Lecture 3: Thermodynamics and Weak Molecular Interactions Flashcards
What do thermodynamics tell us?
- Which reactions are possible 2. What directions do reactions take
What is the 1st Law of Thermodynamics (law + equation)?
- Energy is conserved - it is neither created nor destroyed
- ΔU = Ufinal – Uinitial = q - w
ΔU = total energy of the universe, unit = Joules (J)
q = heat absorbed by a reaction
w = work done by the reaction
What does ΔU = 0 mean?
It means that the heat absorbed by the reaction is equal to the work done by the reaction
What does it mean when a unit is capitalized?
It is a state function, meaning it is INDEPENDENT of path
What are examples of non-state functions?
Work and rate of rxn
What is the definition of enthalpy?
The total heat content of a system, H
What is the equation to calculate enthalpy? Unit?
H = U + P.V Unit = J
What is bond enthalpy?
The energy stored in chemical bonds
What is the sign of ΔH for exothermic reactions?
-
What is the sign of ΔH for endothermic reactions?
+
What is an example of an exothermic rxn?
Bond breaking
What is an example of an endothermic rxn?
Bond formation
Can endothermic reactions occur spontaneously?
Yes!
What is the 2nd Law of Thermodynamics? Why?
The universe tends towards maximum disorder because there are many more probable ways of being disordered than ordered.
What is entropy, S?
It is a measure of disorder or randomness
What is the equation to calculate entropy?
S = kB.ln W
unit = Joules/Kelvin (J/K)
kB = Boltzmann constant (1.3807 x 10-23 J/K)
W = number of ways
What does the Boltzmann constant correspond to?
The gas constant divided by Avogadro’s number
What are examples of energy investments to maintain order?
DNA repair, ordering books in a library
What is the Boltzmann constant? What does it correspond to?
kB = 1.3807 x 10-23 J/K
Corresponds to the gas constant divided by Abogadro’s number
How do temperature and entropy relate to each other?
Entropy increases as temperature increases
What are the 2 mathematical ways of saying that entropy always increases? What do they mean?
- For ΔU = 0, ΔSsystem + ΔSsurroundings = ΔSuniverse > 0
- ΔS >/= q/T q: heat absorbed by the system
They mean that not all of thermal energy in a system can be converted to useful work
What is an example of a system gaining order at the expense of its surroundings?
Protein folding disorders the aqueous surrounding, formation of lipid bilayer disorders the water surrounding
What is Gibbs free energy used for?
To determine spontaneity
What is the equation to calculate G?
ΔG = ΔH – TΔS
What is the sign of ΔG for spontaneous reactions?
-
What is the sign of ΔG for non-spontaneous reactions?
+
In what direction do rxns go?
Direction of lower free energy
How can one make an endergonic rxn happen? 2 ways
- Couple it to an exergonic rxn 2. Change the concentrations of reactants/products
Draw the chart of spontaneity based on the signs of ΔH and ΔS
What determines ΔG?
Nature AND concentrations of the reactants/products
What is the equation to calculcate ΔG?
ΔG = ΔGº’ + R.T.ln [Pi] . [Qi] / [Ai] . [Bi]
What is ΔGº’?
The standard free energy of formation: free energy when forming 1M of reactants and products under standard conditions (1 atm, pH 7.0, 25ºC, 1M of each substrate and product (adjusted for their stoichiometry in the reaction). ).
What is the free energy of formation, ΔGfº’?
Change in free energy accompanying the formation of 1 mol of the substance in its standard state
How do you calculate the standard free energy change, ΔGº? What is important to note when using this equation?
ΔGº = Σ ΔGfº (products) - Σ ΔGfº (reactants)
To note: COEFFICIENT IS MULTIPLIED!
What are the 2 properties of the chemical equilibrium? What is it expressed by
- Rate of forward rxn = rate of reverse rxn
- Concentrations of reactants/products are constant
Expressed by Keq
How do you calculate Keq?
Keq = [Peq]p . [Qeq]q / [Aeq]a . [Beq]b
What does a large Keq mean?
Formation of PRODUCTS is favored
What does a small Keq mean?
Formation of REACTANTS is favored
What is the equation that relates Keq and ΔGº’?
ΔGº’ = -R.T.ln Keq
What is ΔG equal to at equilibrium? Why?
0 because ln 1 = 0
What is Le Chateler’s principle?
Reactions, like many biochemical reactions in our body, that are
not at equilibrium will move TOWARD that equilibrium.
What measure is binding affinity described by? How is this calculated? What does this number represent?
The dissociation constant Kd:
Kd = [A].[B]/[AB] = koff / kon
It is the concentration of reactant necessary (ligand usally) that brings half max binding and also the concentration of the species when the binding reaction is at equilibrium and there are no longer any net changes in the concentrations of any of the species
What does a low Kd mean? Why?
Strong binding affinity because you can reach max binding at a lower concentration of reactant (ligand usually)
What is Ka? What is it equal to?
The affinity constant, the reciprocal of Kd
Ka = Keq
How do you calculate the free energy change of a bond formation?
ΔG = R.T. ln Kd = - R.T. ln Ka
What is the bond energy of an H bond? Why is this such a large range?
5 - 30 kJ/mol
Because energy varies on length and orientation of the bond
What is the equation to calculate the energy of electrostatic interactions?
U = k.q1.q2/D.r
k: 9 . 109J.m/C2
U: energy required to pull the bond apart
D: dielectric constant (water had the highest one)
What type of solvent favors electrostatic forces?
Hydrophobic environments
What type of dipoles are Van der waal’s reactions?
Induced dipole interactions that occur between all groups in direct contact
What are electrostatic interactions?
Favorable bonds between molecules of opposite charges
Describe interactions between permanent dipoles.
The partial negative charge of one carbonyl group interacts with the partial positive charge of another carbonyl group (two fixed dipoles and orientation specific).
Describe dipole-induced dipole interactions.
The partial negative charge of one carbonyl group interacts with a non-polar methyl group to induce a dipole (one fixed dipole and one induced dipole).
Describe London dispersion forces. What are these dependent on?
Induced dipoles between two non-polar methyl groups that are in DIRECT contact with one another.
Dependent on close distance.
Also called van der waals interactions
What are induced dipoles important for? Where are they usually located?
Protein folding - usually located in the interior of the protein
What is the impact of the hydrophobic effect on entropy of water?
Increase entropy of water
What is the hydrophobic effect driven by?
Entropy!
What is the gas constant in J/K?
8.314 J/K
What is ΔG’s units?
J/mol
How to calculate the free energy of binding?
∆GB = RT ln Kd
What is the difference between isolated systems and open systems?
Isolated systems must reach equilibrium vs open systems are not at equilibrium w/ their surroundings, but are continually consuming energy which is subsequently disordered into its constituent molecular components and expelled as waste (energy is harvested to do work and maintain order)
What kind of H bonds are less favorable?
Those that restrain the movement of otherwise highly mobile species because of the decrease in conformational entropy
Moving hydrophobic molecules from water to a non-polar solvent: exothermic or endothermic? Why?
Endotermic because nonpolar species make favorable enthalpic interactions with water (induced dipole and van der Waals interactions) –> this decreases the stability of the hydrophobic bonds
On average, how many AAs in a protein are hydrophobic?
Half
What is the hydrophobic effect a result of?
Increased entropy when water molecules are free
Why is water a good solvent for salts?
Because it has a high dielectric constant
Does the entropy of water increase or decrease when it dissolves salts?
Decreases!!!
What forces are involved in maintenance of membrane integrity?
Weak molecular forces: hydrophobic, electrostatic
How can we determine Kd empirically?
On a binding curve of [A.B]/[A] vs [B] Kd is the concentration when 50% of A is bound to B
What happens to the binding curve if you lower the affinity?
Right shift
What happens to the binding curve if you increase the affinity?
Left shift
