Introduction to the Principles of Chemistry


Plant metabolism, like that of all organisms, is based on the fundamental principles of physics and chemistry that govern inanimate matter.

All living creatures:

  • grow
  • respond to stimuli
  • reproduce


The bodies of plants and other organisms are made of atoms drawn from the:

  • soil
  • air
  • water

The energy that drives their metabolism is produced by ordinary chemical reactions.



  • Atoms & Molecules




  • Chemical Bonds



The lightest, hydrogen (H), has only one proton.

The heaviest, uranium (U), has 92 protons.

Atomic nuclei also contain neutrons in numbers roughly equal to protons:


  • Neutrons 
  • Electrons
    • Noble gasses




Chlorine, however, even when it is electrically neutral with 17 electrons matching its 17 protons, is not stable.


In plants and animals, chlorine almost always has an extra electron, making it the chloride ion Cl-.

An atom or molecule that carries a charge is an ion.

A negative ion is an anion.





Sodium is just the opposite.

When electrically neutral, it has one electron in an orbital by itself.


A positive ion is a cation.


  • Electronegativity

The element with the greatest affinity for electrons, fluorine, has an electronegativity of 4.0.

Noble gasses, with no affinity for extra electrons, have electronegativities of 0.0.

Only electrons in the highest, partially filled energy level, called valence electrons*, are involved.

They are responsible for forming chemical bonds.




Imagine a reaction between an atom with low electronegativity, such as sodium and one with high electronegativity, such as chlorine.

Both elements become more stable by the transfer of a valence electron from sodium to chlorine (see figure, below).



* Khan Academy video on electron orbitals:






Another exergonic reaction is the burning of hydrogen with oxygen.

Two hydrogen atoms transfer one electron each to an oxygen atom, resulting in water:

2H + O2 H2O + energy






Another endergonic reaction is the formation of carbohydrates in leaves during photosynthesis.

The exergonic reactions for this are thermonuclear reactions in the sun.



Sodium/Chlorine Reaction:



A bond in which electrons are shared is described as a covalent bond.

Whether an ionic bond or a covalent bond forms depends to a large degree on the difference in electronegativities of the two reactants.





  • Water

polar molecule with a slightly negative end and slightly positive end.




  • Hydrogen Bonding

When two water molecules come close to each other, the positive charge from one slightly attracts the negative charge of the other

It's not nearly enough force to pull electrons from one to the other, but is sufficient to cause them to adhere slightly.



The force causes water to:

  • water is sticky and viscous.
  • water absorbs a great deal of energy without warming rapidly.
  • water requires a large amount of energy to convert from a liquid to a gas.


Nonpolar substances move easily past each other and flow with little viscosity.

Examples are methane, and acetylene.







  • Water Solubility & Lipid Solubility

When a polar material like ordinary table salt is placed in water, the formation between negative and positive ends and the ions have weak bonds.



water soluble.

When a nonpolar substance, which can not form hydrogen bonds, is placed in water, no interaction occurs between the two types of molecules.

The substance does not dissolve.


If a molecule of the substance diffuses into the water, it disrupts the water's own hydrogen bonds .

This would be an energy-consuming, endergonic reaction that destabilizes the water.



If the molecule diffuses out of the water, the water molecules can form new hydrogen bonds and release energy, becoming more stable.

If the substance is placed in water and agitated,, it may mix temporarily, but gradually separates.

Oil in water is an example.





  • Acids & Bases


acidity of a solution.





A base is anything that decreases the concentration of free protons.

This is usually accomplished by giving off hydroxyl (OH-) ions that combine with protons and form water.

This effectively removes free protons.

NaOH breaks down into Na+ and OH-.

The OH- indicates that it is a base.