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Animal Physiology 3. Digestion and metabolism

How animals obtain, process and absorb the nutrients needed to sustain their metabolic work.
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Animal physiology is, to use a common phrase, how animals work. 

Animals are, in one sense, machines, and the aim of the science of physiology is to understand how these machines function—what drives them, how they operate, the interaction of the various systems they comprise, and the physical and chemical constraints on how they work. 

Animals are also organisms, and this course is intended to help you understand how animals work as integrated units, i.e. as organisms. We will be concerned with how organisms’ various components work to keep an animal alive, with how these are coordinated, and how the various types of animals, despite their disparate evolutionary histories, solve common physiological problems, sometimes in remarkably innovative ways.

This course is the third in a series of courses that, together, would be the equivalent of a one-semester course in animal physiology. I strongly recommend that you take the first two courses in the series, Animal Physiology 1. Respiration and gas exchange, and Animal Physiology 2. Blood and circulation, before you take this course. The next course in the series is Animal Physiology 4. Temperature, water and metabolic rate

This course is intended for the upper-division biology student. It is also a good course for graduate students and practicing professionals looking for a brush-up course in animal physiology. I presume that you come into this course with the background in chemistry, physics, mathematics and biology that can be reasonably expected of a senior biology student.

The course consists of about six  hours of video clips, parceled into seven lectures.

Who is the target audience?
  • This course is aimed at the upper-division and graduate student in the life sciences.
  • Life-long learners interested in the nature of adaptation and the biology of animals can also profit from this course.
  • This course is not intended for the lower-division college biology student, or for students in high school biology.
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What Will I Learn?
Understand the nature of metabolic fuels and their role in sustaining metabolism.
Understand how the oxidation of carboydrates differs from oxidation of lipids, and how they are similar.
Understand the unique metabolic challenges of using amino acids as fuels.
Understand the fundamentals of digestion, including how food is broken down into absorbable nutrients in the gut.
Understand how carbohydrates, amino acids and lipids are absorbed across the intestinal epithelium, and the mechanisms that power absorption.
Understand the optimization principles underlying gut design, and how these principles guide the adaptations of guts to varying food quality.
Understand how gut function is controlled by the network of neural and hormonal feedbacks within the gut.
Understand the higher level control of appetite, including how these integrate with gut level control mechanisms.
Understand the nature of the metabolic rate, including that it is fundamentally an energy consumption rate.
Understand the major sources of variation in metabolic rate among the animals, including body size and metabolic 'lifestyle.'
View Curriculum
  • A basic knowledge of physics, biology and mathematics through algebra. High school level is adequate, introductory college level is preferable.
Curriculum For This Course
Expand All 40 Lectures Collapse All 40 Lectures 06:16:16
Lecture 14 Digestion
6 Lectures 58:56

Carbohydrates are one of three major classes of molecules that can serve as sources of energy and materials for animals. Carbohydrates are very versatile molecules, existing in a variety of stereoisomers. They can also polymerize in various ways, enabling them to serve as stores of energy and structures.

KW: metabolism; nutrition; carbohydrate; lipid; protein; energy; monosaccharide; disaccharide; glucose; fructose; galactose; lactose; glycosidic linkage; polysaccharide; starch; glycogen;

Preview 14:48

Lipids or water insoluble molecules can also serve as stores of energy. Lipids exist in a variety of forms, including fats, fatty acids, sterols, and waxes.

KW: metabolism; nutrition; lipid; fat; fatty acid; saturated; unsaturated; sterols; cholesterol; steroid hormones; honey guide; honey badger;

Preview 09:16

Proteins are the only food molecule that can serve as a source of nitrogen. Proteins are polymers of amino acids. Proteins are broken down into their constituent amino acids, and the amino acids can be degraded for fuel.

KW: metabolism; nutrition; protein; amino acid; peptide linkage; hydrolysis; dehydration;

Lecture 14_3 Proteins

Carbohydrates can be metabolized anaerobically through the glycolytic pathway. They can also feed in carbon through the Krebs cycle and electron transport chain in the mitochondria to be metabolized aerobically. Carbohydrates and fatty acids have certain common points in their metabolism that allow them to share common pathways for capturing energy.

KW: metabolism; nutrition; carbohydrate; fatty acid; glycolysis; aerobic respiration; acetate; pyruvate; Krebs cycle; acetyl coenzyme A; mitochondrion; and a symbiosis; lactic acid; ethanol;

Lecture 14_4 Carbohydrate and fatty acid metabolism

Proteins can also be metabolized for energy, but metabolizing amino acids poses a significant problem in the generation of a toxic waste product, ammonia. Metabolizing amino acids involves a complicated relationship between the mitochondrion and the cytoplasm. The toxic ammonia generated by protein metabolism can be detoxified in various ways, including conversion to urea and uric acid.

KW: metabolism; nutrition; protein; amino acid; peptide linkage; ammonia; urea; ornithine; mitochondrion; uric acid; purine metabolism; energy cost;

Lecture 14_5 Protein metabolism
Lecture 15 Digestion and absorption
6 Lectures 01:05:00
Lecture 15 Intro. Digestion and absorption

Nutrition involves taking food in the form of meals and converting them into nutrients that can be of sort across the intestinal wall. This is done through a sequence of different processes, ranging from physical rendering of the food, to acid digestion in the stomach, to absorption of amino acids and sugars in the small intestine, to emulsification of fats, and then to the recovery of water, salts, and other nutrients in the colon.

KW: digestion; food; nutrients; mouth; salivary gland; amylase; saliva; stomach; acid; pepsin; protein digestion; small intestine; exocrine pancreas; bicarbonate; bile salts; liver; emulsification; proteins; amino acids; fat; fatty acids; micelle; complete digestive tract; incomplete digestive tract; deuterostome; protostome; chime; trypsin; gut flora; reabsorption;

Lecture 15_1 Digestion

Absorption of nutrients across intestinal wall uses energy to actively transport sugars and amino acids across the intestinal epithelium. Central to this is the standing gradient mechanism, in which a cell uses energy to establish a potential energy gradient in one form that can be used to actively transport other materials. The standing gradient mechanism is illustrated by the absorption of water across the intestinal epithelium, in which ATP energy is used to transport sodium and establish a potential energy gradient and osmotic potential, which drives water absorption across the intestinal epithelium.

KW: digestion; standing gradient; belly patch; water reabsorption; sodium transport; intestinal epithelium; aquaporin; sodium channel; water balance; colon; crypt; active transport;

Lecture 15_2 The standing gradient

Absorption of sugars in amino acids across the intestinal wall uses a standing gradient mechanism in which glucose and amino acids are piggybacked onto a sodium carrier, which translocates both sodium and the sugar or amino acid into the epithelial cell. The standing potential energy gradient is maintained by sodium transport out of the cell which keeps the sodium concentration within the cell low. In addition to the standing gradient mechanism, absorption of sugars involves a series of complex enzymatic reactions that ultimately convert various disaccharides and stereoisomers of glucose into glucose.

KW: digestion; sugar absorption; amino acid absorption; standing gradient; sodium transport; fructose transport; galactose; lactose; hydrolase; sucrose; isomerization; brush border; facilitated diffusion; lactose intolerance; cultural evolution; dairy husbandry;

Lecture 15_3 Sugar and amino acid absorption

Absorption of fats involves the physical translocation of the micelles formed in the small intestine across the intestinal wall, and into the lacteal vessels. In the process, the lipid micelles are turned into a lipoprotein known as a chylomicron, which is transported to the liver for further modification. Fat absorption and metabolism continues through the use of lipoproteins acting as shuttles for lipids between cells, adipose tissue, and the liver. Specifically, fat transport involves the conversion between two common classes of lipoproteins, the very low density lipoproteins, or VLDLs and the intermediate density lipoproteins, or IDLs.

KW: digestion; micelles; endocytosis; exocytosis; chylomicron; lacteal; liver; adipose tissue; cells; very low density lipoprotein; VLDL; intermediate density lipoprotein; IDL; dietary fat; shuttle; bile salt; protein; phospholipid; VLDL to IDL ratio;

Lecture 15_4 Fat & fatty acid absorption

Cholesterol metabolism is a special case of lipid metabolism, in part because cholesterol plays a vital role in a number of cell functions. Cholesterol is absorbed in the diet, and is transported around the body on a lipoprotein shuttle system, similar to that for dietary fats. The lipoproteins involved in the cholesterol metabolism are in a different class of lipoproteins called the low density lipoproteins or LDLs, and the high density lipoproteins, or HDLs. These form part of a larger regulatory system in which cholesterol levels within the cells and blood are regulated.

KW: digestion; cholesterol; HDL; IDL; high density lipoprotein; low density lipoprotein; shuttle; liver; cells; cardiovascular disease; LDL to HDL ratio; bile salts; cholesterol export; dietary cholesterol;

Lecture 15_5 Cholesterol
Lecture 16 Optimizing gut function
5 Lectures 51:05
Lecture 16 Intro. Optimizing gut function

Optimizing gut function can be modeled by using diminishing returns theory. Specifically, diminishing returns theory seeks to ask the question “For how long should a meal be retained within the digestive system to optimize the obtaining of nutrients from it?” Optimum gut function can sometimes mean expelling a meal even if there are considerable undigested nutrients left in it.

KW: digestion; sea anemone; incomplete digestive tract; diminishing returns theory; chemical kinetics; nutrient extraction rate;

Lecture 16_1 Optimizing digestive tracts

In the complete digestive tract, diminishing returns theory accounts for all the costs of obtaining the meal and having a digestive tract ready to process it, as well as nutrient and energy that can be extracted from the meal. Guts can be optimized for two different functions: for increasing the maximum yield of energy, or maximizing the net energy yield rate. Each propose an optimum retention time for digesting food, which sets, among other things, and optimum that links.

KW: digestion; complete digestive tract; diminishing returns theory; chemical kinetics; net energy yield; net energy yield rate; optimum retention time;

Lecture 16_2 Optimizing tubular digestive tracts

Diminishing returns theory lets us calculate how diet quality affects optimum retention time, and from there, optimum gut length. Optimum gut length is set by a combination of a foods energy density, and metabolic demand. Low-quality foods generally require high-quality foods.

KW: digestion; food quality; energy density; bulk flow rate; optimum retention time; optimum gut length; metabolic rate;

Lecture 16_3 Food quality

Many diets contain a mixture of high-quality foods and low-quality foods. It’s therefore difficult to provide an optimum gut length for such mixed quality diets. The high-quality component require short retention times, while the low-quality component requires long retention times. Animals balance these conflicting demands by essentially building two digestive tract into one, providing diversion chambers for the low-quality components to digest longer. In animals, this adaptation arises in three different ways:-hindgut fermenters, foregut fermenters, and coprophagy.

KW: digestion; mixed diet quality; hindgut fermenters; fore gut fermenters; cecum; ruminant; stomach; esophagus; fundus; cardia; pylorus; rabbit; coprophagy;

Lecture 16_4 Mixed quality diets
Lecture 17 Control of digestion & appetite
4 Lectures 33:47
Lecture 17 Intro. Control of digestion & appetite

Digestion involves a coordinated and sequential processing of a meal as it passes through the gut. There are three basic phases to digestion: a cephalic phase, a gastric phase, and an intestinal phase. Digestion is characterized by various levels of hormonal control and interaction between these phases. The endocrine glands behind this control are the tissues of the digestive tract itself.

KW: digestion; cephalic phase; gastric phase; intestinal phase; gastrin; cholecystokinin; CCK; pancreas; gallbladder; bile; stomach acid; gastric motility; duodenum; secretin; gastrointestinal peptide; GIP;

Lecture 17_1 Control of digestion

Control of appetite is tied in with the bodys system of pleasure, reward, and learning. Appetite is regulated through an interaction between the brain’s limbic system, and systems of appetite regulation located in the medulla of the spinal cord.

KW: digestion; cephalic phase; pleasure reward system; limbic system; medulla; ventral tegmentum; nucleus accumbens; appetite regulatory network; orexigenesis; anorexigenesis; anorexia; neuropeptide Y; melanocyte stimulating hormone;POMC; MSH; pro-opiomelanocortin;

lecture 17_2 Appetite control 1

Control of appetite is also tied in with feedbacks onto the cephalic phase of digestion from the stomach and intestines. There are various levels of hormonal control, with hormones secreted from adipose tissue, the stomach, and the large intestine that feedback onto the appetite control centers of the brain.

KW: digestion; cephalic phase; appetite regulatory network; orexigenesis; anorexigenesis; anorexia; neuropeptide Y; melanocyte stimulating hormone; POMC; MSH; pro-opiomelanocortin; adipose tissue; leptin; fundus; ghrelin; colon; peptide YY; pancreas; insulin; glucagon;

Lecture 17_3 Appetite control 2
The metabolic rate
6 Lectures 56:38
Lecture 18 Intro. The metabolic rate

The metabolic rate is fundamentally a rate of energy consumption, energy used to do the order producing work that underlies all of life. Thermodynamically, all this energy is ultimately released as heat. This enables one to measure and animals total metabolic rate by measuring its total rate of heat production, a method known as direct calorimetry.

KW: energetics; metabolic rate; free energy; second law of thermodynamics; entropy; heat production; direct calorimetry; ice calorimeter; Antoine Lavoisier;

Lecture 18_1 The metabolic rate

The thermodynamic aspect of metabolic rate is inevitably coupled to chemical metabolism, that is the oxidation of metabolic fuels such as carbohydrates, lipids, and proteins, to provide free energy to do order-producing work. Because the oxidation of metabolic fuels is a chemical process, chemical metabolism has a stoichiometric relationship to energy metabolism. One can measure metabolic rate, therefore, by measuring the consumption rate of metabolic fuels, and their oxidants, mostly oxygen, or by measuring the production rate of chemical wastes, such as carbon dioxide. This is a method known as indirect calorimetry.

KW: energetics; metabolic rate; chemical metabolism; carbohydrates; lipids; indirect calorimetry; stoichiometry;

Lecture 18_2 Indirect calorimetry

Methods of measuring metabolic rate through heat production rate, or oxygen consumption rate, always involve restraint of the animal, either in a metabolic chamber, or tied to an instrument via a respiratory mask. These methods do not allow the measurement of metabolic rates of animals in their natural environments, or engaging in their normal behaviors. There is a method of indirect calorimetry, known as the doubly-labeled water technique, which allows the measurement of metabolic rates of free ranging animals in their natural environments. This method uses clearance rates of isotopes of oxygen and hydrogen from the body. Here, we explain how tracer isotopes can be used to estimate the water turnover rate in an animal’s body.

KW: energetics; metabolic rate; isotope; protium; tritium; oxygen 18; turnover rate; water balance; evaporation; respiration; defecation; urination; indirect calorimetry; doubly labeled water;

Lecture 18_3 Doubly-labeled water 1

The method of doubly-labeled water involves measuring the turnover rates of two isotopes contained within water, tritium for hydrogen, and oxygen 18 for oxygen. By measuring the clearance rate of these two isotopes, one can estimate both the water turnover rate of the body, and the carbon dioxide turnover rate of the body. The latter is related stoichiometrically to the metabolic rate. The technique of doubly labeled water, therefore, allows one to measure the metabolic rates of animals in their natural environments and engaging in their natural behaviors.

KW: energetics; doubly labeled water; isotopes; tritium; oxygen 18; turnover rate; carbon dioxide turnover rate; stoichiometry; indirect calorimetry;

Lecture 18_4 Doubly-labeled water 2

Respiratory quotient is the ratio of carbon dioxide production over oxygen consumption. This value differs between metabolic fuels. Carbohydrates, for example, have respiratory quotients of 1. Lipids, on the other hand, have respiratory quotients that are considerably less, about 0.7. By measuring the respiratory quotient one can estimate several important things about an animal’s chemical metabolism. For example, one can estimate the mix of metabolic fuels, that is, the proportions of carbohydrates and lipids being consumed. The respiratory quotient also enables one to estimate the energy equivalence between moles of oxygen consumed, and joules of energy produced. This quantity also varies depending upon the mix of metabolic fuels.

KW: energetics; respiratory quotient;, RQ; oxygen consumption rate; carbon dioxide consumption rate; energy equivalence; proteins; amino acids;

Lecture 18_5 The respiratory quotient
Body size and metabolic rate
6 Lectures 53:34
Lecture 19 Intro. Body size and metabolic rate

Compared to the remarkable diversity of form amongst animals, variation of metabolic rate among animals is reducible to just two dimensions: body size, and metabolic lifestyle. Body sizes of animals range over nearly 18 orders of magnitude of mass. This requires us to think about variation in a different way. In this lecture, we introduce you to some important mathematical and conceptual tools you will need to be able to analyze any variation that is due to body size, metabolic rate included.

KW: body size; scaling; allometry; power equation; logarithm; body mass; body length;

Lecture 19_1 Body size and metabolic rate 1

How should metabolic rate scale with body size? There are many likely possibilities, which we explore here. For example, for many years, variation of metabolic rate was assumed to be limited by the surface area of the skin through which an animal can lose metabolic heat. This relationship, in which metabolic rate scales to the two thirds power of body mass, was known as the surface law. As it turns out, metabolic rate scales by unusual exponent that is close to three fourths. This stands out as one of the major unresolved problems in comparative physiology.

KW: scaling; surface law; two thirds power; three fourths power; metabolic rate; body size; power equation; logarithm; Kleiber;

Lecture 19_2 Body size and metabolic rate 2

One prominent explanation for the three fourths power law is that it is a statistical error. Specifically, it has been argued that variation of metabolic rate within animal types follows the surface law, namely two thirds power scaling. This explanation does not account for the three fourths power scaling of metabolic rate that seems to characterize variation across different animal types.

KW: surface law; Heusner; statistical artefact; regression analysis; metabolic rate; variance; scaling;

Lecture 19_3 A statistical artefact?

An ingenious explanation for the three fourths power law can be derived from mechanical considerations. Animals and trees are elastically similar, that is their risk of elastic failure appears to be the same across all body sizes and animal types. Applying elastic similarity criteria to the muscles, which are the major source of the metabolic consumption of energy, yields a scaling exponent of three fourths.

KW: elastic similarity; three fourths power law; muscle mechanics; buckling failure; animal shape; metabolic rate; scaling;

Lecture 19_4 Elastic similarity?

Fractal scaling represents a peculiar kind of geometry in which shape can vary with size, but form is held constant. The exchange surfaces of animals for respiratory gasses, nutrients and wastes are fractal surfaces. This may put a peculiar scaling limitation on metabolic exchange rates, which may explain a three fourths power scaling in a physiologically meaningful way. It seems not to be a complete explanation, however.

KW: fractal geometry; Koch snowflake; similarity; lung; exchange; metabolic rate; scaling;

Lecture 19_5 Fractal scaling?
Metabolic lifestyle
6 Lectures 50:47
Lecture 20 Intro. Metabolic lifestyle

Another major source of variation of metabolic rate is the so-called metabolic lifestyle. Animals metabolic rates parse into two dramatically different energy use patterns. On the one hand are mammals and birds, which generate considerable amounts of metabolic heat to maintain a warm and steady body temperature. On the other hand are nearly every other animal of the animal kingdom, which use metabolic energy sparingly, and do not expend considerable amounts of energy on regulation of the body temperature. These two very different energy lifestyles correlate with significant differences of mitochondrial density.

KW: metabolic rate; energy misers; energy wastrels; mitochondria; body size;

Lecture 20_1 Metabolic lifestyle

The existence of energy wastrels poses an interesting evolutionary question. What are the selective advantages of expending 90% of your metabolic energy budget to the wasteful production of heat rather than the production of offspring? There is a plausible explanation for this, but only if the high metabolic rate of energy wastrels enables them to command enough energy to outcompete the more energetically efficient energy misers.

KW: metabolic rate; energy misers; energy wastrels; reproduction; fitness; selection; growth; energy budget; homeostasis;

Lecture 20_2 Energy budgets and fitness

The selective advantage of being an energy wastrel is predicated on the ability it confers to command a large metabolic stream of resources and energy. How this ability comes about is probably due to the effects of high metabolic rate on efficiency of locomotion. Specifically, animals that are energy wastrels should be able to run faster more efficiently than energy misers can. The evolutionary question turns, therefore, on how metabolic lifestyle affects the locomotory capacity of animals.

KW: metabolic rate; energy misers; energy wastrels; fitness; running speed; aerobic scope; cost of transport; momentum;

Lecture 20_3 Aerobic scope

Animals with high metabolic lifestyles have the same aerobic scopes as do animals with low metabolic lifestyles. However, because of the height resting metabolism of energy wastrels, their ability to run a robust we at higher speeds is much greater than that for energy misers. This difference is the key to understanding how animals with a high-energy metabolic lifestyle can outcompete those animals that are more efficient and sparing in their use of metabolic energy.

KW: metabolic rate; energy misers; energy wastrels; fitness; running speed; symmorphosis;

Lecture 20_4 Locomotory capacity

The selective advantage of a high metabolic rate lifestyle is predicated on the ability of energy wastrels to cover large amounts of territory. This ecological dimension of metabolic lifestyle can be quantified by estimating the effects of metabolic rate and body size on the daily movement distance and home range of sizes of different kinds of animals.

KW: metabolic rate; energy misers; energy wastrels; fitness; daily movement distance; daily energy expenditure; snakes; colubrid; Brown racer; reproduction; carnivore; non-carnivore;

Lecture 20_5 Selection on metabolic lifestyle
Animal Physiology 3: Wrap up
1 Lecture 06:29
Animal Physiology 3: Wrap up
About the Instructor
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Physiologist, Scientist, Writer, Media Maker

I am a Professor of Biology at the State University of New York College of Environmental Science and Forestry in Syracuse, New York.

I am a physiologist by training but with a deep interest in the interface of physiology, ecology, adaptation and evolution. You can read some of my thoughts in two books I have published: The Extended Organism: The Physiology of Animal-Built Structures (2007) and The Tinkerer's Accomplice: How Design Emerges from Life Itself (2007), both published by Harvard University Press. I have completed a third book, Purpose and Desire: Biology's Second Law, which I hope will be published soon.

My current research focuses on the problem of emergent physiology in social insect colonies. specifically the mound building termites of southern Africa.

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