La Termodinmica y la Vida

Prof. Mirko Zimic

mzimic@jhsph.edu
La Biologa est basada en la
materia suave viviente
Auto-ensamblaje
Alta especificidad
Informacin
Los objetos vivientes estn
compuestos por molculas inertes
Albert Lehninger
El problema es:

Cmo estas molculas
confieren la admirable
combinacin de
caractersticas que
denominamos vida???


Cmo es que un
organismo vivo aparece
ser ms que la suma de
sus partes inanimadas???

La Fsica procura entender y reducir la
Biologa en leyes fundamentales


Pero este es un problema muy
complicado !

Son demasiadas las variables y resulta
imposible describir un sistema de un
nmero tan grande de partculas
SOLUCIN:
Descripcin estadstica del mundo aleatorio
La ACTIVIDAD COLECTIVA de muchos objetos de
Movimiento aleatorio puede ser predicho, aun cuando el
movimiento exacto de un slo objeto es desconocido
Si todo en el nano-mundo de las clulas es aleatorio,
cmo podemos realizar predicciones?
TERMODINMICA
Permite predecir la ACTIVIDAD
COLECTIVA de muchos objetos de
movimiento aleatorio, aun cuando el
movimiento exacto de un slo objeto es
desconocido



Todo en el Universo esta
compuesto por Materia y Energa

Materia: - Medida de la inercia
Energa: - Energa cintica (movimiento)
- Energa potencial (reposo)

E = M C
2


Trabajo
Trabajo = Fuerza Distancia
W = F Ax

La unidad del trabajo es el Newton-metro
conocido tambin como Joule.
Trabajo mecnico
F
F
A x
Kinetic Energy
Kinetic Energy is the energy of motion.
Kinetic Energy = mass speed
2

2
mv
2
1
KE =
Potential Energy
The energy that is stored is called
potential energy.
Examples:
Rubber bands
Springs
Bows
Batteries
Gravitational Potential PE=mgh
Conversin entre la Energa cintica y
la Energa potencial
Qu es la Bioenergtica?
Es la disciplina que estudia los aspectos
energticos en los sistemas vivos, tanto a
nivel molecular como a nivel celular.
Interacciones moleculares
ATP como biomolcula almacenadora de
energa
Biocatlisis
Reacciones acopladas

Interacciones Fundamentales
Interaccin Gravitacional (masa-masa)
Interaccin Electromagntica (carga-dipolo)
Interaccin Nuclear Dbil (electrones-ncleo)
Interaccin Nuclear Fuerte (protones-neutrones)

Los Sistemas Biolgicos son guiados
fundamentalmente por Interacciones
Electromagnticas
Enlaces Covalentes
Enlaces No-covalentes (Interacciones Dbiles):
Puentes de Hidrgeno
Efecto Hidrofbico
Interacciones Inicas
Interacciones In-Dipolo
Interacciones Dipolo-Dipolo
Fuerzas de Van der Waals

Enlace Covalente
Las interacciones Inicas se dan
entre partculas cargadas
PUENTE DE
HIDRGENO
Participacin de los Puentes de Hidrgeno:
Replicacin, Transcripcin y Traduccin
Las interacciones dbiles dirigen el
proceso de docking molecular
El efecto hidrofbico colabora en
el plegamiento de las protenas
Revisin de algunos conceptos
Termodinmicos
Sistemas termodinmicos
Equilibrio termodinmico
Temperatura
Calor
Entalpa
Energa Libre
Entropa
Clasificacin de los sistemas
termodinmicos
Sistemas Abiertos
Intercambian materia y energa con el exterior
Sistemas Cerrados
Slo intercambian energa con el exterior
Sistemas Aislados
No tienen ningun tipo de intercambio con el
exterior
Equilibrio Termodinmico
Un sistema se encuentra en equilibrio
termodinmico cuando la distribucin
espacial y temporal de la materia y la
energa es uniforme
En el equilibrio termodinmico se
reducen las gradientes y con ello se
reduce la energa potencial
Qu esta ms fro?
El metal o la madera?
Temperatura
Es la medida de la energa cintica
interna de un sistema molecular
E
k
= N K T /2
Cool Hot
Qu es el cero absoluto?
Escalas de temperatura
Fahrenheit Celsius Kelvin
Boiling Point
of Water
Freezing Point
of Water
Absolute Zero
212F
32F
-459F
100C
0C
-273C
373 K
273 K
0 K
Los estados de la materia
Slido Lquido
Gas Plasma
Calor
Es la energa cintica
que se propaga debido a
un gradiente de
temperatura, cuya
direccin es de mayor
temperatura a menor
temperatura
El flujo del calor
T = 100
o
C
T = 0
o
C
Temperature
Profile in Rod
Heat
Vibrating copper atom
Copper rod
Reversibilidad
Reversibility is the ability to run a process
back and forth infinitely without losses.
Reversible Process
Example: Perfect Pendulum
Irreversible Process
Example: Dropping a ball of clay
Procesos reversibles
Examples:
Perfect Pendulum
Mass on a Spring
Dropping a perfectly elastic ball
Perpetual motion machines
More?
Procesos irreversibles
Examples:
Dropping a ball of clay
Hammering a nail
Applying the brakes to your car
Breaking a glass
More?
Primera Ley de la Termodinmica
La energa no se crea ni se destruye, slo
se transforma
Q = W + dE
First Law: Energy conservation
Internal energy (E).- Total energy content of a system. It
can be changed by exchanging heat or work with the
system:
E
Heat-up the system
Do work on the system
E
Cool-off the system
Extract work from the system
AE = q + w
w
-PAV
w
Entalpa
H=E+PV
La entalpa es la fraccin de la energa
que se puede utilizar para realizar
trabajo en condiciones de presin y
volumen constante

dH<0 proceso exotrmico
dH>0 proceso endotrmico
Entropa
S = K Ln(W)
La entropa es la medida del grado de
desorden de un sistema molecular
S
1
> S
2

La entropa es la medida del grado
de desorden de un sistema

Ordered Solid
Disordered Liquid
Hard-sphere crystal
Hard-sphere liquid
Hard-sphere freezing is driven
by entropy !
Higher Entropy
Lower Entropy
Segunda Ley de la Termodinmica
En todo sistema
aislado, la entropa
siempre aumenta
hasta alcanzar el
estado de equilibrio

dS>=0 (dS>=dQ/T)
Ordering and 2
nd
law of thermodynamics
- Condensation into liquid (more ordered).

- Entropy of subsystem decreased

- Total entropy increased! Gives off heat to room.
System in thermal contact with environment
Equilibration
Initially high
Cools to room
Algunos eventos bioqumicos contradicen
la segunda ley de la termodinmica?
Second Law of Thermodynamics
naturally occurring processes are
directional
these processes are naturally irreversible

Energa Libre de Gibbs
G=H-TS
La energa libre es
la fraccin de la
energa que se
puede utilizar para
realizar trabajo en
condiciones de
presion, volumen y
temperatura
constante


Lo importante es la variacin de la
energa libre

dG<0 proceso exergnico (espontneo)
dG>0 proceso endergnico

dG<0 perder capacidad de hacer trabajo ==
perder energa potencial == aumentar el desorden
(entropa)
G= H - T S
G+ (exergnico) H +(endotrmico)
G (endergnico) H- (exotrmico)
S +(sube entropa) S (baja entropa)

Table 3.2



La paradoja del Demonio de Maxwell
Segunda ley: Entropa y desorden
Las Enzimas o biocatalizadores,
reducen la Energa de Activacin
La molcula de ATP
Los seres vivos utilizan la
molcula de ATP como
medio principal para
almacenar energa
potencial proveniente de
la degradacin de los
alimentos
La manera de utilizarse la energa en la
molcula de ATP es mediante la separacin de
un grupo fosfato el cual est unido mediante
un enlace covalente de alta energa
La sntesis de
ATP ocurre
durante la
gliclisis y la
respiracin
celular en la
mitocondria
usualmente
En las plantas, la sntesis
de ATP ocurre asistida por
luz durante la fotosntesis,
la cual es luego empleada
en las denominadas
reacciones oscuras. Este es
un ejemplo de
transformacin de energa
radiante en energa
qumica.
El ATP participa en una serie de
reacciones acopladas
Diversas molculas
biolgicas requieren la
capacidad de moverse
para cumplir sus
funciones Por lo
tanto hace falta energa
para realizar esta
funcin.
La fuente de energa
para el movimiento
molecular es
fundamentalmente el
ATP
El ATP contribuye a diversos
tipos de reacciones
El ATP suele participar en el
correcto plegamiento de las
protenas
Thermodynamics
First Law: Energy conservation
Internal energy (E).- Total energy content of a system. It
can be changed by exchanging heat or work with the
system:
E
Heat-up the system
Do work on the system
E
Cool-off the system
Extract work from the system
AE = q + w
w
-PAV
w
Thermodynamics
A more useful concept is: ENTHALPY (H)
H = E + PV
At constant
pressure
P V V P w V P - q H
p
A + A +
'
+ A = A
AE
0 0
Only P-V work involved w = 0
(as in most biological systems)
So
p
q H= A
At constant pressure, the enthalpy change in a process is
equal to amount of heat exchanged in the process by the
system.
Thermodynamics
We have
H = E + PV
AH = AE + PAV + VAP

AP = 0
AV ~ 0
in biological
systems
0 0
AH ~ AE

at AP = 0 and since AV ~ 0
Q: How is this energy stored in the system?
1) As kinetic energy of the molecules. In isothermal (AT =
0) processes this kinetic energy does not change.
2) As energy stored in chemical bonds and interactions. This
potential energy could be released or increased in chemical
reactions
A:
Thermodynamics
Second Law: Entropy and Disorder
Energy conservation is not a criterion to decide if a process will
occur or not:
Examples
q
Hot
T
Cold
T
T T
AE = AH = 0
This rxn occurs in one
direction and not in the
opposite
these processes
occur because
the final state
( with T = T &
P = P) are the
most probable
states of these
systems
Let us study a simpler case
tossing 4 coins
Thermodynamics
All permutations of tossing 4 coins
1 way to obtain 4 heads
4 ways to obtain 3 heads, 1 tail
6 ways to obtain 2 heads, 2 tails
4 ways to obtain 1 head, 3 tails
1 way to obtain 4 tails
Macroscopic states


H T T H
H H T T
H T H T
T H H T
T T H H
T H T H
2! 2!
4!
6
=
Microscopic states
1
4
6
4
1
4 H, 0 T
3 H, 1 T
2 H, 2 T
1 H, 3 T
0 H, 4 T
The most probable
state is also the
most disordered
In this case we see that AH = 0,
i.e.:

there is not exchange of heat between the system and its
surroundings, (the system is isolated ) yet, there is an
unequivocal answer as to which is the most
probable result of the experiment
The most probable state of the system is also the most
disordered, i.e. ability to predict the microscopic outcome
is the poorest.
Thermodynamics
Thermodynamics
A measure of how disordered is the final state is also a measure of
how probable it is:
16
6
P
2T 2H,
=
Entropy provides that measure
(Boltzmann)
ln W k S
B

Number of
microscopic
ways in which
a particular
outcome
(macroscopic
state) can be
attained
Boltzmann
Constant
Molecular
Entropy
For Avogadro numbers
of molecules
ln W ) k (N S
B Avogadro
=
R (gas constant)
Therefore: the most probable
outcome maximizes entropy
of isolated systems
AS > 0 (spontaneous)
AS < 0 (non-spontaneous)
Criterion for Spontaneity:
Thermodynamics
The macroscopic (thermodynamic) definition
of entropy:

dS = dq
rev
/T
i.e., for a system undergoing a change from an initial state
A to a final state B, the change in entropy is calculated
using the heat exchanged by the system between these
two states when the process is carried out reversibly.
Thermodynamics

AS =
dq
rev
T
initial
fina l
}
(Carried t hrough a reversible path)
AS =
C
P
T
initial
fina l
}
dT (If process occurs at contant pressure)
AS =
C
V
T
initial
fina l
}
dT (If process occurs at const ant volume)

Spont aneity Criteria
In these equat ions, the equal sign applies for reversible
processes. The inequalities apply for irreversible, spontaneous, processes :
AS(system) + AS(surroundings) > 0
AS(isolated system) > 0
Thermodynamics
Free-energy
Provides a way to determine spontaneity whether system is
isolated or not
Combining enthalpic and entropic changes
S T - H G A A A
What are the criteria for spontaneity?
Take the case of AH = 0:
S T - G A = A
< 0 > 0
AG > 0
AG < 0
AG = 0
non-spontaneous process
spontaneous process
process at equilibrium
(Gibbs free energy)
Thermodynamics
Free energy and chemical equilibrium
Consider this rxn:
A + B C + D
Suppose we mix arbitrary concentrations of products and reactants
These are not equilibrium concentrations
Reaction will proceed in search of equilibrium
What is the AG is associated with this search and finding?:
[A][B]
[C][D]
ln RT G G
o
+ A = A
is the Standard Free Energy of reaction
o
G A
i.e. AG when A, B,
C, D are mixed in
their standard state:
Biochemistry: 1M,
25
o
C, pH = 7.0
1 1
1 1
ln RT G G
o
Rxn

+ A = A
o
Rxn
G G A = A
Thermodynamics
Now Suppose we start with equilibrium concentrations:
Reaction will not proceed forward or backward
0 G
Rxn
= A
Then
eq eq
eq eq
o
[B] [A]
[D] [C]
ln RT G 0 + A =
eq eq
eq eq
o
[B] [A]
[D] [C]
ln RT - G = A
eq
o
K ln RT - G = A
RT
o
S T -
o
H

eq
e K
|
.
|

\
|
A A

=
|
.
|

\
|
|
.
|

\
|
=
A A
+
R
o
S
RT
o
H
e e K
eq
RT
o
G
eq
e K
A

=
R
e
a
r
r
a
n
g
i
n
g

Thermodynamics
(

|
.
|

\
|
|
.
|

\
|
=
A A
+
R
o
S
RT
o
H
e e K ln
eq
Graph:
R
S

RT
H
- K ln
o o
eq
A
+
A
=
( )
1 - o
K
T
1
eq
K ln
R
S
o
A
-
AH
o
R
Slope =
Vant Hoff Plot
Thermodynamics
1) Change in potential
energy stored in bonds
and interactions
2) Accounts for T-dependence
of K
eq

3) Reflects: #, type, and
quality of bonds
4) If AH
o
< 0: |T K
eq
+
If AH
o
> 0: |T K
eq
|
1) Measure of disorder
S = R ln (# of microscopic ways of
macroscopic states can be attained)
2) T-independent contribution
to K
eq

3) Reflects order-disorder in
bonding, conformational
flexibility, solvation
4) AS
o
| K
eq
|
Rxn is favored
Summary: in chemical processes
AH
o
AS
o
Thermodynamics
Examples:
A B
Consider the Reaction
[A]
initial
= 1M
[B]
initial
= 10
-5
M
K
eq
= 1000
eq
o
K ln RT - G = A
Free energy change
when products and
reactants are present at
standard conditions
( )( ) ( ) 1000 ln K 298 1.98 - G
K mol
cal
o
= A
mol
Kcal
o
4.076 - G = A
Spontaneous rxn
How about AG
Rxn

[A]
[B]
ln RT G G
o
Rxn + A = A
( ) ( )( )
1
10
ln K 298 10 1.98 4.076 - G
-5
K mol
Kcal
3 -
mol
Kcal
Rxn
+ = A
mol
Kcal
Rxn
10.9 - G = A
Even more spontaneous
Thermodynamics
Another question What are [A]
eq
and [B]
eq
?
1M 10 1 [B] A] [
-5
~ + = +
[B] - 1 A] [ =
1000
[A]
[B]
K
eq
eq
eq
= =
( )
eq eq
[B] - 1 1000 B] [ =
1000 B] [ 1001
eq
=
1M 0.999M
1001
1000
B] [
eq
~ = =
0.001M A] [
eq
=
Thermodynamics
Another Example Acetic Acid Dissociation
AH
o
~ 0
CH
3
COOH + H
2
O CH
3
COO
-
+ H
3
O
+

5 -
3
3
-
3
eq
10 ~
COOH] [CH
] O ][H COO [CH
K

=
+
Creation of charges Requires ion solvation
Organizes H
2
O around ions
At 1M concentration, this is entropically unfavorable.
K
eq
~ 10
-5


If [CH
3
COOH]
total
~ 10
-5
50% ionized
Percent ionization is concentration dependent. We can favor
the forward rxn (ionization) by diluting the mixture
If [CH
3
COOH]
total
~ 10
-8
90% ionized
Thermodynamics
CH
3
COOH + H
2
O CH
3
COO
-
+ H
3
O
+

K
eq
=
[CH
3
COO
-
][H
3
O
+
]
[CH
3
COOH]
=
[CH
3
COO
-
][H
3
O
+
]
[CH
3
COOH]
T
2
[CH
3
COOH]
T
[CH
3
COO
-
]
[CH
3
COOH]
T
2
K
eq
=
o
2
[CH
3
COOH]
T
1 o
with o
[CH
3
COO
-
]
[CH
3
COOH]
T
and o =
-K
eq
+ K
2
eq + 4[CH
3
COOH]
T
K
eq
2[CH
3
COOH]
T
o
CH3 -COOH total
Thermodynamics
Thermodynamics
Third Example Amine Reactions
R N H + H
2
O R NH
2
+ H
3
O
+

H
H
+
AS
o
~ 0

mol
Kcal
o
14 H = A
-10
eq
10 K =
not favorable
Backbone Conformational Flexibility
N
C
R
H
O
N
H
H
C
u +
For the process
folded unfolded
(native) (denatured)
folded
unfolded
o
conf. backbone
W
W
ln R S = A
How many ways to form the unfolded state?
Backbone Conformational Flexibility
degrees of freedom = 2
u
+
Assume 2 possible values for each degree of freedom. Then
residue
isomers onal conformati
4 of Total
For 100 amino acids
4
100
~ 10
60
conformations
These results do not take into account excluded volume effects.
When these effects are considered the number of accessible
configurations for the chain is quite a bit smaller
W
unfolded
~ 10
16
conformations
Backbone Conformational Flexibility
Thermodynamic considerations
16 o
conf. backbone
10 ln R S = A
2.303 16 1.987 ~
K mol
cal
73 =
C 25 at 22 - S T - G
o
mol
Kcal
o o
conf. backbone
= A = A
In addition other degrees of freedom may be quite important,
for example
N
C
R
H
O
N
H
H
C
e
We will see this
later in more detail
] ][OH O [H K
-
3 w
+
=
Ionization of Water
Water is the silent, most important component in the cell
Its properties influence the behavior and properties of all other
components in the cell.
H
2
O + H
2
O H
3
O
+
+ OH
-

Here we concern ourselves with its ionization properties:
O] [H
] ][OH O [H
K
2
-
3
eq
+
=
Since in the cell, [H
2
O] ~ 55M, and ionization is very weak, then
[H
2
O] ~ constant, so se can define
the ionic
product of
water
] O [H log -
] O [H
1
log pH
3
3
10
+
+
= =
Ionization of Water
From the previous equation
] ][OH O [H K
-
3 w
+
=
-14
w
10 K = For pure water
M 10 ] [OH ] O [H ] [H
-7 -
3
= = =
+ +
i.e. in a neutral soln: M 10 ] O [H
-7
3
=
+
M 10 ] [OH
-7 -
=
The overall acidity of the medium greatly affects many biochemical
reactions, because most biological components can function either
as bases or acids.
A measure of acidity is given by the pH scale, defined as
7
10
1
log pH
7 -
10
= =
So, in fact for
pure water:
Weak Acids and Bases
All biological acids and bases belong to this category
Consider acetic acid
AH A
-
+ H
+

The Dissociation Constant
AH]

[

]

A

][

[H


K

-

a

+

=

[AH]
] [A
log pK pH
-
a
+ =
rearrange
Henderson-
Hasselbalch
equation
where, pK
a
= - logK
a
Fraction of deprotonated acid is
[AH] ] A [
] [A

A
+
=

f
Weak Acids and Bases
Also
=
A
AH
1 f f

+ =
A
A
a
- 1
log pK pH
f
f
pH
0.5
A
f
1.0
0
pK
a

i.e. pK
a
is the pH at
which the acid is
50% ionized
So, we can re-write the
Henderson-Hasselbalch
equation
Weak Acids and Bases
Based on the previous page
90%
11
10
; 1 pK pH
A
a
~ = + =

f
9% ; 1 pK pH
A
a
~ =

f
etc. 0.9%, ; 2 pK pH
A
a
~ =

f
If
Morever the lower the pK
a
, the stronger the acid
pH
0.5
A
f
1.0
0
stronger
acid
weaker
acid

+ =
A
A
a
- 1
log pK pH
f
f
Weak Acids and Bases
Some useful relationships

f
AH
=
AH
A

+ AH
=
H
+
| |
K
a
+ H
+
| |
f
A
-
K
a

f
AH

K
a


f
A

=
A

+ AH
=
K
a
K
a
+ H
+
| |
Multiple Acid-Base Equilibria
Consider Alanine
NH
3
+

CH
3

CH

COOH
Titrate a solution of ala, using a gas electrode (pH meter), and a
buret to add a strong base of known concentration:
=

2
.
3

=

9
.
7

pK
1
pK
2

pH
(
f
r
a
c
t
i
o
n

d
e
p
r
o
t
o
n
a
t
e
d
)

m
L

o
f

b
a
s
e

a
d
d
e
d

Macroscopic
experiment shows
2 inflection points
(2 pKs)
Please correct in your
notes
Multiple Acid-Base Equilibria
N
+

CH
3

CH

COOH
H
H
H
N
+

CH
3

CH

COO

H
H
H
N
CH
3

CH

COO

H
H
Cation Zwitterion Anion
If we assume that the ionization of a given group is independent
of the state of ionization of the others, then
As we vary the pH of the solution from low to high:
So, in fact the two inflection points seen correspond to the
deprotonation of the carboxylic group (at low pH) and then
to the deprotonation of the amine group (at high pH).
So, How can we estimate the fraction of these different species in solution?
Multiple Acid-Base Equilibria
f
+
HAH


=
f
COOH


f
NH
3
+

=

H
+
K
a 1

+
H
+
|
\

|
.
|
H
+
K
a 2

+
H
+
|
\

|
.
|
f
+
HA


=
f
COO



f
NH
3
+

=

K
a
1
K
a 1

+
H
+
|
\

|
.
|
H
+
K
a 2

+
H
+
|
\

|
.
|
f
AH

=
f
COOH


f
NH 2

=

H
+
K
a 1

+
H
+
|
\

|
.
|
K
a
2
K
a 2

+
H
+
|
\

|
.
|
f
A


=
f
COO



f
NH 2

=

K
a
1
K
a 1

+
H
+
|
\

|
.
|
K
a
2
K
a 2

+
H
+
|
\

|
.
|
1
A
AH
HA HAH
= + + +
+ +
f f f f