Thermodynamics

Question 1

Define system

Answer 1

Consists of matter at a given temperature, pressure and volume. It is the part of the Universe under study.

Question 2

What are the 3 types of system

Answer 2

1. Isolated- cannot exchange energy or matter with its surroundings
2. Closed- can exchange energy in the form of q- heat to or from surroundings or w- work done by system on surroundings or w done on system
3. Open- Exchange energy and matter with surroundings, all biological systems are OPEN and exchange substrates and end products with their environment.

Question 3

Define boundary

Answer 3

Separates system and surroundings.

Question 4

Define process

Answer 4

Any change that occurs within a system

Question 5

Define heat and work

Answer 5

heat= energy transfer by random motion
work= energy transfer by organised motion

Question 6

Define the first law of thermodynamics

Answer 6

1. Energy can neither be created nor destroyed
2. But it can be changed from one form to another or transported from one region to another
3. Deals with energy balance in a reaction but does not say anything about preferred direction of the reaction
4. It is a mathematical statement:
   Delta U = Q - W
   (Q= heat absorbed by system from surroundings, W=work done by system on surroundings, U is energy)

Question 7

What is a state function

Answer 7

1. A state function depends only on the current properties or state of a system, not on how the system reached that state.
2. Energy is a state function as it depends only on current properties or state not how it reached it
3. Work and heat are not state functions- depend on path followed by a system in changing from one state to another

Question 8

What is the name of a process with no net change in energy

Answer 8

1. Cyclic process

2. Any process which the system returns to its initial state

Question 9

Define enthalpy

Answer 9

1. H=U + PV
2. V= volume of system
3. P= pressure of system
4. It is a state function - it can be added and subtracted for a sequence of reactions

Question 10

Define enthalpy change

Answer 10

1. The heat change of a reaction at constant pressure is equal to the enthalpy change, DH: DH = DU + PDV (D=delta)

Question 11

Define the Second law of thermodynamics

Answer 11

1. Spontaneous change in system occurs in a direction that increases the combined entropy of the system and surroundings
2. Conversion of order to disorder. Spontaneous process occur in direction that increase the overall disorder of the universe

Question 12

What results in a spontaneous change

Answer 12

1. For a constant energy process DU=0, a spontaneous process is where DS > 0
2. DSsystem + DSsurrounding = DS univers>0

Question 13

Define entropy

Answer 13

1. S= k loge W (k= Boltzmann constant) (W=number of ways of arranging system)
2. Entropy is a state function as it depends only on parameters that describe a state.

Question 14

What is the maximal energy principle

Answer 14

1. The laws of random chance cause any system of reasonable size to spontaneously adopt its most probable arrangement, the one in which entropy is maximum, as this state is so overwhelmingly probable.
2. The entropy of the system and surroundings has a maximum value at equilibrium

Question 15

Why do we need Gibbs free energy

Answer 15

1. The spontaneity of a process cannot be predicted from a knowledge of the system’s entropy change alone
2. An exothermic process may be spontaneous even if DSsystem<0

Question 16

Define Gibbs free energy

Answer 16

1. G= H -TS

2. It is a state function

Question 17

What is equation for DeltaG

Answer 17

1. At a constant temperature and pressure 
DG = DH – TDS
2. Delta G= free energy change  Jmol-1
3. DH= enthalpy change Jmol-1
4. T= absolute temperature K 	
5. DS= entropy change Jmol-1K-1

Question 18

What is the criteria for a spontaneous process

Answer 18

1. The general condition for a process to occur spontaneously at constant temperature and pressure is DHsys – TDSsys < 0.
2. DG≤0

Question 19

What does it mean when DG<0

Answer 19

1. Exergonic process
2. Forward reaction is energetically favourable
3. Forward process proceeds spontaneously

Question 20

What does it mean when DG>0

Answer 20

1. Endergonic process
2. Forward process is energetically unfavourable
3. Reverse process proceeds spontaneously

Question 21

What does it mean when DG=0

Answer 21

1. System is at equilibrium
2. No further change
3. The process is reversible and can be made to go in either direction under small changes in conditions
4. When a system is far from equilibrium, it will tend to move to equilibrium by an irreversible process unless there is a major change in conditions.

Question 22

Describe where the point of equilibrium is on a graph of Gibbs free energy/progress of reaction

Answer 22

1. The equilibrium point is the minimum point of a curve
2. The derivative of G with respect to X is zero when G is either maximal or minimal.
3. When free energy is at a minimum, small fluctuations in the system parameters will increase DG and the system will relax back to equilibrium spontaneously
4. The maximal point is unstable however, as small fluctuations in the system will cause the system to move away from that point.

Question 23

What is the difference between ΔG˚ and ΔG˚’

Answer 23

1. ΔG˚ is the physical chemistry free energy change
2. ΔG˚’ is the biochemistry convention for standard free energy change
3. Because biochemical reactions occur in dilute aqueous solutions in near neutral pH there are differences in standard conditions used
4. Water’s standard state is that of pure liquid so it’s activity is taken to be unity so it doesn’t need to be used in the equation
5. H+ activity is defined at the physiologically relevant pH 7 instead of 0 (which would be [H+]=1) where many biological systems are unstable.
6. Corresponding equilibrium state to ΔG˚’ is Keq’

Question 24

What are two strategies that can be used to make a specific reaction proceed in the direction required by the organism

Answer 24

1. Alter concentrations so that DG becomes negative.
2. Couple a reaction with a positive DG value to one that has a negative DG value, so that overall the DG is negative.
3. Normally temperature and pressure are relatively stable

Question 25

What equation links free energy and concentration

Answer 25

1. a A + b B c C + d D 2. DG = DGº + RT loge [C]c[D]d / [A]a[B]b 3. a, b, c, d represent numbers of moles of substances A, B, C, D 4. [C]c[D]d / [A]a[B]b is called the mass action ratio 5. R is the gas constant 6. T is temperature in Kelvin 7. DGº represents DG at standard free energy change

Question 26

When does DGº = DG

Answer 26

1. When all concentrations = 1M

Question 27

What is the equation linking DG and the equilibrium constant

Answer 27

At equilibrium: 1. DG = 0 2. [C]c[D]d / [A]a[B]b = Keq (mass action ratio = equilibrium constant) 3. DGº = –RT ln Keq 4. Equilibrium constant, Keq, can be calculated from DGº

Question 28

What is the relationship between DGº and Keq

Answer 28

1. When DG° is large and negative, Keq is very large. 2. When DG° is large and positive, Keq is very small. 3. DG° < 0, Keq>1 4. DG° > 0, Keq<1 5. DG° = 0, Keq=1 6. Rule of thumb: if Keq > 10^4, reaction will go to completion (but not necessarily at a favourable rate).

Question 29

What are the standard conditions in biochemistry

Answer 29

1. The º in DGº denotes that reactants and products are all at 1 M concentration, 2. temp = 298 K, 3. pressure = 1 atmosphere. 4. Activity of water is taken to be unity for reactions in dilute solutions – justified since the concentration of water is essentially constant. 5. pH = 7 indicated by ʹ, e.g. DGºʹ, Keqʹ = MEANS if protons are in reaction concentration won’t be 1M but would need to be the right concentration for pH 7, 10^-7

Question 30

Describe the importance of coupled reactions

Answer 30

1. DG values are additive, Keq values are multiplicative 2. This allows an endergonic reaction to be driven by an exergonic reaction under proper conditions 3. Many metabolic reactions have unfavourable DG values 4. The thermodynamic basis of operation of metabolic pathways is the coupling of an endergonic reaction to an exergonic reaction with a more negative DG, exploiting the fact that free energies are additive. 5. Reactions in a metabolic cycle are coupled in that the product of one reaction becomes the reactant for the next reaction in the cycle. e. g. p51

Question 31

Give an example of coupled/sequential reactions

Answer 31

1. ATP occupies the middle rank in the thermodynamic hierarchy of phosphoryl-transfer agents 2. This allows it to serve as an energy conduit between high energy phosphate donors and low energy phosphate acceptors. 3. Net flow of phosphate is always from high energy to low energy compounds 4. Catalysed by enzymes called kinases. e. g. a) Endergonic half reaction= Pi + glucose glucose-6-p + H2O (DG=+13.8) b) Exergonic half reaction= ATP + H2O ADP + Pi (DG=-30.5) c) Overall coupled reaction= ATP + glucose ADP + glucose-6-P (DG=-16.7) 5. 2 reactions separately won't happen but when coupled have overall DG<0

Question 32

Describe the basis of other important coupled reactions

Answer 32

1. Other important coupled reactions in bioenergetics use oxidation/reduction reactions involving electrons as common intermediates 2. Chemiosmotic coupling where exergonic and endergonic reactions are coupled through a shared gradient of ions across a membrane

Question 33

Why is the DG of ATP hydrolysis negative

Answer 33

1. Relatively negative due to highly charged ATP polyphosphate group: a) Relief of electrostatic repulsion when terminal phosphate bond is hydrolysed b) Inorganic phosphate (Pi) undergoes stabilisation as a resonance hybrid. c) Releasing protons into low proton concentration environment d) 3 product molecules from 2 reactant molecules, more ways to distribute translational and rotational energy among 3 molecules– makes positive contribution to DS°’. e) Greater degree of solvation of products ADP and Pi compared to ATP

Question 34

What is the scale of scale of phosphate transfer potentials

Answer 34

1. Ranking of phosphorylated compounds according to their values of DGºʹ for hydrolysis = scale of PHOSPHATE TRANSFER POTENTIALS. 2. Each compound is capable of driving the phosphorylation of compounds lower on the scale provided a suitable coupling mechanism is available 3. e.g Hydrolysis of PEP DGºʹ = -61kJmol^-1 Phosphorylation of ADP DGºʹ= +30.5 kJmol^-1 Coupled phosphorylation of ADP by PEP DGºʹ=-31.5 kJmol^-1 4. PEP is able to transfer phosphate to ADP to form ATP in a thermodynamically favoured process. ATP can then transfer phosphate to a compound lower down on the phosphate transfer potential scale, for example glucose.

Question 35

What is the scale of scale of phosphate transfer potentials

Answer 35

1. Ranking of phosphorylated compounds according to their values of DGºʹ for hydrolysis = scale of PHOSPHATE TRANSFER POTENTIALS. 2. Each compound is capable of driving the phosphorylation of compounds lower on the scale provided a suitable coupling mechanism is available 3. e.g Hydrolysis of PEP DGºʹ = -61kJmol^-1 Phosphorylation of ADP DGºʹ= +30.5 kJmol^-1 Coupled phosphorylation of ADP by PEP DGºʹ=-31.5 kJmol^-1 4. PEP is able to transfer phosphate to ADP to form ATP in a thermodynamically favoured process. ATP can then transfer phosphate to a compound lower down on the phosphate transfer potential scale, for example glucose.