School of Traditional Western Herbalism: Organic Chemistry Basics sp 2010
Organic molecules are carbon based molecules produced by living organism, in this case, plants.
Where it all starts
Specialized organs in plant cells called chloroplasts use the energy of sunlight to combine water with
CO2 to form a glucose molecule and the waste product of O2. The glucose is broken down in a series of
biochemical pathways called glycolosis. From this humble beginning emerges the immense array of
organic molecules present in plants.
Valence;
The carbon atom, in order to remain stable needs to be bonded in 4 sites. This is the fundamental
organization of life. It can bond to another atom or have multiple bonds with another atom as long as in
total it is connected in 4 ways. Electrons like to be in pairs. Every element has a certain amount of
electrons traveling around its nucleus in different levels, some even, some not. When those levels
contain unpaired electrons that element actively seeks a way to balance the situation either by giving it
away, stealing one or sharing it. Each of these different arrangements create the bonds between atoms.
Elements each have their own bonding requirements to remain stable, this is defined as their valence
and has to do with the number of unpaired electrons available to interact with other elements. For
example Carbon has 4, Nitrogen 3, Oxygen 2 and Hydrogen 1. A carbon is most stable connected to 4
hydrogen atoms. Hydrogens just need one connection. Replacement of any of those hydrogen atoms on
a carbon with something else is the basis of organic chemistry.
Bonding;
A bond is formed when atoms share an electron in a way that makes them both stable. There are
several different kinds of bonds but in organic chemistry we mainly see covalent bonds which is when
the electrons are equally shared between the atoms. Bonds can be single, double or triple. Each bond
has its own level of stability and reactivity. The more multiple the bond is the less stable and the more
easily it can be persuaded to uncouple and join in a bond that promises more stability. Saturated bonds
are happy stable carbons locked into their 4 bonded relationships. In unsaturated bonds the hydrogens
have been replaced with multiple bonds which leave the carbons less fulfilled and interested in looking
for a more stable relationship.
Geometry
Organic molecules are basically chains of carbon atoms. Complexity builds based on what the carbons
are connected to. They can form chains, acyclic or in rings or a combination of chain and ring called ,
heterocyclic.
Benzene rings are an exception to the reactivity of unsaturated molecules. A benzene ring is a 6 carbon
ring with 3 double bonds. Normally this unsaturated molecule would be willing to react and join other
molecules but the ring structure allows enough sharing between all the molecules that the complete
unit is extremely stable and unchanging. That said the double bonded carbons can be persuaded to
attach to other fancy groups which we call functional groups.
Sharon Woodard ND sp2010
School of Traditional Western Herbalism: Organic Chemistry Basics sp 2010
Functional groups
What differentiates different organic molecules is the fancy accessories they each sport in the form of
different groups of atoms replacing hydrogen atoms on the molecule.
Alcohol; OH attached to either a carbon at the end of the chain or any carbon on a ring.
Ketone:
Aldehyde:
Carboxyl group:
methyl:
Amine:
How it all gets complicated:
Isomerism
Molecules are 3 dimensional shapes allowing the same chemical formula to be arranged in different
shapes. These different shapes can react to other molecules in different ways because areas willing to
bond could be available or not depending on the shape of the molecules. Thus molecules with the same
formula could lead very different lives.
Structural isomers; same formula but the multiple bonds or elements are in different areas
Positional isomers; the functional groups are in different places
Stereoisomers: same bonds or functional groups but they are positioned differently
Geometric ; different placing on the sides of the double bonds. This is important in unsaturated
fats. The placement of the functional groups can determine the difference between a
healthy unsaturated fat and a dangerous trans fat.
Sharon Woodard ND sp2010
School of Traditional Western Herbalism: Organic Chemistry Basics sp 2010
Enantiomers: isomers that are mirror images of each other. They look the same but can’t be
superimposed on each other in the way that the right hand is not the same as the left hand.
This shows up in the effect of essential oils on the olfactory lobes. Enantiomers can smell
completely different because they attach to completely different configured receptors.
Diastereomers; stereo isomers that don’t have a mirror because they are more complicated and
have multiple centers that could be different. Examples are maleic acid and fumaric acid.
Fumaric acid
Sharon Woodard ND sp2010
maliec acid