Chapter 3 Slides - University of Virginia

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Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Chapter 3

Thermodynamics of Biological
Systems

to accompany

Biochemistry, 2/e

by

Reginald Garrett and Charles Grisham

All rights reserved. Requests for permission to make copies of any part of the work
should be mailed to: Permissions Department, Harcourt Brace & Company, 6277
Sea Harbor Drive, Orlando, Florida 32887
-
6777

Biochemistry 2/e
-

Garrett & Grisham

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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


E
2

-

E
1

=

E = q + w


q is heat absorbed
BY

the system


w is work done
ON

the system

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Entropy


A measure of disorder


An ordered state is
low
entropy


A disordered state is
high

entropy


dS
reversible

= dq/T

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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:

C
p

= dH/dT

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

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


G versus

G
o



How can we calculate the free energy
change for rxns not at standard state?


Consider a reaction: A + B


C + D


Then:


G =

G
o
’ + RT ln ([C][D]/[A][B])

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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,

FADH
2
)



High
-
energy phosphate compounds
-

free
energy of hydrolysis larger than
-
25 kJ/mol
)

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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!

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

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

Copyright © 1999 by Harcourt Brace & Company

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company

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

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

Ionization States of ATP


ATP has five
dissociable

protons


pK
a

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

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

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

Biochemistry 2/e
-

Garrett & Grisham

Copyright © 1999 by Harcourt Brace & Company