Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2010

Lecture Notes: 3 February

© R. Paselk 2006


Water, cont.

Ionization of Water, pH & Buffers

Dissociation of water molecules: One aspect of water we have yet to talk about is its dissociation or ionization. In normal aqueous solution there is a certain probability that a hydrogen nucleus (a proton) can exchange between two hydrogen bonded molecules:

(Of course the hydronium ion, H3O+, will be associated with additional water molecules as well through H-bonding. For simplicity we will just write H+, with the understanding that it refers in fact to hydrated hydronium ions in aqueous solution. ) Note the reaction is not highly favored, in neutral solution (no excess H+or OH-) there will only be 10-7 molar hydronium ions, in other words only about 2 of every billion water molecules will be protonated!

For aqueous solution [H+][OH-]= 10-14;

Brönsted acid: we will be using the Brönsted definition for acids and bases:

pH & Buffers

The strengths (ability to donate protons) of acids vary considerably.

The equilibrium equation for a mixture of a weak acid and its conjugate base can be rewritten by taking logs of both sides and rearranging to give the Henderson-Hasselbalch equation: pH = pKa + log [A-]/[HA]

We frequently represent the reaction of an acid with a base as a titration curve (Fig. 2.16). You should understand these curves and be able to label them for axis, percent dissociation at beginning, middle and end, buffer region, end-point, and how to find pKa. An exercise to help you to review titrations curves is available.

Amino Acids 1

The amino acids are the building blocks for proteins - nearly all proteins studied are made from the twenty "standard" amino acids we will look at now. Other amino acids are also found in proteins, but most arise by modification from the twenty after they have been incorporated in the protein. All of the standard amino acids are alpha amino acids (except for proline, an imino acid). That is they have an amino group alpha to the carboxyl group (they are 2-amino acids). Thus all 20 of these amino acids share the basic structure below: [Figure 3.1]

Fischer and wedge structural diagrams of amino acids

At neutral pH (pH =7) both the acid and amine groups will be ionized to give the so-called zwitterion form. [Figure 3.1] Note that there is no pH at which the amino acid structure will have no ionized groups! Note the titration behavior of amino acids, and be able to draw the structure for an amino acid at each point in the curve. [Fig. 3.6]

With four different substituents on the central (alpha) carbon all of the amino acids except one, where R = H, will be chiral. All chiral protein amino acids are "L" as shown in the figure. (Recall the Fischer structure convention for drawing chiral molecules.) Most, but not all of the 20 amino acids are also "S." But since not all amino acids are the same configuration in the RS system, but still have the same relationships of the R- group, carboxyl group and amino group the DL system is used more frequently by biochemists.

Pathway Diagrams

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Lecture Notes

Last modified 3 February 2010