Learning Strategies in Biochemistry:
Amino Acids

Revised 2008/05/22

Essential Review

From Organic Chemistry

If you are not familiar with the following topics, look them up in the index of your organic chemistry text, and review them thoroughly:

Amines: structure and ionization
Carboxylic acids: structure and ionization
Amides: structure, synthesis, and hydrolysis

Essential Memory Work: The 20 Amino Acids

Click HERE for a handy table with all amino acid structures in one place.

Sorry, but there's no way around it: if you are going to be able to read and retain any material in biochemistry, you'll just have to memorize the structures of those 20 amino acids, along with their 3-letter abbreviations. This is essential vocabulary in biochemistry, like learning to conjugate the verb to be in a foreign language. And while you're at it, you'd better memorize the ionization states of all ionizable groups at pH's above and below their pKa's: the groups you need to know are the alpha amino and alpha carboxyl groups, and the side chains of arginine, histidine, lysine, aspartic acid, glutamic acid, cysteine, and tyrosine. These are the only amino acids whose side chains ionize near physiological pH. Each group will exist predominantly in its protonated state if the pH is lower than the pKa of the group, and predominantly in the unprotonated state when the pH is higher than the pKa of the group.

Carry out this memory work BEFORE you try to read the chapter. Most texts provide a table of the amino-acid structures, and another table of the ionizable groups, showing their structures and charges when protonated and unprotonated. To make you work easier, first memorize the general structure of an alpha amino acid, then memorize all the side chains as they exist at pH 7, and finally, memorize how the ionizable groups (listed in boldface above) change as the pH changes. Then begin studying the chapter.

The authors of your text, and your instructor as well, will quickly start treating you like a biochemist, which means that they will use the names of amino acids freely, and will assume that you translate names into structures automatically. Refresh you memory on the structures regularly, especially before each exam. There's nothing more frustrating than not being able to get started on a ten-point exam problem simply because you can't come up with the structure of an amino acid.


(At beginning of first class on this topic)

1. Draw the complete structure of the two amino acids whose 3-letter abbreviations are given on the board. Draw each in the ionization state that predominates at pH 7.

2. One of these two amino acids possesses an ionizable side chain with a pKa value between 3 and 10. Draw the complete structure of its side chain at pH 2.0. Then draw the complete structure of the side chain at pH 12.0.


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