General Biology Notes

Chapter 2: Basic Chemistry and Chemical Bonds


All matter is composed of substances called atoms.


Atom: Pure matter that cannot be broken down or changed into simpler substances.




The composition of an atom includes three subatomic particles: protons, neutrons, and electrons.




Element: A pure substance that consists entirely of one type of atom that cannot be broken down or changed into simpler substances.


100 Elements occur naturally but only about 24 are commonly found in living organisms.

The most important elements that compose the majority of living cells are:

*Carbon = C                    *Oxygen = O

 Hydrogen = H                 Phosphorus = P

*Nitrogen = N                  *Sulfur = S


Others elements that exist in living cells are:

Potassium = K               Chloride = Cl

Sodium = Na                  Iron = Fe

Calcium = Ca                 Zinc = Zn






Electrons are found in energy levels or electron clouds outside the nucleus of the atom.  They are in constant motion. 

·      Each energy level has a limited capacity of electrons that it can hold.   

·      The electrons will always fill the energy levels closest to the nucleus first.

·      Electrons like to be in pairs.

·      The outside energy level is called the valence level or shell.

·      The Octet Rule says the valence level cannot have more than 8 electrons (e-).

·      An energy level is stable if an energy level is full.

·      The first energy level is stable with 2 e-, all other energy levels are stable with 8 e-.


Chemical Compounds:


A chemical compound is a substance formed by the chemical combination of two or more elements.


Compounds are held together by chemical bonds. Chemical bonds are the result of atoms trying to fill their valence level and become stable.


There are 2 basic types of chemical bonds:

1.    Ionic Bonding: One or more electrons are transferred from one atom to another.
Ex. Sodium Chloride (NaCl) = Salt


Na has one valence e-.  To be stable it needs to lose one e- so the outer energy level disappears and the next energy level has 8 e-.  Cl needs to gain one e- to be stable since is already has 7.  This transfer of e- will give Sodium a (+) charge and the Chlorine a (-) charge.  This bond makes both atoms stable.

·      When atoms become charged they are then called ions.

·      The attraction between the opposite ions (charges) holds the ionic bond together.

·      This bond is strongest only if it is in a non-aqueous environment.  The body however is mainly composed of water so it is rare that ionic bonds are strong inside organisms.


2.    Covalent Bonding: Electrons are shared between atoms.

·      Single covalent bond: two electrons are shared.  Ex.     Methane CH4         









·      Double covalent bond: four electrons are shared.           Ex.                O=C=O




·      Triple covalent bond: six electrons are shared          Ex.          





·      The movement of the shared electrons holds

the covalent bond together.

·      Covalent bonds are not weakened by water so most of the compounds that make up organisms are held together by covalent bonds.

·      The term molecule refers to atoms that are joined together by covalent bonds.

Ex.  A Water Molecule 


Water is a polar molecule.  This is an extremely important property of water.


Polarity: A molecule in which the charges (electrons) are unevenly distributed causing the molecule to have poles.  


Why is water a polar molecule?

Water is a polar molecule because

       O contains 8 p+ in its nucleus and therefore has a much stronger attraction for e- .

       H contains a single p+ in its nucleus so e- spend less time around H.



This unequal distribution of charge causes the oxygen end to become slightly negatively charged and the hydrogen ends to become slightly positively charged.

How is water unique?

Hydrogen Bonding: water molecules are attracted to each other forming multiple hydrogen bonds between the oxygen of one water molecule and the hydrogen of another water molecule. 


Water’s polarity gives it the ability to dissolve both ionic compounds and other 

polar molecules.


Water dissolves ionic compounds by causing the ions (charged atoms) to break away and water surrounds them. 
The breaking apart is called dissociation.
The loose ions also allows ionic solutions to conduct electricity.


Solute = Salt  Solvent = Water




Water dissolves other polar molecules because “likes dissolve likes”.

Polar molecules dissolve other polar molecules.
Polar molecules do NOT dissolve non-polar molecules.

The slightly negative end of a water molecule is attracted to the slightly positive end of another polar molecule and vice versa.

Solute = Sugar     Solvent = Water


Chemical Formula = shows the types of atoms and how many of each atom but does not show how the atoms are bonded. 

EX: H2O or C6H12O6




Structural Formula = shows the types of atoms and how many of each atom but also shows how the atoms are bonded and whether the bonds are single, double or triple covalent bonds.