Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 31 January

© R. Paselk 2006


Amino Acids 2

Lets now look at the amino acid side chains as shown in the side chain handout in your packet [overheads S 5&6 - 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.
*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.)
Amino Acid Chemistry: All aa's share two chemically functional groups, the carboxyl group and the amino group. Thus they will share the chemical reactions of these groups familiar from organic chemistry. Many of these reactions are exploited in the laboratory manipulation of amino acids, peptides, and proteins. Note that these reactions are also common to the side chains of asp, glu (-COOH), and lys (-NH2). Another side-chain with important chemistry is cys (-SH). Biologically the most important reactions are those required for protein formation, particularly the peptide bond.
pKa's: Note that the pKa's for carboxylic acids tend to have values of about 5, while the pKa of the amino acid -COOH is around 2. What's going on? The shift in pKa can be assigned to the nearby protonated amine. Recall that 'naked' charges are very unstable, while nearby counter-charges stabilize them. Also, from organic chemistry you may recall that negative charges can be stabilized by inductive effects of nearby electron withdrawing groups, such as a protonated, positively charged, nitrogen. Because of the extra intervening carbons the side chain -COOH's of asp and glu are not similarly stabilized, and thus have pKa values closer to the expected 5. Of course we would also expect analogous effects of the negative charge on the carboxyl group on the charged amine.

Pathway Diagrams

C438 Home

Lecture Notes

Last modified 1 February 2007