∞ generated and posted on 2016.04.09 ∞

The kidneys are responsible for filtering blood, which they turn, at least initially, into a product that is known as glomerular filtrate.

The kidneys, going from the outside in, consist of the renal cortex, the renal medulla, including the renal pyramids, and the renal pelvis. Nephrons, the functional units of urine formation, are found first in the renal cortex, including in terms of glomeruli and Bowman's capsule, along with within the renal medulla.

This page contains the following terms: Excretion, Excretory organs, Urinary system, Nitrogenous waste, Ammonia, Urea, Kidneys, Nephron, Blood filtration, Glomeruli, Glomerular filtrate, Bowman's capsule, Tubular reabsorption, Tubular secretion, Renal cortex, Renal medulla, Renal pyramids, Renal pelvis


Removal of small substances from the body such as via the kidneys.
Excretion is a normal function of the body, one which in concert with what can be described as metabolism — removal of materials from the body by breaking down those materials — is responsible for making sure that substances that would be toxic to the body at high densities do not build up within the body.

Excretion is effected by a number of organs that together can be described as having excretory functions and, thus, are excretory organs. The primary excretory organ, however, is the kidney and the primary excretory organ system is the associated urinary system.

Excretion and metabolism are terms used as well within the context of pharmacology, that is, the study of drug function. There excretion, a.k.a., elimination, is removal of a drug from the body in an intact form, and therefore which can have environmental consequences! Metabolism, by contrast, is the chemical breaking down of a drug, often by the liver, into a different, often less harmful form. Yes, drugs typically are harmful to the body as well as helpful, and particularly harmful if present within the body at too-high concentrations.

Links to terms of possible interest: Active transport, Ascending limb of loop of Henle, Amino acids kidneys, Collecting duct, Descending limb of loop of Henle, Distal tubule, Drugs, elimination, Excretion, Excretory organ, Glucose kidneys, H>+ kidneys, H>2O kidneys, HCO>3 kidneys, Kidneys, Inner medulla, K>+ kidneys, NaCl kidneys, NH>3 kidneys, Nutrients kidneys, Outer medulla, Passive transport, Proximal tubule, Renal cortex, Renal medulla, Salts kidneys, Urea kidneys, Urinary system

The above video is provides a quick overview of excretion, particularly in terms of the urinary system.

The above video is more of a why kidneys are important video rather than one that describes the anatomy of the urinary system. Still, it provides an admittedly somewhat superficial explanation of why or at least what we do or don't excrete, while at 4:00 minutes there is a sad but actually slightly relevant story of sea monkeys.

Excretory organs

Kidneys, large intestine, liver, lungs, lymph nodes, skin, and spleen.
The kidneys filter the blood, removing especially excess salts, water, and nitrogenous waste. The large intestine excretes especially materials deposited into the alimentary canal by the liver, particularly breakdown products of heme as otherwise associated, e.g., with hemoglobin. Heme in particular is broken down into the fecal pigments, bilirubin and biliverdin. The liver additionally detoxifies various chemicals including numerous drugs, but crucially generates urea as well.

The lungs "excrete" carbon dioxide in the course of gas exchange. The lymph nodes and immune system more generally can convert foreign materials, such as infecting microorganisms, into breakdown products that are then deposited into the blood for subsequent excretion. The skin excretes salts as well as some nitrogenous wastes—indeed you can conceptualize the kidneys in part as an elaboration on the functioning of the skin. The spleen is involved in red blood cell breakdown and associated heme destruction for subsequent breakdown and excretion.

Links to terms of possible interest: Artery, Bilirubin, Biliverdin, Bronchiole, Bronchus, Carbon dioxide, Common bile duct, Dermis, Epidermis, Excretion, Excretory organ, Excretory system, Gallbladder, Hair, Hair follicle, Hepatic artery, Hepatic vein, Large intestine, Liver, Lungs, Lymph nodes, Nitrogenous waste, Portal vein, Skin, Spleen, Sweat gland, Trachea, Urea, Vein

The above video provides a broad overview of excretory organs, particularly not focusing solely on the urinary system.

Urinary system

Kidneys, ureters, bladder, and urethra.
The kidneys are a primary excretory organs which are involved in the removal of excess salts (ions, ones that in this case are present in blood), nitrogenous wastes, and excess water (again as found in the blood). The urinary system in terrestrial vertebrates, such as ourselves, is substantially involved as well in the retention of water by the body, just as is the large intestine. Excess ions along with nitrogenous waste thus are excreted using relatively small amounts of water such that urinating does not result in body dehydration any more than it has to.

As noted, and as presumably is obvious, the primary product of the urinary system is urine, with the kidneys generating urine and the ureters, bladder, and urethra involved in a combination of directing the flow of urine (to out of the body) and otherwise storing urine prior to its movement out of the body.

Links to terms of possible interest: Aorta, Bladder, Excretion, Excretory organs, Kidney, Nitrogenous waste, Renal artery, Renal vein, Ureter, Urethra, Urinary system, Urine, Vena cava

The above video is an excellent introduction to the urinary system.

The above video mostly does a good job of providing an overview of the functioning and importance of the urinary system though I'm not convinced that they use all of their terms or arrows accurately, so watch with an, ahem, grain of salt.

Nitrogenous waste

Breakdown products of especially amino acids but also nucleic acids that must be removed from the body.
The primary nitrogenous waste is the compound ammonia (NH3), which is generated from amino groups (–NH2) that partly make up, for example, amino acids (hence the name, amino acid). Ammonia is particularly damaging to body tissues so ammonia, towards body protection, is quickly converted by the liver, via what is known as the urea cycle, to the less-toxic compound, urea. Urea is less toxic but is still dangerous if it accumulates within the body so is eliminated from the body via excretion by the kidneys.

Links to terms of possible interest: Amino acids, Amino groups, Ammonia, Excretion, Nitrogenous excretory products, Nitrogenous waste, Toxic, Urea, Uric acid

The above video is a little off topic, answering the question (sort of) of why nitrogen is so important that we end up with having to put up with its wastes, i.e., in the course of covering the nitrogen cycle (though the phosphorus cycle as well). It also helps to connect the dots by providing some clue as to what happens to urine once it's released from bodies.


Nitrogenous waste that, if allowed to accumulate, results in a rising of the pH of tissues.
Ammonia is a product of the breakdown of amine-carrying molecules such as amino acids. It has the chemical formula of NH3 but can be more stable if it acquires an additional hydrogen ion (H+) to become an ammonium ion (NH4+).

Because hydrogen ions are key determinants of a solution's pH, with more hydrogen ions meaning a lower pH and therefore a more acidic solution, the removal of hydrogen ions by ammonia has the opposite effect, raising the pH and therefore making a solution less acidic. Though that might not sound like a bad thing, if we assume acid is bad so less acid must be good, in fact in normal body tissues this essentially is too much of a "good" thing. A pH that is raised by ammonia to above the normal, healthy, more or less neutral pH, that is, makes the blood too basic, which essentially means too not acidic.

As too high a blood pH is not a good thing, excess ammonia within the body must be eliminated, either via excretion or instead via chemical conversion into something less noxious. That chemical conversion, in ourselves, is into urea, though this conversion can be impaired given liver dysfunction, resulting in a condition known as hyperammonemia. Aquatic organisms, such as fish, instead simply excrete ammonia, but are not happy critters should ammonia build up in their environment such as their fishtank!

Links to terms of possible interest: Ammonia, Ammonium ion, Bacterial proteins, Cellular protein, Colon, Dietary proteins, Endogenous, Hyperammonemia, Kidney excretion, Liver, NH>3 urea cycle, NH>4+ urea cycle, Nitrogenous waste, Portal circulation, Proteases, Systemic circulation, Urea, Urea cycle, Ureases

Biochemistry of the urea cycle, truly simplified but still a tiny bit complicated.


Less-toxic nitrogenous waste product of the chemical reaction between two molecules of ammonia and one of carbon dioxide.
Urea is synthesized in the liver from ammonia that is generated when amino acids are used as a source of energy, necessitating the removal and then disposal of their associated amino group. Urea then is synthesized in the course of removal of ammonia from the blood.

It is noteworthy that urea, as well as its chemical relative, uric acid, address the requirement by land animals to conserve water since ammonia on its own is relatively easy to excrete from the body if sufficient water is excreted at the same time, something that aquatic organisms can get away with, but land animals, except those living in very moist environments, are much less able to.

Urea has the distinction of being the first organic molecule that previously had been thought to be generatable only by living things that was generated instead via chemical synthesis within the laboratory from non-organic materials. This effort helped, literally, to demystify the body and its functioning, ultimately ushering in the idea that the body could be mechanistically understood based upon chemical and physical principles, versus the concept known as vitalism.

This first laboratory synthesis of an organic molecule took place in the early 19>th century (1828). The discovery also represents what essentially is the key, early step towards development of the field of organic chemistry.

Links to terms of possible interest: Amino acids, Amino group, Ammonia, Carbon dioxide, CO>2 urea cycle, NH>3 urea cycle, NH>4+ urea cycle, Nitrogenous waste, Urea, Urea cycle

Biochemistry of the urea cycle, simplified but still pretty complicated!


Primary excretory organs involved especially in the production of urine.
The kidneys are located in the wall in the back (or dorsal wall) of the abdominal cavity. Their function is primarily in maintaining blood chemistry, that is, contributing (substantially) to the homeostasis of the blood. This contribution includes, of course, the removal of urea, while ammonia is passively removed as well. The kidneys also maintain the salt balance of the blood (i.e., that of electrolytes) and water balance of the blood and thereby the body generally.

Part of this latter function is prevention of loss of those substances found in blood that the body does not want to excrete. This includes water but also glucose (which the body transports within the blood) and amino acids (which the body also transports within the blood)

The pathway of filtration of blood and then elimination of wastes is literally convoluted but begins with the glomeruli and ends within entrance of fully formed urine into the ureters and then bladder.

Links to terms of possible interest: Adrenal gland, Ammonia, Bladder, Descending aorta, Diaphragm, Excretory organs, Glomeruli, Inferior vena cava, Kidney, Renal arteries, Renal cortex, Renal pelvis, Renal pyramid, Renal veins, Salt balance of the blood, Ureter, Urine

The above video provides a nice overview of especially kidney function.

The above video considers kidney anatomy.

The above video provides a nice overview of the external anatomy of the kidneys along with surrounding structures and organs.


The blood filtration, tubular secretion, and tubular reabsorption functional units of the kidney.
The nephron consists of the Bowman's capsule and associated glomerulus, the proximal convoluted tubule, the loop of Henle, the distal convoluted tubule, and associated peritubular capillaries. These structures are adjacent to and to varying degrees interact with collecting ducts. Their function is the generation of glomerular filtrate from blood and subsequent modification of that filtrate into urine. The kidneys together contain on the order of one million nephrons.

Links to terms of possible interest: Ascending limb of loop of Henle, Afferent arteriole, Blood filtration, Bowman's capsule, Collecting duct, Descending limb of loop of Henle, Distal convoluted tubule, Efferent arteriole, Functional units, Glomerular filtrate, Glomerulus, Kidneys, Loop of Henle, Nephrons, Peritubular capillaries, Proximal convoluted tubule, Renal artery, Renal vein, SEM, Tubular reabsorption, Tubular secretion, μm, Urine, Vasa recta

The above video provides a nice overview of the anatomy of nephrons.

The above video provides an overview of the basic functioning of the of a nephron.

Blood filtration

Removal of relatively small substances from plasma.
The first step of urine formation is to remove relatively small substances from blood including water, electrolytes, and urea. This occurs via a mechanism that represents an elaboration of what normally occurs within the vicinity of capillaries, that is, blood pressure forces fluids out of capillaries and into the interstitial environment (this mechanism, as it occurs in the kidneys, also provides a clue as to why excessive blood pressure can result in kidney damage). The difference between what occurs with these capillaries, possessing fenestrated endothelium, versus ordinary capillaries possessing continuous endothelium is that this pushing is more efficient in the kidneys due to the porous nature (fenestrations) of the associated capillaries (referred to collectively as glomeruli) along with the sustained high blood pressure across these capillaries.

The resulting "filtrate", known as glomerular filtrate, is collected into the nephron via a collecting cup known as the Bowman's capsule. At this point the urine contains both waste materials along with materials that are still valuable to the body. The blood that leaves the glomerulus thus is depleted in these substances. Some materials are then returned to the blood and additional removal of materials from the blood takes place in the course of what are known as tubular reabsorption and tubular secretion, respectively. The result, ultimately, is formation of urine which is depleted in materials that are useful to the body and concentrated with materials that are harmful to the body.

The above video provides a nice overview of the process known as glomerular filtration.

The above video looks at blood filtration that is not equivalent to glomerular filtration since, though formed elements are retained by a filter, blood proteins are free to flow through to the capillary tube. Thus, blood plasma is created by the devise rather that glomerular filtrate.


Network of capillaries from which the initial step of kidney function, blood filtration, occurs.
Glomeruli, or glomerulus as the singular, possess capillaries with particularly porous endothelia (fenestrated epithelium). In addition, the rest of the associated nephron, especially the proximal convoluted tubule, pulls the glomerular filtrate away from the receiving Bowman's capsule. The result is efficient generation of glomerular filtrate as pushed out of the glomeruli by blood pressure. The step is explicitly one of membrane filtration of the blood.

Links to terms of possible interest: Afferent arteriole, Blood filtration, Blood pressure, Bowman's capsule, Capillaries, Efferent arteriole, Excretion, Fenestrated endothelium, Glomerular filtrate, Glomeruli, Glomerulus, Kidney, Renal secretion, Renal vein, Tubular Reabsorption, Renal filtration, Glomerular capillaries, Peritubular capillaries, Urinary excretion

The above video provides a very nice overview of what a glomerulus is all about; it gets a little technical towards the end, though.

The above video depiction of a glomerulus is more pretty than helpful, as well as short in duration.

Glomerular filtrate

Material received by Bowman's capsule representing the product of the first step of kidney-mediated filtration of blood.
Following its generation as a more-or-less random sampling of smaller-sized components of blood, the glomerular filtrate is then modified over the course of its passage through the various tubes making up the nephron as well as the subsequent collecting duct. This modification occurs via what is known as tubular reabsorption and tubular secretion, which are processes that either remove materials from glomerular filtrate (called tubular reabsorption) or instead which add additional materials to glomerular filtrate (called tubular secretion).

In short, over the course of its movement from the renal cortex to the renal pelvis the glomerular filtrate is converted via highly specific as well as well-defined steps into urine. Because of these processes, only a fairly small fraction, about 1% of the original glomerular filtrate, remains as the fully formed urine. The original crude, size-based filtration effected by the glomeruli thus is refined over the course of a much more elaborate filtration processes as effected by the nephron and subsequent collecting duct.

Links to terms of possible interest: Afferent arteriole, Blood filtration, Blood flow, Bowman's capsule, Capillary endothelium, Collecting duct, Efferent arteriole, Fenestrae, Glomerular capsule, Glomerular filtrate, Glomerulus, Kidney, Nephron, Proximal convoluted tubule, Renal cortex, Renal pelvis, Tubular reabsorption, Tubular secretion

The above video is a visually stunning look at kidney function, with substantial emphasis on the formation of glomerular filtrate.

The above video (repeated from above) provides a nice overview of the process known as glomerular filtration.

Bowman's capsule

Nephron receiving point of glomerular filtrate.
The Bowman's capsule is a cup-shaped structure that partially encloses a single glomerulus, with a single Bowman's capsule present per nephron. The path of glomerular filtrate thus is out of the capillaries making up the glomerulus and into the Bowman's capsule. From there it passes into the proximal convoluted tubule and then to the rest of the nephron.

Links to terms of possible interest: Afferent arteriole, Bowman's capsule, Capillaries, Capsular space, Efferent arteriole, Glomerular filtrate, Glomerulus, Kidney, Nephron, Podocyte, Proximal convoluted tubule, Visceral layer

The above video provides a look at some of nephron functioning, with arguably emphasis on the role of Bowman's capsule.

Tubular reabsorption

Facilitated removal of substances from forming urine into the blood.
The majority of material that enters the nephron from the glomerulus is then removed from the glomerular filtrate via various intentionally nephron- or collecting duct-effected processes. The result is a recovery of the vast majority of material originally lost from the blood during glomerular filtration. In this way the initial filtration step need not be highly selective other than in terms of the size and, to a degree, the electrical charge of materials that are able to move out of the blood. Subsequent selectivity is a function, at least in part, of this reabsorption of valuable materials back out of the nephron.

Tubular reabsorption specifically is the movement of materials out of glomerular filtrate to reduce losses of materials from the blood during filtration at the kidneys. Nearly all of the material originally received by the Bowman's capsule as glomerular filtrate, other than a substantial amount of water, is reabsorbed back into the blood in the course of this process of tubular reabsorption. This in fact is a key means by which the kidneys regulate the chemistry of the blood. Whereas the glomerular filtrate represents a very crude mechanism of initial urine formation, removing substances from the blood almost indiscriminately, a great deal of discrimination is introduced in the course of removal from the filtrate via tubular reabsorption of those substances that are valuable to the body, so that only that which either represents waste or instead is currently found in excess within the blood is allowed to remain in the forming urine.

Much of this reabsorption occurs within the portion of the nephron known as the proximal convoluted tubule. The removal is facilitated by processes involving either passive transport or active transport depending on the substance being reabsorbed.

Links to terms of possible interest: Active transport, Afferent arteriole, Bowman's capsule, Collecting duct, Efferent arteriole, Glomerular filtrate, Glomerulus, Kidneys, Loop of Henle, Nephron, Passive transport, Peritubular capillaries, Proximal convoluted tubule, Renal filtration, Tubular reabsorption, Tubular secretion

In the above video the story of reabsorption from the glomerular filtrate is explored in moderate detail. Yes, no matter what, the function of the kidney is a fairly complicated story to recount.

Tubular secretion

Active movement of substances from the blood into the forming urine.
These are materials that are removed from the blood, particularly from peritubular capillaries, where that removal is in addition to that removed during the formation of glomerular filtrate. These are materials that either the body is "desperately" attempting to remove from the blood or instead which the body is removing from the blood in the course of more refined regulation of blood chemistry.

The latter includes particularly removal of hydrogen ions (H+), whose removal has the effect of raising the pH of blood. This occurs in response to too low blood pH, e.g., increases in blood acidity as can follow anaerobic exercise, which releases lactic acid from muscles into blood. Other ions that are removed from blood via tubular secretion are potassium (K+), which once upon a time was so abundant in our diets that our bodies were desperate to get rid of it (so still are), and ammonia (NH4+), which of course is a particularly nasty nitrogenous waste.

Links to terms of possible interest: Amino acids kidneys, Ammonia, ATP, Blood chemistry, Bloodstream, Ca2+ kidneys, Calcium kidneys, Cl kidneys, Chloride kidneys, Glomerular filtrate, Glucose kidneys, H+, Hydrogen ions kidneys, H>20, Interstitial space, Lumen, Mg3+ kidneys, Magnesium kidneys, Na+ kidneys, Nitrogenous waste, Peritubular capillaries, Sodium kidneys, PO43– kidneys, Phosphate kidneys, Protons kidneys, Proximal convoluted tubule Tubular secretion,

The above video provides a very short overview of tubular secretion.

Renal cortex

The outer layer of the kidney where blood filtration begins.
It is within the renal cortex that one finds all aspects of nephrons except what is known as the loop of Henle and associated capillaries. This includes the initial filtration of the blood as found within Bowman's capsule and associated glomerulus, the proximal convoluted tubule, the distal convoluted tubule (and associated peritubular capillaries), and the start of the collecting duct.

Links to terms of possible interest: Distal convoluted tubule, Glomerulus, Kidney, Proximal convoluted tubule, Renal cortex, Renal medulla, Renal pelvis, Ureter

The above video introduces the kidney anatomy, starting (approximately) with the renal cortex.

Renal medulla

The middle layer of the kidney where secretion and reabsorption takes place.
It is within the renal medulla that the renal pyramids are located, including the loop of Henle, along with much of the collecting duct. The collecting ducts then pass into the underlying renal pelvis where fully formed urine is deposited. Overlying the renal medulla, by contrast, is the renal cortex, where much of urine formation takes place and the majority of nephrons are located.

Renal pyramids

Macroscopic structures making up a large portion of the renal medulla, containing loops of Henle.
Primarily within the renal pyramids are found what is known as the loop of Henle (and associated straight rather than convoluted capillaries known as the vasa recta) along with the majority of the collecting duct. The renal pyramids are found, as noted, within the renal medulla. They are pyramidal in shape with the broad portion facing the renal cortex and narrow portion facing the renal pelvis.

Links to terms of possible interest: Arcuate artery, Arcuate vein, Bowman's capsule, Collecting duct, Distal convoluted tubule, Glomerulus, Interlobular artery, Kidney, Loop of Henle, Peritubular capillaries, Proximal convoluted tubule, Renal medulla, Renal pyramid, Vasa recta

Renal pelvis

The base of the kidney where collection of urine into ureters begins.
It is at the point of passage of forming urine into the renal pelvis that urine in fact is fully formed and ready for passage through the ureters into the urinary bladder. Note that the transition from the renal pelvis into the narrower ureter is a point at which kidney stones can lodge.

Links to terms of possible interest: Bladder, Kidney, Renal pelvis, Ureter, Urethra, Urine