
at the same rate
The time-constant for a reaction is the time required for
concentration of the reactant to decrease by a factor of 1/e Fancy T = 1/ kr
A multi-step reaction is often referred to as a ______ reaction.
consecutive
Adding 150 mM NaCl into the reaction mixture of A(+) + B(-) <---> C^ (⌶) will _____ the rate of C^ (⌶2+) formation.
decrease
Increase the viscosity of a reaction buffer will ____ the reaction constant for diffusion.
decrease
How to determine if the reaction is the first step of a consecutive reaction, might it be rate limiting and why?
determine Q and K and if Q < K then it is possible and could be the rate limiting step.
A rate law is an _____ relationship between reactant concentration and reaction rate.
empirical
Principle of Microscopic Reversibility At equilibrium, reactions between any pair of species must occur with
equal frequency in both directions. The forward and reverse mechanisms must be the same. All steps must be reversible.
For a single-substrate enzyme-catalyzed reaction, when the rates of formation of the ES encounter complex greatly exceed the rate of product formation, the value of Michaelis constant approaches the value of the ....
equilibrium constant
The ration of the forward- and reverse rate-constants is equal to the ________ for the forward reaction.
equilibrium constant
If both reactions 1 and 2 in the figure above are reversible, the [P1] / [P2] is determined by their relative
equilibrium constants
In the first-order conversion of A -> B, the concentration of A decreases _______ with time.
exponentially
The rate of an enzyme-catalyzed reaction is ______ -order with respect to the total enzyme concentration.
first
In a ________, a reaction is allowed to run for a defined period of time, then quenched (terminated) and analyzed.
fixed-time assays
A competitive enzyme inhibitor binds only to the ________ form of the enzyme.
free
Adding 150 mM NaCl into the reaction mixture of A(+) + B(+) <---> C^ (⌶2+) will _____ the rate of C^ (⌶2+) formation.
increase
The fraction, f of collision that occur with the minimum kinetic energy Ea __________ when temperature increases.
increases
In this method for elucidating rate-laws, none of the reactants need be present in large excess. The instantaneous reaction rate is measured before there has been any significant decrease in reactant concentrations (or significant accumulation of products). This strategy is called the
isolation method and pseudo-order reactions.
If A is in vast excess, the rate law simplifies to
k' = k[A] (subscript) 0
If B is in vast excess, its concentration will be essentially constant, equal to its initial concentration [B](subscript)0. The rate law simplifies to
k' = k[B]^2 (subscript) 0
The catalytic efficiency of an enzyme, symbolized, is defined as the ratio
kcat/Km a. n=kcat/Km = kakb/ka' +kb b. catalytic efficiency is maximal when kb >> ka'. Then, n=ka, which is the same as saying that the reaction is diffusion-controlled. c. For molecules the size of enzymes encountering low MW substrates, the upper limit for ka is 10^8 - 10^9 M^-1 *S^-1 with a value of n of 4.0 x 10^8 M^-1 *S^-1, catalase is often said to have attained catalytic perfection
The rate of product formation, kb[ES], requires
knowledge of [ES]
In the zeroth-order conversion of A -> B, the concentration of A decreases _______ with time until it is zero.
linearly
Given kr at two temperatures, it is straightforward to calculate Ea:
ln k2/k1 = - Ea/R * (1/T2 - 1/T1)
For the first-order conversion of A -> B, a plot of ________ will be linear with time.
ln[A]
The Swedish chemist Svante Arrhenius noted that many chemical reactions showed a similar temperature-dependence- specifically that a plot of __________ was linear with a slope characteristic of the particular type of reaction.
lnk vs. 1/T
Debye-Huckel Limiting Law
logkf = logkf^º + 2AZ(sub A) Z (sub B) I ^(1/2) or log (kf / kf^º) = 2AZ(sub A) Z (sub B) I ^(1/2) kf^º = rate constant in the absence of added salt A = 0.0509 for water at 25º C I - ionic strength, expressed in molality
All catalysts work by...
lowering the activation energy
Molecularity
means the number of molecules that react in an elementary reaction
_____ refers to the number of molecules that react in an elementary reaction.
molecularity
The principle of microscopic reversibility requires that, at equilibrium, reactions between any pair of species....
must occur with equal frequency in both directions
In ________ competition, the inhibitor binds to a site that may overlap the substrate binding site.
noncompetitive
According to transition-state theory (a.k.a Eyring theory or the theory of absolute reaction rates), the activated complex is an aggregate of atoms, which may be viewed as similar to an ordinary molecules, except that it has....
one particular vibration with respect to which it is unstable.
Elementary reaction
one that takes place in a single step
If the velocity of an enzyme-catalyzed reaction exhibits a sigmoid dependence on substate concentration, substrate binding must be ___________.
positively cooperative did not cover in class, not required for exam 3
The intercept of the linear form of the Arrhenius equation is equal to the natural logarithm of
pre-exponential factor A
Assume A is the limiting reactant and all other reactants are present in large excess. If the reaction rate is proportional to [A], the reaction is said to be ______.
pseudo-first-order
The reaction is said to be ________ because the assumption of constant [B] causes the rate law to take on an apparent first-order form.
pseudo-first-order
If the reaction rate is proportional to [A]^2, the reaction is said to be _____.
pseudo-second-order
The reaction is said to be ______ because the assumption of constant [A] produces an apparent second order rate law.
pseudo-second-order
If both reactions 1 and 2 in the figure below are irreversible, the [P1] / [P2] is determined by
rate constants
The exponent of the concentration term for a particular reactant in a rate-law expression is call the _____ with respect to that reactant.
reaction order
Parallel reactions
reactions that produce two or more distinct products.
Real-time analysis
refers to the analysis of the reaction composition while the reaction is in progress
A competitive enzyme inhibitor changes only the _______ of a lineweaver-burk plot.
slope
In general, reaction orders have no relationship to the
stoichiometric coefficients
The rate of a single-substrate enzyme-catalyzed reaction is zero-order with respect to the substrate when...
substrate is way bigger than Km [S]o >> Km
The rate of a single-substrate enzyme-catalyzed reaction is first-order with respect to the substrate when...
substrate is way smaller than km [S]o << Km
An uncompetitive enzyme inhibitor binds only to ...
the ES complex (a site distinct from the substrate binding site)
All enzymes work by lowering
the activation energy of the reaction.
The half-life for a reaction is the time required for...
the concentration of the reactant to decrease to half of its initial value t1/2= ln2 / kr
The equilibrium constant is the ratio of
the forward and reverse rate constants
The activation energy is the potential-energy difference between
the reactants and the transition state
The fundamental postulate of transition-state theory is that....
the reactants are always in equilibrium with the activated complex.
The activation energy can be viewed as the minimum energy that
the reactants must have in order to form products
In kinetics, the term "relaxation" refers to
the return of a system to equilibrium
Time constant (fancy T)
time required for concentration of ractant to decrease by a factor of 1/e fancy T= 1/ kr
Half-life (t1/2)
time required for the concentration of the reactant to decrease to half of its initial value t1/2 = ln2 / kr the half-life of a reactant in a first-order reaction is independent of its concentration
What is usually the rate limiting step of protein unfolding?
transition of helix-to-coil in the middle of the chain
Overall reaction order is ⍺ + ℬ +....
v= k[A] first order in A v= k[A][B] first order in A, first oder in B v= k[A]^2 second order in A
Reaction orders need not be integers If a rate law is not of the general form, it does not have an overall order. E.g., consider the rate law for a typical enzyme-catalyzed reaction:
v= k[E][S]/ [S] + K (subscript)m This rate law is first-order with respect to E, but has no specific order with respect to S.
Instantaneous reaction rate is given by
v= ⎮d [J] ⎮ ------------ dt
Many apparent first- or second-order reactions in aqueous solution are only pseudo-first- or pseudo-second order because
water is a reactant, but it's concentration if constant
An uncompetitive enzyme inhibitor alters _______ of a lineweaver-burk plot.
y-intercept
Vmax for an enzyme-catalyzed reaction can be deduced from the _______ of a Lineweaver-Burk plot.
y-intercept
The fraction amount of each products (⍬) is given by
⍬i = ki / (Zig Zag E) (n) kn
In transition-state theory, _______ serves the same function as the activation energy in Arrhenius rate theory.
△G =/ activation Gibbs energy
Rate Limiting Step (RDS)
- In a multi-step reaction, one step often dictates the overall reaction rate a. If kb >> ka, then the rate of product formation is dependent solely on the rate at which I is formed, independent of the rate of conversion of I to P b. The reaction behaves like a simple first-order reaction c. The conversion of A to I is the rate-determining, or rate-limiting, step d. Rate-determining step (RDS) : slowest elementary reaction in a complex reaction e. The designation of a slow reaction as the RDS assumes that there is no alternative pathway to products
Folding Kinetics of a-Lactalbumin case study
- The overall decay of the methyl-bulk peak follows a single-exponential kinetic with k=0.33/s and a half time of t(1/2)=2.10 s -Kinetic traces of individual peaks in he methyl group region
The x-intercept of a Lineweaver-Burk plot equals
-1/Km
Unimolecular
-A single molecule decomposed or undergoes an isomerization or conformational change -Rate law: v=kf[A]
Concentrating reactants at the active site
-Binding energy is used to overcome the unfavorable △S associated with immobilizing the substrate(s) at the active site.
Collision Theory continued:
-Given that the reaction rate must be proportional to the product of the collision frequency and the fraction of successful collision, we write v (weird circle symbol) [A][B]e^(-Ea/RT) -Comparing this expression to the rate law for second-order reaction: v=kr[A][B] -Rest on lecture notes.
The Arrhenius Equation
-Swedish chemist Svante Arrhenius noted that much of the chemical kinetic data that had been collected to that time showed a similar dependence on temperature plot of lnk vs 1/T was linear with a slope characteristic of the reaction
Transition State Theory
-The activated complex C=/ is formed from the reactants A and B - There is an equilibrium between the concentrations of A, B, and C=/ -Not every motion along the reaction coordinate takes the complex through the transition state and to the product P -Rest on lecture notes
Bimolecular
-Two molecules collide and undergo some type of chemical change -Rate law: v=kf[A]^2
Summary of 0, 1st, 2nd, 3rd orders
1. 0 order [A] decreases linearly with t 2. 1st order [A] decreases exponentially with t plot: ln [A] vs. t slope= -kr t (1/2) is independent on [A] 3. 2nd order: Type I plot: 1/ [A] vs. t linear plot slope= kr t (1/2) is dependent on [A]
Collision Theory
1. Adequately describes the behavior of gas-phase reactions molecules 2. The theory proposes that reaction occurs only if the reactants collide with some minimum energy, sufficient to surmount the activation barrier (i.e., the peak in the reaction profile) 3. As we have suggested previously, it can be demonstrated that the activation barrier height is the activation energy for the reaction 4. The collision frequency for reactants A, B is proportional to their concentrations: collision frequency
The isolation method and pseudo-order reactions
1. All reactants except one are present in large excess. 2. The rate dependence for each reactant is found by isolating each in turn. 3. Consider the rate law v=k[A][B]^2
Strategies for Achieving Rate Enhancements
1. Concentrating reactants at the active site. 2. Reducing electrostatic repulsion between reactant molecules 3. Transition-state binding 4. Sequestration 5. Strategic orientation of chemical groups
Relaxation techniques
A reaction at equilibrium is subjected to a rapid change in temperature or pressure ("T-jump" or "p-jump") and the return to equilibrium under the new reaction condition is monitored spectrophotometrically. Reactions can be monitored on the s timescale.
Noncompetitive inhibition
Also called mixed inhibition, the inhibitor binds to a site that is not identical to, but may overlap, the substrate binding site. As a result, its presence interferes with substrate binding. 1. ⍺ > 1. Thus the slope of the L-B plot is increased. ⍺ ' > 1. Thus the y-intercept is also increased. 2. Noncompetitive inhibition (at several inhibitor concentrations) produces a set of lines that intersect to the left of the y axis. The point of intersection can be on, above, or below the x-axis, depending on the relative magnitudes of KI and KI'
Case Study: protein folding kinetics by T-jump
Amyloid fibrils FBP28 WW protein T-jumped-induced of unfolding from 37 degrees C to 39.5 degrees C T=30 µs (ultrafast folding) biological significance is unclear.
Integrated Rate Law
An integrated rate law is an expression that gives the concentration of a species as a function of the time
What impact does a mixed inhibitor have on a lineweaver-burk plot?
Both the slope and the y-intercept increase.
Briefly describe a strategy for determining whether a chemical reaction is diffusion-limited.
Calculate the rate constant (kd) for diffusional encounter, and compare its value with the rate constant (kr) of the reaction. If kd is close to kr, then the reaction is diffusion limited. If kd is much larger than kr, then the reaction is activation- controlled.
______ reactions produce two or more distinct products.
Parallel
How does a ping-pong enzyme-reaction mechanism differ from sequential one?
Product released before all reactants are bound to the enzyme
In a multi-step reaction, one step often dictates the overall reaction rate. That step is called the
Rate limiting/ determining step (RDS)
Nucleation Model
Rather loose and unstable helices and sheets form early in the folding process and can be stabilized by some degree of tertiary contacts
_____ refers to the analysis of the reaction composition while a reaction is in progress.
Real-time analysis
Framework Model
Regions with well-defined and stable secondary structure form independently and then coalesce to yield the correct tertiary structure
A reaction at equilibrium is subjected to a rapid change in temperature, and the return of the system to equilibrium at the new temperature is monitored spectroscopically. What is the name of this technique?
Relaxation techniques
What two properties of the reacting species determine the magnitude of the rate constant for diffusional encounter?
Sizes of the reacting species and their diffusion coefficients.
Which approximation is generally used if the concentrations of substances involved in a consecutive reaction: Reactants -> Intermediates -> Products ? (figure)
Steady-State approximation
In many chemical reactions, the reactants must collide with a specific orientation. To account for this requirement, the mathematical formula for the Arrhenius pre-exponential factor includes a term known as the __________.
Steric Factor P
Motor-driven syringes propel a small volume of the reactants through a mixing chamber into a capillary immediately adjacent to the mixing chamber. The subsequent progress of the reaction is then monitored by an optical detector. What is the name of this technique?
Stopped- flow
_____ techniques are capable of monitoring reactions that occur on the ms timescale. Reactions that occur on faster timescales (µs) must be studied by _____.
Stopped-flow Relaxation techniques
Competitive Inhibition
The inhibitor binds only to the free form of the enzyme, preventing binding of substrate. (i.e. the inhibitor competes with the substrate for the active site. 1. ⍺ > 1. Thus the slope of the L-B plot is increased. ⍺ ' = 1. Thus the y-intercept is unaffected. 2. competitive inhibition (at several concentrations of I) gives rise to a pattern of lines intersecting on the y axis.
Kinetic Salt Effect
The kinetic salt effect describes the effect of adding an inert salt on the rate of a reaction involving charged reactants. The physical origin is the difference in stabilization of the reactant ions and the activated complex by the surrounding ionic atmosphere.
