Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431	Biochemistry	Fall 2008
Lecture Notes: 12 September	© R. Paselk 2008
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pH & Buffers, cont.

• For reactions involving a strong acid or base we can assume, for practical purposes, that all of the strong acid or base added to a mixture will react until the base or acid originally present in solution is completely consumed. (Of course this is an approximation, all reactions actually approach an equilibrium condition, so that, in theory, there is always some reactant and some product present.) For example, if we start with a solution containing 0.100 mole of acetic acid and add 0.050 moles of sodium hydroxide the resulting mixture will contain 0.050 moles acetic acid, 0.050 moles sodium acetate and 0.000 moles sodium hydroxide (actually about 10^-10 moles, which is 0.000 for our thousandths place significant figure calculation).

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 = pK_a + log [A^-]/[HA]

We frequently represent the reaction of an acid with a base as a titration curve [text 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 pK_a. 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: [text Figure 3-9]

At neutral pH (pH =7) both the acid and amine groups will be ionized to give the so-called zwitterion form. [text Figure 3-9] 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. [text Figure 3-10]

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, though RS is often used for "side chains."

Lets now look at the amino acid side chains as shown in the side chain handout in your packet [Models] Can group the side chains as nonpolar (hydrophobic or water hating) and polar (hydrophilic or water loving).

Hydrophobicity is a measure of relative solubilities of substances in water. Turns out to be the quantitatively most important weak force in biological systems. Often see term "hydrophobic bond" but really isn't a bond since force arises by exclusion from water - thus no attraction, as seen in bonds, takes place. Hydrophobic force has two components: 1) enthalpic (heat energy) due to the breaking of hydrogen bonds and dipole-dipole bonds etc. when nonpolar substances are inserted into water and disrupt its structure; 2) entropy due to the relative loss of mobility of water molecules forced into "cage" structures surrounding nonpolar molecules or groups inserted into water, as seen in our last lecture.

• Nonpolar side chains [text Figure 3-5 part 1, 2]: these will tend to be found on interior of protein, except that glycine and alanine are so small that they can fit into interior or on surface. Compare these amino acids: note how these side chains build in size from gly (glycine), ala (alanine), val (valine), to leu (leucine), then have two which have about same size but different shapes: ile (isoleucine) and met (methionine - met has a nearly identical shape to the linear analogue of leucine, norleucine). Met of course also has possibility of liganding metal ions through sulfur. Next have phe (phenylalanine) and trp (tryptophan). These are aromatic, which enables stacking interactions with other aromatic groups as well as being very hydrophobic. Trp also has an amine group which needs to form a hydrogen bond. Thus trp is often found with the -NH at the surface but with the remainder in a hydrophobic cleft. If trp is interior it will generally hydrogen bond with another functional group. Finally pro (proline) is also hydrophobic, but its main characteristic of interest is its tendency to put a near right angle in the direction of a peptide chain. It thus generally disrupts particular structural elements of proteins. As such it is often near the surface, since it forces structural elements to turn at the surface (defining the surface).*

*Just for your interest: You can briefly look at hydrophobicities of the nonpolar amino acids quantitatively by comparing their solubilities to glycine in a relatively "nonpolar solvent" such as ethanol or dioxane [values from Alan G. Marshall Biophysical Chemistry, Wiley (1978) pp 64-5]. The values in parenthesis are in cal/mole @ 25°C: Ala (-500), His (-500, uncharged), Met (-1300), Val (-1500), Leu (-1800), Tyr (-2300), Phe (-2500), Trp (-3400), and for comparison, Ser (+300). Plotting accessible surface area vs. hydrophobicity one finds that the hydrophobicities of the amino acid residues in proteins turn out to be about -2500 cal/mole/nm2 of accessible surface.)

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Last modified 12 September 2008