Proteins are long chains of hundreds of amino acids, the sequence of the protein primary structure. These amino acids chains form either spiral springs of alpha-helices or switch-backed beta-sheets. Helices and sheets are the rigid parts of a protein that fold and bring together the chemical functional groups that hold molecules and catalyze chemical reactions. It is the folding of the secondary structure to make a compact tertiary structure that makes a protein an enzyme.
Biochemical Reactions Involve the Rearrangement of the Atoms of Molecules
The molecules of cells, sugars, amino acids, nucleotides and their polymers, polysaccharides, proteins and nucleic acids, are made up of just six different elements (carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus). Bacteria can convert a simple sugar, e.g. glucose, and inorganic sources of the other elements, into all of the molecules found in their cells. The atoms of carbon, hydrogen and oxygen present in glucose can interact with the other chemical nutrient and rearrange into amino acids, nucleic acids, etc.
Reactions Result from the Random Collision of Molecules – Thermal Energy
Laboratory experiments have confirmed that most of the simpler molecules present in cells will form spontaneously if a simple combination of carbon dioxide, ammonia and methane is heated and an electrical discharge is sparked through the vapor in the closed flask. This illustrates that most of the chemical reactions that rearrange atoms in the molecules of cells will occur as the molecules collide randomly, i.e. due to their thermal/kinetic energy. These reactions will occur naturally, but the reactions will be very slow.
Catalysts Orient Molecules and Enhance Biochemical Reactions
Biochemical reactions will occur more quickly if the reacting molecules are properly oriented and held together. Catalysts are molecular surfaces to which reacting molecules can bind. The catalysts display groups of atoms, functional groups, that form bonds with the reacting molecules, so that subsequent thermal collisions by solvent water will bring the reacting molecules together and trigger the biochemical reaction. The product molecule with a new structure will then break the multiple weak bonds with the catalyst.
Enzymes Are Rigid Molecular Platforms That Catalyze Biochemical Reactions
The rigid secondary and tertiary structure of enzymes displays the functional groups of particular amino acids in one domain of the enzyme, the active site. Each of the amino acids of the active site can make only one or two weak bonds. Thus, it is the simultaneous formation of several weak bonds in the rigid framework of the enzyme that determines the molecular specificity of the enzyme.
The enzyme active site binds small molecules, substrates, in a highly specific orientation. The result is that only particular biochemical reactions are accelerated by a particular enzyme.
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