Thermodynamics

Question 1

What is thermodyanamics? Kinetics?

Answer 1

Thermodynamics - Tells us whether a given change can occur spontaneously

Kinetics - Tells us how quickly that change occurs

Question 2

What is the first law of thermodynamics?

Answer 2

Energy must be conserved but it can take different forms

Question 3

Give an overview of cellular energetics?

Answer 3

Life involves order and for living systems to maintain this, they release heat to the surrounding which increases entropy of the surroundings (energy for this is provided by metabolism)
Cellular metabolism breaks respiration down into many steps - at each step energy is released, being used to generate high energy molecules
Open system

Question 4

What are the types of system?

Answer 4

Isolated system: no exchange of heat or matter with the surroundings
Closed system: system exchanges heat with the surroundings but not matter
Open system: system exchanges matter and heat with surroundings

Question 5

What is work? and the types of work?

Answer 5

Work - energy transfer to/from the system by any other means

Expansion work - work done by the system on the surroundings when the system changes volume

Useful work - all the other types of work done by the system during the change

Question 6

What is state function?

Answer 6

A quantity that has a unique value for each state of the system, Its value depends only on the state of the system
e.g. Internal energy (U), Enthalpy (H), Entropy (S) and Gibbs free energy (G)

Question 7

What is Hess’ Law?

Answer 7

the enthalpy change in a chemical process is independent of the route by which that change occurs

Question 8

What is internal energy (U)?

Answer 8

The total energy of the system: kinetic energy of molecules, vibration and potential energy due to intermolecular interactions
KJ/mole

Question 9

What is enthalpy (H)?

Answer 9

The internal energy of system plus the work done by or against surroundings to create it
KJ/mole

Question 10

What is the relationship between internal energy and enthalpy?

Answer 10

The differences between ΔU and ΔH are negligible in most biochemical systems
Therefore the energy/heat change of the reacting system is equivalent to the enthalpy change

Question 11

What is the second law of thermodynamics?

Answer 11

Spontaneous processes are characterised by the conversion of order to disorder

The total entropy of the universe can never decrease

Question 12

What is entropy?

Answer 12

A system is a measure of how disordered it is

Question 13

What is gibbs free energy?

Answer 13

∆G = ∆H - T∆S

Determined by both entropy and enthalpy

Question 14

What does ∆G tell us?

Answer 14

Exergonic - negative ∆G and therefore spontaneous reaction (favourable)

Endergonic - positive ∆G and therefore not spontaneous reaction (unfavourable)

Question 15

What does entropy depend on?

Answer 15

The free energy change of a chemical reaction depends on the concentrations of both its reactants and its products

Question 16

What is Le Chatelier’s Principal?

Answer 16

Any deviation from equilibrium stimulates a process that will restore the system to equilibrium

The system does the opposite of what is being done to it

Question 17

What equation shows free energy under the influence of concentrations?

Answer 17

ΔG° = −RT ln Keq

ΔG° - free energy change when all reactants/products are in their standard states
R - gas constant (8.314)
T - temp (kelvin)
Keq - equilibrium constant

Question 18

How to work out Keq?

Answer 18

Keq = [C]c [D]d / [A]a [B]b

Question 19

What are standard state conditions?

Answer 19

25 degrees celcius
1 atmosphere
pH 7

Question 20

What are some rules to follow with standard state conditions?

Answer 20

Pure water us assigned a value of 1 - even though the conc is 55.5 M, in order to be ignored in calculations

H+ ion is assigned a value of 1 at pH 7

The standard state of a substance that can undergo an acid–base reaction is defined in terms of the total concentration of its naturally occurring ion mixture at pH 7

Question 21

Describe reversible and irreversible reactions?

Answer 21

Reversible: fully reversible at equilibrium, fast enzyme and concentrations are the equilibrium concentrations

Irreversible: ΔG not = 0, slow enzyme and concentrations are different from equilibrium concentrations

Question 22

Describe sequential reactions?

Answer 22

The products of one reaction are substrates for the next
∆G values for each reaction add to give the total ∆G for whole pathway
Unfavourable reactions can be driven forward by coupling to the next reaction provided that overall ∆G is negative

Question 23

Describe metabolic flux?

Answer 23

A living organism needs at least one irreversible reaction
As if all reactions were reversible then there is no net flux of material = useless for a living organism

They reach a steady state: concentrations of metabolic intermediates don’t change over time but now have net flux through the pathway

Question 24

Describe flux regulation?

Answer 24

The main regulatory point in a pathway is usually the slowest irreversible reaction (the rate determining step) - this limits the limits flux
Flux control is achieved by regulating the activity of the corresponding enzyme e.g. allosterically, covalent modification or gene expression

Question 25

What is macrostate and microstate?

Answer 25

Macrostate - any macroscopic state of the system e.g. pressure, density and temperature

Microstate - one configuration of all the components (atoms and molecules) of the system e.g. an ideal gas

Question 26

What is linked to macro/microstates?

Answer 26

Statistical weight - the number of microstates compatible with that macrostate

The greater the statistical weight of a macrostate, the greater the number of ways it can occur so the higher the probability of finding the system in that macrostate
As the system samples its microstates, the macrostate of the system evolves over time in the direction of increasing statistical weight

The greatest statistical weight achieved = equilibrium

Question 27

What is the entropy of a system in a macrostate?

Answer 27

S = Kb lnΩ

S - entropy
Kb - Boltzmann constant (1.38 x10^-23)
Ω - statistical weight

Question 28

How does the Maxwell-Boltzmann distribution change with temperature?

Answer 28

As temperature increases the distribution become broader and shifts to higher speeds/kinetic energy
Chemical reactions have an activation energy, which can be overcome by increasing temperature increasing the rate of reaction

Question 29

What are some examples of two state systems, showing how to use the Boltzmann factor?

Answer 29

Example - proton NMR
Protons in a magnetic field align either with or against the externally applied field
When parallel to the field each proton has energy E1
When antiparallel to the field the proton has energy E2
The energy difference between the antiparallel and parallel states is (E2-E1) = ∆

Example - Cis/Trans isomerism of proline in proteins
We can use this to calculate the proportions of Cis to Trans in a polypeptide