ORGANIC CHEMISTRY REVIEW

by Frank Deis


It is apparent that many of the students who take Biochemistry have done a good job of totally extirpating all memory of their two semesters of organic chemistry. Also, a few people take Organic as a co-requisite, so it should be helpful to state what you need to know from Organic for this course. It is not necessary to know any of the "named" reactions except perhaps the Aldol Condensation, but a large proportion of the students did not know the structure of formic acid or ethyl acetate when not covered in class. This sheet is an attempt to lay out the basics of organic chemistry which I will assume that everyone knows.

Alkyl Groups:methyl, ethyl, propyl, butyl, pentyl, hexyl

Acyl Groups:formic, acetic, propionic, butyric, pentanoic

Dibasic Acids:oxalic, malonic, succinic, glutaric

Functional Groups:ether, amide, ester, anhydride, ketal, acetal, 
hemiacetal, hemiketal

If you can draw a simple version of each of the functional and connecting groups, and have some understanding of its properties, then the more complex compounds found in the study of biochemistry will be easy for you. For example, if you know what an ester is well enough to be able to draw ethyl acetate, then you can draw a wax like stearyl palmitate simply by adding carbons to both ends. Likewise, if you understand that glycerol is a triple alcohol which can esterify with three fatty acids, you should have no trouble understanding the structure of fats or membrane phosphatidyl lipids.

Starch is a very large molecule held together by acetal linkages (related to ether). Proteins are held together by amide linkages (known in context as peptide bonds). If you bear in mind that phosphate is really an acid, phosphoric acid, then it is easy to see that DNA and RNA are held together by ester linkages, just as fats and waxes are.

Anhydrides are easily hydrolyzed, which is to say that they have a large negative free energy of hydrolysis. Anhydrides are stable enough that most can be bottled and sold by chemical companies with a reasonable shelf life, but in the cell they are used mainly as energy storage forms like ATP, Adenosine triphosphate. ATP has phosphate-phosphate anhydrides, and other high energy compounds like 1,3 BPG have mixed (carboxy phosphate) anhydrides.

The mistake students make most often in drawing amides is forgetting to subtract the H and OH necessary to form water when the compound is made.