BCH 330 Exam 1
Assume that the acid-base dissociation constant (pKa) of pyruvic acid is 2.0. Using pH as the x axis and
"number of protons removed (from pyruvic acid)" as the y axis, draw the pH dependence curve for this
equilibrium - correct answer ✔✔-at pH 2, pH = pKa (50/50 distribution)
-pryuvic acid = associated/ protonated version
-pyruvate = dissociated version / conjugate base
-pH+/- 1 : 90/10
-pH+/- 2 : 99/1
What is the pKa precisely in terms of concentrations of pyruvic acid, pyruvate, and H+? What is the
practical significance of the pKa? - correct answer ✔✔-pKa: acid-base dissociation constant
-measures affinity of a proton for the conjugate base
-pKa = -log(Ka)
-Ka = [pyruvate][H+] / [pyruvic acid]
-Ka is the acid-base dissociation equilibrium
-at low pKa: higher concentration of pyruvate
-at high pKa: higher concentration of pyruvic acid
-mass action: determines distributions of the two
-mass action coefficient (Q): Q= [C'][D']/[A'][B']
How would one calculate the Gibbs free energy change (ΔGd) for dissociation from pyruvate using the
pKa value? Show how you manipulated the relevant equations to determine ΔGd. What is the numerical
value of ΔGd at 20 degrees C (include units)? - correct answer ✔✔-ΔGd = -RTlnKa (define variables too)
-when we know pKa, use: Ka = 10^-pKa
-T = degrees C + 273.4K
-units for ΔGd: J/mol
Write out the Gibbs equation and define each of the terms. Explain what each of the terms represents in
the context of the "hydrophobic effect". Explain the enthalpic and entropic energy contribution to the
,net free energy stabilization of globular protein structures at temperatures between approximately 10
and 50 degrees C. - correct answer ✔✔-ΔGu = ΔHu - TΔSu (define variable - H enthalpy, S entropy)
-hydrophobic effect explains energies of protein folding
-Folded state (Pf) <--> Unfolded state (Pu)
- -ΔGu: favors unfolded
- +ΔGu: favors folded
-hydrophobic effect is affected by the enthalpic factor (ΔHu) and the entropic factor (-TΔS)
-enthalpic factor favors folded state; changes are due to changed in bonding (covalent, ionic, hydrogen
bonding, vdw)
-enthalpy of hydrogen bonds forces proteins to fold due to a hydrogen cage
-Chaotropes (urea & guandinium) disrupt cage & cause unfolding
-entropic factor favors unfolded state & is the change in the number of conformations
Explain why temperatures above about 60 degree C typically result in protein denaturation. - correct
answer ✔✔-temperature impacts the entropic term (-TΔSu) of the Gibbs equation (ΔGu = ΔHu -TΔSu)
-at high temperatures, temperature factor becomes a large multiplier
-hydrophobic effect / enthalpic term is offset & results in a negative ΔGu, causing proteins to denature
-in this denatured/ unfolded state, there are more configurations
What is the "mass action coefficient" and how is it used to convert the standard state free energy (ΔG*)
to the actual value of ΔG? Provide the equation. - correct answer ✔✔-mass action coefficient (Q) is used
to convert standard state free energy (ΔG*) to actual free energy (ΔG)
-accounts for poise of the reactants and products in equilibrium
-aka the partition coefficient
-can only use ΔG* in stead state conditions (1 atm, 298.1 K, 1 M)
-ΔG = ΔG* + RTlnQ
-Q = [C]^c[D]^d / [A]^a[B]^b
-Q = πiCi,p / πiCir (p is product concentration, r is reactant concentration, Ci is concentration of all
components of i)
, Explain why one must make the relevant calculation of converting from ΔG* to ΔG to use ΔG information
to understand the energetic progression of, for example, the glycolysis pathway. - correct answer ✔✔-
understand why glycolysis is energetically favorable
-reactions 1, 3, and 10 drive glycolysis (metabolically irreversible reactions bc they have large -ΔG's)
-metabolically irreversible reactions: hexokinase, PFK-1, pyruvate kinase (all catalyzed by kinases)
-other reactions: near equilibrium
-more efficient because less energy is used
-easier for reverse process, gluconeogenesis, to occur bc 7/11 enzymes needed are the exact same as
the ones for glycolysis
-thermodynamic linkage is required for only 3 reactions to drive the whole process
What is a partial specific volume of a solute? Is it ever smaller than the molecular volume? If so, when? -
correct answer ✔✔-ratio of volume over number of moles, which is also inversely proportional to
density
-⊽ = v/n = 1/ρ
-⊽ can be smaller than the molecular volume due to electrostriction, which occurs in the Donnan sphere
-water in the Donnan sphere has a much larger concentration than the bilk solution
What is the ionic strength? - correct answer ✔✔- i = 1/2 Σ_j c_j z_j^2
-c_j: concentration
-z_j: charger
-different ions have different chargers and effective concentrations
-important when neutralizing nucleic acids, which are negative due to phosphate backbone
-donnan sphere around the nucleic acid increases the water and ion concentration
-Mg2+ is a better neutralizer than Na+ because it has a higher ionic strength
-histones and spermine also neutralize nucleic acids
Is the concentration of ions close to a macromolecule the same as in the bulk solution? Explain. - correct
answer ✔✔-concentration of ions is higher close to a macromolecule due to the donnan sphere
-donnan sphere increases concentration of water to be higher near the molecule
-because the water concentration is increased, the ion concentration is increased as well
Assume that the acid-base dissociation constant (pKa) of pyruvic acid is 2.0. Using pH as the x axis and
"number of protons removed (from pyruvic acid)" as the y axis, draw the pH dependence curve for this
equilibrium - correct answer ✔✔-at pH 2, pH = pKa (50/50 distribution)
-pryuvic acid = associated/ protonated version
-pyruvate = dissociated version / conjugate base
-pH+/- 1 : 90/10
-pH+/- 2 : 99/1
What is the pKa precisely in terms of concentrations of pyruvic acid, pyruvate, and H+? What is the
practical significance of the pKa? - correct answer ✔✔-pKa: acid-base dissociation constant
-measures affinity of a proton for the conjugate base
-pKa = -log(Ka)
-Ka = [pyruvate][H+] / [pyruvic acid]
-Ka is the acid-base dissociation equilibrium
-at low pKa: higher concentration of pyruvate
-at high pKa: higher concentration of pyruvic acid
-mass action: determines distributions of the two
-mass action coefficient (Q): Q= [C'][D']/[A'][B']
How would one calculate the Gibbs free energy change (ΔGd) for dissociation from pyruvate using the
pKa value? Show how you manipulated the relevant equations to determine ΔGd. What is the numerical
value of ΔGd at 20 degrees C (include units)? - correct answer ✔✔-ΔGd = -RTlnKa (define variables too)
-when we know pKa, use: Ka = 10^-pKa
-T = degrees C + 273.4K
-units for ΔGd: J/mol
Write out the Gibbs equation and define each of the terms. Explain what each of the terms represents in
the context of the "hydrophobic effect". Explain the enthalpic and entropic energy contribution to the
,net free energy stabilization of globular protein structures at temperatures between approximately 10
and 50 degrees C. - correct answer ✔✔-ΔGu = ΔHu - TΔSu (define variable - H enthalpy, S entropy)
-hydrophobic effect explains energies of protein folding
-Folded state (Pf) <--> Unfolded state (Pu)
- -ΔGu: favors unfolded
- +ΔGu: favors folded
-hydrophobic effect is affected by the enthalpic factor (ΔHu) and the entropic factor (-TΔS)
-enthalpic factor favors folded state; changes are due to changed in bonding (covalent, ionic, hydrogen
bonding, vdw)
-enthalpy of hydrogen bonds forces proteins to fold due to a hydrogen cage
-Chaotropes (urea & guandinium) disrupt cage & cause unfolding
-entropic factor favors unfolded state & is the change in the number of conformations
Explain why temperatures above about 60 degree C typically result in protein denaturation. - correct
answer ✔✔-temperature impacts the entropic term (-TΔSu) of the Gibbs equation (ΔGu = ΔHu -TΔSu)
-at high temperatures, temperature factor becomes a large multiplier
-hydrophobic effect / enthalpic term is offset & results in a negative ΔGu, causing proteins to denature
-in this denatured/ unfolded state, there are more configurations
What is the "mass action coefficient" and how is it used to convert the standard state free energy (ΔG*)
to the actual value of ΔG? Provide the equation. - correct answer ✔✔-mass action coefficient (Q) is used
to convert standard state free energy (ΔG*) to actual free energy (ΔG)
-accounts for poise of the reactants and products in equilibrium
-aka the partition coefficient
-can only use ΔG* in stead state conditions (1 atm, 298.1 K, 1 M)
-ΔG = ΔG* + RTlnQ
-Q = [C]^c[D]^d / [A]^a[B]^b
-Q = πiCi,p / πiCir (p is product concentration, r is reactant concentration, Ci is concentration of all
components of i)
, Explain why one must make the relevant calculation of converting from ΔG* to ΔG to use ΔG information
to understand the energetic progression of, for example, the glycolysis pathway. - correct answer ✔✔-
understand why glycolysis is energetically favorable
-reactions 1, 3, and 10 drive glycolysis (metabolically irreversible reactions bc they have large -ΔG's)
-metabolically irreversible reactions: hexokinase, PFK-1, pyruvate kinase (all catalyzed by kinases)
-other reactions: near equilibrium
-more efficient because less energy is used
-easier for reverse process, gluconeogenesis, to occur bc 7/11 enzymes needed are the exact same as
the ones for glycolysis
-thermodynamic linkage is required for only 3 reactions to drive the whole process
What is a partial specific volume of a solute? Is it ever smaller than the molecular volume? If so, when? -
correct answer ✔✔-ratio of volume over number of moles, which is also inversely proportional to
density
-⊽ = v/n = 1/ρ
-⊽ can be smaller than the molecular volume due to electrostriction, which occurs in the Donnan sphere
-water in the Donnan sphere has a much larger concentration than the bilk solution
What is the ionic strength? - correct answer ✔✔- i = 1/2 Σ_j c_j z_j^2
-c_j: concentration
-z_j: charger
-different ions have different chargers and effective concentrations
-important when neutralizing nucleic acids, which are negative due to phosphate backbone
-donnan sphere around the nucleic acid increases the water and ion concentration
-Mg2+ is a better neutralizer than Na+ because it has a higher ionic strength
-histones and spermine also neutralize nucleic acids
Is the concentration of ions close to a macromolecule the same as in the bulk solution? Explain. - correct
answer ✔✔-concentration of ions is higher close to a macromolecule due to the donnan sphere
-donnan sphere increases concentration of water to be higher near the molecule
-because the water concentration is increased, the ion concentration is increased as well
