Learning Strategies in Biochemistry:
Water and Biomolecules

Revised 2008/05/22

Essential Review or Remedial Work

From Your Full-Year General Chemistry Course

Review equilibrium constant expressions, including K_a expressions for weak acids. Also review pH, pK_a, titration curves, and buffers.

From Your Full-Year Organic Chemistry Course

Review Lewis diagrams, formal charge, and resonance. If you are given a partial or shorthand structure of an organic molecule, you should be able to complete the structure, indicating the location of all multiple bonds and unshared electron pairs, and drawing complete sets of resonance structures where applicable.

Review noncovalent interactions: ionic attraction, hydrogen bonding, attractions between permanent, induced, and momentary dipoles. Look up these terms: van der Waals forces, London dispersion forces.

Essential Memory Work

As you read the assignment for the first time (once is never enough), do your memory work as soon as you encounter the material you need to learn.

Derive the Henderson-Hasselbalch Equation

Learn to derive the Henderson-Hasselbalch equation from the K_a expression for a weak acid. Learning this derivation will help you to understand ionization and its relation to pH. You must call on the Henderson-Hasselbalch equation repeatedly in assessing the ionization state of complex molecules.

Estimating Percent Ionization

Once you have learned to derive the equation, solve it for the ratio ([A^-]/[HA]). This ratio is called the ionization state -- it reflects the extent to which the acid is ionized. Once you solve for this ratio, you will see from that relationship that the unprotonated form of a weak acid/base pair predominates 10-fold for each unit by which the pH exceeds the Pka (there's a mouthful!). Examples will help:

If the pK_a of a weak acid HA (like RCOOH) is 5.0, then A^- (RCOO^-)predominates over HA (RCOOH) by 10-fold at pH 6.0 (one unit higher than the pKa, so 10¹-fold excess), 1000-fold at pH 8.0 (3 units higher, so 10³-fold excess), and so forth. In like manner, the protonated form predominates by 10-fold at pH 4.0, and 1000-fold at pH 2.0. Knowing this rule of thumb makes it easy to estimate the ionization state -- the relative amounts of both forms of a conjugate acid-base pair -- from the pH, if you know the pK_a.

Estimating Net Charge of Many Ionizable Groups

Later on, we'll use this same reasoning to figure out the ionization state and net charge of complex molecules that contain several or many ionizable groups (weakly acidic or basic groups like carboxyl and amino). We'll just figure out the charge on the predominant form of each ionizable group at the pH of interest (you'll need a table of pK_a values), and then add up the individual charges to get the net charge on the complex molecule.

In biological systems, we always assume that the strongly buffered medium--cytosol, blood, or [eeww!] urine) controls the pH and thus determines the ionization state of functional groups on biomolecules. In blood, this buffer system is mostly carbonic acid/carbonate, and it may be primarily phosphates in the cytosol.

Quiz

Derive the Henderson-Hasselbalch equation from the acidity constant expression for the dissociation of a simple monoprotic acid: HA <==> H⁺ + A^- . Show all steps in your derivation. Especially, make it clear that you know how to apply the properties of logarithms and the definitions of pH and pK in this derivation.

At class time, you'll want to know this derivation cold. Come to class prepared to write out the derivation in no more than 5 minutes.

Biochemistry Resources