From Chemistry to Biology

Life is Complex Chemistry

    Life, at its most fundamental level, is a chemical phenomenon. In fact, the discipline of biology is often described as applied chemistry. But how does something as seemingly complex as an organism arise out of chemistry? The answer lies in life’s polymers.

Biological Polymers have Emergent Properties

    In biology polymers are king; they make all of the functions of life possible. Polymers are long molecules built from repeating units of monomers. Synthetic examples include polyethylene plastic, which is built from repeating ethylene monomers.

Two-Dimensional Structure of RNA

     Biological polymers have emergent properties. Take for example RNA. RNA is a linear, biological polymer built from nucleotide monomers. The ribose sugar and phosphate portions of the nucleotides form the backbone of the polymer, termed the sugar phosphate backbone (purple stripe). Nucleotides also have another portion, a nitrogenous base that emanates from the sugar molecule. There are four of these bases, adenosine (A), guanosine (G), cytidine (C), and uridine (U).  These four nucleotides can be present in any order in the linear polymer, the order is known as the RNA’s sequence. The order of bases is like the order of words in this sentence; if they are rearranged their individual meaning remains the same but the meaning of the sentence would change.

Three-Dimensional Structure of RNA

    The bases in an RNA sequence give rise to the first emergent property of RNA: three-dimensional folding. First picture a two-dimensional sheet of origami paper. There are only a few dozen folds an origamist could perform; yet when these folds are used together on the same paper, there are nearly infinite unique sculptures that could arise. Similarly two-dimensional RNA polymers fold by complimentary base pairing, supported by a base’s chemical properties. Base pairing is the attraction and hydrogen bonding of bases: A pairs with U, while G pairs with C (and sometimes weakly with U). The attraction of bases within the molecule cause it to fold up into a three-dimensional shape. The figure below shows a representation of base pairing in two and thee-dimensions.

Catalytic Activity Comes from Three-Dimensional Structure

    The three dimensional folding of RNA gives rise to a second emergent property of RNA: catalytic activity. The three-dimensional folding brings together chemical groups in specific geometries, forming an active site that can promote the chemical conversion of substrate molecules to some other form; like a large molecule breaking into two molecules or rearranging chemical groups on a substrate molecule. Catalytic RNA polymers are known as ribozymes. The example below shows the catalytic RNA known as the hammerhead ribozyme and its active site. The hammerhead ribozyme catalyzes the cleavage of its own sugar phosphate backbone at the site indicated.

Protein Polymers are often highly efficient Enzymes

    RNA is a simple example of the emergent properties of biological polymers. In living organisms though, proteins do most catalysis. Protein is biological polymer built from amino acid monomers. It has a backbone of peptide bonds with amino acid side chains stemming from the backbone.  In RNA there are four nucleotides to provide chemical groups for folding and active sites. There are twenty one amino acids built into proteins, the interactions between them are much more complicated than the four nucleotides making for more complex folding patterns. Because they have more diverse side chains, they make for better catalysts than RNA. Catalytic proteins are called enzymes. Proteins are typically very long polymers with hundred or thousands of amino acids.

Networks of Enzymes

    The chemical reactions preformed by the enzymes have another layer of complexity: biochemical pathways. The products of enzyme are often substrate for another; therefor a chemical reaction will flow into the next reaction and so on. This chain of reactions is known as a pathway. The pathways also all feed into each other, resulting in a complex web of chemical reactions. The image below shows a condensed map of some very common metabolic pathways. The black lines represent chemical reactions catalyzed by enzymes. At this level, the system starts to display the kind of control we associate with living systems, such as homeostasis. The individual protien sequences of the enzymes become less important than the relationships between them.