Atoms interact with other atoms to form molecules by forming bonds.

A molecule containing more than one kind of element is called a compound.

The combining activity of atoms that form molecules and compounds reflects three chemical forces:

1. the tendency of electrons to occur in pairs
2. the tendency of atoms to balance positive and negative charges
3. the tendency of the outer shell of electrons to be full (see the table below) or be "happy" for awhile with eight electrons in the outer shell (the octet rule
   

Let's look at a couple of elements and their atomic structure.

When atoms of an element combine to satisfy the octet rule, they make a chemical bond.

There are two kinds of chemical bonds: covalent and ionic or electrovalent. Some elements such as sodium and chlorine readily gain or lose an electron to form ions. They become charged and once this occurs, positive ions attract negative ions. They associate with one another to form compounds by means of ionic or electrovalent bonds. We often refer to these compounds as "salts" or "salt-like." They are often quite soluble in water.

Most of the mineral nutrition required by plants is provided by electrovalent or ionic compounds.

When electrons are shared between atoms, a different bond type is found-- a covalent bond.

An atom of H with its single electron can fill its outer shell with another H atom to form a molecule of hydrogen. O can do a similar thing to form O₂, having a double bond. Nitrogen does it with a triple bond.

Quadruple covalent bonds, however, do not exist so one never sees for example, C₄.

Carbon, with four electrons in its outer shell, can, however, form four single covalent bonds. Carbon, then, can share its electrons with four atoms of hydrogen to form methane, CH₄.

The sharing of electrons between C and H in methane is pretty equal. Some atoms are more strongly electron attracting than others (O, N, P, for example). This allows for a phenomenon called polarity to occur. Methane is non-polar but let us look at water, H₂O.

Water is among the most polar of molecules. This is because the "sharing" of electrons between the hydrogens and oxygen are rather unequal. Oxygen is such a strong electron attracter that it hogs the electrons and effects a partial negative charge. The hydrogens, being unable to have their proper share of the electrons, effect a slightly positive charge. This lends a charge asymmetry to the water molecule and makes it a polar molecule.

Water is the cradle of life. The most common atoms in living material are H and O. Water has some pretty neat properties. For example, of all the common molecules on earth, only water exists as liquid at the relatively cool temperatures that prevail on its surface.

Life, as it evolved on earth, is inextricably tied to water. The chemistry of life is in a real sense, water chemistry.

There are several properties of water that you must be conversant with:

1. Water has the ability to form weak chemical associations with only 5-10 percent the strength of covalent bonds. These associations are referred to as hydrogen bonding. This property derives from its structure and is responsible for much of the organization of life chemistry.



2. Water is a simple structure: one oxygen atom bound by single covalent bonds to two hydrogen atoms. The resulting molecule is stable. It satisfies the octet rule, has no unpaired electrons, and does not carry a net electrostatic charge.



3. The electron attracting power of oxygen is so strong, however, that the electrons of hydrogen are more likely to be associated with the oxygen than the hydrogens. This leads to the oxygen acquiring a partial negative charge (electrons are negatively charged) and leaves the hydrogens with a partial positive charge (from the protons in their nuclei). This charge separation creates a negative and positive region for the molecule. The partial charges are small. The result though is a molecule with distinct, charged ends. We refer to such molecules as polar molecules. Once again, water is one of the most polar molecules known.



4. Polar molecules such as water interact with each other via hydrogen bonding.



5. Thermal properties - water is a good heat absorber. Much of energy absorbed by water is used to break hydrogen bonds rather than increase molecular motion (a measure of heat) at first. Lots of hydrogen bonds are found in water. Water also cools well. In order to evaporate, water must absorb a large amount of thermal energy which cools the liquid that is left behind.



6. Ice formation - as water cools, the movement of molecules slows and the molecules are able to crowd closer together. In other words, as water cools it becomes more dense. Water reaches a maximum density at 4°C. As the temperature gets colder, it increases its volume, and lessens its density. This is why ice floats. Why this is the case has to do with bond angles of hydrogen to oxygen during crystal formation at freezing and an open, i.e., less compact association. Ice insulates and this change in density phenomenon has implications for oxygenation in lakes.

When chemistry was an infant science at the end of the 18th century, two broad classes of materials were recognized: minerals or substances of mineral origin in rocks and oceans were found to be stable against strong heating, except when they underwent specific chemical transformations.

In contrast, substances derived from living or once-living things often would char or burn when heated. Such decompositions often were confusingly complicated. These same substances derived from living things were also known to undergo other reactions which were well characterized, such as the formation of alcohol from sugar solutions by fermentation.

It was also recognized that substances of this second type could be converted into mineral type substances; i.e., candle wax or alcohol burns to form carbon dioxide and water.

In 1807, Berzelius proposed the terms inorganic and organic for these two classes.

Berzelius argued that organic materials could only be synthesized under the influence of a presiding "vital force". Once formed and present in dead matter, organic substances could be converted to inorganic but the reverse had never been observed. Here was one of the earliest speculations about what life was! Berzelius' vitalism theory started off as an all-encompassing principle supposedly governing the behavior of atoms and molecules in living material by some unique rules.

Within 20 years, one of Berzelius' students, Friedrich Wöhler, a German, produced evidence to prove the master was wrong. Wöhler heated ammonium cyanate (an unmistakable inorganic, salt-like material) and found the product to be urea.

This conversion of an inorganic material to organic was the first evidence for what has since been found to universally true:

Atoms follow only one set of rules for chemical combinations. Matter at the atomic and molecular level is the same whether manipulated within a living organism or not.

In spite of this, the name organic chemistry has survived as an anachronism. Since carbon forms so many varied compounds, their study constitutes a whole branch of chemistry; the label given the study of these compounds is organic chemistry.

A living organism is a remarkable chemical factory. A single cell can synthesize precisely and efficiently a bewildering variety of highly complicated products.

Organic molecules produced by living cells are called biochemicals.

Carbon's chemical properties make it an ideal central element upon which to base life. Carbons have the ability to bond with one another to form a backbone for biological molecules which may be linear, cyclic or branched.

These bonded carbons still have space for additional bonds. Often hydrogen is bonded but sometimes other functional chemical groups are bonded.

Functional groups give an organic molecule its chemical properties and reactivity.

Most functional groups are charged or highly polar, making organic molecules much more soluble in aqueous solutions and more chemically reactive than are those composed only of carbon and hydrogen.

The chemicals that form the structure and perform the functions of life are highly organized molecules. Many are enormous, containing hundreds to millions of carbon atoms. These enormous chemicals are called macromolecules and they have special properties that their smaller cousins lack.

Macromolecules are constructed by assembling together small molecular subunits. Subunits are referred to as monomers. The macromolecule is referred to as a polymer.

Macromolecules fall into four fundamental classes or families of organic compounds: carbohydrates, lipids, proteins and nucleic acids.

A group of substances which include simple sugars and all larger molecules constructed of sugar subunits. This includes things like glucose, fructose and sucrose as well as starch, glycogen and cellulose.

Individual sugars are called monosaccharides and can be linked together to form larger molecules. A molecule composed of two sugar units is a disaccharide. Polysaccharides are macromolecular carbohydrates.

Plants have starch, also a polymer of glucose. Starch is much less branched than glycogen. Animals don't produce starch but they are able to readily convert it to glucose. Starch is the primary energy source for humans in many parts of the world.

Two of the most important structural polysaccharides are cellulose and chitin. Cellulose is the earth's most abundant polysaccharide and is an unbranched polymer of glucose. Cellulose differs from starch and glycogen in the kind of linkage between individual sugars also. Animals lack the enzyme capable of digesting cellulose but some bacteria possess the enzyme. Cows and termites depend on these bacteria for their cellulose digesting enzymes.

Chitin is a polymer of an amino sugar, a nitrogen containing sugar. It is a major part of the exoskeleton of insects and crustaceans.

Lipids are a fairly diverse group of molecules that share one common property--they don't dissolve in water. They include such things as fats, oils, phospholipids, steroids and waxes.

Fats consist of three fatty acids linked together in a particular manner. These are generally long chained fatty acids. Each fatty acid is linked to one of the three carbons of a glycerol backbone.

Fats are very different from carbohydrates in terms of energy storage. Fat contains over twice the energy of carbohydrate. This is why it takes so much exercise to "burn" fat.

Liquid fats are called oils. Saturated fats are often solids at room temperature. Unsaturated fats are often liquid at room temperature. Some people say that unsaturated fats are less likely to promote heart disease but the matter is not at all settled in the scientific literature.

Phospholipids are rather similar to fats in their structure. The exception is that only two fatty acids join the glycerol backbone. The third glycerol carbon is joined to a phosphate group which in turn is joined to one of several possible polar chemical groups.

One can rotate the -OH and -H groups on glycerol. Notice this second glycerol where such a rotation has been done.

To this second glycerol molecule, one can then substitute in a phosphate group and a charged functional group to form a substituted glycerol molecule.

You might wish to go back and re-examine the structures of glycerol, the second glycerol and the substituted glycerol molecule.

Finally, the remaining two -OH groups on the substituted glycerol molecule will be replaced with fatty acids (abbreviated R2 and R3). R2 and R3 are really long chain fatty acids just as you saw earlier in this section. The resulting molecule is a phospholipid, a molecule of great importance in biological membrane structure.

The phosphate side of the molecule is soluble in water; the fatty acid side is not. Biological membranes are phosopholipid bilayers. You can examine a model of this sort of membrane structure if you wish (Sorry, 2-3 minute download for typical dial-up connection).

Steroids are molecules built around a characteristic 4-ringed skeleton. One of the most common animal steroids is cholesterol, an important part of animal cell membranes and a precursor for the synthesis of several hormones. Cholesterol, testerosterone and estrogen are quite similar, chemically.

Waxes are similar in structure to fats. They have more fatty acids linked to a longer carbon chain backbone. A heterogeneous group of waxes cover insect exoskeletons, bird feathers, and leaves.

More than one-half of an organism's body is protein. A typical mammalian cell has more than 10,000 different proteins. Proteins are of two general classes: structural and enzymatic. Hair, feathers, fingernails these are all structural proteins. Then, there are thousands of different enzyme proteins which collaborate to direct metabolic processes controlling development and cellular maintenance.

Proteins are polymers of amino acids. There are, in general, 20 common amino acids that are assembled in strikingly different sequences to produce the protein diversity seen in living organisms. The same 20 amino acids are found everywhere in life, whether it be a plant, an animal or a bacterium.

All free or unlinked amino acids have a carboxyl group and an amino group separated by a single carbon atom. A variable R group defines which of the 20 amino acids one is examining. You might want to examine and compare the structure of amino acids.

Amino acids are joined during protein synthesis. Chemically, the reaction involves removal of a molecule of water.

Most proteins contain at least 100 amino acids; some as many as 20,000. Protein structure has four levels: primary, secondary, tertiary and quaternary.

The sequence of amino acids makes up the primary structure of a protein.

The spatial organization of regions of the polypeptide make up the secondary structure. These organizations are: alpha helix, beta pleated sheet, and random coil.

The tertiary structure describes the shape of an entire polypeptide molecule. Globular proteins versus linear proteins and conformational changes are notions to consider here.

Finally, many proteins are composed of more than 1 polypeptide chain. Hemoglobin, for example, consists of four polypeptide chains.

One can denature proteins-- cause them to lose their secondary and tertiary structure. Enzyme digestion can do this as can treatment with acids, bases, strong salt solutions, heat and cold. Some kinds of denaturation are reversible; others such as the unfrying of an egg are not.

A given primary structure of a protein dictates the secondary and tertiary structure of a protein spontaneously. Amino acid sequences are extremely important. A single amino acid change (valine for a glutamic acid) causes sickle cell anemia. A change in hemoglobin conformation makes the cells have a sickle shape.

Deoxyribonucleic acid is the material in which heredity information resides. Ribonucleic acid is a chemically similar material that is a key player in the transmission/translation of genetic information into protein.

Both DNA and RNA are nucleic acids, molecules constructed as a long chain or strand of nucleotide monomers.

A nucleotide consists of 3 parts: a 5-carbon sugar, deoxyribose or ribose; a phosphate group; and a nitrogenous base.

The sugars and phosphate groups are identical in all nucleotides but there are four different nitrogenous bases:

Note that in RNA, uracil replaces thymine.

Nucleotides are covalently bound to one another through sugar-phosphate linkages to form long strands. DNA is a double stranded molecule with a helical configuration; RNA is a single stranded molecule.

There is a flow of information in a cell from DNA to RNA to protein. The sequence of nucleotides in DNA determines the sequence in RNA which in turn determines the sequence of amino acids in a protein.

While nucleotides are important as monomers for nucleic acids they are also significant as "energy carrier compounds", such as adenosine triphosphate or ATP.

That's it for the chemistry. You might wish to go back to the first chemistry module.

You may take a quiz on the material in this module. No record of the quiz is made. You decide after the quiz if you really know this material.

Or you can return to the Syllabus Page.