thermodynamic concepts biophisics

8/13/2019 Thermodynamic Concepts biophisics

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THERMODYNAMIC CONCEPTS

In thermodynamics three types of systems are studied:

ISOLATEDISOLATED (or adiabatic) : systems completely autonomous, exchangingneither material nor energy with their surroundings.

CLOSEDCLOSED: materially self-contained, but exchange energy across their

boundaries.

OPENOPEN: exchange both energy and material with the environment


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It is the manifestation of the internal energy of a system.In 1842 Julius Meyer established the equivalence between heat and energy: 1stprinciple of thermodynamic: principle of conservation of energy

SETTING UP THE ENERGY IS NEITHER CREATED NOR DESTROYED, JUSTSETTING UP THE ENERGY IS NEITHER CREATED NOR DESTROYED, JUST

CHANGINGCHANGING..

The heat spreads through 3 mechanisms: conduction, convection and radiation

ConductionConduction: direct contact between the heat source and the body: FOURIER LAW

ConvectionConvection: when there is a translation of particles presents in a fluid moving

from cold to hot spots and vice.

RadiationRadiation: It is the process by which the heat in the form of radiant energy istransmitted into the vacuum, using electromagnetic waves.

1st thermodynamic principle: HEAT: ENTHALPY concept



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The internal energy E of a system is altered by exchange of work, W and heat Qwith the surroundings.

E or U = Q+W dE =Q+

W

The pressure-volume work (pV) done on the surroundings by a systems changing itsvolume against an external pressure p is:

W= -pdV

H=E + pVENTHALPY concept

dH = E+pdV

(1) and (2)

H=Q

(1)

(2)

.H < 0--> the reaction isexothermic and heat is given off.

H > 0--> the reaction is

endothermic and heat isabsorbed

E is an extensive property, whose units in thermodynamic problems are calories or joules

(1 cal = 4.184 J or electron-volts (1 eV = 1.6 x 10-19 J).


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2nd thermodynamic principle: ENTROPY

For any spontaneous process, the Entropy(disorder) of the universe,.Suniverse, must increase.

"The amount of entropy of any isolated system thermodynamically tends toincrease with time

ENTROPY: it is the disorder DEGREE OF A SYSTEM: BOLZMAN law

S=klnW

where k = Boltzmanns constant, which equals R, the gas constant (8.31 J K-1mol-1)divided by Avogadros number, = 1.38 X 10-23 J/K.

S = S(2)- S(1)= kln W2/W1


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MORE ENTROPY-----MORE DISORDER----LOW INFORMATION

In a CLOSED systems a process will occur SPONTANEOUSLY if the entropy

of the system + its surroundings increases.

In an open system (alive systems), the disorder is the return results of twoprocesses: the exchange-system environment and changes that occur in theinterior.

Non-Isolated System (dS dQ/T)

In an isolated system, the art on the inside moves to a state of equilibriumwhere the disorder is maximum


dS= dQrev/T

Relation between Heat and Entropy Change:

The 19th century physicist, Clausius, proposed that the differential entropychange, dS, is proportional to the heat absorbed,dQrev, for a reversible process,with 1/T :

(dS 0)


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however ===> we need a criterion of spontaneity which applies toour system (organism).

At constant Temperature and Pressure (conditions under whichwe exist, more or less):

Gibbs Free Energy = . G G = H-T S

???????? HOW WE ARE GOING TO MEASURE THE ENTROPY CHANGES INTHE REST OF THE UNIVERSE CAUSED BY THE ENERGY FLOW ACROSS THEBOUNDARY OF THE SYSTEM??????-------- NOT POSSIBLE !!!

it is possible to calculate the entropy from the flow of ENTHALPY (heat)across the boundaries of the system.

The thermodynamic function that links ENTHALPYENTROPY:

GIIBBS ENERGY: information about if a process is or not favourable, andis a quentitative measure of the net driving force flow at constant

temperature and pressure conditions.


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G 0 -- The net reaction will be in the reverse directionG = 0 -- The reaction is at equilibrium, and no net change in either direction occurs


R = Ideal Gas Const. (1.99 cal mole-1 deg-1);

T = is the Absolute Temperature (Kelvin)

aA + bB === cC + dD

= observed mass action rationot equilibrium

Keq= equilibrium

Gibbs Free Energy = . G G = H-T S


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A B


Gibbs energy content of a reaction Vs displacement from equilibrium

(a) Any change in away fromthe equilibrium requires anincrease in the Gibbs

energy : not spontaneous

(b) Slope=0 : Equilibrium

(c) When the reaction has not

yet proceeded as far asequilibrium, a conversion ofA to B results is a decreasein G : the mechanism exist

(d) The slope of the curve

decreases as equilibium isapproached.

(e) The reaction requiere aninput of Gibbs energy: notspontaneaus

G = - R T ln [B]b / [A]a= - R T

ln Keq


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BIOCHEMICAL EXEMPLESCATABOLIC REACTIONS OF METABOLISM

ATP + H2O ADP + Pi

ATP has more free energy than

ADP and Pi

The free energychange for this reaction, G, isless than 0 and the reaction isfavorable, i.e. it is Exergonic.


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ATP Provides Energy for:

Mechanical Work: Muscle contraction, flagella and cilia movement etc.

Transport Work: Pumping ions and molecules across membranes against aconcentration gradient

Chemical Work: Coupling energy from ATP to Endergonic reactions to makethem go

BIOCHEMICAL EXEMPLES

CATABOLIC REACTIONS OF METABOLISM


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BIOCHEMICAL EXEMPLES Energy coupling by phosphate transfer

Go = +3.4 kcal/mole

Glutamate + Ammonia Glutamine

This reaction is catalyzed by an enzyme in two steps

Energetically, this can bedescribed as the sum of thefollowing two reactions :

Glu + NH3 ----> Glu-NH2 + H2O Go = +3.4 kcal/mole

ATP + H2O ----> ADP + Pi Go = -7.3 kcal/mole

Glu + NH3 + ATP ----> Glu-NH2 + ADP + PiGo = - 3.9 kcal/mole


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BIOCHEMICAL EXEMPLESPROTEIN DENATURATION

Protein denaturation. (A) Schematic diagram ofthe initial and final final states of a nativedenatured transition

Tm=

H/

S

Tm is defined by the temperature of the

equilibrium, G=0 between the nativeand denatured states


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BIBLIOGRAPHY

Molecular biophysics part: Biophysics, W. Hoppe, W. Lohmann, H. Markl,H. Ziegler (eds). Springer-Verlag, Berlin, 1983. Chapter 3. (Chapters 1 and

2 are recommended for students with no previous exposure tobiology/biochemistry although in this case a better introduction would be a

general Biochemistry book such as Lehningers Biochemistry).

Bioenergetics part: Bioenergetics3, D.G. Nicholls, S.J. Ferguson,Academic Press, Amstedam, 3rd ed, 2002. Chapters 3 and 4.

Bioelectrochemistry: Electrode Dynamics, A.C. Fisher, Oxford UniversityPress, Oxford, 1996.

thermodynamic concepts biophisics

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