Termodinmica

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Termodinámica
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Biology is living soft matter
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Statistical description of random World
The collective activity of many randomly moving
objects can be effectively predictable, even if
the individual motions are not.
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Interacciones Fundamentales

• Interacción Gravitacional (masa-masa)
• Interacción Electromagnética (carga-dipolo)
• Interacción Nuclear Débil (electrones-núcleo)
• Interacción Nuclear Fuerte (protones-neutrones)

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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

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Enlace Covalente
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La Energía de Activación es el resultado de la
repulsión de las nubes electrónicas
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Las interacciones Iónicas se dan entre partículas
cargadas
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Participación de los Puentes de
HidrógenoReplicación, Transcripción y Traducción
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Las interacciones débiles dirigen el proceso de
docking molecular
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El efecto hidrofóbico colabora en el plegamiento
de las proteínas
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Which is colder?

• Metal or Wood?

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Temperatura

• Es la medida de la energía cinética interna de un
  sistema molecular

Ek N K T /2
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11.3 Temperature

• Measured in Fahrenheit, Celsius, and Kelvin
• Rapidly moving molecules have a high temperature
• Slowly moving molecules have a low temperature

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Cool Hot
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What is absolute zero?
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Temperature Scales
Fahrenheit
Celsius
Kelvin
Boiling Point of Water
212?F
100?C
373 K
Freezing Point of Water
273 K
32?F
0?C
Absolute Zero
-459?F
-273?C
0 K
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Calor

• Es la energía cinética que se propaga debido a un
  gradiente de temperatura, cuya dirección es de
  mayor temperatura a menor temperatura

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Entropía

• S K Ln(W)
• La entropía es la medida del grado de desorden de
  un sistema molecular

S1 gt S2
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Entalpía

• HEPV
• La entalpía es la fracción de la energía que se
  puede utilizar para realizar trabajo en
  condiciones de presión y volumen constante
• dHlt0 proceso exotérmico
• dHgt0 proceso endotérmico

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Energía Libre

• GH-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
• dGlt0 proceso exergónico (espontáneo)
• dGgt0 proceso endergónico

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11.4 Pressure

• Pressure - force per unit area
• It has units of N/m2 or Pascals (Pa)

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Pressure

• What are the possible units for pressure?
• N/m2
• Pascal 1 Pa 1 N/m2
• atm 1 atm 1 105 Pa
• psi 1 psi 1 lb/inch2
• mm Hg 1 atm 760 mm Hg

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11.5 Density

• Density - mass per unit volume
• It has units of g/cm3

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11.6 States of Matter
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Questions

• Is it possible to boil water at room temperature?
  
• Answer Yes. How?
• Is it possible to freeze water at room
  temperature?
• Answer Maybe. How?

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Gas Laws

• Perfect (ideal) Gases
• Boyles Law
• Charles Law
• Gay-Lussacs Law
• Mole Proportionality Law

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Boyles Law
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Charles Law
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Gay-Lussacs Law
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Mole Proportionality Law
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Perfect Gas Law

• The physical observations described by the gas
  laws are summarized by the perfect gas law
  (a.k.a. ideal gas law)
• PV nRT
• P absolute pressure
• V volume
• n number of moles
• R universal gas constant
• T absolute temperature

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Table 11.3 Values for R
J
3
Pam

314
.
8

314
.
8
molK
molK

cal
atmL
1.987

08205
.
0
molK
molK
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Work

• Work Force Distance
• W F Dx
• The unit for work is the Newton-meter which is
  also called a Joule.

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Types of Work
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Mechanical Work
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Mechanical Work
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Hydraulic Work
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Joules Experiment
Joule showed that mechanical energy could
be converted into heat energy.
DT
M
F
Dx
H2O
W FDx
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11.11 Energy

• Energy is the ability to do work.
• It has units of Joules.
• It is a Unit of Exchange.
• Example
• 1 car 20k
• 1 house 100k
• 5 cars 1 house

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11.11 Energy Equivalents

• What is the case for nuclear power?
• 1 kg coal 42,000,000 joules
• 1 kg uranium 82,000,000,000,000 joules
• 1 kg uranium 2,000,000 kg coal!!

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11.11 Energy

• Energy has several forms
• Kinetic
• Potential
• Electrical
• Heat
• etc.

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Kinetic Energy

• Kinetic Energy is the energy of motion.
• Kinetic Energy ½ mass speed2

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Potential Energy

• The energy that is stored is called potential
  energy.
• Examples
• Rubber bands
• Springs
• Bows
• Batteries
• Gravitational Potential PEmgh

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Conversión entre la Energía cinética y la Energía
potencial
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11.11.3 Energy Flow

• Heat is the energy flow resulting from a
  temperature difference.
• Note Heat and temperature are not the same.

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Heat Flow
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11.12 Reversibility

• 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

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Reversible Process

• Examples
• Perfect Pendulum
• Mass on a Spring
• Dropping a perfectly elastic ball
• Perpetual motion machines
• More?

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Irreversible Processes

• Examples
• Dropping a ball of clay
• Hammering a nail
• Applying the brakes to your car
• Breaking a glass
• More?

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Example Popping a Balloon
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Sources of Irreversibilities

• Friction (force drops)
• Voltage drops
• Pressure drops
• Temperature drops
• Concentration drops

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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 q w
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• Second Law of Thermodynamics
• naturally occurring processes are directional
• these processes are naturally irreversible

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Heat into Work
W
Thot
Heat Engine
Tcold
Qcold
Qhot
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Entropy. The 2nd law of thermodynamics
Isolated system always evolve to
thermodynamic equilibrium. In equilibrium
isolated system has the greatest possible
ENTROPY (disorder) allowed by the physical
constraints on the system.
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Entropy as measure of disorder
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Entropy of ideal gas
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Disordered Liquid
Ordered Solid
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Hard-sphere liquid
Hard-sphere freezing is driven by entropy !
Hard-sphere crystal
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Entropy and Temperature
Isolated (closed) system
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Ordering and 2nd law of thermodynamics
System in thermal contact with environment
Cools to room
Initially high

• Condensation into liquid (more ordered).
• Entropy of subsystem decreased
• Total entropy increased! Gives off heat to room.

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The first law of thermodynamics tells us that
energy is conserved The law of conservation of
energy in every physical or chemical change, the
total amount of energy in the universe remains
constant, although the form of energy may change.
In other words, convertible but not creatable or
destroyable For an open system like a cell
energy out energy in energy stored (5-1) or
energy stored energy in energy
out (5-2) or ?E E2 E1 (5-3) Change in
internal energy E or ?E Eproducts
Ereactants (5-4) Enthalpy (H) heat content
is the description of energy change during
biological reactions. H E PV (P,
pressure V, volume) (5-5) ? H ?E ?( PV)
? ?E (Constant P V) (5-6) ?H
Hproducts Hreactants (5-7)
Endothermic reaction ?H positive, products have
higher energy the reaction needs
energy Exothermic reaction ?H negative,
products have lower energy the reaction releases
energy
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Thermodynamic spontaneity is a measure of whether
a reaction or process can go, but says nothing
about whether it will go. The second law of
thermodynamics or the law of thermodynamic
spontaneity tells us that reactions have
directionality in every physical or chemical
change, the universe always tends toward greater
disorder or randomness.
The second step in glycolysis to break down
glucose
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Entropy and free energy are two alternative means
of assessing thermodynamic spontaneity Entropy
(S) is a measure of randomness or disorder, such
as when ice melts the volume becomes larger and
there is more randomness for the water
molecules. For the whole universe, all processes
or reactions that occur spontaneously result in
an increase in the total entropy of the universe,
i.e. ?Suniverse is always positive. For a
particular system, however, ?S can be positive or
negative. Due to the conservative of energy, the
surroundings have to be considered when using
entropy to describe a biological system. Free
energy is one of the most useful thermodynamic
concepts in biology, a better way to describe
thermodynamic spontaneity of a reaction based
solely on the properties of the system. ?G ?H
- T ?S (T, temperature in Kelvin K oC 273)
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Thermodynamics
Second Law
Entropy and Disorder
Energy conservation is not a criterion to decide
if a process will occur or not
these processes occur because the final state
( with T T P P) are the most probable
states of these systems
Examples
?E ?H 0
This rxn occurs in one direction and not in the
opposite
Let us study a simpler case
tossing 4 coins
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Thermodynamics
All permutations of tossing 4 coins
Microscopic states


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Thermodynamics
In this case we see that DH 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.
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Thermodynamics
A measure of how disordered is the final state is
also a measure of how probable it is
Entropy provides that measure (Boltzmann)
For Avogadro numbers of molecules
Number of microscopic ways in which a
particular outcome (macroscopic state) can be
attained
Therefore the most probable outcome maximizes
entropy of isolated systems
?S gt 0 (spontaneous)?S lt 0 (non-spontaneous)
Criterion for Spontaneity
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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.
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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

(Gibbs free energy)
What are the criteria for spontaneity?
Take the case of ?H 0
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Thermodynamics
Free energy and chemical equilibrium
Consider this rxn
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?

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Thermodynamics
Now Suppose we start with equilibrium
concentrations
Reaction will not proceed forward or backward
Then
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Thermodynamics
Graph
Vant Hoff Plot
Slope
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Thermodynamics
Summary in chemical processes

• Change in potential energy stored in bonds and
  interactions

2) Accounts for T-dependence
of Keq
2) T-independent contribution to Keq
3) Reflects , type, and quality of bonds
3) Reflects order-disorder in bonding,
conformational flexibility, solvation
4) ?So? ? Keq? Rxn is favored
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Thermodynamics
Examples
Consider the Reaction
Ainitial 1M Binitial 10-5MKeq 1000
How about ?GRxn
B
o
ln

RT


G


G

D

D
Rxn
A
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Thermodynamics
Another question
What are Aeq and Beq?
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Thermodynamics
Another Example
Acetic Acid Dissociation
?Ho 0
CH3 COOH H2O CH3 COO- H3O
At 1M concentration, this is entropically
unfavorable. Keq 10-5
If CH3 COOHtotal 10-5 ? 50 ionized
Percent ionization is concentration dependent.
We can favor the forward rxn (ionization) by
diluting the mixture
If CH3 COOHtotal 10-8 ? 90 ionized
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Thermodynamics
Third Example
Amine Reactions
?So ? 0
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Backbone Conformational Flexibility
For the process
How many ways to form the unfolded state?
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Backbone Conformational Flexibility
?
degrees of freedom 2
?
Assume 2 possible values for each degree of
freedom. Then
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
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Backbone Conformational Flexibility
Thermodynamic considerations
In addition other degrees of freedom may be quite
important, for example
We will see this later in more detail