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8/3/2019 bioenergetica 2007 I
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Bioenergética
Mirko Zimic
8/3/2019 bioenergetica 2007 I
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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
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Conversión entre la Energía cinética y
la Energía potencial
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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 Hidrógeno:
Replicación, 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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Temperatura
Es la medida de la energía cinética
interna de un sistema molecular
Ek = N K T /2
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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 > S2
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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
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Energía Libre
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
dG<0 proceso exergónico (espontáneo)
dG>0 proceso endergónico
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Las Enzimas o biocatalizadores,
reducen la Energía de Activación
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La molécula de ATP
Los seres vivos utilizan la
molécula de ATP como
medio principal para
almacenar energíapotencial proveniente de
la degradación de los
alimentos
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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
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La síntesis de
ATP ocurre
durante la
glicólisis y larespiración
celular en la
mitocondria
usualmente
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En las plantas, la síntesis
de ATP ocurre asistida por
luz durante la fotosíntesis,
la cual es luego empleada
en las denominadasreacciones oscuras. Este es
un ejemplo de
transformación de energíaradiante en energía
química.
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El ATP participa en una serie de
reacciones acopladas
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Diversas moléculasbiológicas requieren la
capacidad de
„moverse‟ para cumplir sus funciones… Por lo
tanto hace falta energía
para realizar estafunción.
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La fuente de energía
para el movimiento
molecular es
fundamentalmente el
ATP
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El ATP contribuye a diversos
tipos de reacciones
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El ATP suele participar en el
correcto plegamiento de las
proteínas
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Thermodynamics
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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
Heat-up the system
Do work on the system
E
Cool-off the system
Extract work from the system
E = q + ww
-PV
w´
Thermodynamics
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Thermodynamics
A more useful concept is: ENTHALPY (H)
H = E + PV
At constant
pressure… PVVPwVP-qH p
E
00
Only P-V work involved… w´ = 0
(as in most biological systems)
So…
pqH
At constant pressure, the enthalpy change in a process is
equal to amount of heat exchanged in the process by the
system.
Thermodynamics
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Thermodynamics
We have…
H = E + PV
H = E + PV + VPP = 0
V 0
in biological
systems
0 0
H E
at P = 0 and since V 0
Q: How is this energy stored in the system?
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
A:
Thermodynamics
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Thermodynamics
Second Law: Entropy and Disorder
Energy conservation is not a criterion to decide if a process willoccur or not:
Examples…
q
HotT ColdT T T
E = H = 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 thesesystems
Let us study a simpler case…
tossing 4 coins
Thermodynamics
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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
14 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
Thermodynamics
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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 mostdisordered, i.e. ability to predict the microscopic outcome
is the poorest.
Thermodynamics
Thermodynamics
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Thermodynamics
A measure of how disordered is the final state is also a measure of
how probable it is:
166 P 2T2H,
Entropy provides that measure
(Boltzmann)…
ln Wk S B Number of
microscopic
ways in which
a particular
outcome
(macroscopic
state) can be
attained
Boltzmann
Constant
Molecular
Entropy
For Avogadro number‟s
of molecules…
ln W)k (NS BAvogadroR (gas constant)
Therefore: the most probable
outcome maximizes entropyof isolated systems
S > 0 (spontaneous)
S < 0 (non-spontaneous) Criterion for Spontaneity:
Thermodynamics
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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.
Thermodynamics
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Thermodynamics
S dq
rev
T initial
fina l
(Carried through a reversible path)
S C
P
T initial
fina l
dT (If process occurs at contant pressure
S C
V
T initial
fina l
dT (If process occurs at const ant volume
Spontaneity Criteria
In these equat ions, the equal sign applies for reversible
processes. The inequalities apply for ir reversible, spontaneous, processes :
S ( system) S ( surroundings) 0
S (isolated system) 0
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
ST-HG
What are the criteria for spontaneity?
Take the case of H = 0:
ST-G
< 0 > 0G > 0
G < 0
G = 0
non-spontaneous process
spontaneous process
process at equilibrium
(Gibbs free energy)
Thermodynamics
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Thermodynamics
Free energy and chemical equilibrium…
Consider this rxn:
A + B C + DSuppose 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?:
[A][B]
[C][D]lnRTGG o
is the Standard Free Energy of reaction
o
G
i.e. G when A, B,
C, D are mixed in
their standard state:Biochemistry: 1M,
25oC, pH = 7.0
11
11lnRTGG o
Rxn
o
Rxn GG
Thermodynamics
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Thermodynamics
Now… Suppose we start with equilibrium concentrations:
Reaction will not proceed forward or backward…
0GRxn
Then…
eqeq
eqeqo
[B][A]
[D][C]lnRTG0
eqeq
eqeqo
[B][A]
[D][C]lnRT-G
eq
o KlnRT-G
RT
oST-oH
eq eK
R
oSRT
oH
eeKeq
RT
oG
eq eK
R e a r r a n g i n g
Thermodynamics
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Thermodynamics
R
oSRT
oH
eeKln eq
Graph:
R
S
RT
H -Kln
oo
eq
1-o K
T
1
eqKln
R
So
-Ho
R
Slope =
Van‟t Hoff Plot
Thermodynamics
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Thermodynamics
1) Change in potential
energy stored in bonds
and interactions
2) Accounts for T-dependenceof Keq
3) Reflects: #, type, and
quality of bonds
4) If Ho < 0: T Keq
If Ho > 0: T Keq
1) Measure of disorder
S = R ln (# of microscopic ways of
macroscopic states can be attained)
2) T-independent contributionto Keq
3) Reflects order-disorder in
bonding, conformational
flexibility, solvation
4) So Keq
Rxn is favored
Summary: in chemical processes
Ho So
Thermodynamics
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y
Examples:
A B
Consider the Reaction… [A]initial = 1M [B]initial = 10-5M
Keq = 1000
eq
o KlnRT-G
Free energy change
when products and
reactants are present at
standard conditions
1000lnK2981.98-G Kmolca lo
molKcalo 4.076-G Spontaneous rxn
How about GRxn…
[A]
[B]
lnRTGG
o
Rxn
1
10lnK298101.984.076-G
-5
Kmol
Kcal3-
mol
Kcal
Rxn
molKcal
Rxn 10.9-G Even more spontaneous
Thermodynamics
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y
Another question… What are [A]eq and [B]eq?
1M101[B]A][-5
[B]-1A][
1000
[A]
[B] K
eq
eq
eq
eqeq [B]-11000B][
1000B][1001 eq
1M0.999M1001
1000 B][ eq
0.001MA][ eq
Thermodynamics
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y
Another Example… Acetic Acid Dissociation
Ho ~ 0
CH3 – COOH + H2O CH3 – COO- + H3O+
5-
3
3
-
3eq 10~
COOH][CH
]O][HCOO[CH K
Creation of charges Requires ion solvation
Organizes H2O around ions
At 1M concentration, this is entropically unfavorable.
Keq ~ 10-5
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
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y
CH3 – COOH + H2O CH3 – COO- + H3O+
K eq [CH3 COO
-][H 3O
]
[CH3 COOH]=
[CH3
COO-][H3O ]
[CH 3 COOH]T2
[CH3 COOH]T [CH3 COO-]
[CH 3 COOH]T 2
K eq
2[CH3 COOH]T
1
with [CH3 COO
-]
[CH 3 COOH]T
and =-K eq K
2eq + 4[CH 3 COOH]T K eq
2[CH3
COOH]T
Thermodynamics
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CH3 -COOH total
y
Thermodynamics
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y
Third Example… Amine Reactions
R – N – H + H2O R – NH2 + H3O+
H
H+
So 0
molKcalo 14H
-10
eq 10K not favorable
Backbone Conformational Flexibility
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y
NC
R
HO
N
H
H
C
For the process… folded unfolded(native) (denatured)
folded
unfoldedoconf. backbone
WWlnRS
How many ways to form the unfolded state?…
Backbone Conformational Flexibility
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y
degrees of freedom = 2
Assume 2 possible values for each degree of freedom. Then…
residueisomers onalconformati 4of Total
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 accessibleconfigurations for the chain is quite a bit smaller…
Wunfolded ~ 1016 conformations
Backbone Conformational Flexibility
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y
Thermodynamic considerations…
16o
conf. backbone 10lnRS 2.303161.987
Kmolca l 73
C25at22-ST-Go
molKcaloo
conf. backbone
In addition other degrees of freedom may be quite important,
for example…
N
C
R
HO
N
H
H
C
We will see this
later in more detail
Ionization of Water
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]][OHO[HK -
3w
•Water is the silent, most important component in the cell
•Its properties influence the behavior and properties of all other
components in the cell.
H2O + H2O H3O+ + OH-
Here we concern ourselves with its ionization properties:
O][H
]][OHO[H K
2
-
3eq
Since in the cell, [H2
O] ~ 55M, and ionization is very weak, then
[H2O] ~ constant, so se can define… “the ionic
product of
water”
Ionization of Water
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]O[Hlog-]O[H
1 logpH 3
3
10
From the previous equation…
]][OHO[HK -
3w
-14
w 10K For pure water…
M10][OH]O[H][H -7-
3
i.e. in a neutral soln: M10]O[H -7
3 M10][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 logpH
7-10 So, in fact for
pure water:
Weak Acids and Bases
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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 logpKpH
-
a rearrange… Henderson-Hasselbalch
equation
where, pKa = - logKa
Weak Acids and Bases
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Fraction of deprotonated acid is…
[AH]]A[][A
A
f Also… AAH 1 f f
A
Aa
-1
logpKpH
f
f
pH
0.5A f
1.0
0
pKa
i.e. pKa
is the pH at
which the acid is
50% ionized
So, we can re-write the
Henderson-Hasselbalch
equation
Weak Acids and Bases
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Based on the previous page…
90%11
10
; 1pKpH Aa f
9% ; 1pKpHAa f
etc.0.9%, ; 2pKpHAa f
If…
Morever… the lower the pK a, the stronger the acid
pH
0.5A f
1.0
0
stronger
acid
weaker
acid
A
Aa
-1 logpKpH
f
f
Weak Acids and Bases
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Some useful relationships…
f AH AH
A AH
H
K a H
f A-
Ka
f AH
Ka
f A A
A AH
K a
K a H
Multiple Acid-Base Equilibria
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Consider Alanine…
NH3+
CH3
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
pK1 pK2 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
Macroscopicexperiment shows
2 inflection points
(2 pKs)
Please correct in your
notes
Multiple Acid-Base Equilibria
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N+
CH3
CH COOH
H
H
H
N+
CH3
CH COO –
H
H
H
N
CH3
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
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f HAH
f COOH f
NH3
H
K a1
H
H
K a2
H
f HA
f
COO f
NH3
K a1
K a 1 H
H
K a 2 H
f AH f COOH f NH2
H
K a 1 H
K a 2
K a 2 H
f A
f COO
f NH2
K a1
K a1 H
K a 2
K a 2 H
1AAHHAHAH
f f f f