An Intro Into Energy and Metabolism
Any organism is nothing more than a series of chemical reactions - some related and some not related. The sum of all of these reactions - the organism's metabolism - is very integral in maintaining the specific organism. We should think of organisms as being billions of chemically complex reactions. There are two classifications of reactions that occur within living organisms: catabolic reactions are reactions that break down complex molecules into much simpler molecules - anabolic reactions are reactions that create complex molecules from much simpler molecules.
Energy and the Laws that Govern It
There are various forms of energy within the universe, and regardless of the state in which the energy appears, it still is under subtle laws. The First Law of Thermodynamics states that energy cannot be created or destroyed - energy can only change form as it passes through various systems. The Second Law of Thermodynamics states that entropy (disorder) in the universe is always increasing.
Why Is Energy Important?
Energy must be present to complete reactions that naturally exist as non-spontaneous. A spontaneous reaction does not require additional energy (from an outside source) to proceed - a non-spontaneous reaction does require this help. Regardless of whether or not a reaction is spontaneous (exergonic) or non-spontaneous (endergonic), an activated complex must be attained by supplying the reaction with the correct amount of activation energy.
ATP (adenosine triphosphate) is closely related to one type of nucleotide found in nucleic acids - ATP has the nitrogenous base, adenine, bonded to ribose (just like in RNA - except that ATP has three phosphates). The bonds between the phosphate groups of ATP's tail can be broken by hydrolysis (using water to break the bond - a type of catabolic reaction). When the ATP is hydrolyzed (it is now ADP), energy is released - this reaction has a free energy value deltaG = -31kj/mol (-7.3kcal/mol). Please note that this deltaG value is negative - which means that this reactions occurs spontaneously. Therefore, we can consider the phosphate bonds on ATP to have an ability to create a substantial amount of energy if ATP is hydrolyzed.
ATP is usually depleted very quickly - not to worry, ATP can be regenerated very quickly. In this backwards reaction, ADP can combine with an inorganic phosphate group - the energy required to complete this anabolic reaction generally comes from catabolism of organic nutrients.
There are many reactions that are non-spontaneous - in other words, such reaction cannot proceed without an input of energy. Many times, such a reaction is coupled (placed with) a reaction that is highly spontaneous (ATP hydrolysis). Coupling reactions in this method helps reactions that would not usually proceed to proceed.
Enzymes are catalytic proteins - agents that help to speed up the rates of various reactions without being consumed in the reaction. They are able to be successful with this increase in speed because they are able to lower the activation energy required to reach the transition state of the molecules. Note that without enzymes, a reaction would require more energy to attain the required transition state. When an enzyme is used, neither the equilibrium concentrations nor the energy released by the reaction changes.
Enzymes are proteins and are only able to help speed up reactions because of their specific interactions to the substrate - the actual reactant in the molecule. For the above reaction, it proceeds very slowly without an enzyme - however, once the enzyme sucrase is added in the reaction vessel, the reaction proceeds very quickly. Note that the substrate, sucrose, has been broken down at the end of the reaction.
Most enzymes are proteins - which have specific three-dimensional shapes (conformations) that give them their unique and precise ability to bond accurately with their specific substrate. It can be assumed that only one enzyme can catalyze one specific substrate. The substrate bonds to the enzyme at the active site - the region of the protein that usually appears as a pocket or groove. The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and shape of the substrate. This specificity is known as the lock and key model.
Enzymes are proteins that have specific 3D shapes. Such shapes, as mentioned above, are very specific should not be disrupted. If the conformation changes, the enzyme will no longer be able to adequately bind to the substrate - leading to a failed reaction. Enzymes can be affected by both temperature and pH. Usually, enzymes have specific conditions under which they can operate (there is a little fluctuation in the conditions - but not much). When the conditions are no longer optimal for the specific enzyme, it will cease to function correctly.
Many enzymes require nonprotein helpers (cofactors and coenzymes). Enzymes may also be regulated (a good idea to conserve valuable resources within a cell). Certain chemical selectively inhibit the action of specific enzymes. A competitive inhibitor will bind to the active site to stop the protein from being able to bind with the substrate. A noncompetitive inhibitor binds to the enzyme at some other location other than the active site - this changes the shape of the active site, thus stopping the reaction.
The allosteric site is a receptor site on an enzyme - this site may have a regulatory molecule bond to it - thus allowing for allosteric regulation.
Enzymes also utilize a system in which end products can be used to inhibit earlier processes within the reaction chain. This process of using a product along a pathway to stop the pathway at a primary reaction is known as feedback inhibition.