Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2010

Lecture Notes: 5 February

© 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.)

Pathway Diagrams

C438 Home

Lecture Notes

Last modified 5 February 2010