Richard David Feinman

The themes in my blog are the scientific issues in nutrition, how to interpret data in the literature and my take on policy issues like taxing fat and taxing sugar.  The most important thing, though, is the basic science because you really can’t understand nutrition without biochemistry and you really can’t do biochemistry without organic chemistry. Organic chemistry refers to the chemistry of carbon compounds. The term once referred to the chemistry of living organisms but now would includes polyethylene as much as fructose and, in the extreme case, the plastic bottles made from corn. I am going to try to present the science and I will start from scratch and make it very elementary. My experience is that chemists don’t mind very elementary — at professional seminars, it is the Nobel prize winner who asks the really simple question (because he doesn’t care what you think of him, he just wants to know the answer). I am interested in reader feedback as to whether this is what you want to know and if this and subsequent blogs help.

The good news is that, contrary to the college myth, organic chemistry is easy.  It is freshman chemistry that is hard (because it depends more on physical chemistry, that is, physics), so I think I can get you up to speed on biochemistry and nutrition pretty fast. I am duplicating some of the material on my YouTube presentation but people told me that that is not always the best format.  So, organic chemistry is easy. That’s the first thing.

The second thing is that chemistry is  structural, that is, visual and what a chemist sees in chemical formulas is visual objects.  I am going to show what a chemist is thinking about in dealing with chemical formulas.  It’s graphic, so I will try to use as few words as possible. Comments on the figures at the end of the post.

 

Start with H₂O

What a chemist sees in the formula H₂O is a diagram, or structural formula. What a chemist thinks of when they see that diagram is the ball and stick model  or maybe the so-called space-filling model which is supposed to be closer to what you would see if it weren’t that molecules of water  are too small to be seen.

Methane is the simplest organic compound – The formula is CH₄ – carbon always forms 4 chemical bonds. Different views of methane below. Methane is a colorless, odorless gas, the major component of natural gas (the odor of cooking gas comes from an added compound as a safety warning). Various representations below. (The wedge (coming out of the paper) and dotted line (behind the plane of the paper) is a shorthand representation of the 3D structure

Carbon Forms bonds with Other Carbons and Carbon Atoms Can Form Chains – Think of two methane molecules tied together by replacing one of the carbon-hydrogen bonds in each with a carbon-carbon chemical bond.  The two carbon compound (C₂H₆) is called ethane. We can, similarly build up chains of carbon atoms. which will be the skeletons on which millions of organic compounds will be constructed.  Carbon always forms four chemical bonds.  A compound that has only carbon and hydrogen is called a hydrocarbon.  The series built up from ethane are called saturated hydrocarbons (other name: alkanes) meaning that they have as many hydrogens as possible.

There is a Family of Organic Compounds – everything is organized as if it came from the chain of carbons known as saturated hydrocarbons.  (IUPAC is the International Union of Pure and Applied Chemists who standardizes chemical names).  Propane is a gas but it can be compressed into a liquid and is used as a fuel for various kinds of engines or for barbecues or welding torches. The higher hydrocarbons are fuels; you recognize the name octane as a component of gasoline which is a mixture of the higher saturated hydrocarbons. Much larger hydrocarbons are the major constituent in industrial and motor oils. The first ten hydrocarbons are shown in this table:

 

STOP.  Are you with me so far? If so, you should commit to memory the names of the ten hydrocarbons.  Everything else depends on this.  Most organic compounds are given names based on this system.

The Secret of Organic Chemistry: Functional Groups

Organic compounds have two parts: a hydrocarbon backbone and a functional group, the non-hydrocarbon part that contains the chemically reactive part of the molecule, the functional groups. The assumption is that all compounds with the same functional group have similar chemistry. The millions of organic compounds are grouped into classes: alcohols, aldehydes, acids, sugars, amino acids, etc. based on which functional groups they contain. It’s easiest to understand by example.  Look at the alcohols.

What Alcohols Look Like

Start with the simplest functional group. The combination of oxygen and hydrogen as a functional group is called hydroxyl.  Any compound that has an hydroxyl group is called an alcohol.  The common term “alcohol” refers to ethanol, one specific type of chemical alcohol.  The simplest series of alcohols are those derived from the saturated hydrocarbons.  If the hydroxyl group is added at the end of the chain, the compound is called a primary alcohol.  To name such compounds, you count the number of carbons, use the name from the hydrocarbon, e.g., ethane and remove the “-e” at the end and add “-ol.”   The figure below shows you that no matter how complicated the hydrocarbon backbone, if there is an OH group, the compound is an alcohol.  Cholesterol is an alcohol (you can figure out that if you know that a structure has only CH groups, they can be indicated just with the geometry without writing the symbols, each vertex in the figure representing one carbon atom).

Next chemistry post:

Aldehydes, sugars and sugar alcohols.

Do I get it?  Answers in the comments.

1. Can you write the structural formula for octanol?
2. When there is more than one hydroxyl group, the number of groups may be indicated by “di-, tri-” etc. The common compound glycerol would be called propane triol.  What does it look like?