CAUTION: ENZYMES AT WORK
PART V: DIGESTION


We live in a world made from matter.  Matter is made up of atoms and molecules that follow the laws of nature.  All life is made up of atoms and molecules that are organized into cells.  Our body has trillions of them.  Everyone knows that we must eat food and drink liquids to keep the cells in our body alive and working properly.  And most people know that what we swallow contains nutrients that are vital for life.  There are even some who know that most of these nutrients are contained in large molecules that must first be broken down into much smaller ones before they can be taken into the body.  But what most people do not understand, or appreciate, is how the body actually accomplishes this task.  One of the most important set of molecules in the body is the enzymes.  Let’s first look at what enzymes are and what they do and then we’ll be able to better understand how they work in our digestive system to let us to take in the vital nutrients we need to survive within the laws of nature.  

Enzymes

Enzymes are special molecules (mostly proteins) that are made in the cell which help other molecules undergo chemical reactions when they come in contact with each other.  When these reactions occur energy is either released or used up and different molecules are produced.  Every biochemical process in the body requires enzymes to work properly.

Molecules are made up of atoms joined together by chemical bonds.  There are very small molecules, like molecular oxygen, which is made up of two oxygen atoms joined together (O2) and water, which is made up of two hydrogen atoms joined to one oxygen atom (H2O).  There are also slightly larger molecules, like glucose, a sugar that is made up of six atoms of carbon and oxygen joined to twelve atoms of hydrogen (C6H12O6).  And there are very large molecules, like carbohydrates, fats, and proteins, many of which are made up of hundreds or even thousands of atoms joined together. 

When molecules meet up with each other they sometimes react.  A reaction between molecules simply means that chemical bonds between atoms are created and destroyed.  This usually causes some of the atoms in the reacting molecules to change places with each other to form different molecules.  Enzymes help chemical bonds be destroyed in larger molecules to form smaller ones and be created between smaller molecules to make larger ones.  During this process energy may be released or used up.  At the end of the reaction the enzymes are not altered so they can continue to promote more reactions.  And, the total number of atoms present in the molecules that are produced at the end of the reaction is the same as there were in the molecules that reacted in the first place.  In other words, in a chemical reaction no new atoms are created or destroyed, just the bonds between them, and this often results in the release or use of energy and the atoms involved changing partners to form different molecules.       

One important example of a chemical reaction that occurs within our cells involves how they get the energy they need from the chemical bonds within the glucose molecule.  Cellular respiration uses specific enzymes to help breakdown one glucose molecule (C6H12O6), in the presence of six oxygen molecules (6 O2), to release the energy the cell needs, while at the same time producing six carbon dioxide molecules (6 CO2) and six molecules of water (6 H2O).  Notice that the chemical reaction starts off with a total of six carbon atoms, twelve hydrogen atoms and eighteen oxygen atoms from one molecule of glucose (C6H12O6) and six molecules of oxygen gas (6 O2).  And it ends up with the same total amount of carbon, hydrogen and oxygen atoms, but instead they make up the six molecules of carbon dioxide gas (6 CO2) and the six molecules of water (6 H2O).

The laws of nature determine how fast specific molecules will react with each other.  But the addition of an enzyme makes this reaction take place much faster.  By speeding things up, enzymes help to produce many more new molecules, usually in the order of thousands or millions of times more, than what would normally happen at random.  This is why enzymes are called catalysts.  They help bring molecules together to react much faster than what would happen if they were dependent on the random forces of nature alone.    

If our body were left only to the random laws of nature the thousands of chemical reactions we need to help keep us alive would not take place fast enough and we would die.  Enzymes can catalyze chemical reactions because their specific chemical nature and shape allows them to bring specific molecules together to react in a specific way.  This is similar to how hormones have their specific effect(s) in the specific cells of specific target tissues by locking on to specific receptors (see prior articles entitled Caution: Hormones At Work).  It is also important to note here that the body also produces different proteins called “enzyme inhibitors” as well.  It is the specific chemical nature and shape of the enzyme inhibitor that enables it to bind to a specific type of enzyme and by doing so either slow down or totally block its metabolic effect.  Enzyme inhibition is one of the ways the body is able to control many of its metabolic processes.

There are thousands of different enzymes in the body each of which have a specific effect on a specific molecule.  As noted above, it is the shape and chemical nature of the enzyme that determines which molecules it works on and what type of reaction it will catalyze.  The first part of the chemical name of an enzyme usually indicates the specific molecule or class of molecules for which it catalyzes reactions.   And the last part of its name usually ends in “ase”.  For example, lactase is the enzyme that helps to breakdown lactose, a sugar in milk that is made up of one molecule of glucose joined to one molecule of galactose.  And a protease is a class of enzymes that helps to breakdown proteins which are made up of two or more amino acids joined together. 

The body often uses several specific enzymes in a specific order (pathway), in a chain reaction, to bring about what is needed for survival.  The first molecule undergoes a reaction catalyzed by the first enzyme, and one of the products of that reaction becomes the second molecule in the pathway.  The second molecule, in turn, undergoes a reaction catalyzed by the second enzyme, and one of the products of that reaction becomes the third molecule in the pathway.  The third molecule, in turn, undergoes a reaction catalyzed by the third enzyme, and one of the products becomes the fourth molecule in the pathway, and so on.  This process continues until the required molecule is produced so it can do what the body needs it to do.  Note that if any one of the enzymes in the chemical pathway were to be missing or not working properly then not enough of the final product would be produced and life could hang in the balance. 

Finally, it is important to understand that since enzymes, themselves, are made up of hundreds or thousands of atoms chemically bonded together, their chemical stability and capacity to work properly can be affected by the laws of nature as well.  Things like temperature, hydrogen ion concentration and the body’s water content can affect the chemical structure of enzymes. When any of these three important parameters falls out of the normal range the enzymes in our body start to malfunction and so does our body.  Serious deviations can even result in death.  That is why our body must be able to control these three, and other vital parameters to allow us to survive within the laws of nature.  (see prior articles called Caution: Hormones At Work). 

http://highered.mheducation.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

Now that we know what enzymes are and what they do let’s see how enzymes work in our digestive system to allow us to take in the vital nutrients we need to go on living.  

Nutrients: How the Body Uses Some of Them

The three main categories of nutrients the body needs besides water, vitamins, minerals and electrolytes are carbohydrates, fats and proteins. 

Carbohydrates are generally made up of two or more sugar molecules joined together by chemical bonds.  The body uses sugar molecules, like glucose, as the main source of energy for its cells.  It also uses other sugar molecules as part of DNA and RNA and also ATP, the main molecule that stores and transfers energy within the cell.  In addition the body takes certain sugar molecules and attaches them to specific proteins and uses them as part of the tissue that makes up the bones and connective tissue.  And when the body takes certain sugar molecules and attaches them to specific lipids they become part of the tissue that insulates the nerves to help them work properly. 

Fats are complex molecules consisting mainly of carbon, hydrogen and oxygen and some of them also have phosphorus and nitrogen as well.  The body uses some of the molecules it gets from fats to provide the structure for the plasma membrane of the cell.  They are also used for storing energy that can be accessed by the body when it needs it.  The body uses these molecules to make some of the lipids it needs and places them in a fatty layer within the skin to provide insulation.  And, as noted above, some of the lipids the body produces insulate the nerves to help them work properly.  The body also uses some of the molecules it gets from fats to produce steroid hormones which help to control its growth, development and metabolism. 

Proteins are made up of amino acids, of which there are twenty different kinds, joined together by chemical bonds.  The proteins that the body produces do many different things.  Most of the enzymes needed to catalyze the chemical reactions of the body’s metabolism are proteins.  Proteins also make up a large amount of the plasma membrane of the cell.  The cytoskeleton, which gives strength and support to the cell and allows for cell division are proteins.  The molecules that transport ions (like sodium) and molecules (like glucose) across the plasma membrane are proteins.  The structures that allow muscles to contract are proteins.  The antibodies in the blood that help the immune system defend the body from foreign invasion are proteins.  The clotting factors that prevent the body from bleeding after injury are proteins.  And many of the hormones that affect the metabolism (like insulin) are proteins.  So, one can see that proteins do a lot of work in the body.  

Digestive Enzymes

Before the body can take in and use the sugars it needs from carbohydrates, the various molecules it needs from fats, and the amino acids it needs from proteins, it must first breakdown the large molecules that contain them.  If you’ve ever been to a car wash then you have an idea of how your digestive system works.  Just as the car wash applies water and soap, turns on scrubbers, and then waxes and blow dries your car as it passes through, so too, your digestive system applies various liquids and chemicals to your food and moves it along by muscular action to do its job.  And just like a car wash, instead of wasting material and energy, the body only turns on the digestive system when there’s actually something there to be worked on.  But unlike a car wash, the digestive system’s job is not to clean your food (although the acid in the stomach kills off most of the bacteria).  Its job is to breakdown the large molecules we ingest into very small ones and then bring the nutrients the body needs into the bloodstream.  It’s like a pulp and paper mill that takes huge logs and chops and mashes them up into pulp that can be used for paper and other products.  The digestive system has to chemically chop and mash up the large molecules we eat and drink so the body can get the nutrients it needs to live and work properly.  To do this job the digestive system uses many different digestive enzymes. 

The process of digestion starts as soon as food enters the mouth.  Its presence, along with its taste and smell, are detected by the nervous system which stimulates the release of saliva.  Saliva is a fluid that contains many different chemicals which not only help oral and dental health but also the swallowing of food as well.  Saliva also contains digestive enzymes, like amylase and lipase, which are the first enzymes to start working on the large molecules taken into the digestive system.  Amylase (Gk: amylon = starch) is an enzyme that helps break the chemical bonds between sugar molecules, like glucose, that are joined together in large carbohydrate molecules like starch.  And lipase is an enzyme that helps break the chemical bonds between molecules, like fatty acids and glycerol that are joined together in large fat molecules. 

Seeing, tasting and smelling food also causes the nervous system to stimulate the stomach as well.  It responds by producing gastric juice which mainly contains mucus, acid and inactive enzymes called pepsinogens.  When the pepsinogens are exposed to the acid in the stomach they become activated as pepsins which are proteases that help break the chemical bonds between amino acids that are joined together in proteins.  If pepsin were to be produced in the active state it could literally digest the stomach cells that produce it. 

The stomach also produces lipase that works on fat molecules like the lipase in saliva.  Moreover, the nervous system also triggers the stomach to send out a hormone called gastrin which tells the stomach to make even more gastric juice containing more mucus, acid and  pepsinogens.  As the stomach fills up with food and more gastric juice this causes its walls to stretch.  The stretching of the stomach wall, along with the chemical contents of the food, is detected by the nervous system and it stimulates the stomach further.  This makes it, not only produce more gastric juice, but also causes regular muscle contraction (peristalsis) so the stomach churns and mixes its contents (chyme) to help digestion.          

As the stomach works on the acidic chyme and sends it slowly into the intestine the resulting stretching of the intestinal walls signals it to start producing its own fluid.  Intestinal juice mainly contains saline, mucus, bicarbonate and digestive enzymes.  The bicarbonate is alkaline and begins to neutralize the acidic chyme the intestine is receiving from the stomach.  The enzymes produced in the lining of the intestine mainly help to break up the bonds between molecules that contain two sugars.  Maltase breaks up the bonds between the two glucose molecules that make up maltose.  Lactase breaks up the bonds between glucose and galactose which make up lactose.  And sucrase breaks up the bonds between glucose and fructose which make up sucrose (regular sugar).  The intestine also produces other enzymes as well, in particular enterokinase, a protease that is important for activating many of the enzymes that come from the pancreas.

As the mixture of chyme moves from the stomach into the first part of the intestine (duodenum) the simpler molecules that have been released, like fatty acids and amino acids, are detected by sensors on specialized gland cells.  These gland cells respond to these chemicals by sending out two hormones, secretin and cholecystokinin, which tell the pancreas to deposit its fluid into the digestive tract.  Pancreatic juice is very alkaline (as opposed to acidic) and contains high amounts of bicarbonate.  The addition of the alkaline pancreatic juice helps to neutralize the acidic chyme that has come into the duodenum from the stomach.  The pancreatic juice also contains most of the enzymes needed to finish off the digestion of the carbohydrates, fats and proteins.  In addition to amylases and various lipases, the pancreatic juice contains different proteases that break down proteins.  This includes trypsin, chymotrypsins, elastases and carboxypeptidases.  All of these proteases are produced inside the pancreatic cells in the inactive form so they won’t digest the pancreas itself.  Trypsin enters the intestine as trypsinogen and becomes activated by the alkaline environment and the enzyme enterokinase which by snipping a few atoms off changes its shape making it ready to go to work.  Trypsin then activates the other proteases mentioned above including many of the lipases as well.  Finally, since lipids are not very soluble in water they require the presence of bile, which comes from the liver and gall bladder, to help in fat digestion.  The presence of broken down fat molecules in the duodenum contributes to the release of cholecystokinin which, as mentioned above, not only tells the pancreas to release its juice but also tells the gall bladder to contract and send its concentrated bile into the intestine to help in fat digestion.  Once the carbohydrates, fats and proteins have been digested and broken down into very simple molecules, like glucose, fatty acids, glycerol and amino acids, they are readily absorbed into the bloodstream through the lining of the intestine.  

In summary, many of the vital nutrients we need to survive make up the large molecules such as carbohydrates, fats and proteins that we ingest.  The digestive system uses many different enzymes to help break the bonds between the smaller molecules contained in carbohydrates (e,g, sugars), fats (e,g, fatty acids and glycerol) and proteins (e.g. amino acids)  allowing them to be taken into the bloodstream through the intestine.  Without these digestive enzymes we could not survive.

http://highered.mheducation.com/sites/0072495855/student_view0/chapter26/animation__organs_of_digestion.html

Points to Ponder

It was the extremely high improbability of any one of the thousands of biologically significant molecules, like all the different enzymes needed for digestion, being formed by just chance and the laws of nature (never mind the need for the untold millions of each one of them to allow for life) that alerted scientists to, there having to be an intelligent agent within the cells telling them how to make them.  This is what first motivated scientists to search for and find the DNA molecule and everything else connected to it that has been, and continues to be, discovered.  But, paradoxically, modern evolutionary biologists see all of the information packed into the DNA molecule and still conclude that it all came about by just chance and the laws of nature alone rather than “a mind at work” i.e. an intelligence.  In other words, scientists, using their ability to detect intelligence, recognized that there had to be an intelligent agent inside the cell instructing it on how and when to produce these complex and vital molecules, but after finding it concluded that this intelligent agent itself had come about by chance and the laws of nature alone.  Alternatively, many people now believe and teach that it was nature itself, as the intelligent agent that through evolution, brought about DNA and all of the innovations needed for life because that was what was needed.  They seem to forget that, by definition, evolution is a blind process which has no goals.

Take a good look at yourself.  Think about the organs and tissues of your body.  How your lungs breathe air in and out.  How your heart pumps blood throughout your body to feed your cells what they need to live.  And how your nerves and muscles allow you to be aware of, and move within, your surroundings.  Now consider where all the material that makes up your body came from.  Yes, almost every molecule in your body had to first come into it through your digestive tract.  In other words, you literally are what you eat.  But most of the molecules you ingest (carbohydrates, fats and proteins) are too large to enter your body through your digestive system and into your bloodstream.  They must first be broken down (digested) into their individual parts (sugars, fatty acids, glycerol and amino acids) so they can be brought into your body so it can use them as it sees fit. 

Digestion is a controlled process that requires the body to turn on its machinery when there is actually something present to be digested and then do what it is supposed to do.  This requires the coordinated activity of (1) the nervous system and (2) several different hormones (e.g. gastrin, secretin and cholecystokinin), the release of (3) specific chemicals (e.g. acid in the stomach, bicarbonate from the intestine and the pancreas and bile from the liver and gall bladder) in addition to (4) several different classes of digestive enzymes (e.g. amylases, lipases, and proteases).  The actions of these chemicals must take place in the right part of the digestive system and be synchronized so that  proper digestion can take place to allow the body to absorb the nutrients it needs to live.

Besides the main parts of the digestive system (esophagus, stomach, intestine and colon) and the main organs that help it function (liver and pancreas) if any one of these four major parts of digestion were to be missing, or not working properly, the whole system would fail and absorbing enough nutrients would be impossible.  Dr. Michael Behe has called a system where the absence of any one part renders it useless as being irreducibly complex.  The system involved in digestion demonstrates irreducible complexity.  One must then wonder how an irreducibly complex system with so many vital parts could have come into existence while remaining functional every step along the way?  Does it make sense that this system could have come about one step at a time?  The idea is totally absurd.  They must have all come together as a system to perform a function to keep the human race alive.  But if a system is irreducibly complex does that make it automatically capable of supporting life?  If you think about it you’ll realize that there are more pieces to the puzzle that are needed, pieces that go beyond irreducible complexity, to enable these systems to keep us alive within the laws of nature.             

If instead of using several gallons of water and lots of concentrated soap a car wash splashed on just a quart of water and very small amounts of dilute soap, how likely would it be to properly clean your car?   And if the log cutters and chippers were too dull and the chemicals used to break down wood fibers in the pulp and paper mill were too weak then how could it do its job properly?  In other words, when dealing with the forces of nature, real numbers have real consequences.  The same applies to the body and how it survives in a world consisting of physical and chemical laws.  When it comes to digestion the carbohydrates, fats and proteins we take in must be acted upon by a minimum amount of chemicals and enzymes that are strong enough to get the job done.  Not just any concentration of chemicals or enzymatic activity will do.  It has to be the right amount.  Just because a system is irreducibly complex does not automatically mean it will be able to function well enough to allow for life.  Besides being irreducibly complex, systems that allow for life must also have a “natural survival capacity”.  By this I mean that each system must give the organism the capacity to survive by taking into account the laws of nature.  This usually involves having knowledge of what is needed to keep the organism alive within the laws of nature and then being able to do what needs to be done.  The organs that help proper digestion take place so the body can take in the nutrients it needs to live seem to inherently know how much chemicals and what kinds of enzymes are needed to get the job done, and they do it naturally.  The same can be said for many other control systems in the body, each of which is necessary for survival.

Given what we know about how life actually works and how easily it dies when it doesn’t have the components it needs for digestion, it is evident that there must have been several innovations within intermediate organisms with respect to them obtaining the molecules  they needed to survive.  What those innovations were and exactly how these organisms were able to get the molecules they needed in these intermediate phases may never be known.  This is because further changes which may have come about have since gone by the wayside of evolution and we can only see what is present now.  This is one way to explain how digestion may have evolved without having to seriously consider the biomolecular physiology of the now extinct intermediate organisms.  But this is not Science, where every aspect of the reverse engineering needed to come up with a plausible explanation for life should be explored before a theory is proclaimed to the public.  No, this is just faux science and wishful thinking.  It’s also how evolutionary biologists have been able to convince themselves, and others, of the supposed irrelevance or even impossibility of irreducible complexity.  Some scientists have argued that the positions of intelligent design and irreducible complexity are arguments from ignorance which lack enough imagination.  I would submit that the concerns put forth above are based on, not ignorance, but what we actually do know about how life actually works and how easily it dies.  But I wholeheartedly agree that based on current evolutionary theory in the face of the incredible complexity of life that the scientists involved do indeed have very good imaginations.  Alas, we who believe that the design seen in nature is real, and not an illusion, are forced to limit our imaginings to what is already known about what it takes for life to survive within the laws of nature.  Case in point is the innovation of having the right organs and enzymes in place, with proper control to obtain the molecules the body needs to survive.

The laws of nature have put up many obstacles to prevent life from existing.  Just as a car can die from not having enough gas for energy, or oil for seizing parts, or anti-freeze for engine overheating, so too, all physicians know that there are many different pathways to death.  If you really want to begin to understand how life came into existence, you first have to understand how easily it can become non-existent.  Did life really come about solely by random chemicals coming together to form cells, then simple organisms, and then complex ones like us?  In other words, without “a mind at work” to make it happen?  Do you think the people who own car washes just leave it up to chance as to how much soap and water they use to clean cars?   Or the owners of pulp and paper mills leave it up to chance as to how effective their equipment and chemicals are for breaking down wood fibers into pulp?  No, when it comes to the origin of life it seems to me that Science still has a lot of explaining to do.  Meanwhile, our children and the whole world, are being led astray!


Be sure to catch all of the articles in Dr. Glicksman's series, "Beyond Irreducible Complexity."



Howard Glicksman M. D. graduated from the University of Toronto in 1978. He practiced primary care medicine for almost 25 yrs in Oakville, Ontario and Spring Hill, Florida. He now practices palliative medicine for a Hospice organization in his community. He has a special interest in how the ethos of our culture has been influenced by modern science’s understanding and promotion of what it means to be a human being.

Comments and questions about this article or any of the previous ones are welcome.

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Copyright 2015 Dr. Howard Glicksman. All rights reserved. International copyright secured.

November 2015