Chapter 8

Metabolism is involved in managing the material and energy resources of the cell.

Catabolic pathways involve breaking down complex molecules to simpler molecules.

Anabolic pathways build complex molecules from simpler molecules.

To understand chemical energy we must understand energy.

The First Law of Thermodynamics: Energy can be transferred and transformed but it cannot be created or destroyed. This is referred to as the Principle of Conservation of Energy.

The Second Law of Thermodynamics: Every energy transfer or transformation makes the universe more disordered (or reduces the amount of usable energy).

Entropy is a measure of disorder, and the second law states that entropy is always increasing in the universe. Life is very ordered, therefore to maintain life processes a continuous input of energy is required.

Each molecule has some potential (stored) energy called Enthalpy. Both reactants and products of chemical reactions represent levels of disorder (entropy).

To determine if a reaction will occur spontaneously we must simultaneously consider changes in both enthalpy and entropy. Free Energy combines both of these concepts in a single term and can be defined as that portion of a system’s energy that can be used to do work. (Fig 8.5) In exergonic reactions the free energy is less in the products than in the reactants. In endergonic reactions the free energy is greater in the products than in the reactants. (Fig 8.6) Reactions are in equilibrium when the free energy in the products equals the free energy in the reactants.

The maintenance of life requires that energy released from exergonic reactions, be used to supply the energetic needs of endergonic reactions. Usually this energy is transferred from the exergonic reaction to the endergonic reaction via an intermediate molecule called Adenosine triphosphate (ATP). ATP is an adenine containing nucleotide that has two additional phosphates bound to the nucleotide’s phosphate via high energy bonds (symbolized with squiggly lines). Typically ATP is produced from ADP (Adenosine diphosphate) by the process of phosphorylation. (Fig 8.9) This is an endergonic reaction and is driven by the energy released from another exergonic reaction. The phosphate obtained is in turn usually transferred from ATP to another molecule thereby increasing the latter molecules free energy and making it more reactive.

The following reactions are continuously occurring in cells:

ATP à ADP + Phosphate + Energy

ADP + Phosphate + Energy à ATP

Consider how ATP works to allow the combination of Glutamic Acid and Ammonia to occur (Fig. 8.10). This is a typical scenario for ATP functioning.

Energy is often needed to break the bonds of reactants before chemical reactions will take place. The necessary energy is referred to as activation energy. (Fig 8.14) Activation energy must be provided even before otherwise spontaneous reactions (exergonic) will take place. Enzymes speed up the rates of particular reactions by reducing the amount of activation energy necessary. Enzymes act as catalysts in that they speed up reactions but are unchanged by the reaction itself. (Fig 8.15) It was long thought that all enzymes are proteins, but it is now realized that some RNA may have enzymatic activity.

The three dimensional structure of proteins may create a region that serves as the active site for the enzyme. It is the active site where the reactants bind and their bonds stressed such that the activation energy required for reactions are diminished. Often when substrates bind at the active site the entire complex changes shape and it is this shape change that reduces the required amount of activation energy. This shape change is called induced fit and is analogous to the shape changes in hands when a handshake takes place. (Fig 8.17)

Life forms control the rate of chemical reactions that occur in their cells by having appropriate collections of enzymes. The set of enzymes present in cells is determined by the genetic blueprint (DNA). The efficiency of enzymes is determined by environmental factors, such as temperature and pH.

Sometimes, molecules other than the normal substrate molecules may bind to the enzyme’s active site. When this happens the substrate will not access the active site and the enzyme will be ineffective in speeding up the reaction. Competitive inhibitors and substrate gain access to the active site with a frequency that is proportional to their relative concentrations. (Fig 8.19)

In addition to the active site, enzymes may have remote regions referred to as allosteric sites. If certain molecules bind allosterically, they may cause the three dimensional shape of the enzyme to change at the active site. If this makes the active site less attractive to the substrate the process is noncompetitive inhibition. If the active site becomes more attractive the process is called activation. These allosteric functions are independent of the relative concentration of substrates and inhibitors.

Sometimes polypeptide chains must bind to other molecules before they can function as enzymes. These supplementary molecules are called cofactors. If cofactors are organic they are called coenzymes.