Biology 101 Chapter 2

The Chemical Basis of Life


Chemistry = the study of matter and the changes matter undergoes.  Chemistry is the universal study of two things: what is matter and how it is formed, and what types of reactions does matter undergo and what products are made.  By far chemistry is the most important field and discipline out there.  Everything is based on chemistry, it is the basic building block of all other sciences (even biology).


Nature of Matter:  Matter is anything in the universe that has mass and occupies space (has volume).


Two of the most important words and concepts in chemistry and the general world are Element and Atom.  Often people will confuse these two terms and use them interchangeably, though this practice is incorrect.  They are two distinctively different things.

Element defined: the basic kinds or types of matter, a substance that cannot be broken down further by chemical means.  Element is more of a conceptual item than an actual thing.  Like the color blue.  Is there really such a thing as “blue”?  We have blue cars and blue shirts and blue ink, but do we have blue?  Notice in each case the word is used as an adjective or descriptor.  The word blue is never by itself when used in context, though things can be classified by the color blue.  “Blue” has no mass, cannot be moved, and things are not made out of “blue”.  On the other hand, things are made out of atoms.  Atoms are the physical building blocks of the universe.  Atoms have mass, can move and be moved, connect to one another and collide.  Atoms are the building blocks, but there are different types of atoms available to build from.  Hence elements, the different types of matter or in other words the different types of atoms we can use.  I like to think this is analogous to Lego building blocks.  Most people at one time in childhood played with Legos.  Imagine you have a pile of Lego Blocks, all of the same size and shape (basic block with 4 prongs), but different colors (red, black, blue, white, yellow, etc.).  The blocks represent your atoms.  You can put them together in any shape or form you want, in any combination you desire, in any proportion or number of blocks you fancy.  But you also want to classify them, based on their color.  So you have several plastic containers for your blocks, each labeled a different color.  A red container for red blocks, a white container for white blocks, etc. and you place each block into its appropriate container.  If someone walked up and placed a brown block in the yellow container, you would be upset and recognize that the block is out of place.  The containers represent your elements; the distinctive types of Legos (or atoms) that exist.  Each block goes to its own container.  Elements represent the different kinds of atoms we have to play with in chemistry and each atom belongs to its particular element.  Here are some general notes on elements:


-          substances whose atoms have the same # of protons (this will be explained later)

-          92 elements occur naturally, 25 found in living things

-          118 known elements (this number varies a lot and is an estimate, because the higher elements are unstable and are synthetically made)

-          the 4 most important elements (>97% mass)

1)      Carbon [C]

2)      Oxygen [O]

3)      Hydrogen [H]

4)      Nitrogen [N]

-          trace elements (these include iron, zinc, copper, sodium for examples)


Atom defined: the smallest fundamental particles of matter that still retain the identity of an element.  Atoms have already been discussed to some extent.  “Things” are made up or out of atoms.  They ARE the basic building block.  All compounds that exist are made up of atoms.  Atoms represent the smallest thing you can have that is used to construct material.  Even though there are things in the universe smaller than an atom, atoms cannot be broken down any further by chemical means.  Every atom can be said to have the identity of a particular element, the one it can be classified as, so an atom has and retains the identity of that element.  Can atoms be broken down at all?  Yes, they can be split into their smaller fundamental particles, but this is technically a nuclear reaction (fission or fusion), not chemical, and the atoms will no longer have the identity of that element.  Because of this there are some baseline rules to atoms:

  1. Every atom is classified as belonging to an element.
  2. Every atom can be classified as one and only one element, never two.
  3. Atoms cannot change from one element into another, so they cannot swing between elements.
  4. Every element is represented by its own cadre of atoms.
  5. If you discover an atom that cannot be classified into an existing element, you have discovered a new element.


Atomic Structure

Now, there are smaller particles than atoms.  They actually make them up, so atoms have structure themselves.  The general principles of structure apply to every atom.

Same for all atoms

Atoms have two basic regions

1)      Nucleus (a tight central core in the middle of the atom)

2)      Orbitals (shells) (a region of vast space occupied by one of the particles in orbit)


Composed of 3 smaller particles (subatomic particles) (here they are)

  1. Protons
  2. Electrons
  3. Neutrons






# in atom










Lost or Gained





Can alter

The preceding table is vastly important.  It gives you the basic 3 subatomic (smaller than an atom) particles, their respective charge, their mass, where to find them within the atom, and if the number of them can be altered.  There are several subtle things to note about the table:

  1. There is only positive charge, the proton, and negative charge, the electron.  Neutrons are neutral, they have no charge.
  2. The charges between the protons and electrons are perfectly matched at 1.  We say they have the same magnitude charge but of opposite sign.  The charge is 1, not 0.99 or ¾.  It is exactly one for both.  Note an equal number of protons and electrons would cancel each other out as far as charge is concerned.
  3. The proton and neutron have the same mass, 1 amu (atomic mass unit), but the mass of the electron is insignificant compared to the other two.  The electron does have mass, but of such a negligible amount that it is not considered in calculating the mass of objects.  I find this fascinating, that something so much smaller than a proton could contain the same degree of charge.
  4. Both the proton and neutron are located in the nucleus, and they are the two with any mass.  So, nearly all the mass (practically all) is located within the nucleus.
  5. The electrons are the ones moving incredibly fast in orbits.  The orbitals are vast though, like the planets in orbit around the sun, most is empty space.
  6. The number of protons cannot be changed, they are constant.  Electrons can be gained or loss by an atom, which makes sense considering where they are found.  Neutrons cannot be gained or lost by an individual atom, but may vary from one atom to another of the same element.


Considering what was mentioned above, here are more interesting things.

Atoms in an uncombined state have the same number of protons and electrons; therefore they are electrically neutral.  An uncombined state means they are not chemically bonded to another atom.  In this case the number of electrons in an atom will always match the number of protons.  Sense their charges cancel this would lead to a neutral atom.  Typically this is how they are represented on the Periodic Table.


Most of the mass of an atom is in the nucleus.

Most of the volume is empty space occupied by orbitals.

Periodic table always refers to atoms in an uncombined state.


The Periodic Table:  The Periodic Table is one of the most important information sources in chemistry.  It is a large table listing all the elements that exist in a particular order.  Each element is represented on the table by a box that contains several pieces of information on that element.  The sequence, or order, of the elements also has significance.


Atomic Symbols:  Within each box is the name of the element and its Atomic Symbol.  The Atomic Symbol is usually a one to two letter abbreviation for that element, but the letters do not always correspond to the name of the element.  For example sodium is Na and potassium is K.  Three letter designations are used for elements that do not have official names yet.  The Atomic Symbol is one of the chief ways atoms are identified.  They are used to communicate what elements are involved in reactions, chemical formulas and chemical equations.


The Atomic Number:  This is more important for chemistry.  Note as mentioned earlier that atoms are classified into elements based on certain characteristics, which we call identity, and they retain this identity through chemical reactions.  Atoms of one element are different from atoms of another element.  However, all atoms of the same element have some identifying mark in common.  Also note that of all the subatomic particles, only the proton did not change.  All atoms have the same basic structure, a nucleus and orbitals, composed of the same three particles, protons, electrons and neutrons.  If every atom has the same three particles, how do they differ from one another?  They differ based on the proportion, or mount, of each particle present, not on the ones it has.  Electrons are not good for this, since they can be lost or gained by atoms.  Neutrons also are not reliable, since their numbers may vary from atom to atom of the same element.  However, protons cannot be gained or lost or altered.  So, it is the actual number of protons in an atom that defines it.  This number is represented by the Atomic Number on the Periodic Table.  For example the first element is Hydrogen and its number is 1.  This tells me that atoms of Hydrogen have 1 proton in them.  Not 2 or 3, just 1.  Every atom of Hydrogen has 1 proton and any atom in the universe that has only 1 proton in it is an atom of Hydrogen.  Carbon’s Atomic Number is 6, so atoms of Carbon have 6 protons, etc.  Note: the Atomic Number gives you specifically the number of protons in an atom.  Since atoms uncombined would be neutral and have the same number of electrons and protons, the Atomic Number also gives you the number of electrons in an atom of that element, but only in an indirect way.  Hence, Carbon has 6 protons and 6 electrons.  The Atomic Number is another chief way to identify atoms.


The Atomic Mass:  The Atomic Mass of atoms is their relative mass expressed in AMUs or atomic mass units.  The Atomic Mass is determined by combining the mass of the neutrons with the mass of the protons.  Since each has a mass of one, the Atomic Mass is simply the sum of the number of protons and neutrons in an atom.  In reality the Atomic Mass is an average.  On the Periodic Table the mass is given for each element, but is not used to really identify that element.  Note: if the mass of a proton is one and a neutron is one and you simply add them together, you should get a whole number.  The Atomic Masses given in the table are actually decimals and fractions.  Why?  Because it is an average.  Neutrons cannot be gained or lost by individual atoms, but because they have no charge they play no real role in chemical reactions and their number can be different than a norm.  The number does not have to match the number of protons and electrons, and may even be different from one atom to another atom of the same element.  The only criteria for atoms to belong to a particular element is the number of protons it possesses.  On the table the mass is always the larger number.


                        Isotopes and mass number:  Atoms of the same element that have different numbers of neutrons are called isotopes.  Think of isotopes as subtypes of an element.  Every element has two to four isotopes.  Some are radioactive while others are not.  An isotope’s mass is always a whole number and is called the mass number.  The Atomic Mass for an element is determined by taking all the masses of the different isotopes and multiplying them by their relative percentage of occurrence, then adding the results.  See the text book for examples.


Molecule defined:  A molecule is composed of two or more atoms chemically bonded together.  As simple as that.  Technically speaking, nothing occurs as a single atom (monoatomic), so everything is a molecule by default.  When in doubt, err on the side of caution and call it a molecule.  The simplest, smallest molecules you can get are composed of only two atoms specifically of the same element.  There are only seven of these that exist and are called the diatomics.

                        Diatomic molecules: H2, O2, N2, F2, Cl2, Br2, I2


Compound defined:  A compound is a material made up of two or more atoms from two or more different elements bonded together.  Note the definition of a compound is very similar to that of a molecule, just a little more complex.  Also note that technically all compounds are still molecules, but not all molecules are necessarily compounds.  For example: hydrogen gas, H2, is a molecule but not a compound since it is composed of only one type of element, whereas water, H2O, is a compound and a molecule.


Atomic Structure Part II


Electron Arrangements  The electrons in orbitals around the nucleus of an atom do not all orbit at the same altitude or speed.  They would get too crowded and electrostatic repulsion would cause them to repel from each other (like holding the same charge end of two magnets towards one another).  So they orbit in distinctive layers or shells.  Each layer or shell represents a particular speed for the electrons, the further away from the nucleus the faster they are moving.  Because of this phenomenon, we refer to the shells as energy levels or energy shells.  They also hold only a specific amount of electrons at each level.  The first holds only 2 electrons.  It increases from there, but the last or outermost layer will never exceed 8 electrons.

Electron shells:

-          certain energy levels

-          2e- in 1st

-          8e- in outermost

Valence electrons = bonding electrons and the octet rule.  Even though a level can hold more than 8 electrons, before the ninth is put in place the next level will have already started.  Like an apartment building that fills from the ground floor up.  It has one rule, before the ninth or tenth tenant can move into an apartment on a particular floor; one apartment in the next floor up has to have someone move in.  This tendency to never exceed 8 electrons in the outermost level of an atom is called the octet rule, and the electrons found in this level are called the valence electrons.  Why are they important?  The valence electrons are the only ones involved in chemical bonding.


Chemical Bonds  There are three (really two) principle chemical bonds, or connections between atoms.

3 types:

Ionic                Covalent                      Hydrogen


Ionic bonds and ions:  Ionic bonds are the most common and require the formation of ions.

-          atoms can gain or lose electrons and become charged

-          ions can form independent of ionic bonds

Remember, atoms can gain or lose electrons.  This unbalances the numbers or protons and electrons, resulting in the atom acquiring an electrical charge.  If an atom gains electrons it becomes negatively charged.  If it loses electrons it becomes positively charged.  Note: although the formation of ions is necessary to form ionic bonds, it is not a guarantee that a bond will form.


Ion = an atom or molecule with an electrical charge resulting from the gain or loss of 1 or more electrons.


Ionic bond: attraction of opposite charges, fairly strong, most common, found in metals and salts.  Ionic bonds are formed by the mutual attraction of opposite charges of positive and negative ions.  The bond will only form between opposite charges, but may form between multiple atoms.  The overall driving force for this is that atoms want to be electrically neutral.  But they gain or lose electrons and become charged.  Atoms don’t like being charged.  So to compensate for this they will form bonds with atoms of opposite charge in an attempt to neutralize themselves.  This is the rule: ions of opposite charge will combine in whole number ratios to that the entire molecule is neutral.   Ex. NaCl


Covalent bond: (molecular bond) in which two atoms share 1 or more pairs of electrons, strongest bond, organic compounds.  The covalent bond is seen as the best relationship one could hope for.  The bond is stronger than an ionic, with the atoms actually physically closer together than an ionic.  In a covalent bond, a pair of electrons (one each from either atom forming the bond) is shared between the atoms making the bond.  The electrons are neither gained nor lost, but shared.  Each atom donates equally one electron to the pair.  And the pair of electrons forms a figure 8 orbit that goes around each atom’s nucleus, orbiting both part of the time equally.

                        Structure of a covalent bond

                        Single, double and triple bonds

Two atoms can actually form more than one covalent bond between them.  Regardless of the charge, you only ever have one ionic bond.  With covalent you can have single, double or triple bonds form between two atoms.  Each is more powerful that the proceeding.


Hydrogen bond: most rare, weakest, water and some organics.  Mostly water.

·         Always formed between an H atom already covalently bonded and an atom in another molecule

·         Unique because of H atom structure

The hydrogen bond is barely a bond and is not technically classified as a chemical bond because it is neither strong enough to form molecules nor is it permanent.  Hydrogen bonds form between a hydrogen atom already covalently bonded in one molecule and another atom in another molecule.  They flip on and off like a light switch, making them unpredictable and really weak.  Though, the hydrogen bonds formed between water molecules does lend water some interesting properties.


The Properties of Water (due to H-bonds)

  1. Polarity: water molecules are polar; they have distinctive charged ends to the molecule, like a Duracell battery.  This gives water the ability to conduct electric current and dissolve compounds that are also polar, like salts and sugars.
  2. Cohesion + surface tension: water is cohesive at its surface, it sticks to itself.  This creates surface tension at the water’s surface.  This is why water beads after you wax your car and crawls up the side of a glass of water, and you can skip stones on a lake.
  3. Temperature Stability: water can absorb a tremendous amount of heat while its temperature only rises slightly, and it can lose great quantities of heat without dropping its temperature much.  This stabilizes the temperature of the environment locally around large bodies of water.  This is why coastal cities are so nice year round compared to landlocked cities.
  4. Universal Solvent: Basically, water can dissolve just about anything given enough time, even rock (we call it erosion).

Three basic terms to know concerning water.

Solution, solvent and solute

Solvent = that substance that does the dissolving

Solute = that substance dissolved by the solvent

Solution = the combination of solvent and one or more solutes dissolved in it


Acids and Bases

Some solutions create acids and bases.  We measure the acidity of substances using a measurement called pH.  The actual measure is placed on a scale called the pH Scale.

pH = measures the level of acidity of a solution, level of H+ (hydrogen ion) in solution.


Hydrogen ion (H+) plus Hydroxide ion (OH-) = H2O


Acid: any compound that releases H+ to solution

An acid is any substance that when dissolved in solution will release or give off hydrogen ions.  These substances are typically recognizable by having H in the beginning of the formula.  Examples of acids include HCl (hydrochloric), HNO3 (nitric), H2SO4 (sulfuric) and H3PO4 (phosphoric).  Sugar, C6H12O6, is not an acid.

Base: or alkali, any compound that removes H+ from solution (most have OH-)

A base will usually balance and neutralize an acid of similar strength.  Usually bases are thought of as having OH in them like sodium hydroxide, NaOH, one of the worlds most common and powerful bases.  But not all bases have hydroxide in them, like ammonia, NH3.  Bases are technically defined as any substance that can absorb or remove hydrogen ions from solutions.


pH Scale: Here are some notes on the pH scale and its ranges.

-          ranges from 0-14

-          0-6.9 acidic, 7 neutral, 7.1-14 basic

-          Water is neutral