La Termodinámica y la Vida

Prof. Mirko Zimic

mzimic@jhsph.edu
 La Biología está basada en la
materia ´suave´ viviente

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Alta especificidad
Información
 “Los objetos vivientes están
compuestos por moléculas inertes”
Albert Lehninger
El problema es:

Cómo estas moléculas

confieren la admirable
combinación de
características que
denominamos vida???

Cómo es que un
organismo vivo aparece
ser más que la suma de
sus partes inanimadas???
La Física procura entender y reducir la
Biología en leyes fundamentales

Pero este es un problema muy

complicado !

Son demasiadas las variables y resulta

imposible describir un sistema de un
número tan grande de partículas
 SOLUCIÓN:
Descripción estadística del mundo ´aleatorio´
Si todo en el nano-mundo de las células es aleatorio,
cómo podemos realizar predicciones?

La ACTIVIDAD COLECTIVA de ‘muchos’ objetos de

Movimiento aleatorio puede ser predicho, aun cuando el
movimiento exacto de un sólo objeto es desconocido
 TERMODINÁMICA
• Permite predecir la ACTIVIDAD
COLECTIVA de ‘muchos’ objetos de
movimiento aleatorio, aun cuando el
movimiento exacto de un sólo objeto es
desconocido
 Todo en el Universo esta
compuesto por Materia y Energía

• Materia: - Medida de la ‘inercia’

• Energía: - Energía cinética (movimiento)
- Energía potencial (reposo)

E = M C2
 Trabajo

• Trabajo = Fuerza × Distancia

• W=F∆ x

• La unidad del trabajo es el Newton-metro

conocido también como Joule.
 Trabajo mecánico

∆ x F
 Kinetic Energy

• Kinetic Energy is the energy of motion.

• Kinetic Energy = ½ mass × speed2
1
KE = mv 2

2
 Potential Energy

• The energy that is stored is called

potential energy.
• Examples:
– Rubber bands
– Springs
– Bows
– Batteries
– Gravitational Potential PE=mgh
Conversión entre la Energía cinética y
la Energía potencial
 Qué es la Bioenergética?
• Es la disciplina que estudia los aspectos
energéticos en los sistemas vivos, tanto a nivel
molecular como a nivel celular.
– Interacciones moleculares
– ATP como biomolécula almacenadora de energía
– Biocatálisis
– Reacciones acopladas
 Interacciones Fundamentales
• Interacción Gravitacional (masa-masa)
• Interacción Electromagnética (carga-dipolo)
• Interacción Nuclear Débil (electrones-núcleo)
• Interacción Nuclear Fuerte (protones-
neutrones)
 Los Sistemas Biológicos son guiados
fundamentalmente por Interacciones
Electromagnéticas
– Enlaces Covalentes
– Enlaces No-covalentes (Interacciones Débiles):
• Puentes de Hidrógeno
• Efecto Hidrofóbico
• Interacciones Iónicas
• Interacciones Ión-Dipolo
• Interacciones Dipolo-Dipolo
• Fuerzas de Van der Waals
Enlace Covalente
Las interacciones Iónicas se dan
entre partículas cargadas
PUENTE DE
HIDRÓGENO
Participación de los Puentes de Hidrógeno:
Replicación, Transcripción y Traducción
Las interacciones débiles dirigen el
proceso de ‘docking’ molecular
El efecto hidrofóbico colabora en
el plegamiento de las proteínas
 Revisión de algunos conceptos
Termodinámicos
• Sistemas termodinámicos
• Equilibrio termodinámico
• Temperatura
• Calor
• Entalpía
• Energía Libre
• Entropía
 Clasificación de los sistemas
termodinámicos
• Sistemas Abiertos
– Intercambian materia y energía con el exterior
• Sistemas Cerrados
– Sólo intercambian energía con el exterior
• Sistemas Aislados
– No tienen ningun tipo de intercambio con el
exterior
 Equilibrio Termodinámico

Un sistema se encuentra en equilibrio

termodinámico cuando la distribución
espacial y temporal de la materia y la
energía es uniforme
 En el equilibrio termodinámico se
reducen las gradientes y con ello se
reduce la energía potencial
 Qué esta más frío?

El metal o la madera?
 Temperatura
Es la medida de la energía cinética
interna de un sistema molecular

Ek = N K T /2
Cool Hot
Qué es el “cero absoluto”?
 Escalas de temperatura

Fahrenheit Celsius Kelvin

Boiling Point 212°F 100°C 373 K

of Water

Freezing Point 273 K

32°F 0°C
of Water

Absolute Zero -459°F -273°C 0K

Los estados de la materia

Sólido Líquido

Gas Plasma
 Calor

Es la energía cinética
que se propaga debido a
un gradiente de
temperatura, cuya
dirección es de mayor
temperatura a menor
temperatura
 El flujo del calor
T = 100oC
Temperature
Profile in Rod
T = 0oC

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 Termodinámica
“ La energía no se crea ni se destruye, sólo
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:

Heat-up the system Cool-off the system

E E
Do work on the system Extract work from the system

∆ E=q+w -P∆ V
w
w´
 Entalpía
H=E+PV
La entalpía es la fracción de la energía
que se puede utilizar para realizar
trabajo en condiciones de presión y
volumen constante

dH<0 proceso exotérmico

dH>0 proceso endotérmico
 Entropía
S = K Ln(W)
La entropía es la medida del grado de
desorden de un sistema molecular

S1 > S2
La entropía es la medida del grado
de desorden de un sistema
 Disordered Liquid

Ordered Solid
 Hard-sphere liquid

Higher Entropy… Hard-sphere freezing is driven

by entropy !

Lower Entropy…

Hard-sphere crystal
Segunda Ley de la Termodinámica

“En todo sistema

aislado, la entropía
siempre aumenta
hasta alcanzar el
estado de equilibrio”

dS>=0 (dS>=dQ/T)
Ordering and 2nd law of thermodynamics
System in thermal contact with environment

Equilibration

Initially high Cools to room

- Condensation into liquid (more ordered).

- Entropy of subsystem decreased…

- Total entropy increased! Gives off heat to room.

Algunos eventos bioquímicos contradicen
la segunda ley de la termodinámica?
• Second Law of Thermodynamics
– naturally occurring processes are directional
– these processes are naturally irreversible
 Energía Libre de Gibbs

G=H-TS
La energía libre es
la fracción de la
energía que se
puede utilizar para
realizar trabajo en
condiciones de
presion, volumen y
temperatura
constante
Lo importante es la variación de la
energía libre…

dG<0 proceso exergónico (espontáneo)

dG>0 proceso endergónico

dG<0  perder capacidad de hacer trabajo ==

perder energía potencial == aumentar el desorden
(entropía)
 ∆G= ∆H - T ∆S
∆G+ (exergónico) ∆H +(endotérmico)
∆G – (endergónico) ∆H- (exotérmico)
∆S +(sube entropía) ∆S – (baja
entropía)
Table 3.2
 La paradoja del ¨Demonio de Maxwell¨
Segunda ley: Entropía y desorden
 Las Enzimas o biocatalizadores,
reducen la Energía de Activación
La molécula de ATP
Los seres vivos utilizan la
molécula de ATP como
medio principal para
almacenar energía
potencial proveniente de
la degradación de los
alimentos
 La manera de utilizarse la energía en la
molécula de ATP es mediante la separación
de un grupo fosfato el cual está unido
mediante un enlace covalente de alta energía
La síntesis de
ATP ocurre
durante la
glicólisis y la
respiración
celular en la
mitocondria
usualmente
 En las plantas, la síntesis
de ATP ocurre asistida por
luz durante la fotosíntesis,
la cual es luego empleada
en las denominadas
reacciones oscuras. Este es
un ejemplo de
transformación de energía
radiante en energía
química.
El ATP participa en una serie de
reacciones acopladas
 Diversas moléculas
biológicas requieren la
capacidad de
‘moverse’ para cumplir
sus funciones… Por lo
tanto hace falta energía
para realizar esta
función.
La fuente de energía
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
proteínas
 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:

Heat-up the system Cool-off the system

E E
Do work on the system Extract work from the system

∆ E=q+w -P∆ V
w
w´
 Thermodynamics
A more useful concept is: ENTHALPY (H)

H = E + PV
0 0
At constant
∆H = q p - P∆V + w ′ + P∆V + V∆P
pressure…

∆E
Only P-V work involved… w´ = 0
(as in most biological systems)

So…
∆H = q p

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

0 0
in biological ∆ P=0
∆ H = ∆ E + P∆ V + systems ∆ V≈ 0
V∆ P
∆ H≅ ∆ E
at ∆ P = 0 and since ∆ V ≈ 0

Q: How is this energy stored in the system?

A: 1) As kinetic energy of the molecules. In isothermal (∆ T =

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
 Thermodynamics
Second Law: Entropy and Disorder

Energy conservation is not a criterion to decide if a process will

occur or not:

Examples… these processes

occur because
THot TCold T T the final state
( with T = T &
P = P) are the
q most probable
∆ E=∆ H= states of these
0 systems
This rxn occurs in one
direction and not in the
Let us study a simpler case…
opposite
tossing 4 coins
 Thermodynamics
All permutations of tossing 4 coins…
Microscopic states…
Macroscopic states…
HTTH
1 way to obtain 4 heads
HHTT
4 ways to obtain 3 heads, 1 tail
HTHT 4!
6 ways to obtain 2 heads, 2 tails 6=
THHT 2! 2!
4 ways to obtain 1 head, 3 tails
TTHH
1 way to obtain 4 tails
THTH

6
The most probable
4 4 state is also the
3 H, 1 T
2 H, 2 T
1 H, 3 T
most disordered
1 1
4 H, 0 T 0 H, 4 T
 Thermodynamics
In this case we see that ∆ H = 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
A measure of how disordered is the final state is also a measure of
how probable it is:
6
P2H, 2T =
16
Entropy provides that measure For Avogadro number’s
(Boltzmann)… of molecules…

S ≡ k B ln W Number of S = (N Avogadrok B ) ln W
microscopic
ways in which
Molecular a particular R (gas constant)
Boltzmann
Entropy
Constant
outcome Therefore: the most probable
(macroscopic
state) can be
outcome maximizes entropy
attained of isolated systems

∆ S > 0 (spontaneous)
Criterion for Spontaneity:
∆ S < 0 (non-
spontaneous)
 Thermodynamics
The macroscopic (thermodynamic) definition
of entropy:

dS = dqrev /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
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 Thermodynamics
Free-energy…
•Provides a way to determine spontaneity whether system is
isolated or not
•Combining enthalpic and entropic changes

∆G ≡ ∆H - T∆S (Gibbsfreeenergy)

What are the criteria for spontaneity?

Take the case of ∆ H = 0:
∆G = - T∆S
∆ G> non-spontaneous process
<0 >0
0 spontaneous process
∆ G< process at equilibrium
0
∆ G=
 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 ∆ G is associated with this search and finding?:
[C][D]
∆G = ∆G + RT ln
o
i.e. ∆ G when A, B,
[A][B]
C, D are mixed in
∆G is the Standard Free Energy of reaction
o
their standard state:
Biochemistry: 1M,
1× 1 25oC, pH = 7.0
∆G Rxn = ∆G + RT ln
o

1× 1
∆G Rxn = ∆G o
 Thermodynamics
Now… Suppose we start with equilibrium concentrations:
Reaction will not proceed forward or backward…
∆G Rxn = 0
Then…
[C]eq [D]eq o
0 = ∆G + RT ln
o − ∆RT
G
K eq = e
[A]eq [B]eq
 ∆Ho - T∆So 

Rearranging
 
−
[C]eq [D]eq K eq = e RT

∆G = - RT ln
o

[A]eq [B]eq
  + ∆RS 
o o
− ∆RT
H
K eq =  e  e 
∆G o = - RT ln K eq   
 Thermodynamics
Graph:
 
ln K eq =  e
Ho
− ∆RT  + ∆RS  
o

 e 
   

∆H o ∆So
ln K eq = - +
RT R
∆So
Van’t HoffPlot R
∆Ho
Slope = -
ln K eq R

( K )
1 o -1
T
 Thermodynamics
Summary: in chemical processes
∆ Ho ∆ So
1) Change in potential 1) Measure of disorder
energy stored in bonds S = R ln (# of microscopic ways of
and interactions macroscopic states can be attained)

2) Accounts for T-dependence 2) T-independent contribution

of Keq to Keq
3) Reflects: #, type, and 3) Reflects order-disorder in
quality of bonds bonding, conformational
flexibility, solvation
4) If ∆ Ho < 0: ↑T ⇒ Keq ↓ 4) ∆ So↑ ⇒ Keq ↑
If ∆ Ho > 0: ↑T ⇒ Keq ↑ Rxn is favored
 Thermodynamics
Examples:
Consider the Reaction… [A]initial = 1M
A B [B]initial = 10-5 M
Free energy change
when products and Keq = 1000
reactants are present at
standard conditions
∆G o = - RT ln K eq

∆G o = - (1.98 mol
cal
)( ) (
K 298 K ln 1000
)
∆G o = - 4.076 Kcal
mol
Spontaneous rxn
How about ∆ GRxn …
o [B]
∆ G Rxn = ∆ G + RT ln
[A]
) + (1.98 ×10 -3 mol K ) 298 K ln
-5
10
∆G Rxn = - ( 4.076 Kcal
mol
Kcal
( )
1
∆G Rxn = - 10.9 Kcal
mol
Even more spontaneous
 Thermodynamics
Another question… What are [A]eq and [B]eq ?

[A] + [B] = 1 + 10-5 ≈ 1M

[A] = 1 - [B]
[B]eq
K eq = = 1000
[A]eq

[B]eq = 1000 (1 - [B]eq )

1001[B]eq = 1000
1000
[B]eq = = 0.999M ≈ 1M
1001
[A]eq = 0.001M
 Thermodynamics
Another Example… Acetic Acid Dissociation
∆ Ho ~ 0
CH3 – COOH + H2O CH3 – COO- + H3O+
Creation of charges ⇒ Requires ion solvation
⇒ Organizes H2O around ions
At 1M concentration, this is entropically unfavorable.
Keq ~ 10-5
[CH 3 − COO - ][H 3O + ]
K eq = ~ 10-5
[CH 3 − COOH]
If [CH3 – COOH]total ~ 10-5 → 50% ionized
Percent ionization is concentration dependent. We can favor
the forward rxn (ionization) by diluting the mixture

If [CH3 – COOH]total ~ 10-8 → 90% ionized

 Thermodynamics
CH3 – COOH + H2O CH3 – COO- + H3O+

[CH −COO -][H O+]

3 3
- + 2
[CH 3 −COO ][H3O ] [CH 3 −COOH] T
Keq = = -
[CH 3 −COOH] [CH 3 −COOH] T −[CH 3 −COO ]
2
[CH −COOH]
3 T
2 -
α [CH 3 −COOH] T [CH 3 −COO ]
Keq = with α ≡
1−α [CH 3 −COOH] T

2
-Keq + K eq +4[CH 3 −COOH] T Keq
and α =
2[CH −COOH]
3 T
 Thermodynamics

CH3-COOHtotal
 Thermodynamics
Third Example… Amine Reactions

H
+
R – N – H + H2O → R – NH2 + H3O+
H

∆ So ≈
0

∆H o = 14 Kcal
mol
not favorable
K eq = 10 -10
 Backbone Conformational Flexibility
Φ R Ψ H

C N
N C
H
H O

For the process…

folded unfolded
(native) (denatured)

Wunfolded
∆S o
backbone conf. = R ln
Wfolded

How many ways to form the unfolded state?…

 Backbone Conformational Flexibility
Φ
degrees of freedom = 2
Ψ
Assume 2 possible values for each degree of freedom. Then…

Total of 4 conformational isomers residue

For 100 amino acids…
4100 ~ 1060 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…

Wunfolded ~ 1016 conformations

 Backbone Conformational Flexibility
Thermodynamic considerations…

∆Sobackbone conf. = R ln 1016

≅ 1.987 × 16 × 2.303
= 73 mol
cal
K

∆G obackbone conf. = - T∆So = - 22 Kcal

mol at 25 o
C

In addition other degrees of freedom may be quite important,

for example…
R ω H

C N We will see this

N C later in more detail
H
H O
 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.
Here we concern ourselves with its ionization properties:

H2O + H2O H3O+ + OH-

[H 3O + ][OH - ]
K eq =
[H 2 O]
Since in the cell, [H2O] ~ 55M, and ionization is very weak, then
[H2O] ~ constant, so se can define…
“the ionic
K w = [H 3O + ][OH - ] product of
water”
 Ionization of Water
From the previous equation…
K w = [H 3O + ][OH - ]
K w = 10-14 For pure water…
[H + ] = [H 3O + ] = [OH - ] = 10-7 M
i.e. in a neutral soln: [H 3O + ] = 10 -7 M [OH - ] = 10-7 M
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…
1 +
pH = log 10 +
= - log [H 3 O ]
[H 3O ]
1
So, in fact for pH = log 10 -7 = 7
pure water: 10
 Weak Acids and Bases
All biological acids and bases belong to this category
Consider acetic acid…
AH A- + H+

The Dissociation Constant…

[H+ ][A- ]
Ka =
[AH]

[A - ] Henderson-
rearrange… pH = pK a + log Hasselbalch
[AH]
equation
where, pKa = - logKa
 Weak Acids and Bases
Fraction of deprotonated acid is…

[A − ]
f A− = − Also… f AH = 1 − f A −
[A ] + [AH]

f A−
So, wecanre-writethe pH = pK a + log
1 - fA−
Henderson-Hasselbalch

equation
1.0

i.e. pKa is the pH at

f A− 0.5
which the acid is
pKa 50% ionized
0
pH
 Weak Acids and Bases
Based on the previous page…
10
pH = pK a + 1 ; f A − = ≈ 90%
11 f A−
pH = pK a + log
If… pH = pK a − 1 ; f A − ≈ 9% 1 - f A−

pH = pK a − 2 ; f A − ≈ 0.9%, etc.

Morever… the lower the pKa, the stronger the acid

1.0
stronger
acid

f A− 0.5

weaker
acid
0
pH
 Weak Acids and Bases
Some useful relationships…

A
H []
H+
fAH
H= −
f =
A
A +A
H Ka+[]
H+

Ka

−
A K
− =− =
f a fA-
A
A+A
H K a+[]
H+

Ka
 Multiple Acid-Base Equilibria
Consider Alanine…
CH3

NH3+ CH COOH

Titrate a solution of ala, using a gas electrode (pH meter), and a

buret to add a strong base of known concentration:
(fraction deprotonated)

= 9.7
mL of base added

Pleasecorrect inyournotes
= 2.3

Macroscopic
experiment shows
pK1 pK2 pH
2 inflection points
(2 pKs)
 Multiple Acid-Base Equilibria
As we vary the pH of the solution from low to high:

H CH3 H CH3 H CH3

H N+ CH COOH H N+ CH COO – N CH COO –

H H H

Cation Zwitterion Anion

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?

If we assume that the ionization of a given group is independent

of the state of ionization of the others, then…
 Multiple Acid-Base Equilibria
 +  + 
f + HAH − = fCOOH × fNH 3+ =  H  H 
 Ka1 + H+ Ka 2 + H+
   + 
f + HA − = fCOO − × fNH 3+ =  
K a1 H 
Ka 1 + H 
+
 Ka2 + H
+

 +   
f AH = fCOOH × =
fNH 2   H   K a 2 
Ka 1 + H   K a 2 + H 
+ +

   
f A− = f COO − × fNH 2 =  
K a1
K a 2 
Ka 1 + H
+
  Ka 2 + H
+

f + HAH − + f + HA − + f AH + f A − = 1