Basic Chemistry

Part I


Atomic Structure


The universe from stars to humans is made of matter composed of various elements. There are about 110 known elements, but only 90 are found on the surface of the earth. The unit of structure of an element is the atom.

All atoms (except hydrogen's) are composed of 3 subatomic particles; protons, electrons, and neutrons (the most common isotope of hydrogen lacks neutrons).


Click on the letters in the diagram of a nitrogen atom to see which subatomic particle it represents (hint, count the electrons). To learn more about protons, neutrons and electrons follow this link to see the structure of an atom of neon

Each element is made of similar atoms, all having the same number of protons in a relatively massive central core called the nucleus. The element carbon will always have 6 protons. If one of these protons could be removed then the element's properties change dramatically to reflect the new element, nitrogen, which has 5 protons in its nucleus.

Of the 90 or so elements found on the earth six make up 99% of living matter? These are oxygen, carbon, hydrogen, nitrogen, sulfur, and phosphorus. You should already know their symbols.




Percent of atoms in cells
Role in Living Systems

Constituent of most proteins


Energy Transfers


Redox Reactions, respiration, constituent of nearly all organic molecules


Constituent of proteins and nucleic acids


Backbone of all organic molecules


Part of water and all organic molecules

Study the table "Elements Essential to the Processes of Life." pg.26 in Wallace. You should familiarize yourself with these elements and learn about their roles over the next month. Be prepared to add several more to this list.

Special Project. Learn what you can of the role calcium ions play in biological systems. Start with this article about calcium.

Molecules and Compounds

 A molecule is a unit formed by two or more atoms joined together by covalent bonds (Covalent bonding will be discussed later). The atoms in an molecule may be the same or different elements.

Molecules remain separate particles until a combination of low temperatures and/or high pressures result in the formation of a solid. The weak intermolecular forces between molecules only have enough strength to form bonds when temperatures are low and/or pressures are high. Most small molecules are gases or liquids at normal temperatures and pressure on the surface of the earth.

The following elements are diatomic, that is two atoms of the element combine to share their outer electrons.

  • Hydrogen - H2
  • Fluorine - F2
  • Nitrogen - N2
  • Oxygen - O2
  • Chlorine - Cl2
  • Bromine - Br2
  • Iodine - I2


A molecule of water is also a compound because it is a pure substance in which each molecule contains atoms of two or more different elements in specific proportions. Water has 2 parts hydrogen to one part oxygen.

 Click to see animation of water molecule

The sugar, glucose, is a molecular compound with the following ratio: 1 part carbon to 2 parts hydrogen to 1 part oxygen or CH2O. Sugars are generally known as carbohydrates. Can you see why? Glucose's molecular formula is (CH2O)6 but is normally written C6H12O6.

Click on this structural formula for a sugar molecule for greater detail.




Occasionally you will find among the atoms comprising an element one which has a different mass. This atom is an isotope of that element. Isotopes differ only in the number of neutrons, uncharged particles, interacting with the protons in the nucleus. Thus the vast majority of carbon atoms have 6 protons and 6 neutrons in the nucleus and collectively is called carbon-12 (12 being the atomic mass of this isotope of carbon). But if a neutron is added to the nucleus of carbon-12, the isotope carbon-13 would be formed.

As you may have guessed or perhaps already know, protons and neutrons are very similar in mass. To simplify our calculations each is considered to weigh 1 atomic mass unit or amu.

In biochemistry the atomic mass unit is called a dalton and is one twelfth the mass of the isotope carbon-12. Thus an atom of sulfur would weigh 34 daltons.


Atomic Symbol


The most common isotope of hydrogen has a proton but lacks a neutron. It is the only atom missing one of the subatomic particles. A rare isotope of hydrogen, deuterium, does have one neutron in its nucleus. Its atomic mass is 2 (its atomic number is still one, because all atoms of the element hydrogen must have only one proton.) Find out what tritium is.

The nuclei of some isotopes are unstable or radioactive. "Unstable" refers to the decomposition or decay of the atomic nucleus which may release either alpha, beta, or gamma radiation.

 Table of Properties Radioactive Decay Products

What it is
What it does to living tissue
alpha particles
helium nucleus

little or no effect, can just penetrate paper.

beta particles

may effect skin surface, can penetrate no more than a mm of lead

gamma radiation
powerful radiation

great penetrating power, can cause damage to any tissue by breaking bonds and ionizing molecules


The time required for half of the atoms of any radioactive material to decay is called its half life. This period varies greatly from isotope to isotope ranging from milliseconds to billions of years for certain isotopes of uranium and potassium.


Electrons and Chemical Characteristics of Elements


All biochemistry concerns what happens to the outer electrons of the atoms and molecules involved.

Atoms have electrons buzzing around the nucleus, attracted, but usually unable to interact with the positive protons within. Hydrogen with only one proton, has but one electron circling about.



Carbon with 6 protons will have 6 electrons orbiting about its nucleus.




To simplify; electrons orbiting outside the nucleus, are located in energy levels which occur at various discrete distances called shells. The greater the distance of the electron from the nucleus the more energy it will have.

The number of electrons in the outer shell (valence shell) of all elements must not exceed 8 (except hydrogen and helium where 2 is the max.)

Why atoms behave the way they do

The universal energetic tendency of all matter, regardless of its form, involves a "downhill" trend, tending toward lower energy levels.

Three specific energetic tendencies in the behavior of electrons are:

  • electrons tend to come in pairs. When an electron is paired its energy is less than when it is by itself
  • elements reduce their potential energy by filling their outer shell (end up with 8 electrons - hydrogen only needs 2 electrons for its outer shell)
  • various combinations of atoms (in molecules and compounds) tend to retain the electrically neutral condition they had as individual atoms.




Atoms by definition are neutral particles, each positive charge (a proton) canceled by a negative charge (an electron). When there is, for some reason, an imbalance in the number of protons and electrons the particle is called an ion. For instance sodium, element 11 (atomic number 11) has 11 protons in its nucleus, however sodium rapidly reacts with its environment and so has only 10 electrons. This form of sodium must have a positive charge of one, written Na+.

Sometimes an electron gains so much energy that the nucleus can not hold on to it. When an atom loses an electron it will become a positively charged ion, a cation. Metals, like sodium, usually lose their outer electrons. Some elements, the nonmetals, tend to gain the electrons lost by the metals and become negatively charged. They are called anions.

Which of the following ions are possible or generally considered "impossible"? For those that are impossible can you explain why. Highlight after each ion to "view" the answer.

(a) Na- impossible

(b) N-3 possible

(c) Ca+3 impossible

(d) Cl+5 possible

(e) Ag+ possible


Acids Bases and pH

Acidity is determined by the concentration of hydrogen ions in solution. When hydroxide ions (OH-) exceed the hydrogen ions the solution will be basic. A special scale called the pH scale is used to indicate the relative concentrations of hydrogen to hydroxide ions. The range of this scale is 0 to 14.

If a solution has a pH of 7 it is considered neutral. Each whole number step below 7 increases the hydrogen ion concentration by 10 making the solution more and more acidic, and every whole number step above 7 reduces the hydrogen ion concentration by 10 and the solution becomes more basic.

Thus a solution with a pH of 3 is 100 times more acidic than a solution with a pH of 5, and a solution with a pH of 11 is 1000 times more basic than a solution with a pH of 8.

Chemical reactions


Chemical reactions occur, in large part, to satisfy the energetic tendencies of atoms and their electrons . Thus electrons are often lost, gained, or shared when atoms bond together.

Chemical reactions are changes in the distribution of electrons where the starting substances -- the reactants -- are chemically changed into new substances called the products.

Whether interacting atoms gain, lose, or share electrons the process is predictable, and an atom's ability to hold on to its electrons and to attract more depends on a factor called electronegativity.

The difference in electronegativity between two atoms determines the type of bond which will form between them. If this value is greater that about 1.8 the bond is considered ionic and the electron is found almost entirely around the more electronegative atom. If the difference is less that 1.7 the bond which forms is considered a polar covalent bond and the electron is shared but unequally. Bonds that are purely covalent can occur between atoms of the same element. Diatomic molecules are an example.

Using a table of electronegativities we can specify the type of bond found between the following atoms.


(a) NaCl (0.9 - 3.0 = -2.1) -- ionic bond

(b) HF (2.1 - 4.0 = 1.9) -- ionic bond

(c) S-O (2.5 - 3.5 = -1) -- covalent bond

(d) N-H (3.0 - 2.1 = .9) -- covalent bond

Covalent Bonds


Covalent bonds occur when 2 electrons are shared between the nuclei of two atoms

In situations where sharing occurs but in an unequal manner, the molecule formed has no real net charge on it, but takes on a polar nature. Opposite regions of the molecule are partially negative and partially positive depending upon the relative distribution of electrons.


Because the sharing of electrons between hydrogen in H2 is perfectly equal the molecule is nonpolar (difference in electronegativity = 0)

  • Covalent bonds are stronger than ionic bonds
  • Covalent bonds do not dissociate in water.


Ionic Bonds


An ionic bond forms when the electron(s) in the outer shell of one element (usually a metal) transfer into the outer shell of a more electronegative element (usually a nonmetal). The electrostatic attraction between the ions constitutes the ionic bond.

The chemical equation 2 Li (s) + F2 (g) ----> 2LiF (s) represents the reaction between lithium metal and diatomic fluorine gas. The role of the electron is diagrammed below.



Water causes the disassociation of ionic solids into their respective ions. This property of water is essential for many chemical reactions, especially those in living systems. How is water equipped to break the relatively powerful ionic bonds making up crystals like sodium chloride?

Both salt water and sugar water are clear, odorless solutions, but one conducts electricity and the other cannot? Do you know which one is the conductor?


Calcium is considered a micronutrient for plants but is needed in much larger quantities in animals - compare and contrast the role of calcium in plants and animals.

Links to other Lectures


Links to Self Tests

Modified Nov 2, 2013







The nucleus (central region) of nitrogen must have 7 protons, or it's not nitrogen. As an uncharged atom nitrogen must also have the same number of electrons as it has protons.



















Electrons are nearly massless particles with a negative charge. They are found "orbiting" around the nucleus. The first shell or orbit becomes full when a second electron is added. The second shell fills with 8 electrons. The third shell can have as many as 18 electrons. But if it is the outermost shell or energy level its maximum is 8 (as soon as a 9th electron can be added the third shell can no longer be the outer or valence shell).

Since 8 outer electrons is especially stable most substances share or shift their electrons around to maintain this arrangement known as the octet rule.

















Neutrons are nuclear subatomic particles. They have a mass of 1 amu (dalton) but have no charge. The curious reason that they have no charge is because a neutron is really a combination of 2 other particles, a proton and an electron somehow fused together into a single particle.