In this sub-module we explore some concepts and nomenclature from biochemistry. First we discuss three classes of biological chemicals: fats, sugars, and proteins.

Fats

If you took a long saturated hydrocarbon chain, say

we call this a "paraffin," and find it in crude oil. (Actually any alkane can be called a paraffin, but common usage refers to the longer chains.) You can make a candle out of it or eat it, if you are very hungry. If it had a carboxylic acid on one end, we call it a fatty acid.

You may remember that when a carboxylic acid reacts with an alcohol, a ester is formed. There is a type of alcohol, called glycerol, that has three alcohol moieties in one molecule. If a glycerol molecule reacts with one fatty acid, it forms a mono-glyceride, if that reacts with a second fatty acid, you get a diglyceride, and if that reacts with a third fatty acid you get a . That's plain old fat. The hydrocarbon end of the fatty acid might be saturated, as in the sketches above, or unsaturated, meaning there are some carbon-carbon double bonds in the chain. If you're into health food, you know all about those double bonds and how fish oil (which is fish fat) has those double bonds in just the right places to guarantee you a long happy life. Here a short video on that topic: https://www.youtube.com/watch?v=HGg_WiaSr4U

Now the term biological lipid includes some compounds that are not fatty acids. Cholesterol is one such lipid.

Also, if you took that diglyceride and reacted the third alcohol with a weak inorganic acid, phosphoric acid, you wind up with a phospholipid. The phosphoric moiety is quite polar, so the resulting molecule has two very non-polar tails and a polar head. These are the "self-assembling" molecules you read about earlier, and if the tails are the right length, they self-assemble into a bi-layer. This lipid bilayer forms the outer membrane of all cells, prokaryotes and eukaryotes, and separates what is alive (inside the cell) from what is not alive (outside the cell).

One way to get fat is to eat too many carbohydrates.

Carbohydrates

 

Amino Acids, Polypeptides, and Proteins

"Amino" indicates an organic base, so isn't "amino acid" a contradiction? Nope. There are 20 or so very important biological molecules that have an amine group on one side and a carboxylic acid on the other.

There are only 20 or so "R" groups that are biologically important. Some of these 20 or so R's are acids, some are bases, some are hydrophobic and some a hydrophilic, a few have a sulfur atom.

The acid end of one amino acid can react with the base end of another and so one, forming a chain of amino acids. The bond between amino acids is called a peptide bond.A short chain is called a polypeptide and a long chain is called a protein. If the cartoon character Microman used his molecular fingers to stretch the protein out in water, you would have a chain of amino acids, probably not more interesting then the telephone lines between utility poles. But if Microman lets the ends go, the protein starts to knot up, like my fishing line just after the trout broke the surface. This knotting or folding arises as the the side groups of the various amino acids in the chain find each other and adjust to the surrounding watery solution. The polar R groups seek to turn that group towards the water, or at least other polar R groups, the hydrophobic R's twist to get away from the water and associate with other non-polar R groups. Sometimes the groups with sulfur form covalent bonds with each other, sometimes the acids and bases react, and so on. In a twinkling, the chain had formed a definite shape with characteristics greater than the sum of its parts.These protein shapes or structures might be a structural protein, a hormone, an enzyme or lots of other useful things for use inside or outside the cell. Here's a good overview. Kahn has a good overview, if you don't go too deeply into the chemical details.

Proteins are usually known by a common name, like "hemoglobin" or "collagen," rather than a chemical name related to their chemical structure, although you could write an IUPAC name for them, if you were really, really bored. Sometimes the proteins or rather polypeptides are shown by a string of three letter abbreviations, like -Phe-Gly-Ala-Cys- which would mean phenylalanine attached to glycine attached to alanine attached to cysteine attached to ......"hemoglobin" is much simpler.

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