Thermodynamics of Biological Systems: To Accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham

Biochemistry 2/e - Garrett & Grisham
Chapter 3
Thermodynamics of Biological
Systems
to accompany
Biochemistry, 2/e
by
Reginald Garrett and Charles Grisham
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Copyright © 1999 by Harcourt Brace & Company
Outline
• Basic Thermodynamic Concepts
• Physical Significance of
Thermodynamic Properties
• pH and the Standard State
• The Effect of Concentration
• Coupled Processes
• High-Energy Biomolecules

Basic Concepts
• The system: the portion of the universe
with which we are concerned
• The surroundings: everything else
• Isolated system cannot exchange
matter or energy
• Closed system can exchange energy
• Open system can exchange either or
both

The First Law
The total energy of an isolated system is
conserved.
• E (or U) is the internal energy - a function
that keeps track of heat transfer and work
expenditure in the system
• E is heat exchanged at constant volume
• E is independent of path
• E2 - E1 = E = q + w
• q is heat absorbed BY the system
• w is work done ON the system


Enthalpy
A better function for constant pressure
• H = E + PV
• If P is constant, H = q
• H is the heat absorbed at constant P
• Volume is approx. constant for
biochemical reactions (in solution)
• So H is approx. same as E


The Second Law

• Systems tend to proceed from ordered to
disordered states
• The entropy change for (system +
surroundings) is unchanged in reversible
processes and positive for irreversible
processes
• All processes proceed toward equilibrium
- i.e., minimum potential energy

Entropy
• A measure of disorder
• An ordered state is low entropy
• A disordered state is high entropy
• dSreversible = dq/T

The Third Law

• The entropy of any crystalline, perfectly
ordered substance must approach zero
as the temperature approaches 0 K
• At T = 0 K, entropy is exactly zero
• For a constant pressure process:
Cp = dH/dT

Free Energy
• Hypothetical quantity - allows chemists
to asses whether reactions will occur
• G = H - TS
• For any process at constant P and T:
G = H - TS
• If G = 0, reaction is at equilibrium
• If G < 0, reaction proceeds as written



G versus Go’
• How can we calculate the free energy
change for rxns not at standard state?
• Consider a reaction: A + B  C + D
• Then:
G = Go’ + RT ln ([C][D]/[A][B])

Energy Transfer
A Crucial Biological Need
• Energy acquired from sunlight or food
must be used to drive endergonic
(energy-requiring) processes in the
organism
• Two classes of biomolecules do this:
– Reduced coenzymes (NADH, FADH2)
– High-energy phosphate compounds - free
energy of hydrolysis larger than -25 kJ/mol)

High-Energy Biomolecules
Study Table 3.3!
• Note what's high - PEP and 1,3-BPG
• Note what's low - sugar phosphates,
etc.
• Note what's in between - ATP!
• Note difference (Figure 3.8) between
overall free energy change - noted in
Table 3.3 - and the energy of activation
for phosphoryl-group transfer!


ATP
An Intermediate Energy Shuttle Device
• PEP and 1,3-BPG are created in the
course of glucose breakdown
• Their energy (and phosphates) are
transferred to ADP to form ATP
• But ATP is only a transient energy
carrier - it quickly passes its energy to a
host of energy-requiring processes
Phosphoric Acid Anhydrides

Why ATP does what it does!
• ADP and ATP are examples of phosphoric
acid anhydrides
• Note the similarity to acyl anhydrides
• Large negative free energy change on
hydrolysis is due to:
– electrostatic repulsion
– stabilization of products by ionization and
resonance
– entropy factors



Phosphoric-Carboxylic
Anhydrides
• These mixed anhydrides - also called
acyl phosphates - are very energy-rich
• Acetyl-phosphate: G°´ = -43.3 kJ/mol
• 1,3-BPG: G°´ = -49.6 kJ/mol
• Bond strain, electrostatics, and
resonance are responsible


Enol Phosphates
• Phosphoenolpyruvate (PEP) has the
largest free energy of hydrolysis of any
biomolecule
• Formed by dehydration of 2-phospho-
glycerate
• Hydrolysis of PEP yields the enol form
of pyruvate - and tautomerization to the
keto form is very favorable


Ionization States of ATP

• ATP has five dissociable protons
• pKa values range from 0-1 to 6.95
• Free energy of hydrolysis of ATP is
relatively constant from pH 1 to 6, but
rises steeply at high pH
• Since most biological reactions occur
near pH 7, this variation is usually of
little consequence


The Effect of Concentration

Free energy changes are concentration
dependent
• We will use the value of -30.5 kJ/mol for the
standard free energy of hydrolysis of ATP
• But at non-standard-state conditions (in a cell,
for example), the G is different!
• Equation 3.12 is crucial - be sure you can use
it properly
• In typical cells, the free energy change for
ATP hydrolysis is typically -50 kJ/mol


Thermodynamics of Biological Systems: To Accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham

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Thermodynamics of Biological Systems: To Accompany Biochemistry, 2/e by Reginald Garrett and Charles Grisham

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Biochemistry 2/e - Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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The Second Law

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The Third Law

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Phosphoric Acid Anhydrides

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Ionization States of ATP

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The Effect of Concentration

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