Basic biological thermodynamics Thermodynamics

Theory that is concerned with energetic and macroscopic, bulk properties of matter Deals especially well with large amount of matter and properties of matter under changes in temperature and pressure Link between thermodynamics and molecular process = statistical mechanics

Basic concepts
System part of universe with which experimentalist is concerned Open system both matter and heat exchange with surroundings Closed system only heat exchanges with surroundings Isolated or adiabatic system neither matter nor heat exchange with surroundings State functions properties relating to changes in a system which are dependent only on its initial and final states e.g. internal energy, enthalpy, entropy and Gibbs free energy

First Law of Thermodynamics

Total energy of a system and its surroundings is constant energy cannot be created or destroyed but can only be changed from one form into another System exchange heat with surroundings or does works on surroundings change in internal energy U = U!"#$% U!"!#!$% = q + w q = positive when heat has been transferred to system (endothermic) = negative when heat has been transferred to surroundings (exothermic) w = positive when work has been done on system = negative when work has been done on surroundings

Enthalpy
Heat content of a system H = U + pV = U + nRT As most biochemical reactions occur in solution, volume change is negligible H = U

Second Law of Thermodynamics

Total entropy of a system and its surroundings always increases for a spontaneous process Entropy = indication of disorder or randomness of a system q S T Equality applies in cases of reversible processes Inequality applies in case of irreversible processes For ideal gas, S = k ln W where k is the Boltzmann constant, W is no. of microstates Entropy of gas > liquid > solid * Entropy of perfect crystal = 0 (Third law of thermodynamics) The more diluted solution, the greater entropy

Basic biological thermodynamics

Gibbs Free Energy
Second law of thermodynamics indicates that a process will occur spontaneously if q < !! For processes occurring at constant temperature and pressure, q = H H TS <0 (for spontaneous process) G = H TS Value of G gives max. work available from the process non-PV work * Work associated with changes in pressure or volume is negligible generally not important in biological systems G < 0, spontaneous, exergonic; G > 0, non-spontaneous, endergonic G = 0, at equilibrium * G only indicates the reaction is thermodynamically favorable, but not necessary kinetically favorable

Standard states
For a substance = form of substance at a specified temperature that is stable at 1 atm of pressure For a solute = solution of concentration 1M G! = H ! TS !

Biochemical standard states

-

Thermodynamical activity of solute in solution at a concentration of 1M at 25oC and 1 atm of pressure is assigned 1.0 Standard state of H+ in solution is originally defined as 1M solution but as the pH = 0 incompatible with most forms of life define biological standard state for solutes in which all components except H+ are at a concentration of 1M, while H+ is present at 10-7M (pH = 7) G!" = H !" TS !"

Chemical potential/ Partial molar free energy

= changes of free energy of a substance when the no. of molecule of it changes by one assuming constant pressure and no charge movement in an electric field ! i.e. ! = ! - consider the case of one mole of substance A (! = !), relationship between chemical potential and concentration is defined as: ! !! !! = !"#$[!]

Equilibrium and free energy

The free energy of the reaction aA + bB cC + dD is G = !! + !! !! !! [C]! [D]! ! = G + RT ln{ ! ! } [A] [B] When equilibrium is attained (i.e. reversible process),G = 0 [C]! [D]! ! G = RT ln{ ! ! } = RT ln K [A] [B] K = e! !"
!!

Basic biological thermodynamics

* There are backward and forward exchanges of molecules in a process at any time (tandem exchange) no net production and depletion only

Temperature dependence of equilibrium constants

Consider ln K =
!!

= !" + ! (vanHoff isochore at constant volume) 0 Assume H and S0 independent of temperature, plot ln K against 1/T

!" !!

!!