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24 Cards in this Set
- Front
- Back
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Henderson Hasselbach Equation
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pH = pKa + log ( [unprotonated] / [protonated] )
note: the ratio of [un]/[prot] is not the same as the fraction of the ionizable grp that is unprotonated. |
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Michaelis-Menten Equation
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V = ( Vmax [S] ) / ( Km + [S] )
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Features of MM Eq
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1. easy to measure V and [S]
2. when [S] >> Km, V = Vmax = k2 x [E]total 3. When V = 1/2Vmax, Km = [S] |
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Definition of Km
for the equation: E + S <> ES > E + P, where k2 is the slow step |
Km = (k-1 + k2) / k1
where k-1 and k2 are the two rate constants for the ways ES can break down, and where k1 is the only rate constant for the way ES can form. |
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Gibbs Function
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dG = dH -TdS
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Positive Allosteric Effectors that favor R-state
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O2, CO
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Negative Allosteric Effectors that favor T-state
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H+, BPG
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Stability of R-state or T-state depends on:
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1. Partial pressure of Oxygen
2. pH 3. [BPG] |
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Define: allosteric regulation
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the binding of a molecule to an enzyme at a site other than the active site, which ultimately changes the conformation of the enzyme, either activating or deactivating the active site.
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Define: Absolute Specificity
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enzyme fits only one reactant. (rare)
ex. urease |
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Define: Absolute Functional Group Specificity
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only a particular functional group will fit into the enzymes binding site, several different molecules that possess this FG can bind and react.
ex. alcohol dehydrogenase |
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Define: Relative Functional Group Specificity
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specificity for bonds of similar geometry and chemistry
ex. esters and peptides |
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Binding Site vs. Catalytic Site
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binding site: where group binds, site of specificity
catalytic site: where actual chemical reaction takes place. when we can't distinguish btwn the two: "active site" |
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Units of Rxn Velocity
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= Rxn Rate are d[CONC]/dt = CONC/time
ex. M/sec |
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for A + B <> C + D
Rxv Velocity = Rxn Rate = V = |
d[C]/dt = d[D]/dt = -d[A]/dt = -d[B]/dt
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beginning with no products,
Vin = ? |
Vin = k1[A][B]
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Use of the Gibbs Function
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∆G = ∆Go + RTln([C]x[D]/[A]x[B])
the tendency for a reaction to occur is measured by the Gibbs function, holding T and P constant. not holding conc fixed, but allowing rxn to go to equiblibrium then all concentrations adjust themselves until ∆Go = - RTln([C]eqx[D]eq/[A]eqx[B]eq) , i.e. "concentrations are on equal footing" with "relative stability of the molecules" in determining whether a rxn goes to the left or to the right, as written. |
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Why do reactions take time to occur?
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1. Because only a small fraction [proportional to e-∆^(GoTS /RT)] of the reactants have enough free energy to react and form the transition state. We have to wait for molecules to acquire this amnt of free E.
2. The correct orientation is required for reaction to occur |
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How do catalysts lower transition state free energy?
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ONLY TWO WAYS TO DO THIS
1. Directly bind the TS, by binding the TS is stabilized and therefore Go is lowered. 2. Change RXN pathway, new mechanism, new transition state with lower free E |
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ks
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dissociation constant of ES
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Competitive Inhibition:
How do we recognize this on a Lineweaver-Burk Plot? |
1. Vm not changed by the inhibitor!
2. intercept on x-axis (1/[S]) is not -1/Km, but instead -1 / Km ( 1 + [I]/Ki ), where Ki = [E][I]/[EI] |
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Non-Competitive Inhibition:
How do we recognize this on a LWBurk Plot? |
1. Km NOT changed by inhibitor.
2. Intercept on y-axis (1/V) is not 1/Vm, but instead (1 + [I]/Ki) / Vm, where where Ki = [E][I]/[EI] |
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Molecule-by-molecule comparison of reactants and products
[A FREE ENERGY COMPARISON] ATP + H2O <> ADP + Pi |
1. more resonance stabilization of hydrolysis products
2. better solvation of products [ADP, Pi react better with water] 3. Decreased electrostatic repulsion in products 4. favorable uptake of H+ by water also [ADP] is kept low in all cells (drives rxn R) -- true, but not a free energy effect |
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HIGH ENERGY MOLECULES
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1,3 - BPG
Phosphocreatine Phosphoenolpyruvate Thioester |
