Quick Review of Thermodynamics

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Quick Review ofThermodynamics Kinetics
Bioenergetics how organisms gain and use energy
All of the chemical and physical reactions that
take place in living organisms can be interpreted
based on the laws of thermodynamics
- thermodynamics dictates whether reactions are
favourable or not
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First law of thermodynamics
conservation of energy Energy cannot be
created or destroyed in chemical processes, but
can only be inter-converted.
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A useful definition enthalpy (H)
- ?H represents the measure of the energy change
in a process that occurs at constant pressure
H E PV or ?H ?E P?V
change in energy
change in volume is essentially zero in most
biological processes (therefore ?H ?E)
- depends only on the initial and final states of
the process (intermediate stages irrelevant) - a
decrease in energy (?H is negative) is usually
favoured
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Second law of thermodynamics
-tells us whether chemical and physical processes
are favourable or not i.e. which direction is
favourable e.g., melting, not freezing, of ice
is favoured at 25ºC But-tells us nothing about
the speed of a process The entropy of an
isolated system will tend to increase to a
maximum value
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Entropy (S)
-Systems of molecules have a tendency towards
randomization (disorder)- measured by
entropy high randomness high entropy -Not
necessarily toward the lowest energy state
S is entropy k is the Boltzmann constant W
is the number of sub-states of equal energy
(i.e., different ways in which
molecules can be arranged in a system)
S k ln W
- an entropy of zero can only occur in a perfect
crystal at a temperature of absolute zero (0K or
-273ºC), where W1
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Diffusion as an entropy-driven process
here the system is at equilibrium because
molecules are distributed randomly
here the system is disturbed and has become more
ordered (non-random)
- the drive toward equilibrium is a consequence
of the tendency of the entropy to increase
entropy never decreases (i.e., the transition
from (c) to (b) would never occur spontaneously)
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Some definitions Gibbs free energy (G)
Free energy is the important function for
describing the Second Law in open systems, ie. in
biological systems - need a function that
includes both energy(enthalpy) and entropy -
living systems can exchange with their
surroundings, and both energy and entropy changes
take place
? G is the difference in free energies ? H is the
change in enthalpy ? S is the change in
entropy T is the absolute temperature (in K)
?G ? H - T ? S
(at constant T and P)
- if ? G is negative, the process is
thermodynamically favoured (but we know nothing
about the rate at which it will occur) - if ? G
is zero, the process is reversible, i.e., at
equilibrium - if ? G is positive, process is
unfavoured reverse process favoured
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Temperature dependence for ?G
? G ? H - T ? S
Again, large negative ? G does not mean that a
reaction will occur quickly consider C(diamond)
C(graphite) free energy change is -2.88
kJ/mol Know these relationships!
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Contribution of Enthalpy and Entropy to Chemical
Reactions
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A more concrete example ice to water transition
Fig. 3.3
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T?S
? H
? G
? G (? H - T ? S)
0
20
? S
? S
-2
0
0
-20
20
-10
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Temperature (ºC)
note that neither ? H nor ? S alone will tell us
what will happen, but the combination (? G) tells
us what form water will take at a given
temperature a positive ? G ice, but a
negative ? G water
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Standard states
?G is influenced by the characteristics of the
reacting molecules, temperature, pressure, and
for biological systems, also by pH it is also
influenced by the initial concentrations of
reactants and products. Standard free energy
?G is calculated under the conditions shown
below Standard States for Biochemists are T
298K (25C) P 1 ATM pH 7.0 1 M
for each reactant R gas constant
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For the simple reaction, reactants products,
?G can be described as ?G
?Go RT ln products
reactants where RT
product of the gas constant, R, and the absolute
temperature, T. In other words- ?G is the sum of
two parts ?Go, which depends upon the intrinsic
properties of the reacting molecules under
standard conditions, plus a function which
depends upon their concentrations. Note that ?G
becomes more negative as the ratio of products to
reactants decreases.
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At equilibrium

• A chemical mixture at equilibrium has minimal
  free energy, so ?G0
• ?Gº and Keq (the equilibrium constant) are
  related (see below)
• If ?Gº is negative, Keq will be more than 1
  (forward reaction was favoured).
• if ?Gº is positive Keq will be less than 1
  (reverse reaction was favoured).

Keq CD AB
where A B C D
??Gº -RT ln Keq
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Coupling of reactions
A thermodynamic quantity (such as ?G, ?H or ?S)
tells you what reaction is allowed thus, A ? B is
allowed B ? A is not allowed, unless coupled to
another favoured reaction (such as ATP ?
ADP) Even so, the net free energy of the coupled
reaction must show a decrease in free energy.
(i.e., the overall ?G must be negative.)
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Brief Introduction to Enzymes
- they are catalysts, that dramatically increase
the rate of reaction (often by a factor of 106
or more) - highly specific in terms of
substrate in terms of reaction - cellular
enzymes are proteins (Except a few which are RNA)
H2O CO2 ? HCO3- H 100 s in solution 10-5
s with carbonic anhydrase.
- enzymes do not drive reactions they allow
favourable reactions to reach equilibrium faster
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Effect of a Catalyst on Activation Energy
transition state
-All chemical reactions proceed through a high
energy intermediate state (activation energy) -
?Go, or the standard free energy of activation,
represents the difference in free energy between
the transition state and the reactant -Enzymes
increase the reaction RATE by decreasing ?Go
(forces reactant into new transition state with
lower ?Go) Enzymes can accelerate reactions in
both directions, but do not change ?G or Keq