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Imperial - Biological Chemistry (Y1) > Topic 5 - Thermodynamics > Flashcards

Topic 5 - Thermodynamics Flashcards

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1
Q

How to convert proportionality into an equation?

A

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

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2
Q

Draw the graph for direct proportionality.

A
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3
Q

Draw the graph for inverse proportionality.

A
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4
Q

What is the relationship between Volume and moles?

A

Volume and moles are directly proportional.

Double the volume –> double the moles.

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5
Q

What is the relationship between volume and the temperature?

A

Volume and temperature are directly proportional.

Increase temperature –> molecules take up a larger volume.

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6
Q

What is heat?

A

Heat is a form of energy that looks ar the motion of individual molecules.

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7
Q

What is temperature?

A

Temperature is a way to compare heat between different objects.

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8
Q

At what temperature is there no movement of heat between two objects?

A

When two objects have the same temperature –> no heat will transfer.

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9
Q

The relationship between kinetic energy and temperature?

Use Boltzmann curve

A

Average kinetic energy is proportional to temperature.

Increase in temperature –> increase kinetic energy.

Shown by Boltzmann distribution curve.

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10
Q

What is the relationship between pressure and volume?

A

Boyle’s law

Pressure and volume are inversely proportional.

P ∝ 1/V

As one can see as volume halves –> pressure doubles.

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11
Q

How is pressure calculated?

A

Pressure = Force/ unit area

Force per unit area

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12
Q

What is the equation for the ideal gas law?

A

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)

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13
Q

What is work? How is it calculated?

A

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.

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14
Q

How can we convert the equation for work into a scale used in biological systems?

A

Convert to the infinitesimal version –> denoted by ‘d’

dw = force x dx

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15
Q

An equation to calculate work done by a volume change or pressure change?

A

The equation for Volume Change:

w = -nRT Ln (V2/V1)

The equation for pressure change:

w = -nRT Ln (P2/P1)

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16
Q

How to Gases, liquids and solid store their energy as?

A

Gasses and liquids –> Store energy as translational motion.

Solid –> store energy as vibrational motion

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17
Q

Difference between heat and work?

A

Heat –> random motion

Work –> directional motion

Heat and work can be interconverted.

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18
Q

What are the characteristics of an isolated system?

A

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.

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19
Q

What are the characteristics of a closed system?

A

Closed system

Exchange of matter = 0

Exchange of energy > 0

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20
Q

What are the characteristics of an open system?

A

Open system –> cells are open systems.

Exchange of matter > 0

Exchange of energy > 0

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21
Q

What is enthalpy? How can it be calculated using internal energy, pressure and volume?

A

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.

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22
Q

In biological system what is the main factor that impact changes in enthalpy?

A

In biological systems, the main change in energy is due to the breaking and making of chemical bonds.

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23
Q

What is enthalpy of formation?

A

Enthalpy of formation is when a compound is made from its elements in their standard state under standard conditions.

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24
Q

What are the two main ways enthalpy can be stored?

A

Enthalpy:

  1. Molecular motion/organisation –> includes:
    - Thermal energy –> motion
    - Energy stored in the form of a Phase transition –> energy stored when a substance changes phase.
  2. Chemical energy

–> Covalent bonds

–> Weak bonds

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25
Q

What is ‘W’ when speaking about entropy? What is it proportional to? How can it be used to calculate entropy?

A

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.

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26
Q

What is an equation that relates entropy change to heat change and temperature? Why is it useful?

A

ΔS = (Δq/T)

Useful –> actually measurable.

Note –> At constant temperature.

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27
Q

What is the second law of thermodynamics in term of an equation?

A

ΔS(Universe) = ΔS(systems) + ΔS(surroundings) > 0

Spontaneous process –> ΔS(Universe) > 0

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28
Q

What is an equation that links enthalpy of system and surroundings to the overall entropy change?

A

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.

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29
Q

The equation for ΔG?

A

ΔG = ΔH - TΔS

For it to be spontaneous ΔG needs to be negative/less than 0.

30
Q

Example of enthalpy and entropy driven reaction?

A
31
Q

Example of enthalpy driven reaction?

A

Even though the entropy change is not favourable –> the reaction is still possible because something in the surroundings takes care of this entropy change.

32
Q

Example of entropy driven reaction?

A
33
Q

What are the favourable and unfavourable changes in enthalpy and entropy when a ligand binds to a receptor?

A
34
Q

Why are proteins formed if it is an entropically unfavourable reaction?

  • Many microstates to 1 microstate
A
35
Q

What is the equation that links ΔG and pressure change?

A

ΔG = nRT Ln(P2/P1)

36
Q

What is the general equation that links ΔG and concentration change?

A

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])

37
Q

What is the equation for chemical potential?

A

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 .

38
Q

What are the two equation for the change in chemical potential?

A
  1. Simply the chemical change of the products minus the chemical change of the reactants.

A + B —> C + D

Δµ = (µc + µD) - (µA + µB​)

  1. Δµ = Δµo + RT Ln Γ

Γ –> symbol represents equilibrium expression.

39
Q

Difference between ΔG and ΔG’?

A
40
Q

What is the reaction quotient?

A

Reaction quotient (q) –> description of how far a reaction has gone –> applicable at anytime.

41
Q

What is a key characteristic of a reaction at equilibrium?

A

The value for ΔG = Δµ = 0

42
Q

How to calculate standard free energy change at equilibrium?

Explain why this is possible.

A

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.

43
Q

Is there energy stored in concentration?

A

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.

44
Q

What two things are needed for a reaction to proceed?

A

Two factors that impact whether a reaction proceeds

  1. ΔGo < 0
  2. Effect of concentration.
45
Q

What is steady state?

A

Steady state –> concentrations of A, B, C and D may be constant but not at their equilibrium concentrations –> this is what happens in cells.

46
Q

What equation is used to calculate ΔG using concentration in an open system?

A

Note that R and T are constants

R = 8.314 J/Mol K

T = 273 + 37 = 310 K

(R)(T) = 2.58 KJ/mole

47
Q

What are the equations to calculate ΔGo from association or dissociation reactions?

A
48
Q

What is the relationship between Kassociation and Kdissociation?

A

There is a inverse relationship

KD = 1/KA

49
Q

What is half saturation? What does it tell us about?

A

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.

50
Q

How do people actually calculate enthalpy change and entropy change?

A

Van Hoff plot

51
Q

Can electrical charge stop a reaction from proceeding?

A

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.

52
Q

How is voltage expressed?

A

Voltage = electrical potential = electromotive force = V = ε.

We use ε usually as otherwise, we might confuse it with V for volume.

53
Q

An equation that links ΔG and moles of electrons?

A

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.

54
Q

The equation that can be used to calculate whether an uncharged molecule will move across a membrane or not?

A

Aout —-> Ain

ΔG = RT ln ([Ain]/[Aout])

55
Q

How to calculate ΔG taking into account concentration and electrical potential?

A

ΔG = Δµ conc. + Δµ electrical

ΔG = RT ln ([A+]in/[A+​]out) + ZFΨ

Z –> charge of ion

F –> Faraday

Ψ –> membrane potential

56
Q

Explain the role of the concentration gradient and electrical potential in determining whether something diffuses or not?

A

Both things influence whether charged ions or molecules move across the membrane –> both things end up balancing out to a specific point.

57
Q

Why does Sodium not pour into cells since both electrical and chemical potential are favourable?

A

Cells actively pump out Na+ in order to maintain the membrane potential –> requires a large amount of ATP.

58
Q

What is the Nernst equation?

A

Equation used to calculate membrane potential.

59
Q

Definition of rate?

A

A —> B

Rate = V = d[B]/dt = -d[A]/dt

Either the appearance of product overtime or the decrease in reactant overtime.

60
Q

A graph for the first-order reaction?

A
61
Q

What is half life? What is the equation?

A

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

62
Q

How do who indicate whether a molecule is a transition state?

A

X ‡ –> double cross symbol.

‡

63
Q

What is an equation that shows us a quantitative way of examining the impact of temperature and transition state on rate?

A

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.
64
Q

Impact of an increase in temperature on the number of molecules with sufficient activation energy?

A

Increase temperature –> more molecules have the energy to reach and pass the transition state.

65
Q

An equation for second order reaction?

A

Second order reactions –> think of them as two first order reactions.

V = K[A][B]

66
Q

The relationship between rates and equilibrium?

A
67
Q

How to calculate work done to compress a gas?

A

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.

68
Q

When given the Δε for two half equations how to you get the overall Δε?

A

Add both values together like you add the equations together.

69
Q

Equation to calculate membrane potential?

A

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.

70
Q

The relationship between initial rate and concentration of reactant for a first order reaction?

A

Imperial - Biological Chemistry (Y1) (7 decks)

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