Topic 5 - Thermodynamics Flashcards
How to convert proportionality into an equation?
y α x –> directly proportional –> multiply a constant to obtain equation –> y = kx
y α 1/x –> inversly proportional –> multiply a constant to obtain equation –> y = k/x
Draw the graph for direct proportionality.
Draw the graph for inverse proportionality.
What is the relationship between Volume and moles?
Volume and moles are directly proportional.
Double the volume –> double the moles.
What is the relationship between volume and the temperature?
Volume and temperature are directly proportional.
Increase temperature –> molecules take up a larger volume.
What is heat?
Heat is a form of energy that looks ar the motion of individual molecules.
What is temperature?
Temperature is a way to compare heat between different objects.
At what temperature is there no movement of heat between two objects?
When two objects have the same temperature –> no heat will transfer.
The relationship between kinetic energy and temperature?
Use Boltzmann curve
Average kinetic energy is proportional to temperature.
Increase in temperature –> increase kinetic energy.
Shown by Boltzmann distribution curve.
What is the relationship between pressure and volume?
Boyle’s law
Pressure and volume are inversely proportional.
P ∝ 1/V
As one can see as volume halves –> pressure doubles.
How is pressure calculated?
Pressure = Force/ unit area
Force per unit area
What is the equation for the ideal gas law?
Combining all the different relationships between Volume, moles, temperature and pressure we get:
PV = nRT
Units:
P –> Pascals (Pa)
V –> m3
R –> J⋅mol−1⋅K−1
T –> Kelvin (k)
What is work? How is it calculated?
Work is a form of energy –> How much energy it take to move an object from point ‘x’ to ‘y’.
Work = Force x distance
Hence, work is the ordered transfer of energy.
How can we convert the equation for work into a scale used in biological systems?
Convert to the infinitesimal version –> denoted by ‘d’
dw = force x dx
An equation to calculate work done by a volume change or pressure change?
The equation for Volume Change:
w = -nRT Ln (V2/V1)
The equation for pressure change:
w = -nRT Ln (P2/P1)
How to Gases, liquids and solid store their energy as?
Gasses and liquids –> Store energy as translational motion.
Solid –> store energy as vibrational motion
Difference between heat and work?
Heat –> random motion
Work –> directional motion
Heat and work can be interconverted.
What are the characteristics of an isolated system?
Isolated system:
Exchange of matter with the surroundings = 0
Exchange of energy with the surroundings = 0
Often used as it is easier to perform calculations.
What are the characteristics of a closed system?
Closed system
Exchange of matter = 0
Exchange of energy > 0
What are the characteristics of an open system?
Open system –> cells are open systems.
Exchange of matter > 0
Exchange of energy > 0
What is enthalpy? How can it be calculated using internal energy, pressure and volume?
Enthalpy (H) is the way that energy is stored in the system, other than in the form of a volume change.
Basically –> enthalpy is internal energy minus pressure/volume work.
H = U + (P)(V)
U –> internal energy
(P)(V) –> negative of work.
In biological system what is the main factor that impact changes in enthalpy?
In biological systems, the main change in energy is due to the breaking and making of chemical bonds.
What is enthalpy of formation?
Enthalpy of formation is when a compound is made from its elements in their standard state under standard conditions.
What are the two main ways enthalpy can be stored?
Enthalpy:
- Molecular motion/organisation –> includes:
- Thermal energy –> motion
- Energy stored in the form of a Phase transition –> energy stored when a substance changes phase. - Chemical energy
–> Covalent bonds
–> Weak bonds
What is ‘W’ when speaking about entropy? What is it proportional to? How can it be used to calculate entropy?
W is the number of microstates corresponding to a particular macrostate.
Basically a way of quantifying the number of positions a molecules/atom can take within a given space.
W ∝ Vn –> W is proportional to the volume to the power of the number of molecules.
Equation for entropy:
S = KBLnW –> KB = Boltzman constant.
What is an equation that relates entropy change to heat change and temperature? Why is it useful?
ΔS = (Δq/T)
Useful –> actually measurable.
Note –> At constant temperature.
What is the second law of thermodynamics in term of an equation?
ΔS(Universe) = ΔS(systems) + ΔS(surroundings) > 0
Spontaneous process –> ΔS(Universe) > 0
What is an equation that links enthalpy of system and surroundings to the overall entropy change?
Note infinitesimals are used –> applicable to biosystems.
dS(universe) = dS(System) - dH(system)/(T)
If the equation is greater than 0 –> spontaenous.
We simply plugged in the following equation and rearranged.
ΔS(surroudings) = Δq/T
Note that dΔq(system) = dH(system)
Note –> All of this is at constant pressure.
The equation for ΔG?
ΔG = ΔH - TΔS
For it to be spontaneous ΔG needs to be negative/less than 0.
Example of enthalpy and entropy driven reaction?
Example of enthalpy driven reaction?
Even though the entropy change is not favourable –> the reaction is still possible because something in the surroundings takes care of this entropy change.
Example of entropy driven reaction?
What are the favourable and unfavourable changes in enthalpy and entropy when a ligand binds to a receptor?
Why are proteins formed if it is an entropically unfavourable reaction?
- Many microstates to 1 microstate
What is the equation that links ΔG and pressure change?
ΔG = nRT Ln(P2/P1)
What is the general equation that links ΔG and concentration change?
ΔG = nRT Ln([A]2/[A]1)
This shows us that there is energy in concentration.
It can also be expressed under standard state conditions.
ΔG = ΔGo + nRT Ln([A])
What is the equation for chemical potential?
Chemical potential –> ΔG expressed under standard molar Gibbs free energy (Per mole, under standard conditions).
µ = µ0 + RT Ln [A]
µ –> chemical potential
µo –> intrinsic property of a molecule –> energy stored in bonds, folds, etc.
RT Ln [A] –> ?
Note –> this equation can be used to calculate the chemical potential of a specific molecules µA .
What are the two equation for the change in chemical potential?
- Simply the chemical change of the products minus the chemical change of the reactants.
A + B —> C + D
Δµ = (µc + µD) - (µA + µB)
- Δµ = Δµo + RT Ln Γ
Γ –> symbol represents equilibrium expression.
Difference between ΔG and ΔG’?
What is the reaction quotient?
Reaction quotient (q) –> description of how far a reaction has gone –> applicable at anytime.
What is a key characteristic of a reaction at equilibrium?
The value for ΔG = Δµ = 0
How to calculate standard free energy change at equilibrium?
Explain why this is possible.
Given that Δµ = 0 –> we can rearrange the following equation to make Δµo the subject.
1) Δµ = Δµo + RT Ln Γ
2) Δµo = - RT Ln Γ / Δµo = - RT Ln Keq
Hence at equilibrium, we can calculate the equilibrium constant using this equation.
Is there energy stored in concentration?
Yes, there is energy stored within the concentration.
ΔG = ΔGo + RT Ln ([C][D]/[A][B])
If the concentration of A and B are high they drive the reaction forward –> visa versa.
What two things are needed for a reaction to proceed?
Two factors that impact whether a reaction proceeds
- ΔGo < 0
- Effect of concentration.
What is steady state?
Steady state –> concentrations of A, B, C and D may be constant but not at their equilibrium concentrations –> this is what happens in cells.
What equation is used to calculate ΔG using concentration in an open system?
Note that R and T are constants
R = 8.314 J/Mol K
T = 273 + 37 = 310 K
(R)(T) = 2.58 KJ/mole
What are the equations to calculate ΔGo from association or dissociation reactions?
What is the relationship between Kassociation and Kdissociation?
There is a inverse relationship
KD = 1/KA
What is half saturation? What does it tell us about?
Half saturation tells us about the strength of interaction between the protein and ligand.
At half saturation [R] = [RL]
Therefore –> KD = [R][L]/[RL] –> KD = [L]
At half saturation KD is equal to the ligand concentration.
Hence…
Low KD means that there is a higher affinity –> tighter binding –> less ligand is needed when designing a drug.
High KD means that there is a Lower affinity –> weaker binding -> more ligand is needed when designing a drug.
How do people actually calculate enthalpy change and entropy change?
Van Hoff plot
Can electrical charge stop a reaction from proceeding?
Yes, electrical charge can prevent a reaction from occurring –> this is because there is a build up in electrical charge which will prevent the movement of a particular ion –> energetically unfavourable.
How is voltage expressed?
Voltage = electrical potential = electromotive force = V = ε.
We use ε usually as otherwise, we might confuse it with V for volume.
An equation that links ΔG and moles of electrons?
ΔG = -nFε
n –> moles of electrons
F –> faradays constant –> 96.48 KJ/mole - volt
ε –> voltage
As we can see ΔG depends on the electrical potential.
The equation that can be used to calculate whether an uncharged molecule will move across a membrane or not?
Aout —-> Ain
ΔG = RT ln ([Ain]/[Aout])
How to calculate ΔG taking into account concentration and electrical potential?
ΔG = Δµ conc. + Δµ electrical
ΔG = RT ln ([A+]in/[A+]out) + ZFΨ
Z –> charge of ion
F –> Faraday
Ψ –> membrane potential
Explain the role of the concentration gradient and electrical potential in determining whether something diffuses or not?
Both things influence whether charged ions or molecules move across the membrane –> both things end up balancing out to a specific point.
Why does Sodium not pour into cells since both electrical and chemical potential are favourable?
Cells actively pump out Na+ in order to maintain the membrane potential –> requires a large amount of ATP.
What is the Nernst equation?
Equation used to calculate membrane potential.
Definition of rate?
A —> B
Rate = V = d[B]/dt = -d[A]/dt
Either the appearance of product overtime or the decrease in reactant overtime.
A graph for the first-order reaction?
What is half life? What is the equation?
The time required for half of a reactant to be converted into product(s).
Equation:
[A] = [A]0 e-kt
[A]0 –> intial concentration
k –> decay constant
t –> time
How do who indicate whether a molecule is a transition state?
X ‡ –> double cross symbol.
‡
What is an equation that shows us a quantitative way of examining the impact of temperature and transition state on rate?
V = (K ‡ e-ΔG‡ /RT)[A]
This shows us that both the temperature and the transition state (-ΔG‡) impact the rate of the reaction.
- If temperature increase –> rate increases
- Greater energy barrier (-ΔG‡) –> rate is lower.
Impact of an increase in temperature on the number of molecules with sufficient activation energy?
Increase temperature –> more molecules have the energy to reach and pass the transition state.
An equation for second order reaction?
Second order reactions –> think of them as two first order reactions.
V = K[A][B]
The relationship between rates and equilibrium?
How to calculate work done to compress a gas?
We know that Pressure = Force/area
So… F = PA
Substitute into work equation.
dw = (P)(A)(dx)
Note (A)(dx) = Volume
dw = -(P)(dV)
We add negative sign –> compressing gas –> sign convention.
When given the Δε for two half equations how to you get the overall Δε?
Add both values together like you add the equations together.
Equation to calculate membrane potential?
ΔG = RT ln ([A+]in/[A+]out) + ZFΨ
Rearange the equation above:
ΔΨ = -(RT/ZF) Ln ([A+]in/[A+]out)
-(RT/ZF) –> constants = +/- 26.9 mV
Depends on charge (Z) of ion/molecule.
The relationship between initial rate and concentration of reactant for a first order reaction?
