Lecture 3. Aqueous acid-base chemistry
Tuesday 22 January 2019
Noncovalent (weak electrostatic) forces. The hydrophobic effect: Nonpolar and amphipathic species in water. Thermodynamic analysis of the hydrophobic effect. Colligative properties; osmosis, diffusion, and dialysis. Autoionization of water. Definition of pH and pH calculations. Weak acid and weak base equilibria. Definition and use of weak acid pKa values. Titration curves.
Reading: Lehninger - Ch.2, pp.47-63
Summary
Reading summary.
§2.3 Buffering against pH changes in biological systems.
Buffers are mixtures of weak acids and their conjugate bases.
Weak acids or bases buffer cells and tissues against pH changes.
Worked example 2-5: Ionization of histidine.
Worked example 2-6: Phosphate buffers.
Untreated diabetes produces life-threatening acidosis.
Box 2-1 -Medicine- On being one's own rabbit (don't try this at home!).
Worked example 2-7: Treatment of acidosis with bicarbonate.
§2.4 Water as a reactant.
§2.5 The fitness of the aqueous environment for living organisms.
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The physical and chemical properties of water are of great relevance to biochemistry. The hydrophobic effect, an especially important case, is a chemical thermodynamic consequence of the properties of water and the behavior of nonpolar solutes in aqueous environments.
The colligative properties pertaining to aqueous solutions are also an important consideration. Colligative properties are determined by the number of solute particles, and not dependent on the identities of the particles. Thus, colligative properties are thought of as physical, rather than chemical properties, at least in an ideal sense. In fact, one important equation of colligative properties, the van't Hoff equation for osmotic pressure, is remarkably similar to the ideal gas law. In the latter, the chemical identities of the gas molecules are also irrelevant.
Water is unquestionably an excellent solvent for many polar and charged species, yet it is a rather poor solvent for nonpolar molecules. Amphipathic molecules such as detergents or phospholipids can form micelles or bilayer structures in which the nonpolar portions of the amphipathic molecules are are sequestered together, while the polar or charged portions are exposed to the aqueous surroundings.
What is the basis of the solvent properties of water? The interactions of water with ions, dipoles, and H-bond acceptors and donors are strong. The dipole of water interacts strongly with charges, and we should note here that the rather large dielectric constant of water weakens electrostatic forces between charged solute groups. Water molecules ought to be able to interact somewhat favorably with nonpolar species by van der Waals attractions.
If we are to understand water as a solvent, we will have to venture beyond "like dissolves like" with some more careful analysis. If we imagine a process in which initially separated water and solute mix, the thermodynamics are tricky because although water interacts so well with solutes, it interacts with quite well with itself, as may some solutes such as salts. Thus, for the case of an ionic solid that dissolves endothermically, ΔH of the process is not favorable, but ΔS of forming the more dispersed solution is positive (and thus favorable). For solutes with nonpolar character, on the other hand, the interactions between solute molecules in the undissolved initial state and between solute molecules and water molecules in the dissolved state are both considerably weaker. Yet it is still possible for the solute-solvent interactions to be a little better than the interactions in the separated materials. ΔH of the process is then slightly negative, even so, the solubility may still be quite low, indicating that ΔG is positive. We would be led in this case to the counterintuitive conclusion that ΔS is negative. This large negative ΔS for the formation of aqueous solutions of nonpolar solutes is the basis of the what is usually called the hydrophobic effect.
Noncovalent forces that determine macromolecular structure
One of the major themes of biochemistry is how biomolecular structure determines function. Of course we must know the covalent structure of the molecules of life, but the functional implications depend on a detailed picture of the conformations adopted by these molecules. Because of the sheer size of biological macromolecules, an astronomical number of conformations are possible in principle. That molecules such as proteins and nucleic acids in fact assume a unique structure, or a very restricted range of conformations, has something to do with the relationship between a particular conformation and the energy associated with it. A knowledge of noncovalent forces is essential to an understanding of biomolecular structure, since these determine the energetics of conformations and the interactions between molecules in defined conformational states. There are several kinds of forces that play predominant roles in defining the energetic landscape that specifies biomolecular structure: electrostatic interactions, van der Waals forces, and hydrogen bonds. These can be thought of as contributing to enthalpy in processes such as protien folding and formation of complementary double-stranded DNA from the separated single strands. In addition, we discuss the hydrophobic effect, which arises as a result of entropic contributions of water solvation of nonpolar surface area.
Chemical properties of water: Acid-base chemistry
Autoionization of water and pH. Acids, bases, and buffers in aqueous systems.