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Animal Physiology 1. Respiration and gas exchange

Energetics, thermodynamics and adaptation
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This is a course in the physiology of animals, or, 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 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 five hours of video clips, parceled into six lectures. This is the first module of four similar courses. This module covers respiration. Subsequent modules cover blood and circulation; digestion and metabolism; and heat and water balance. All four comprise one semester of a two-semester course in animal physiology.

Who is the target audience?
  • This course is intended for upper-division undergraduates in biology, as well as graduate students looking for a brush-up course in animal physiology.
  • Life-long learners interested in the nature of adaptation and the biology of animals can also profit from this course.
Students Who Viewed This Course Also Viewed
What Will I Learn?
understand how life is a thermodynamic phenomenon.
understand why oxygen is important to the evolution of metabolism.
understand what metabolism is and how to quantify it.
understand the difference between respiration and fermentation.
understand diffusion and Fick's law.
understand the Fick principle and how it differs from Fick's law.
understand the derivation of the ventilation / perfusion ratio and how it constrains the performance of gas exchange organs.
View Curriculum
  • Preparation for this course includes the course work an upper-division biology student can reasonably be expected to have. Thisincludes general biology, general chemistry, organic chemistry, physics, perhaps some biochemistry and ecology.
Curriculum For This Course
Expand All 50 Lectures Collapse All 50 Lectures 05:13:47
Section 1. Thermodynamics of life
7 Lectures 28:10

Physiology is a science marked by many divisions. The question we want to explore here is whether there is a unified set of principles that can cover all the different kinds of physiologies that are out there.

KW: reductionism; Ernest Rutherford; thermodynamics;

Preview 04:06

Thermodynamics is a set of principles that unifies all the different kinds of physiology. Physiology is governed by three principles. The first is the law of conservation of energy, or the first law of thermodynamics.

KW: thermodynamics; first law; conservation of energy;

Preview 04:45

Even though energy is conserved as is transformed from one form into another, the conversion is not perfect. Any work producing transaction inevitably involves a certain loss of heat. This is the second law of thermodynamics, or the law of increasing entropy.

KW: second law of thermodynamics; entropy; Sadi Carnot; Rudolf Clausius; salt balance; ATPase; potassium; sodium;

Lecture 1_3 Second law of thermodynamics

There is a third law of thermodynamics that defines the concept of temperature. Rather than a temperature scale set on arbitrary limits, like the freezing or boiling points of water, the third law of thermodynamics allows us to set a thermodynamic temperature that properly describes what temperature is, namely an energy density.

KW: third law of thermodynamics; thermodynamic temperature; Kelvin temperature; Celsius temperature;

Lecture 1_4 Third law of thermodynamics

The three laws of thermodynamics were formulated for so-called closed thermodynamic systems. Closed thermodynamic systems are those in which energy can neither enter nor leave, but this does not describe the typical thermodynamics of living systems. These are so-called open thermodynamic systems in which energy flows through the system and create order in the process.

KW: open thermodynamic system; closed thermodynamic system; salt balance; equilibrium; dynamic;

Lecture 1_5 Open thermodynamic systems

The general definition of physiology we see can be found in thermodynamics, in particular the thermodynamics of open systems, which energy flow is. In this light physiology is the study of the dynamics of systems that spontaneously create order and sustain it.

KW: homeostasis; dynamic disequilibrium; super organisms; scalability; free energy; entropy reduction;

Lecture 1_6. What physiology is
Lecture 2 Respiration and fermentation
7 Lectures 40:55
Lecture 2 Intro. Respiration & Fermentation

Glucose is the principal energetic fuel for all animals. Glucose is oxidized to carbon dioxide and water, consuming oxygen in the process. Glucose is broken down by a complicated set of reactions that basically involves a flow of electricity: taking electrons from their bonds in glucose and oxygen, and allowing them to flow down the electrochemical gradient in a controlled way that enables the animal cell to capture the energy in glucose into ATP.

KW:glucose; oxidative phosphorylation; ATP; glycolysis; Krebs cycle; electron transport; electron flow; oxidation potential; carbon dioxide; water; oxygen;

Lecture 2_1 Oxidation of glucose

Glucose can be oxidized either aerobically, that is in the presence of oxygen, or anaerobically, that is, in the absence of oxygen. Even though the two are related, they are two different types of oxidation reduction reaction. In the absence of oxygen glucose is fermented, while in the presence of oxygen, glucose is oxidized. There’s a fundamental distinction between these two types of breakdown processes. Glycolysis, the principle reaction in the absence of oxygen is a fermentation reaction, while the breakdown of glucose in the presence of oxygen is the phenomenon of respiration.

KW: respiration; fermentation; glycolysis; electron acceptor; oxidation-reduction; redox potential; NAD; electron shuttle;

Lecture 2_2 Fermentation and respiration compared

Despite it being a requirement for oxidative phosphorylation of glucose, oxygen is actually a deadly poison, in part because it has such a strong oxidation potential. They can also generate highly reactive molecules known as oxygen radicals, which can be very damaging to the complex molecules and structures of cells. So why is oxygen so important?

KW: redox potential; oxidation potential; metabolic power; electronegativity;

Lecture 2_3 Why oxygen?

Oxygen is a dangerous molecule because of its tendency to form so-called oxygen radicals. These are highly reactive substances that are formed when oxygen accepts the electrons released from the oxidation glucose. Much of the cells metabolism and health depends upon a complex system of managing these oxygen radicals.

KW: redox potential; mitochondrion; superoxide; oxygen radical; super oxide dismutase; metalloprotein; hydrogen peroxide; peroxisome; peroxidase;

Lecture 2_4 Oxygen radicals

The ability of animal cells to exploit the high oxidation potential of oxygen while managing oxygen’s toxicity requires a very complex metabolism. This complex metabolism is the result of the metabolic merger between two great kingdoms of life, the prokaryotes, or bacteria, and the eukaryotes, the nucleated cell.

KW: prokaryotes; eukaryotes; evolution; symbiosis; symbiogenesis; mitochondrion; flagellum;

Lecture 2_5 The origin of complex metabolism 1

The evolution of animals first required the evolution of the eukaryotic cell. The evolutionary origins of the eukaryotic cell, and the ability to effectively manage oxygen is the end result of a process called symbiogenesis; which stands out as a radically different theory of evolution.

KW: prokaryotes; eukaryotes; symbiogenesis; endosymbiosis; Lynn Margulis; mitochondrion; organelle; photosynthesis; oxygen;

Lecture 2_6 The origin of complex metabolism 2
Lecture 3 Respiratory gas flux
7 Lectures 43:29
Lecture 3 Intro. Respiratory gas flux

Oxidative metabolism requires that oxygen be delivered to the cells at the correct rates, and that carbon dioxide be removed to the environment, also at a similar rate. These rates are determined by the chemical stoichiometry of glucose oxidation. Ultimately this is determined by the animals energy demand, its metabolic rate.

KW: oxidative metabolism; glucose; oxygen flux rate; carbon dioxide flux rate; metabolic rate; stoichiometry;

Lecture 3_1 Respiratory gas fluxes

Measuring the metabolic flux rates of oxygen and carbon dioxide requires us to have a clear understanding of how to express concentration of gas. There are a variety of means of doing so, including partial pressure, molar concentration, small fraction, and many others.

KW: partial pressure; atmospheric pressure; gas mixture; small fraction; ideal gas law; Dalton’s law of partial pressure; energy density; altitude;

Lecture 3_2 Quantifying gas concentrations

Oxygen and carbon dioxide ultimately must dissolve in water to be able to flow from the environment to the cells. This is true whether the animal lives in air or water. We need to be very clear about what governs the solubility of gases, which is quantified by Henry’s law.

KW: Henry’s law; Bunsen solubility; molar flux rate; oxygen; carbon dioxide; nitrogen; temperature; ideal gas law; gas constant; gas constant;

Lecture 3_3 Henry's law

Partial pressure is often used as a measure of gas concentration, but this can be misleading, particularly when the gas makes the transition from the gaseous phase into the aqueous phase. This confusion can be cleared up by realizing what pressure is, it’s a measure of the energy density of gas molecules.

KW: partial pressure; energy density; phase change; gaseous phase; aqueous phase; gas concentration;

Lecture 3_4 More about partial pressure

Gases are generally poorly soluble in water. Carbon dioxide is a special case, because it reacts with water in a manner that is quite different from how other gases like oxygen or nitrogen dissolve in water. We need a special language to talk about how carbon dioxide dissolves in water.

KW: carbon dioxide; carbonic acid; bicarbonate; weak acid; apparent solubility; acid dissociation constant; pH; anion ratio;; Henderson-Hasselbalch equation;

Lecture 3_5 Carbon dioxide solubility

Delivering oxygen to the cell, and taking carbon dioxide away, as well as most of the exchange steps for these gases involves the process of diffusion. Diffusion is governed by Fick’s law, which is a fundamental component of a general theory of respiratory gas exchange.

KW: diffusion; Fick’s law; diffusion coefficient; oxygen; nitrogen; diffusion barrier; shape factor;

Lecture 3_6 Fick's law of diffusion
Lecture 4 Diffusion / solubility gas exchangers
10 Lectures 01:03:38
Lecture 4 Intro. Diffusion-solubility gas exchangers

Some types of animal systems are limited by the diffusion flux of gases. The bird’s egg provides a good example of how Fick’s law can help us understand it basic physiological process. Respiratory gas exchange across the bird’s egg shell is limited by diffusion, and it illustrates the problem of relying solely on diffusion as a medium for respiratory gas exchange.

KW: diffusion; Fick’s law; bird’s egg; porosity; egg membranes; chorioallantois; pores; partial pressure; diffusion barrier;

Lecture 4_1 Diffusion gas exchange in birds' eggs 1

The respiratory gas flux for a bird embryo is limited by diffusion across its porous eggshell. Fick’s law helps us understand the function of this physiological process, as well as the limitations inherent in diffusion gas flux.

KW: diffusion; Fick’s law; bird’s egg; porosity; egg membranes; chorioallantois; pores; partial pressure; diffusion barrier;

Lecture 4_2 Diffusion gas exchange in birds' eggs 2

Diffusion is a process that operates at small scales, at the millimeter scale or smaller. Respiratory gas exchange for animals operates that much larger scales. To be large, it has always been thought that animals needed some additional mechanism to supplement diffusion gas exchange. This is only partly true, which we can see by a deeper exploration of Fick’s law.

KW: Fick’s law; diffusion; diffusion coefficient; air; water; circulatory system; insect; dragonfly; Permian; Mesozoic; atmospheric oxygen concentration;

Lecture 4_3 Diffusion limitations on body size

Insects have a radically different system for delivering respiratory gases to their cells. Whereas the vertebrates rely on a circulatory system that transports respiratory gases in blood, insects have a system that delivers oxygen to the cells solely by diffusion. Given the right conditions, diffusion gas exchange does not limit body size astringently as had always been thought.

KW: Fick’s law; diffusion; diffusion coefficient; air; water; circulatory system; insect; dragonfly; Permian; Mesozoic; atmospheric oxygen concentration; trachea; tracheole;

Lecture 4_4 Diffusion gas exchange in insects

The tracheal system of insects is largely a diffusion-based system, but it is also part of a broader system of gas exchangers known as mixed diffusion solubility pumps. These systems use site differentials in the solubility in diffusion rates of different gases, notably carbon dioxide, to pull off some remarkable tricks of gas exchange. One of these is the phenomenon of discontinuous respiration, which is commonly found in insects that are adapted to arid conditions.

KW: diffusion; tracheal system; insect; mixed diffusion solubility pump; discontinuous respiration; carbon dioxide; oxygen; water vapor; mitochondrion; spiracle; carbon dioxide;

Lecture 4_5 Mechanisms of tracheal gas exchange

One of the most remarkable differential diffusion solubility pumps can be found in aquatic spiders and insects. These creatures are obligate air breathers, however they have secondarily return to water. Key to their ability to do so is the development of the so-called bubble gill. This and the next three lectures will consider how these remarkable structures work. We start here with a remarkable experiment that gave a counter-intuitive and illuminating result.

KW: bubble gill; Richard Ege; tracheal respiration; insect; diving bell spider; back swimmer;

Lecture 4_6 Bubble gills 1 An anomalous experiment

To understand how bubble gills work, we need to understand something about the physics of bubbles. Bubbles are inherently unstable structures and water, owing largely to the very strong surface tension that typically develops at air water interfaces.

KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability;

Lecture 4_7 Bubble gills 2 Instability of bubbles

The bubble gill of insects operates as a true guilt, that is it’s a device for extracting oxygen from water. It’s ability to do so relies on the differential diffusion and solubility coefficient’s of oxygen and nitrogen. This leads to the interesting conclusion that it is nitrogen that makes a bubble gill work as it does.

KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability; gill factor; oxygen; nitrogen;

Lecture 4_8 Bubble gills 3 How a simple bubble gill works

Bubble gills are generally unstable structures, because their ultimate fate is collapse. Animals with bubble gills have to periodically come to the surface, not to pick up more oxygen, but to pick up for nitrogen, which helps keep the bubble inflated for a long time. Certain insects can stay permanently underwater, and they have the ability to prevent the collapse of their bubbles.

KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability; plastron gill; water boatman; cuticle hair; meniscus;

Lecture 4_9 Bubble gills 4 A permanent bubble gill
Lecture 5 Ventilation / perfusion gas exchangers
9 Lectures 56:36
Lecture 5 Intro. Ventilation / perfusion gas exchangers

Most gas exchange organs of animals bring together two streams of fluid: an extra stream of fluid, either air or water, which is called the ventilation stream, and an internal fluid, blood, which is known as the perfusion stream. These represent so-called convection – diffusion – convection exchangers, more compactly expressed as ventilation – perfusion exchangers.

KW: respiratory gas exchange; gill; lung; convection; diffusion; ventilation; perfusion; heart;

Lecture 5_1 Ventilation-perfusion gas exchangers

A ventilation – perfusion gas exchanger requires a different level of analysis than diffusion gas exchangers. In diffusion, gas exchange is analyzed by Fick’s law. Ventilation and perfusion involves another mode of analysis, embodied in what is called the Fick principle.

KW: respiratory gas exchange; Fick principle; ventilation; perfusion; oxygen flux; arteriovenous difference; volume flow rate; oxygen consumption;

Lecture 5_2 The Fick principle

Any physiological oxygen delivery system has to be able to match the delivery of oxygen, calculated with the Fick principle, with cellular demand for oxygen, or metabolic oxygen consumption. Sometimes, changes in demand are more rapid than the circulatory system can deliver. In these cases, a reserve capacity of blood becomes vital.

KW: respiratory gas exchange; Fick principle; ventilation; perfusion; oxygen consumption; oxygen flux; arteriovenous difference; oxygen reserve capacity; venous oxygen concentration;

Lecture 5_3 Matching supply with demand

The fish gill is one of the most efficient gas exchangers to be found among the animals. The structure of the fish gill is important to its function. Among other things, the structure of the fish gill sets up a so-called countercurrent exchange system, in which the flow of the ventilated fluid is opposite in direction to the flow of the perfused fluid.

KW: respiratory gas exchange; fish gill; countercurrent exchange; ventilation; perfusion; gill arch; gill filaments; pharyngeal cavity;

Lecture 5_4 The fish gill 1

The fish gill employs what is called a countercurrent exchange system, in which the flows of blood and water run anti-parallel to one another. Countercurrent exchange is best understood by comparing it with a so-called co-current exchanger system, in which the two fluids run parallel with one another. This analysis reveals that countercurrent exchange can extract a greater proportion of gas from the ventilated fluid, even though both gas exchangers rely simply on diffusion to bring about the exchange.

KW: respiratory gas exchange; fish gill; countercurrent exchange; co-current exchange; ventilation; perfusion; diffusion; efficiency;

Lecture 5_5 The fish gill 2

Gills are ventilated by a complex two-phase pump known as the bucco-pharyngeal pump, which operates in two phases. The first phase is powered by a complicated motion of the jaw, which expands the buccal cavity of the mouth. The second is a complicated motion of the operculum, which expands the opercular cavity behind the gills. The result is a continuous one-way flow of water across the gills.

KW: respiratory gas exchange; fish gill; ventilation; bucco-pharyngeal pump; buccal cavity; opercular cavity; operculum; jaw; mandible; hyomandibular bone; quadrate bone; maxillary bone;

Lecture 5_6 Fish gill ventilation

The function and design of gas exchangers like the fish gill are best understood by the equation known as the ventilation perfusion ratio. The ventilation perfusion ratio is derived from the Fick principle, and combines it with the principle of conservation of mass to yield a very powerful equation which embodies the interplay between fluid flow, storage capacity, and extraction efficiency of gas exchangers.

KW: respiratory gas exchange; ventilation perfusion ratio; metabolic rate; Fick principle; solubility; partial pressure difference; conservation of mass;

Lecture 5_7 The ventilation / perfusion ratio 1

The ventilation/perfusion ratio provides a powerful tool for analyzing the design of gas exchange organs, because conservation of mass demands that the ventilation / perfusion ratio must always tend towards a value of 1. This means that a change of one term of the ventilation perfusion ratio must be accompanied by compensatory changes in the other terms.

KW: respiratory gas exchange; ventilation perfusion ratio; conservation of mass; solubility coefficient; oxygen demand; Bunsen solubility;

Lecture 5_8 The ventilation / perfusion ratio 2
Lecture 6 Blood and the respiratory pigments
9 Lectures 01:17:44
Lecture 6 Intro. Blood and the respiratory pigments

The ice fish inhabits the Antarctic, and it has no hemoglobin in its blood. This fish can tell us quite a bit about ventilation, perfusion and gas exchange.

KW: respiratory gas exchange; hemoglobin; Bunsen solubility; oxygen; ventilation; perfusion; ventilation/perfusion ratio; ice fish

Lecture 6_1 The ice fish

Hemoglobin is a metalloprotein that is involved in respiratory gas exchange, particularly oxygen. It is built around iron, which reversibly exchanges oxygen with the surroundings.

KW: respiratory gas exchange; hemoglobin; porphyrin; heme; iron; copper; embryonic hemoglobin; oxygen binding; carbon monoxide; blood cell size;

Lecture 6_2 Hemoglobin structure

The dissociation curve is a useful tool for quantifying the dynamics of oxygen exchange in respiratory pigments.

KW: respiratory gas exchange; hemoglobin; oxygen affinity; dissociation curve; saturation; p50; myoglobin; sigmoid; cooperativity;

Lecture 6_3 The oxygen-hemoglobin dissociation curve

The Fick principle governs diffusion gas exchange. Hemoglobin enters into the analysis by decoupling oxygen exchange from partial pressure.

KW: respiratory gas exchange; Fick principle; Bohr shift; oxygen affinity; acidification; blood acidity; apparent solubility; beta;

Lecture 6_4 Hemoglobin and the Fick principle

The dissociation curve for hemoglobin is sigmoid, which indicates a complex change of affinity as hemoglobin become saturated. This is unusual among respiratory pigments.

KW: respiratory gas exchange; dissociation curve;, sigmoid; cooperativity; myoglobin; oxygen binding; affinity; fetal hemoglobin; adaptation; evolution; Bohr shift;

Lecture 6_5 Oxygen binding kinetics

The animal kingdom has many different respiratory pigments besides hemoglobin. The common features of these various pigments points to an interesting evolutionary origin of these remarkable pigments.

KW: respiratory gas exchange; hemerythrin; hemocyanin; chlorocruorin; respiratory pigment; iron; copper; evolution; metalloprotein; oxidation reduction potential;

Lecture 6_6 Evolution of respiratory pigments

Hemoglobin does more than transport oxygen. It also plays a significant role in transporting carbon dioxide about the body.

KW: respiratory gas exchange; carbon dioxide; hemoglobin; bicarbonate; acidification; carbamino; chloride shift; carbonic anhydrase; anti-port;

Lecture 6_7 Hemoglobin and CO2 transport

Hemoglobin is a combination of protein and metal. The composition of the protein part, the globin, affects hemoglobin’s oxygen binding kinetics. This means that hemoglobin binding kinetics is subject to adaptation by natural selection.

KW: respiratory gas exchange; evolution; adaptation; body size; Bohr shift; Delta p50; p50; Allometric scaling; mouse; elephant; specific metabolism; capillary density; diffusion;

Lecture 6_8 Adaptation in hemoglobin binding
Animal Physiology 1: Wrap up
1 Lecture 03:15
Animal Physiology 1: 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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