# Chapter 3 Slides - University of Virginia

Mechanics

Oct 27, 2013 (4 years and 8 months ago)

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Biochemistry 2/e
-

Garrett & Grisham

Chapter 3

Thermodynamics of Biological
Systems

to accompany

Biochemistry, 2/e

by

Reginald Garrett and Charles Grisham

should be mailed to: Permissions Department, Harcourt Brace & Company, 6277
Sea Harbor Drive, Orlando, Florida 32887
-
6777

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

Biochemistry 2/e
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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
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Biochemistry 2/e
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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

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Biochemistry 2/e
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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

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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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Entropy

A measure of disorder

An ordered state is
low
entropy

A disordered state is
high

entropy

dS
reversible

= dq/T

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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

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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

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Biochemistry 2/e
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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])

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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 (

2
)

High
-
energy phosphate compounds
-

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

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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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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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Phosphoric Acid Anhydrides

Why ATP does what it does!

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

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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

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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

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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

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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
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