S2C2: The Digestive & Renal Systems

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a) Nutrient absorption

I could start this chapter in the same manner as in the second section of Chapter 1 by stating that “everything evolves for a reason”. And I will. Indeed, the human digestive system developed over generations, through our long animal family tree, to supply us with chemical energy in the form of external nutrients broken down over several steps so they can be used within our internal staple metabolism.

This rationale is correct but it only provides an incomplete story because those familiar with the concept of energy conservation would be right to ask how come we can’t just keep reusing the same quantum of energy we begin with. The answer lies in the fact that whilst energy is indeed conserved, no unexpected violation there, the human body is not an isolated system and not every type of energy can be reused – you may want to revisit Series 1 Section 10.e for a brief explanation about energy dissipation outside of real systems (as opposed to idealized ones).

In our case, most of the energy dissipation outside of the human organism is in the form of heat via the process of sweating and thermal radiation, convection and conduction at the surface of the skin. Not only that but some of the chemical reactions within our body also result in some chemical energy being converted into thermal energy that cannot be made proper use of by our organism. Putting these factors together, such energy dissipation calls for a replenishment from external sources and this is where food comes in.

Food provides living organisms with vital nutrients that can undergo chemical reactions and be converted into energy. However, nutrients aren’t solely about energy, there are other substances we have come to depend on for our metabolism and to maintain homeostasis such as some amino acids, minerals, vitamins, and of course water which makes up over 60% of our body weight and is present in all our tissues and body fluids.

The digestive system spans the chain of processes at play from the time food enters our body through our mouth and extends all the way to either their excretion out of the body or their crossing into the blood, as part of the circulatory systems which we studied in Section 1.d, after which they are absorbed by diffusion into the relevant set of tissues. The main purpose of the digestive system is thus to facilitate the ingestion of food and break it down into smaller, simpler compounds that can ultimately be absorbed.

The workhorse of the digestive system is arguably the enzymes, the topic of the next section.

b) The work and world of enzymes

I will borrow straight from S1 Section 4.a and define enzymes as “proteins catalysing chemical reactions” with the clarification that “the acceleration of the reaction rate, which can reach thousand-fold, million-fold or even many orders of magnitude more, permits the effective transformation of certain kinds of molecules into other types of molecules within the span of a few milliseconds”.

This sets the scene quite neatly I think and surfaces the importance of efficiency. Let’s not forget the central purpose of nutrition in the first place which is to supply the organism with incremental energy. Digestion transforms food intake into usable chemical fuel that can bump up the metabolic rate of the organism thus making it more likely to maintain proper homeostasis, survive by avoiding predators and netting more food, and reproduce. So an organism with a more efficient digestive system will, all else being equal, have higher evolutionary fitness.

Not having a comprehensive suite of enzymes to boost the digestive process would be quite similar in its consequence to lacking food, namely it would result in a diminished metabolism, as is the case with animal torpor, hibernation or aestivation (dormancy taking place in the summer).

Before diving headlong into a short list of the main enzymes involved in human digestion and then describing the mechanics and anatomy of the digestive tract, I think it would be useful to quickly describe an example of chemical reaction being facilitated by an enzyme.

Amylases are enzymes used within our body to break down starches such as potatoes into sugars. You may want to refer to S1 Section 4.d for a description of the various carbohydrates, including polymers such as starches and shorter compounds like sugars. This splitting of macromolecules, and specifically of the glycosidic bond of starches, is achieved by hydrolysis, a chemical reaction involving water molecules that is being catalysed by the enzymes. Essentially, the H₂O molecule ends up reacting at the site of one of the glycosidic bonds and one its hydrogen atoms binds to the previously-binding oxygen atom, thus cleaving the glycosidic bond and the remaining OH becomes part of the liberated monomer.

In the case of alpha-amylase (also written α-amylase), the resulting reaction products are dextrin and maltose. The latter one may sound familiar and indeed, amylase enzymes are used in some brewing processes to produce alcoholic beverages like beer. The enzymes transform starches such as barley into mostly maltose and then a fermentation process takes place using yeast, which transforms the maltose into ethanol with carbon dioxide as one of the by-products.

The enzymes involved in human digestion are broadly grouped under 4 categories:

Lipases are produced in the pancreas and break down lipids into fatty acids and glycerol by hydrolysis.
Proteases help digest proteins by splitting them into amino acids. It starts with pepsin in the stomach, followed by trypsin and peptidase in the small intestine.
Carbohydrases deal with carbohydrates. We have just looked at amylase, which is produced both in the mouth and in the small intestine, and it is complemented by maltase that hydrolyses maltose into glucose units.
Nucleases break down nucleotides into nucleic acids. This affects RNA and DNA contained in food and happens within the small intestine. They are also used in the body for DNA repair and replication.

c) The human digestive tract

Now that the foot soldiers of digestion and the main purpose of the entire process have been introduced, we are properly equipped to follow a top-to-bottom description of the human digestive tract.

It starts right from the mouth, the point of entry of food. Through a combination of mastication (also known as chewing) and softening by the saliva, the texture of the food is altered so it can be swallowed into the oesophagus via the pharynx. By then the food has already been subjected to the action of lipase and amylase enzymes found in the saliva, a liquid secreted by salivary glands which also has other roles, including the cleaning of the mouth and teeth that helps prevent infections.

Both ends of the oesophagus are soft-sealed by sphincters but food is allowed to travel through and into the stomach thanks to the swallowing reflex and rhythmic muscle contractions. After the mouth, the stomach is the second site of active chemical breakdown of food into its constitutive nutrients. This is achieved by the release of enzymes such as pepsin (for proteins) and lipase as well as the gastric acid, a liquid with a very low pH of between 1 and 3; “pH” stands for “potential of hydrogen” and is a logarithmic scale measuring the acidity or basicity of aqueous solutions where pure water is deemed to have a neutral pH of 7. The low pH helps with enzyme activation and also serves as a defence against pathogens. In fact, this acidity is a risk the stomach needs to protect itself against, so to avoid auto-digestion (not an evolutionary recipe for success) the stomach lining produces an alkaline mucus – alkaline is a synonym for a base soluble in water, so the pH in this case would be basic or higher than 7, thus counteracting the acid gastric juice. Some, but little, nutrient absorption happens at the stomach level, mostly it is water and lipid-soluble compounds such as alcohol. Interestingly, aspirin and caffeine are also on the list, hence the rapidity with which they enter our bloodstream and take effect.

Carbohydrates are the fastest type of food to be broken down, followed by proteins, and fats take the longest, something we can all feel depending on the content of our latest meal. After one to two hours on average in the stomach, food starts its long journey through the small intestine, which is where most of the nutrient exchange takes place. This organ has a length of over 5m and folds many times in our abdomen, food will transit there on average for 4h and up to 8h. The upper part of the small intestine is called the duodenum and the very acidic chyme (that’s the technical name of the semi-liquid substance coming in from the stomach) needs to be balanced by the release of bile from the gall bladder and a few other substances. More enzymes come into action to finalize digestion and allow the crossing of nutrients into the blood vessels so they can be carried by the blood throughout the body. The transit continues through the middle section (the jejunum) and ends at the ileum.

What is left is essentially waste, which makes its way into the large intestine where the highest concentration of microbial density can be found, all part of what we generically call gut-flora or gut-microbiota. This is the main component of the human microbiome, an interesting topic deserving a full section but that would be somewhat of a digression so I will simply provide a link to the relevant Wikipedia entry at the end of this chapter. Some fermentation takes place as well in the large intestine as does further absorption of vitamins and minerals, before the faeces are excreted out of the rectum via the anus.

Quite the journey! And yet, I have left out many indispensable parts and parcels of the digestive tract. Among key players left on the bench I would single out the liver and the pancreas, at the very least because those names are well known but also because they play other interesting roles in our organism.

The liver produces the bile that is stored by the gall blader located just underneath and emulsifies dietary fats, thus helping their breakdown. This organ, the largest after the skin, also performs other key metabolic functions including the synthesis and storage of glucose and its release into the blood. It is also involved in the synthesis of cholesterol, proteins and lymph as well as in the degradation and recycling of proteins, including hormones and insulin in particular. In that sense, it truly is a multi-faceted organ indispensable in both digestion and the regulation of the human body.

The pancreas is located behind the stomach and produces digestive enzymes into the upper part of the small intestine. In addition, it is where insulin production takes place; the insulin hormone helps regulate the level of blood sugar by transporting sugar molecules away from the blood and into the muscle. When levels are low, it produces another hormone called glucagon to break down some of the glycogen stored in the liver into glucose, which makes its way to the bloodstream. In this sense, glucagon and insulin work in tandem and the liver and pancreas perform complementary tasks.

d) Fluid control and regulation

This last topic of regulation is far from being exhausted however and this is the matter we now turn our sight towards, specifically the control and regulation of the most important fluid in our body, that flowing through our circulatory system: blood.

We already mentioned the hormones intervening to maintain blood sugar level and we will explore the world of hormones as part of the endocrine system in Chapter 4. The method used by our kidneys to regulate blood content is markedly different, and one could even say much more radical: they filter blood, about 20% of the volume that traverses them in fact and since the circulatory system goes around, eventually all blood gets sifted through.

I am getting slightly ahead of myself here and before discussing filtering, we should spend some time on the regulation aspect. One of those regulation jobs is blood pressure, a subject introduced in Section 1.d, and the kidneys use a two-pronged tactic to achieve this feat: they leverage a hormone causing vasoconstriction of the blood vessels, thus increasing flow resistance and forcing a drop in pressure, and they release aldosterone, which indirectly results in an increase in plasma volume and therefore pushes the blood pressure up. This is achieved by bumping up the water retention thanks to increased concentrations of potassium and sodium.

The second regulation-related job is to maintain the acid-base balance of the blood at a steady level with a pH hovering in the narrow band of 7.32 to 7.42. Part of the homeostatic mechanisms are accomplished via our respiration and its effect on CO₂ gas pressure in the blood plasma; this is important because carbon dioxide reacts with water to form carbonic acid (H₂CO₃) that can split to form hydrogen ions (H⁺) and bicarbonate (HCO₃^–). Since those reactions are reversible, it is possible to control the pH level by removing or injecting the appropriate ions from or into the blood. For reference, a neutral pH of 7 would have an equal concentration of H⁺ hydrogen ions and OH^– hydroxide ions in the blood, and the higher the concentration in H⁺, the lower the pH and the more acidic the solution. By regulating pH, some reactions are made possible and undesirable ones are avoided.

Third among the key professional tasks of kidneys is maintaining not the pH but the electrolyte concentration level in the blood plasma, a measure called osmolality. When the salt level increases too much then it can be brought back to a satisfactory level through a combination of electrolyte removal and an addition of water, effectively diluting the salt concentration. Those mechanisms will become apparent in the next section.

e) Filtering and removing

That responsibility for maintaining the pH level of the blood, part of the second-mentioned job, requires the extraction of some ions and reintroduction of others. This takes place within the nephrons, a collection of microscopic structures that should remind us of the pulmonary alveoli since exchanges with capillaries take place there as well.

The first step in the interaction between capillaries and the nephrons is filtration, a passive mechanistic process caused by the pressure of blood over the membrane of a nephron. The filtrate then goes through another 2-way exchange with blood in different capillaries (called peritubular, literally meaning along the tube). The transfer from the filtrate in the renal tubule to the bloodstream is called reabsorption, actually quite a complex mechanism that one since it relies on pressure, diffusion and active molecular transport. Compounds that are reabsorbed include water, salts, amino acids and glucose. At the same time, some compounds make the opposite journey, from the blood into the tubule, a process called secretion. Items removed from the blood may include surplus hydrogen ions, as part of the acid-basic balance regulation, nitrogenous compounds such as uric acid, urea, creatinine or ammonium, excess electrolytes, and other toxins (defined as a product of our metabolism which is poisonous when reaching too high a concentration).

The name of this filtrate, after reabsorption and secretion, is called urine. It flows out of the kidneys into our bladder via small tubes called ureters and there waits for excretion which takes place after travelling through the urethra located in the respective genitalia of men and women.

When we think about the total volume of blood being filtered on an ongoing basis, it is no surprise we need to urinate rather frequently. And when we think about the purpose and content of urine, it is no surprise either that an analysis can reveal so much information about pathologies or the nature of nutrients or drugs that have been ingested. The yellow colour of urine is due to the end-product, after multiple degradation, of heme, a component of haemoglobin. Nonetheless, when well-hydrated and healthy, the fluid should be nearly colourless.

f) Trivia – Nutrients absorption by plants

It is not just human and other animals that rely on external nutrients, plants and fungi also do. In this section we will look at plants and we should fully expect a lot of the same processes we have just covered in this chapter to be replicated. This we should expect because we share a common ancestor with plants, and therefore a good chunk of our genetic material, and because many of the processes are purely mechanistic, diffusion for instance, so that if not exactly identical, we can foresee that analogous systems would have evolved.

The main chemical elements required by plants to grow and sustain themselves are carbon, oxygen, hydrogen, nitrogen, potassium and phosphorus.

Carbon is very much the usual suspect for any organic life form given its propensity to bind. It can be found in the cellulose, starch and proteins as well as many other compounds and it is mainly sourced from the CO₂ gas in the air during the photosynthesis, a process described in S1 Section 7.f.
Oxygen is required in some biomolecules produced by plants but the primary use is cellular respiration to produce our ubiquitous ATP molecule (for eukaryotic cells). This chemical element can be found in the air, in water and in the soil within compounds such as nitrate (NO₃^–) or sulphate (SO₄^2-).
Hydrogen is mostly sourced from water and find its way in carbohydrates (starches, sugars, cellulose).
Nitrogen goes into the production of a significant proportion of a plant cell content, into proteins, and into the chlorophyll pigment that is so central to photosynthesis. Plants avail nitrogen from the soil, mostly in the form of ammonium NH₄⁺ and nitrate.
Phosphorus is a crucial element for energy production and organic membranes due to its presence in the ATP macromolecules and in phospholipids (refer to S1 Section 4.d), respectively. And of course, it is also present in nucleic acids. The element is found in rocks and minerals, most commonly in the form of orthophosphate (PO₄^3-).
Potassium is mentioned last in this list since it is a little different and acts as both a regulator and an enhancer rather than a building block. It is indeed involved as an enzyme activator, thus speeding up many processes including photosynthesis or the formation of carbohydrates, it plays a role in moisture management, and it is (obviously) the main chemical element involved in the formation of potassium ion channels (K⁺). Thanks to the gradient they create, those are involved in transport of some molecules across the cell membrane and in regulating cell growth and turgidity – the pushing of the cell membrane against the cell wall which provides rigidity to a plant. The source of potassium is soil minerals and it is the main plant macronutrient in potash fertilizer (no prize for guessing that their name is related).

Those elements found in the air like O₂ for respiration and CO₂ for photosynthesis will make their way inside the plant via gas diffusion, similar to what happens in human respiration. For the nutrients in the soil, the entry point is the roots and accessing them entails three different mechanisms: simple diffusion, facilitated diffusion and active transport. The first of the three is the mechanism we are already familiar with and the second relies on the same passive dynamics except that the nutrients hitch a ride on transport proteins. On the other hand, active transport goes against concentration gradients and therefore requires energy in the form of ATP for nutrient uptake.

Finally, we are left with the internal transport aspect. In vascular plants, which encompasses most land plants other than mosses, there are two types of transport tissues providing mobility to nutrients contained in the fluid called sap. Xylem sap contains water and mineral ions and the prevalent scientific view is that the upward movement, against gravity, is due to intermolecular bonding between the polar water molecules (refer to S1 Section 2.d for more info on intermolecular bonding). As for phloem sap, it transports the organic molecules produced during photosynthesis, sugars in particular. The physical processes driving the movement within phloem are less well understood than for xylem and seem to involve gradients between the source of the organic substances creating a flow towards the place where they are used or stored. During a plant’s growth period, this would be from the stored sugars in the roots towards the growing areas and it would reverse when photosynthesis takes place, from the leaves to the storage areas. In reality, it is a little more complex because the push down in the phloem bears some relationship with the upward movement of water in the xylem with water at the top making its way into the phloem by osmosis and reverting back into the xylem after the sugars have exited into the storage area. Biology is complexity, isn’t it?