So What Are Enzymes Anyway?

by Mark (Biscuit Boy) Rogers

Enzymes are among the most important biomolecules found in all living organisms.  They are large, structurally diverse proteins that catalyze or accelerate a wide variety of chemical reactions that are critical to sustaining life.  Enzymes are not living entities,  but they do, however require very stringent conditions in order to maintain their activity.  The scope, diversity, and specificity of the reactions they catalyze make them some of the most complex, fascinating, and essential molecules found within the cells and organs of all living things.  

Enzymes catalyze a truly astounding number of chemical reactions, and it is their ability to speed up these reactions under physiological conditions, (mild temperature, small pH variance, and in essentially aqueous solution) that make them both critical to life and truly remarkable.  The rate enhancement of enzyme catalyzed reactions can be as great as 10¹⁴ times that of the uncatalyzed reaction.  A key feature of catalysis is that the catalyst is unchanged throughout the course of the reaction, and can be used over and over again.  Despite the spectacular advances in our understanding of chemical processes over the last century the laboratory chemists of our age have not developed a repertoire of such diverse and reaction specific catalysts that work under mild conditions that even approaches those of living organisms.  Since structure is key to the understanding of how enzymes function, it is here where we will start our discussion.  

The majority of enzymes are proteins, large molecules made up of amino acids.  Amino acids are multifunctional organic molecules composed of the elements carbon, hydrogen, oxygen, nitrogen, and in some cases sulfur.  Proteins have four levels of structure.  Amino acids bond together in long chains, called peptides, to form the primary structure of proteins.  The order and spatial arrangement of the amino acids is unspecified.  As the chain length increases the proteins take on secondary structure.  Secondary structure  refers to regular, recurring arrangements in space of adjacent amino acids in a polypeptide chain.  Tertiary structure refers to the spatial arrangement among all amino acids in a polypeptide chain. It is the complete three-dimensional structure of the polypeptide.  Proteins with several polypeptide chains have one  more level of structure, quaternary structure, which refers to the spatial relationship of the polypeptide chains or subunits in the protein.  The feature of enzymes that sets them apart from other proteins is that they catalyze chemical reactions.  This is a direct result of the unique structure of each enzyme.  That in turn is a result of the amino acids present, their order, and how this results in the overall three-dimensional structure.  The business end of an enzyme is the active site.

The high rate of molecular turnover, the degree of reaction specificity, and the incredible rate enhancement of enzymes, all arise out of the unique structure of each enzyme.  Although enzymes are large molecules and the overall totality of the structure is critical to its activity, the active site, the place where the reaction that is catalyzed takes place is often comprised of only a small number of amino acids.  Often times only one or two of these actually participate directly in the chemical reaction.  The remaining amino acids are present to carry out two main functions.  First, they help bind the substrate, the molecule undergoing the chemical transformation, and second they stabilize the transition state structure.  The transition state structure is the transitory structure of the molecule being transformed as it goes from reactant, (the molecule before the chemical reaction), to product, (the molecule after the chemical reaction).  Stabilization of the transition state is what produces the incredible rate enhancements exhibited by enzymes.  Transition state stabilization is structure specific and therefore a function of the amino acids present in the active site.  Without the enormous catalytic rate enhancement produced by enzymes enough cellular processes could not take place to sustain the delicate balances required for life, and thus our pets, ourselves and all other life would simply cease to exist.

In addition to catalysis another very important feature of enzymes is the specificity of the reactions they carry out.  The specificity can be broken down into two main components.  The first component relates to the type of reaction the enzyme catalyzes.  Similar to to transition state stabilization, specificity of reaction type is characterized by the amino acids present in the active site as well as any co-enzymes associated with the enzyme and or any metal or metals in the active site.  The second component is related to substrate, (reactant molecule), specificity.  Families of enzymes can can catalyze a specific type of reaction or reactions, but each structurally unique enzyme may only recognize one specific substrate molecule.  For this reason enzymes work in a series.  That is to say they act in organized sequences, each carrying out one step in a series of single step transformations to either build up or breakdown molecules.  One direction takes large molecules and breaks them down into simpler components and the other takes simple building blocks and constructs large complex molecules required for an organism to function.

An important feature in substrate specificity is the energy required in binding the substrate in or near the active site.  The binding energy of the product produced by the chemical reaction catalyzed by the enzyme must be much less then that of the substrate.  This is important to understand.  The binding energy of the substrate to the enzyme must be sufficiently strong and unique to to allow substrate specificity but not to strong that the reaction cannot take place and so that the product molecule can diffuse out of the active site.

The true beauty of enzymes is their ability to meet all these criteria simultaneously.  The amino acids in and around the active site bind the substrate molecule by interacting with its unique structural features.  This is interaction is strong enough and unique enough that the substrate binds near the active site and is held in the correct spatial orientation so that the chemical reaction can proceed.  The binding energy of the product molecule is, in contrast, just weak enough that the product is released leaving the enzyme to carry out another catalytic cycle.  Finally, and perhaps most importantly, the active site is constructed so that the transition state structure (the transient structure that is part way between the reactant molecule and the product) is stabilized.  This lowers the energy required for the chemical reaction to take place and is the basis for the catalytic nature of an enzyme.  The enzyme is unchanged throughout this entire process and is, therefore, ready upon release of the product, to carry out another catalytic cycle.

Although quite remarkable in and of themselves enzymes do not always act alone.  In many instances they need “helper molecules”, or metal ions.  These helper molecules can take the form of metal ions in or near the active site, or co-enzymes, or both.  Metals ions are normally permanently bound to the enzyme and play a vital role in their activity.  Examples include, copper, zinc, iron, magnesium, etc.  Replacement of these ions by heavy metals such as lead, mercury, or thallium, or arsenic, (found in some rat poisons) cause the enzyme to loose activity and are the result of heavy metal poisoning in our pets and ourselves.  Co-enzymes include many of the vitamins used in the supplements we give our pets in addition to the foods we feed them.  Co-enzymes are organic molecules that can either be covalently bonded to the enzyme or diffuse in and out of the active site region as needed.  Both metal ions and co-enzymes are critical to the activity of many enzymes and although they are found in most foods it is also of great benefit to add them to pet foods or administer them separately as supplements.  Because of their critical role in enzymatic activity vitamin deficiency can cause a variety of disease states.  Two common examples are scurvy and rickets - the result of vitamin C and vitamin B₁ deficiency respectively.

As mentioned, enzymes are proteins and, therefore, prone to denaturation.  Denaturation is the break down of the structure of proteins on any of the four structural levels mentioned previously.  Any change in the structure of enzymes, causes a loss in function, and or activity.  Denaturation can occur by heating proteins or by treating them with alkali or acid.  When proteins are heated such as in cooking even at low temperatures, they rapidly lose their structural integrity.  This is not a problem in nutritive proteins but is a series problem with enzymes.  Once an enzymes structure is compromised, it permanently loses activity.  Enzymes are rapidly denatured in the stomach and, thus, lose all activity.  Most digestive enzymes are active in the small intestine, far removed from the caustic effects of stomach acids.  Only a small number of enzymes are so constructed that they can briefly survive the harsh conditions of the stomach, and these have highly specialized “built in” protections.  

For these reasons, the enzymes found in the foodstuffs used in pet food formulations do not survive the cooking process used to prepare canned and kibbled pet foods.  Likewise, they do not survive the conditions in the stomach and are therefore unavailable to aid in digestion or any other process.  In order for enzymes to be of any use as a supplement they must be added to the food after cooking in very large quantities or coated in some way to protect them from the initial digestive process of the stomach.  The only other method of introduction of enzymes or proteins in general is by means of injection - which is of no use with digestive enzymes.  Unless there is a disease state present, all the enzymes needed for digestion are produced by the animal, where and when they are needed.

Enzyme deficiencies can cause a variety of disease states  Some of these disease states are the result of a deficiency of a particular enzyme or family of enzymes.  In other instances, a disease state or malfunction of a particular organ can cause a decrease in the production or release of enzymes.  An example of the latter is pancreatitis, which is an inflammation of the pancreas.  Pacreatitis causes a decrease in the production and/or release of the digestive enzymes protease, lipase, and amylase.  These represent a family of enzymes responsible for the digestion of the three types of foods animals eat.  Proteases digest proteins, lipases digest fats, and amylases digest carbohydrates, (sugars).  They are produced in, and excreted by, the pancreas.  Pancreatitis can sometimes be effectively treated by supplementation of these enzymes by adding them to pet foods just prior to feeding.  They need to be administered in relatively high doses so that some of them survive the acid conditions of the stomach.  In human pancreatitis they are coated so that they do not release until they reach the small intestine.  This is just one example.  There are many problems associated with the lack of production, over production, release of, or regulation of enzymes.

Since enzymes catalyze virtually every biochemical process inside the cell it is no surprise that they are very highly regulated.  This regulation is extremely complex and beyond the scope of this discussion.  However, it is valuable to mention that inhibition of enzymes and modulation of their regulatory processes represents one of the most important areas in drug design.

Remember enzymes are not living entities!  They are truly remarkable molecules that require very specific conditions, co-factors or co-enzymes, and regulatory molecules to keep them functioning properly.  The finely orchestrated interplay of the myriad of conditions that ensure proper enzymatic activity make enzymes one of the most remarkable and fascinating of all biomolecules that make life possible.  Even the slightest disruption of any these conditions can have deleterious or even fatal consequences for living organisms.  Their importance and complexity can not be overstated.  However, their beauty can be simply appreciated!