Bioenergetics
Microorganisms must use chemical reactions to get energy or make compounds. Chemical reactions that give energy are called exergonic reactions. Chemical reactions that require energy are endogonic.
Free Energy of Formation
Free energy is energy that is released an available to do work. If this value is negative, the reaction will proceed. An example of this is corrosion of metal by acid. Put the metal in the acid and it dissolves with no energy addition.
However, it the value of free energy is positive, an addition of energy will be needed to cause the reaction to occur. Burning gasoline in an engine is an example of this. Air and gasoline can be mixed and will not react. Only when a spark is added does the mixture burn and release energy. The energy added in this case is called activation energy. This is illustrated in the left Panel of Appendix 2.
Enzymes
Enzymes are proteins which speed chemical reactions. Enzymes do not cause chemical reactions to occur. Rather, they lower activation energy causing the reactions to proceed more quickly. This is illustrated in the left Panel of Appendix 2.
Substrate and enzymes come into close contact. If an enzyme is causing two molecules to react, if physically brings the reactants into a position to join. If the enzyme is cause in molecule to break down, the enzyme physically causes the molecule to come apart. This is illustrated in Appendix 3.