Humboldt State University ® Department of Chemistry

Richard A. Paselk

VUB Biology

Fall 2001

Lecture Notes:: 19 September

© R. Paselk 2001

Introduction to Chemistry, cont.

The Nature of Organic Compounds
Functional Groups: One of the cool things about organic (carbon) chemistry is that, although there are over 10 million known and characterized organic molecules and an uncounted number of possible organic molecules, the chemistry of all of these molecules is determined by a fairly small number of functional groups. A functional group is a portion of a molecule which reacts in a particular way. The marvelous thing about them is that their chemistry is largely independent of what else is on the same molecule! Thus an -OH group will react pretty much the same whether it is attached to a single -CH3 group or a carbon chain which has thousands of atoms in it. In Table 4.1 on p 54 of your text the most common organic functional groups in biology are shown with examples. More broadly we can organize functional groups by similarity of chemistry (most common in biology are bolded):
Note that nomenclature is also largely based on these Functional groups. As a general rule the most highly oxidized carbon will take precedence in naming. Thus, as we shall see later, a compound with both an acid group and an alcohol group will be named as an acid, etc. Of course with as complex a system as organic chemistry there will be violations to this general rule.


Biomolecules can be looked at in two major categories: small molecules and macromolecules. The small molecules are going to be either metabolites or monomers from which the macromolecules are built.


Small Molecules and Monomers

There are a few critically important small molecular precursors to biomolecules found in the environment: oxygen (O2), water (H2O), carbon dioxide (CO2) ammonia or ammonium ion (NH3 or NH4+), nitrate ion (NO3-, and nitrogen (N2).

These molecules and atoms in turn can be made into metabolites, small organic molecules used in energy transformation and as precursors to monomers and macromolecules.

Right now we'll focus on the monomers and the associated macromolecules. There are four major categories or families based on functional groups or, for lipids, physical properties:

1. the Nitrogenous Bases (purines and pyrimidines) which are components of the nucleic acids (RNA and DNA-used for information storage and processing). The basic nitrogenous rings used to make the various nucleotides (Fig 5.27, p 78) are shown below:

Both purines and pyrimidines are linked to a sugar, ribose or deoxyribose, and phosphate in their active, nucleotide, forms, as in ATP, below:

2. the Amino Acids which are components of the proteins (proteins comprise the machinery of life [enzymes] and much of the structure of life-these are the molecules that do things)

A chart showing the structures of the "R-groups" of the 20 amino acids used to make proteins (Fig 5.15, p 69) can be seen by following this link (use the back button of your browser to return).

3. the Sugars (carbohydrates) which are components of the polysaccharides (together comprising the carbohydrates, which are used for energy storage and structure). Glucose, the most common sugar is shown in a cyclic form. Note that a sugar must have an aldehyde or ketone and two or more alcohol functional groups by definition. (Fig 5.3 & 5.4, pp 60-1)

4. the Lipids (fats) This is a diverse family charecterized by a physical property: solubility in organic solvents.

The most common lipids are the fatty acids which, together with glycerol, make up the common fats of nutrition (used mostly for energy storage) and the phospholipids (the major component of cell membranes). The 16 carbon fatty acid palmitate is shown below (Fig 5.10a, p 65):

A typical phospholipid is shown here (Fig 5.12, p 67), replacement of the phosphate ester group with a third fatty acid would give a fat instead (Fig 5.10b, p 65):


The amino acids, nucleotides, and sugars can all be polymerized to give the macromolecules characteristic of life: proteins, nucleic acids, and polysaccharides, respectively. We will come back to each of these macromolecules in our study, focusing particularly on proteins. Briefly, proteins comprise the machinery and much of the structure of life; nucleic acids provide the information required to specify the proteins, and polysaccharides provide structural fibers and energy storage molecules.

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