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“Los objetos vivientes están
compuestos por moléculas inertes”
Albert Lehninger
El problema es:
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
E = M C2
Trabajo
∆ x F
Kinetic Energy
2
Potential Energy
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
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
∆ 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
S1 > S2
La entropía es la medida del grado
de desorden de un sistema
Disordered Liquid
Ordered Solid
Hard-sphere liquid
Lower Entropy…
Hard-sphere crystal
Segunda Ley de la Termodinámica
dS>=0 (dS>=dQ/T)
Ordering and 2nd law of thermodynamics
System in thermal contact with environment
Equilibration
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…
∆ 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
0 0
in biological ∆ P=0
∆ H = ∆ E + P∆ V + systems ∆ V≈ 0
V∆ P
∆ H≅ ∆ E
at ∆ P = 0 and since ∆ V ≈ 0
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.:
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
S
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∆
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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)
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)
∆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 ?
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
Wunfolded
∆S o
backbone conf. = R ln
Wfolded
[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+
[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
pH = pK a − 2 ; f A − ≈ 0.9%, etc.
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
= 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:
So, How can we estimate the fraction of these different species in solution?
+
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