Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 328

Brief Organic Chemistry

Summer 2004

Lecture Notes: 8 July

© R. Paselk 2004



Memorize the Fischer structures for D-glyceraldehyde (an aldotriose), dihydroxyacetone (a ketotriose), D-glucose (an aldohexose) and D-ribose (an aldopentose). If you look you will see that once you've memorized glucose fructose is very simple.

We also introduce a new representation with the carbohydrates - the Haworth projection. In the Haworth projection the sugar ring is represented as a flat polygon, commonly a pentagon or a hexagon, instead of in proper geometrical conformation like a chair. The advantages of the Haworth projection are that it is easy to draw, and it is very easy to see whether substituent groups on the ring are on the "top" or the "bottom" of the ring (cis or trans).

We use the Haworth projection because most of the time sugars exist as rings rather than open. Why should this be the case? Look at the chemistry possible with sugars. First we have a carbonyl group with an electrophilic carbon. Then, on the same molecule we have nucleophilic hydroxyl groups. Not only that, but the hydroxyl groups are situated such that the natural conformations of the chain will bring the hydroxyl group into an ideal position for attacking the carbonyl carbon.

Thus pentose and hexose sugars generally exist as rings sealed up with hemiacetal linkages:

Note that the ring formation also resulted in the formation of another chiral center, which is designated as alpha (pointing down in a Haworth projection) of beta (pointing up in Haworth projections):

Both represent D-sugars since the methoxy group on the #5 C is pointing up in the Haworth projection (in L isomers it would point down).

Of course as we saw with aldehydes the hemiacetal can react with another alcohol to give an acetal. This is seen in the formation of disaccharides and polysaccharides from individual sugar residues:


Again we see that two disaccharides are possible, one with an alpha linkage the other with a beta linkage. It turns out that the beta linkage is more stable, for example it is more difficult to hydrolyze. But more importantly in biological systems beta glycosidic bonds are generally very difficult to breakdown, they require special enzymes. Thus for glucose based polymers those involving beta linkages are used for structure (e.g. cellulose) and cannot be digested (broken down) by most organisms. On the other hand glucose polymers involving alpha linkages are easily digested and are used for food storage (e.g. starch). There is much biology involved in these differences.


Amino Acids and Peptides

Amino acids: Want to look at the 20 amino acids used to make proteins. There are other amino acids found in proteins, but they arise by modification after the protein is made on the ribosome. All of these amino acids are alpha amino acids (2-amino carboxylic acids):

The problem with this structure is that we have an amino group, which is a base, and an acid group. They cannot exist together in unionized forms, but rather will react with each other. Thus at neutral pH we see a doubly ionized form, the so called zwitterion structure:

At lo pH only the amino group will be charged, while at high pH only the acid group will be charged:

Note that for any amino acid there will be a pH at which the average charge on the amino acid will be zero. This pH is call the isoelectric point (pI), because the amino acid will not migrate in an electric field at its pI. On the other hand at low pH an amino acid will migrate to the cathode (-) while at high pH it will migrate to the anode (+).

The simplest alpha-amino acid is glycine, with H as its R-group:

The next simplest amino acid is alanine, with a methyl group as its side chain:

You should memorize the structure of glycine. Most of the other 18 amino acids can be considered to be derivatives of alanine. Looking at the side chains only (after all in a protein the only difference among the amino acids will be the side chains), we can divide them into non-polar groups with low solubility in water, and polar groups with high solubility in water. (Glycine is special, since the hydrogen should have little effect one way or the other.) When protein chains (chains of amino acid residues) fold up they tend to fold such that the non-polar side chains end up inside, while the polar groups end up outside. The resulting globule is thus reminiscent of the micelles we saw earlier when we looked at fatty acids and micelles.

When you look at alanine you should notice that it will have stereoisomers, that is it is chiral. Once again nature chose to use a single chirality, this time L - all of the 19 chiral amino acids are L.

Peptides: Amino acids can be linked with amide bonds, referred to as peptide bonds when they are in peptides or proteins:

Note that the elements of water have been removed, thus we would not expect the bond to be terribly stable in aqueous solution. Very long chains of amino acids can be linked together in this way to give proteins, the largest of which have over a thousand amino acid residues linked by peptide bonds. In any peptide or protein is is conventional to write it out such that the amino terminus (the N terminus) is on the left end, while the carboxylic acid group (the C terminus) is on the right end.

Another important covalent bond in proteins which are exported into the "harsh" outside world (outside of the cell) is the disulfide bond. This is a bond which can form between the sulfhydral side chains of two cysteine residues:

The resultant cross linkage between different parts of the chain helps to maintain the overall globular shape of the protein under extracellular conditions.


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Last modified 8 July 2004