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BB10235 > Thermodynamics > Flashcards

Thermodynamics Flashcards

1
Q

Define system

A

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

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2
Q

What are the 3 types of system

A
  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.
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3
Q

Define boundary

A

Separates system and surroundings.

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4
Q

Define process

A

Any change that occurs within a system

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5
Q

Define heat and work

A 
heat= energy transfer by random motion
work= energy transfer by organised motion
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6
Q

Define the first law of thermodynamics

A
  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)
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7
Q

What is a state function

A
  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
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8
Q

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

A
  1. Cyclic process

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

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9
Q

Define enthalpy

A
  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
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10
Q

Define enthalpy change

A
  1. The heat change of a reaction at constant pressure is equal to the enthalpy change, DH: DH = DU + PDV (D=delta)
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11
Q

Define the Second law of thermodynamics

A
  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
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12
Q

What results in a spontaneous change

A
  1. For a constant energy process DU=0, a spontaneous process is where DS > 0
  2. DSsystem + DSsurrounding = DS univers>0
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13
Q

Define entropy

A
  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.
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14
Q

What is the maximal energy principle

A
  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
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15
Q

Why do we need Gibbs free energy

A
  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
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16
Q

Define Gibbs free energy

A
  1. G= H -TS

2. It is a state function

17
Q

What is equation for DeltaG

A 
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
18
Q

What is the criteria for a spontaneous process

A
  1. The general condition for a process to occur spontaneously at constant temperature and pressure is DHsys – TDSsys < 0.
  2. DG≤0
19
Q

What does it mean when DG<0

A
  1. Exergonic process
  2. Forward reaction is energetically favourable
  3. Forward process proceeds spontaneously
20
Q

What does it mean when DG>0

A
  1. Endergonic process
  2. Forward process is energetically unfavourable
  3. Reverse process proceeds spontaneously
21
Q

What does it mean when DG=0

A
  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.
22
Q

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

A
  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.
23
Q

What is the difference between ΔG˚ and ΔG˚’

A
  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’
24
Q

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

A
  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
25
Q

What equation links free energy and concentration

A
  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
26
Q

When does DGº = DG

A
  1. When all concentrations = 1M
27
Q

What is the equation linking DG and the equilibrium constant

A

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
28
Q

What is the relationship between DGº and Keq

A
  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).
29
Q

What are the standard conditions in biochemistry

A
  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
30
Q

Describe the importance of coupled reactions

A
  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
31
Q

Give an example of coupled/sequential reactions

A
  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
32
Q

Describe the basis of other important coupled reactions

A
  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
33
Q

Why is the DG of ATP hydrolysis negative

A
  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
34
Q

What is the scale of scale of phosphate transfer potentials

A
  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.
35
Q

What is the scale of scale of phosphate transfer potentials

A
  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.

BB10235 (16 decks)

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