Introduction to Cell & Molecular Biology (BIOL121) - Dr. S.G. Saupe (ssaupe@csbsju.edu); Biology Department, College of St. Benedict/St. John's University, Collegeville, MN 56321

Introduction to General Chemistry

I.   Life is chemically unique
    This is one of the characteristics of life.  Recall that we can determine if something is, or was, alive simply by analyzing its elemental composition. 

    Imagine sampling atoms throughout the universe.  If you could do so, 91 out of 100 atoms (91%) sampled would be hydrogen, 9.1% helium, 0.6 % oxygen, 0.04% nitrogen.  A similar study of materials in the earth's crust would give yield an elemental composition of: 47% oxygen, 28% silicon, 7.9% aluminum, and 4.5% iron.  Values for seawater:  H 66%, O 33%, Cl 0.33%, Na 0.3%.

    Now, consider an organism like a cat.  Place it in a blender, set the selector to puree, and then sample the atoms.  The approximate elemental composition would be:  63% hydrogen, 25.5% oxygen, 9.6% carbon and 1.4% nitrogen.  These four elements make up 95-99% of the elements in any organism.  In addition, there are approximately 20 other elements are also required by living organisms, but in relatively small amounts.   What can we conclude from our experiment with the pureed cat?

• Conclusion 1:  The chemistry of life is selective (i.e., the most abundant elements on the Earth�s surface were not used).

• Conclusion 2:  Certain elements must be more favorable for the evolution of life than others.  

• Conclusion 3:  Life is obviously chemically unique - materials from living organisms can be recognized by their elemental composition.

II.  What's so special about C, H, N, O?

1. These elements occur in gaseous form, alone (nitrogen, oxygen, hydrogen) or combined (water vapor, carbon dioxide).  This allows for rapid biogeochemical cycling through the environment;
   
2. Other elements are unsuitable for various reasons (i.e., radioactive such as plutonium and uranium, inert like argon and neon, too rare, too toxic like the heavy metals);
   
3. C, H, N, O forms stable covalent bonds. (see III below);
   
4. Carbon is uniquely "fit" (properties) for biological systems (see below) enabling it to serve as the backbone for biological molecules
   
5. Water has unique properties (click here for notes on water).  The abundance of H & O in living organisms reflects the importance of water.

III.  A look at bonding
   A chemical bond is an attraction that occurs between atoms to forms aggregates (molecules).  The bonding ability (and chemical properties) of an atom is largely determined by the number of subatomic particles.

• Protons �  positive charge, mass 1.0, number constant for each atom of an element. Occur in the nucleus.  Thus, each element is characterized by the number of protons in the nucleus.
• Neutrons � no charge, mass 1.0, number may vary among atoms of an elements.  Found in nucleus.
• Electrons � negative charge, no mass, usually same number as protons.  Occur in orbitals.
• Atomic number � refers to the number of protons in the nucleus.  This number is unique for each element.  Symbolized by a subscript.  For example, C has 6 protons and an atomic number of 6.  Thus, we symbolize it:  ₆C
• Mass number � refers to the total number of protons and neutrons in the nucleus.  The mass number may vary among atoms of an element (isotopes).  Symbolized by a superscript. A typical carbon atom has 6 neutrons and hence a mass number of 12.  Thus:  ¹²C
• Isotopes - atoms of a given element that differ in mass number are called isotopes.  Examples:  hydrogen (¹H), deuterium (²H), tritium (³H).  They all have an atomic number of one (=1 proton) but they differ in mass number (1, 2, 3, because they have 0, 1 and 2 neutrons, respectively).   
  
       The important thing to remember about isotopes is that they have the same chemical properties, but different physical properties.  In other words, tritium reacts in the same way chemically as hydrogen, but it is radioactive.  This is a crucial factor leading to the utilization of isotopes in medicine and various other areas of biology.

IV.  Life fractionates isotopes
    This is another characteristic of life.  We expect organisms, such as plants, to have the same concentration of isotopes that exists in nature.  As it turns out, they don't - usually they have a lower isotopic concentration.  Thus, plants are able to discriminate against (fractionate) radioactive isotopes and absorb non-radioactive ones.

V.  Chemical Properties
    The arrangement of the electrons in the atom ultimately determines the bonding ability and hence, chemical properties, of the element.  Points to consider:

• Electrons have discrete energy levels.  The greater the energy, the further away from the nucleus it will be.  Electrons can move between energy levels if they gain/loose the necessary energy. 

• Two electrons maximum can occupy the first energy level.  They are closest to the nucleus and have a spherical orbital (1s).

• Eight electrons maximum can occupy the second energy level.  They can occupy any of four orbitals, each orbital holds a max of 2 electrons.  One of the orbitals is spherical (2s), the other three are shaped-like dogbones (2p).

• If there are more than 10 electrons, they occupy higher energy levels.

• An atom is most stable at its minimal energy state, i.e., the electrons fill the innermost shells, and the orbitals are complete.  

• The bonding ability of the atom is determined by the number of electrons in the outer shell

• Atoms "stabilize themselves" by sharing electrons or transferring electrons to other atoms to complete their outer shells.

• Octet rule

• The following table summarizes the bonding ability of C, O, N, and H.  You should remember the atomic number of these elements and then be able to reconstruct the table based on this information

VI.  Covalent Bonds
    This is a bond formed by a pair of shared electrons.  Each pair of shared electrons are symbolized with a dash "-".  Covalent bonds can be: 

• non-polar:  electrons are shared equally between the two atoms
• polarized:  electrons are not shared equally, pulled more to one of the atoms of the pair.  Oxygen and nitrogen are electronegative; they polarize bonds.

VII.  Ionic bonds
    Transfer of electron from one atom to another with a mutual attraction of the ions (charged).  Cations are positively charged, anions are negatively charged (remember � anion = N for negative).  e.g., Sodium (₁₁Na) + chlorine (₁₇Cl) = salt

VIII.  Hydrogen bonds
    Weak electrostatic attraction between a hydrogen covalently bound to an electronegative atom and another electronegative atom.  More on this during the water lecture.

IX.  The importance of covalent bonds

A.  Proper strength.  Covalent bonds are not too strong nor too weak. 

B.  Covalent bonds are not disrupted in water (aqueous solution).  Think what would happen every time we showered if we were made of, say, salt.

C.  Allow a great diversity of chemical structures (i.e., single, double and triple bonds; various shapes including long chains, rings, and branches)

D.  Strength of covalent bond inversely related to atomic weight.  C,N,H,O are the lightest elements capable of forming covalent bonds - and thus they form the strongest covalent bonds.

X.  Why is carbon so special (fitness)?
    More different types of molecules are based on a carbon skeleton than any other element (molecule with carbon � called organic compound; no carbon � inorganic.  At one time chemists thought that carbon containing molecules could only be made by living things.  Louis Pasteur helped to disprove this idea).

     Why carbon?  (especially considering that silicon is 146x more abundant in the earth�s crust and has 4 unshared electrons just like carbon): 

1. Each C can form covalent bonds to as many as 4 others.  Thus, it can make chains, rings, branches, etc.  Silicon can only make short chains; polymers of silicon are not stable in water
   
2. Carbon can readily form double and triple bonds, silicon does not
    
3. C � C covalent bonds are stronger and more stable than S � S bonds (because silicon is a larger atom) 
    
4. C can combine with oxygen to form countless water soluble compounds.  For example, the simplest form is carbon dioxide which readily dissolves in water.  In contrast, silicon is insoluble in water.  When silicon combines with oxygen it forms silicates or polymers of silicon dioxide (quartz).  One reason that this is important is because it provides an easy way for carbon to enter and dissolve in cells for use of organisms.  It also permits carbon dioxide utilization in aquatic systems. 
    
5. Carbon combines with oxygen to form a variety of compounds, many like carbon dioxide, are soluble in water. 
    
6. Carbon has a tetrahedral configuration of bonds � permits 3D structures. This also accounts for the handedness observed in many biological molecules (check out the biological chem notes for more details).