Chapter 3 Slides - University of Virginia

Report
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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Biochemistry 2/e - Garrett & Grisham
Outline
• Basic Thermodynamic Concepts
• Physical Significance of
Thermodynamic Properties
• pH and the Standard State
• The Effect of Concentration
• Coupled Processes
• High-Energy Biomolecules
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Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
Entropy
•
•
•
•
A measure of disorder
An ordered state is low entropy
A disordered state is high entropy
dSreversible = dq/T
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Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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])
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Biochemistry 2/e - Garrett & Grisham
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)
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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!
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Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Enol Phosphates
• Phosphoenolpyruvate (PEP) has the
largest free energy of hydrolysis of any
biomolecule
• Formed by dehydration of 2-phosphoglycerate
• Hydrolysis of PEP yields the enol form
of pyruvate - and tautomerization to the
keto form is very favorable
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
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
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company

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