#11 Origin of biochemistry

Origin of life is about the origin of biochemistry.  Biochemistry is the chemistry of carbon-based molecules, the organic molecules of life.  Carbon is unique in its ability to form stable bonds with other carbon atoms and to form long chains or rings.  The carbon atom forms four bonds, so a carbon atom in a chain is bonded to other carbon atoms on either side, and can still form bonds with other types of atom or with carbon side-chains. 

The types of atoms or elements of life are mainly six: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P) and sulphur (S).

The simplest types of cells –bacterial cells – contain some 5000 different organic molecules.  However, organic molecules fall into only four major categories: carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates, lipids, proteins and nucleic acids are macromolecules.  The largest are polymers synthesized by linking together large numbers of subunits called monomers by dehydration reactions.  Lipids are not polymers, but they can associate to form membranes. 

The subunits of carbohydrates are monosaccharide sugars.  The subunits of lipids are glycerol and fatty acids consisting of long hydrocarbon chains.  The subunits of proteins are amino acids joined to form polypeptides.  A protein may be composed of several polypeptide chains.  The subunits of nucleic acids are nucleotides.  A nucleic acid polymer has a sugar-phosphate backbone with different nitrogen-containing bases attached.  In DNA the four bases are adenine (A), cytosine (C), guanine (G) and thymine (T).  In RNA thymine is replaced by uracil (U).  ATP (adenosine triphosphate) is a nucleotide with three phosphate groups.  The last two phosphate bonds are unstable which means that they can be broken to release energy.

Biochemistry involves two types of chemical bond: covalent bonds which are strong and hydrogen bonds which are weak.  Covalent bonds can be single, double or triple with the double or triple being stronger than the single.

The peptide bonds joining amino acids in a polypeptide chain are covalent bonds.  Proteins may be strengthened by bonding between sulphur atoms to form cross-links between polypeptides.  The folding of proteins involves the formation of many weak hydrogen bonds. 

The highly complex shape of proteins involves four layers of structure.  The primary structure of a protein is the linear sequence of amino acids.  The secondary structure of a protein involves folds held by hydrogen bonds.  The tertiary structure involves packing to form a compact structure by some side chains being hydrophobic and others hydrophilic.  Hydrophobic side chains form a water-free zone in the interior of the protein with hydrogen bonding stabilizing the structure.  The quaternary structure, if present, consists of several polypeptides assembling together to form a protein which functions as a single three-dimensional structure.

Organic macromolecules are synthesized by cells using enzymes as catalysts.  Reactions do not occur haphazardly, but as metabolic pathways where one reaction leads to the next reaction in a highly structured manner to produce the end product.

Enzymes function by forming a complex with their substrate by binding on at the active site.  The enzyme orientates monomers such that a bond can be formed between them.  A polymer made from bonded monomers is thus formed.  ATP is used as a source of energy for the formation of each bond.

For more detailed information on biochemistry see the appendix for this chapter.  This basic understanding of biochemistry serves as an introduction to the discussion on the stereospecific properties of proteins discussed in the next section.