Chapter 3

Energy, Catalysis and Biosynthesis

Essential
Cell Biology
Third Edition
Copyright Garland Science 2010
Learning Objectives
Basic Thermodynamics (!C = !P + 1!S) & Lermlnology

Relationship between !C for reacuon and Lhe keq
Oxidation / reduction (RedOx) reactions
Enzyme catalysis (activation, kinetics)
Binding energy & affinity
Activated carrier molecules
Coupled reactions & energy transfer
Figure 3-3 Essential Cell Biology ( Garland Science 2010)
Life creates order in a chaotic Universe
Second Law of Thermodynamics

Spontaneous processes are characterized by the
conversion of order to disorder

Disorder in the Universe can only increase
!S
universe
> 0
Entropy (S) is dened
as the degree of disorder
in a closed system
Figure 3-4 Essential Cell Biology ( Garland Science 2010)
Second Law of Thermodynamics

Spontaneous processes are characterized by the
conversion of order to disorder

Disorder in the Universe can only increase
Systems will change spontaneously toward those
arrangements that have the greatest probability

H

T
Consider a Coin Toss

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H
1 : 68,000,000,000

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H

H
Once in 10,774 years








































































































































































































































































































































































Ordered (36:0)



Disordered (18:18)

H

T

H

T

H

T

T

H

T

H

T

H

H

T

H

T

H

T

T

H

T

H

T

H

H

T

H

T

H

T

T

H

T

H

T

H
42,000,000,000 times
Second Law of Thermodynamics

Spontaneous processes are characterized by the
conversion of order to disorder

Disorder in the Universe can only increase
Systems will change spontaneously toward those
arrangements that have the greatest probability
1hermodynamlcs was developed Lo undersLand Lhe sLeam englne
nlcolas Leonard Sadl CarnoL
SLeam urlven ump
!u = q - w
!u = q - w
llrsL Law of 1hermodynamlcs

!"#$%& ()" *# "#+,-#$ ($#),#. "/$ .#0,$/&#.

(l.e., only converLed from one form Lo anoLher)
The increase in
internal energy of
a closed system
The heat
supplied to
the system
The work
done by
the system
= -
!u = q - w

AL consLanL pressure .

!u = !P - !v

where !P = q = heaL galned by sysLem
llrsL Law of 1hermodynamlcs

!"#$%& ()" *# "#+,-#$ ($#),#. "/$ .#0,$/&#.

(l.e., only converLed from one form Lo anoLher)

AL consLanL pressure .

!u = !P - !v

where !P = q (aL consLanL )

P = LnLhalpy of sysLem (ln [oules)

!P ls posluve, process ls !"#$%&!'()*
!P ls negauve, process ls !+$%&!'()*



Second Law of Thermodynamics

Spontaneous processes are characterized by the
conversion or order to disorder

Disorder in the Universe can only increase
S = state of disorder of the system = entropy
!S
universe
> 0
Second Law of Thermodynamics

Spontaneous processes are characterized by the
conversion or order to disorder

Disorder in the Universe can only increase
!P - 1!S < 0
For any spontaneous process (constant T & P)
!S
universe
> 0
ConcepL of lree Lnergy
"Lhe rsL Lo apply Lhe second
law of Lhermodynamlcs Lo Lhe
exhausuve dlscusslon of Lhe
relauon beLween chemlcal,
elecLrlcal, and Lhermal energy
and capaclLy for exLernal
work.
!C = !P - 1!S
!. Wlllard Clbbs
Gibbs Free Energy (G)
!G = !H T!S

For a spontaneous process, !G < 0

If the !G is < 0, the process is called exergonic
If the !G is > 0, the process is called endergonic
If the !G is = 0, the process is called equilibrium

Equilibrium is Death
System = Cell + Environment

!C = !P - 1!S < 0
!C will always be negative when !P < 0
when the overall process is exothermic
Cells are able to create internal order because the
processes employed to accomplish this produce heat,
which is released into the environment
!P < 0
!S<0
!S>0
*
Environment
Figure 3-8 Essential Cell Biology ( Garland Science 2010)
Energy enters the living world through Photosynthesis
Energy enters the living world through Photosynthesis
[NAD(P)H]
[ATP]
Figure 3-8 Essential Cell Biology ( Garland Science 2010)
Energy enters the living world through Photosynthesis
[NAD(P)H]
[ATP]
Photosynthesis & Respiration
Figure 3-10 Essential Cell Biology ( Garland Science 2010)
Prokaryotes contain ~ 50% of carbon in living organisms
C
6
H
12
O
6
+ 6 O
2
6 CO
2
+ 6 H
2
O
Cellular Respiration
In the presence of
molecular Oxygen
Most stable form of arbon
Most stable form
of Hydrogen
C
6
H
12
O
6
+ 6 O
2
6 CO
2
+ 6 H
2
O
Combining with oxygen ! oxidation

Oxygen is a strong electron acceptor

Oxidation ! a loss of electrons

Reduction ! a gain of electrons

Cant have one (e.g., Red.) without the other (Ox)

! RedOx Reactions

Cellular Respiration
*
Figure 3-11a Essential Cell Biology ( Garland Science 2010)
Polar covalent bonds indicate partial
intramolecular RedOx condition
C/H
O
*
Figure 3-11b Essential Cell Biology ( Garland Science 2010)
*
C
6
H
12
O
6
+ 6 O
2
6 CO
2
+ 6 H
2
O
C
6
H
12
O
6
+ 6 H
2
O 6 CO
2
+ 24 e
-
+ 24 H
+

6 O
2
+ 24 e
-
+ 24 H
+
6 12 H
2
O
C
6
H
12
O
6
+ 6 O
2
6 CO
2
+ 6 H
2
O
Cellular Respiration
!G
0
= -2870 kJ/mol

Free Energy Yield of Oxidative Metabolism
(glucose)
Controlled Oxidation of Carbohydrate
Energy
Energy
Energy
Energy
Energy
ATP

NAD(P)H
Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
*
36
Lach sLep of a blochemlcal process ls noL
requlred Lo be exergonlc.
As long as Lhe overall process ls exergonlc, lL
wlll operaLe ln a forward manner.




| !G2 + !G4 + !G5 | > | !G1 + !G3 |
*
37
Lach sLep of a blochemlcal process ls noL
requlred Lo be exergonlc.
As long as Lhe overall process ls exergonlc, lL
wlll operaLe ln a forward manner.



1hus, Lhe free energy of A1 hydrolysls, a
hlghly exergonlc reacuon, ls harnessed Lo
drlve many oLherwlse endergonlc blologlcal
processes Lo compleuon!!
*
G
X
< G
Y
!G < 0
Enzymes reduce the activation energy of a specic reaction
Enzymes increase the reaction rate of thermodynamically
favored reactions. They observe the 2
nd
Law.
*
Figure 3-14b Essential Cell Biology ( Garland Science 2010)
Enzymes reduce the frequency of side reactions by
selectively reducing the activation energy creating conditions
that favor a particular outcome
G
X
< G
Y
!G < 0
product
reactant
!G > 0
t
o
t
a
l

e
n
e
r
g
y

a
b
G
Y
> G
X
G
C
> G
D
C
D
C
D
| !G
C-D
| > | !G
X-Y
|

*
Figure 3-18 Essential Cell Biology ( Garland Science 2010)
G
Y
> G
X
K
eq
=

[X]
[Y]
!G < 0
*
Standard Free Energy Change ( !G
0
)

under standard conditions

1. [reactants] remains unchanged @ 1 M

2. Constant T = 37
o
C

!G = !G
0
+ RT ln




[X]
[Y]
!G = !G
0
+ RT ln


@ equilibrium

!G = 0 & = K
eq


!G
0
= - RT ln K
eq





[X]
[Y]
[X]
[Y]
!G = !G
0
+ RT ln


@ equilibrium

!G = 0 & = K
eq


!G
0
= - RT ln K
eq


@ 37
o
C

!G
0
= -1.42 log K
eq




[X]
[Y]
[X]
[Y]
*
lor Lhe reacuon: ? x
3.1
% X @ equil.
99.999 %
99.99 %
99.9 %
99 %
91 %
50 %
*
Hemoglobin
heterotetrameric complex ("
2
#
2
)
Binding Energy

A + B AB
*
Binding Energy

A + B AB
equilibrium constant for association
Figure 3-20 Essential Cell Biology ( Garland Science 2010)
K
eq
= 10
10
K
eq
= 10
8
! = 2.8 kcal/mol
~ 2 3 H-bonds
*
Figure 2-32 Essential Cell Biology ( Garland Science 2010)
Need multiple weak bonds for enzyme and
substrate to bind together at the active site
Noncovalent bonds account for much of the specicity in living cells.
This is also extremely important in drug pharmacology.
Binding Energy

A + B AB
Usually expressed as the equilibrium constant for dissociation

K
D
=

high afnity binding ! small (low) K
D
[A][B]
[AB]
*
X Z
Y
!G = + 5 kcal/mole
!G = - 13 kcal/mole
!G = +5 kcal/mole - 13 kcal/mole = - 8 kcal/mole
2 : 1
2 : 1
1 : 25
1 : 25
*
Figure 3-15 Essential Cell Biology ( Garland Science 2010)
Figure 3-26b Essential Cell Biology ( Garland Science 2010)
*
Figure 3-24 Essential Cell Biology ( Garland Science 2010)
Figure 3-26c Essential Cell Biology ( Garland Science 2010)
Lineweaver Burk Plot
*
Figure 3-31 Essential Cell Biology ( Garland Science 2010)
ATP is the most common activated carrier molecule
Adenosine 5-TriPhosphate
Lots of energy stored
in these bonds
Why is this favorable?
Removes repulsion
P
i
stabilized by resonance + H-bonds
w/ water
!G
0
= -30.5 kJ/mol
The terminal phosphate of ATP can be readily transferred to other
molecules to drive energetically unfavorable reactions
often
unfavorable
*
Figure 3-34 Essential Cell Biology ( Garland Science 2010)
NADH and NADPH carry high energy electrons
and participate in oxidation-reduction reactions
Ring more stable
without hydride
*
NADH and NADPH carry high energy electrons
and participate in oxidation-reduction reactions
NADH and NADPH, while similar, are recognized by
different enzymes and hence play different biological roles.
NADPH plays large role in anabolic reactions.
NADH plays large role in catabolic reactions (often to
generate ATP).
Inside cell, NAD
+
and NADPH levels are high. This
provides oxidizing power for breaking stuff down (ex. food)
and reducing power needed for anabolism (ex. cholesterol
synthesis) respectively.
*
Table 3-2 Essential Cell Biology ( Garland Science 2010)
Many other activated carrier molecules exist
Often activated carriers are generated in reactions
involving ATP hydrolysis.
*
Macromolecule metabolism
Conversely, the breakdown of all of
these macromolecules occurs with the
simply addition of water (hydrolysis)
*
Figure 3-40 Essential Cell Biology ( Garland Science 2010)
ATP hydrolyzed to AMP can be used
if more energy is needed
!G
0
= -45.6 kJ/mol
!G
0
= -19.2 kJ/mol
!G
0
= -64.8 kJ/mol
*
FINI