 H 0 for some Noncovalent Interactions Na + (g) + Cl - (g) NaCl(s)Ionic-785 NaCl(s) Na + (aq) + Cl - (aq) Ionic +ion-dipole+4 Ar(g) Ar(s)London (fluctuation dipole) -8 Acetone(g) Acetone(l)London-van der Waals-30 H 3 C H 3 C (permanent dipole) 2 O O H OHydrogen bond-20 H H CH 3 H H 2 NONH H OH 2 H 2 NONHydrogen bond (aq)-5 H 2 NONH 2 H O(NH 2 ) 2 HOH (Urea (aq)) C 3 H 6 (l) + H 2 O(l)C 3 H 6 (aq)Hydrophobic-10 (TSWP p. 98) ReactionInteraction  H 0 (kJ mol -1 )

Protein Unfolding Proteins have a native state. (Really, they tend to have a tight cluster of native states.) Denaturation occurs when heat or denaturants such as guanidine, urea or detergent are added to solution. Also, the pH can affect folding. When performing a denaturation process non-covalent interactions are broken. Ionic, van der-Waals, dipolar, hydrogen bonding, etc. Solvent is reorganized.

Protein Unfolding Let’s consider denaturation with heat. We can determine a great deal about the nature of the protein from such a consideration. The experimental technique we use for measuring thermodynamic changes here is the differential scanning calorimeter. Basic experiment: Add heat to sample, measure its temperature change. heat

Protein Unfolding In differential scanning calorimetry you have two samples: Your material of interest Control You put in an amount of heat to raise the temperature of the control at a constant rate, then measure the rate of change in temperature of the other sample as a function of the input heat. This is a measure of the heat capacity! Protein + Solvent Heat T1 T2 T1-T2

Protein Unfolding Data for glyceraldehyde-3-phosphate dehydrogenase. pH8.0 pH6.0 Bacillus stearothermophilus E. coli Rabbit Is the protein more stable at pH 8 or 6? Why is B. stear. more stable?

Protein Unfolding We are given the following data for the denaturation of lysozyme: °C  G ° kJ/mol  H ° kJ/mol  S ° J/ K mol T  S ° kJ/mol Where is the denaturation temperature? What then is special about the temperature at which the denaturation is spontaneous?

Nonideal Systems For ideal gases: For all systems define the activity of component A, a A : For a generalized chemical reaction: aA + bBcC + dD

Nonideal Systems What is the activity of a gas? –For ideal gases it is the partial pressure –For real gases it is related to, but not necessarily equal to the partial pressure: –Since all gases become ideal at low enough pressures,  A = 1 in the limit of low pressure. –Standard state for a real gas is extrapolation of properties at low pressure to 1atm. slope = RT at low pressure

Nonideal Systems What is the activity of a solid or liquid? –The standard state for a pure solid or liquid is the pure substance at 1atm. –The activity of a pure solid or liquid is 1 at 1atm and changes only slightly with pressure. –For example, consider water: Molar volume changes slightly with pressure Can we calculate the activity of water at high pressure from this information?

Nonideal Systems What is the activity of a solution? –Solutions can be solid or liquid –They can contain many components –The activity of each component will depend on: Its concentration The concentrations of everything else in the mixture –The activity coefficient can be expressed in terms of the concentration: –Solvent standard state: a A X A as X A 1. Or, equivalently, in the limit as X A approaches 1,  A =1. For dilute solutions, activity of the solvent (e.g. H 2 O) ~ 1 using the solvent standard state.

Nonideal Systems –Solute standard state: The solute standard state for a component is defined as the extrapolated state where the concentration is equal to 1 molar (M) or 1 molal (m), but the properties are those extrapolated from a very dilute solution. It is a hypothetical 1M (or m) solution of A that is behaving ideally. The activity becomes equal to the concentration as the concentration goes to zero. aAaA cAcA 1 1 Solute standard state Ideal solution Real solution

Nonideal Systems If the solute is a strong electrolyte (e.g. NaCl) –Activity coefficients Activity coefficients for divalent ions can be much less than 1,even in the millimolar concentration range. See TSWP p.140.

Nonideal Systems Biochemist’s standard state –Addresses difficulty of partial dissociation H 3 PO 4, H 2 PO 4 -, HPO 4 2-, PO 4 3- Distribution of these species depends strongly on pH (moderate equilibrium) –pH = 7 is chosen as the standard condition for a H + H + activity is 1 for [H + ] = M –Activity of each molecule is set equal to the total concentration of all species of that molecule at pH 7.

Example