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INTRODUCTION
From simple viruses and single-celled organisms to the most complex ecosystems,
biology is the study of living things. The diversity of nature cannot be summed up
in a short chapter in this handbook and so this chapter will explore just a few of
the many interesting topics among the vast range of biological sciences – the very
small (microbiology), the multicellular organism level (comparative anatomy of the
respiratory and digestive systems) and the interactions among different organisms
and their environments (ecology).
MICROBIOLOGY
Microbiology is the study of organisms that are so small that you can’t see them
without a microscope. In this section, we will learn about bacteria, viruses and
prions, which are all too small to see with the naked eye!
Bacteria
Did you know that the number of bacteria living in your mouth is more than the
number of people who have ever lived?
Bacteria have been around for a long, long time. In fact, the earliest fossils of
bacteria are over 3.5 billion years old!! Having been around for so long, bacteria
have had the opportunity to evolve into a wide variety of different types, adapting
to a variety of different environments (including living inside your mouth!).
Bacteria are single-celled organisms – unlike humans, who are made up of trillions
of cells, each bacterium is just one single cell. Bacteria can be classified by their
shape, as well as by something called Gram staining.
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Table 1: Bacteria come in many different shapes!
Bacteria
Description
Example
Shape
Cocci
Sphere
Figure 1: Staphylococcus epidermidis lives in human and
other animal skin and does not commonly cause disease.
Bacilli
Rod
Figure 2: Escherichia coli (often abbreviated as E. coli)
lives in the lower intestines of birds and mammals. Some
strains of E. coli can cause serious disease and even death
(e.g., a strain called E. coli O157:H7)
Spirilla
Helix
Figure 3: Campylobacter sp. can cause food-borne
illnesses (Source: Agriculture & Agri-Food Canada)
Vibrios
Comma
Shaped
Figure 4: Vibrio vulnificus can cause infection after
eating seafood and is closely related to Vibrio cholerae,
the bacteria that causes cholera.
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Gram staining is named for Hans Christian Gram who, in 1884, invented a technique
that is still used today to identify bacteria. Using this special staining technique,
bacteria can be classified as:


Gram positive: cells that appear blue/purple when Gram stained; these
cells possess a second cell wall that contains lipid
Gram negative: cells that appear pink/red when Gram stained; these
cells have a single cell membrane (a cell membrane is the structure
that surrounds a cell, holding in all the contents in) that contains a lot
of peptidoglycan (a large molecule that surrounds the cell membrane
of the bacteria, giving structure and strength to the cell wall)
Figure 5: Gram positive staining.
The purple rods in this figure are
Bacillus anthracis, which are Gram
positive (the other cells in this
photo are white blood cells).
Bacillus anthracis is relatively
common in some animals, and can
cause anthrax, a serious disease, in
humans. Diseases that can be
spread from animals to humans are
called zoonotic diseases.
Figure 6: Gram negative staining.
The red cocci shown here are
Neisseriae sp., which are Gram
negative. Most species within the
Neisseriae family are nonpathogenic (i.e., they don’t cause
disease) and reside in the upper
respiratory tract.
There are four different ways that bacteria can obtain nutrients and energy:
1. photoautotrophs: use light as an energy source and carbon dioxide as their
carbon source to undergo photosynthesis
2. photoheterotrophs: use light as their source of energy and use organic
compounds produced by other organisms as their source of carbon
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3. chemoautotrophs: obtain energy through chemical reactions of inorganic
(chemicals that aren’t carbon-based) substances (such as ammonium and
hydrogen sulphide) and use that energy to fix carbon dioxide in a process
similar to photosynthesis
4. chemoheterotrophs: obtain their energy and carbon from organic compounds
(i.e., chemicals that are carbon-based) (just like you do when you eat food!)
“Good” Bacteria and “Bad” Bacteria
We often think of bacteria as being “bad” because many bacteria are pathogenic
(i.e., they cause disease). Examples of pathogenic bacteria include:
 Clostridium tetani causes tetanus
 Salmonella typhi causes typhoid fever
 Mycobacterium tuberculosis causes tuberculosis
 Streptococcus pyogenes can cause strep throat
 Bacillus anthracis causes anthrax
 A number of bacteria including Vibrio vulnificus, Clostridium perfringens,
Bacteroides fragilis can cause necrotizing fasciitis (more commoly known as
flesh eating disease)
 Escherichia coli O157:H7 can cause very serious food-borne illness and has
even resulted in death (Does anyone remember what happened in Walkerton,
Ontario just a few years ago???)
But did you know that many bacteria are very helpful? For example, we have
harmless bacteria that live in our digestive tract and these bacteria help to
prevent harmful microbes from growing there and making us sick. Bacteria are also
used to make fermented foods, such as vinegar, sauerkraut and yogurt.
Biotechnologists even use bacteria to clean up toxic spills and to produce
therapeutic drugs like insulin.
Viruses
Viruses have a significant impact on humans. Diseases from the common cold to
severe acute respiratory syndrome (SARS) and Acquired Immunodeficiency
Syndrome (AIDS) are products of viral infection. Scientists have worked
tirelessly for centuries to understand how these microorganisms work and to find
better ways of combating them.
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Viruses are very small, generally from 17 to 400 nanometres (a nanometre is
1/1000th of 1/1000th of a millimetre, or “very very tiny”) (define) in diameter,
approximately 1000 times smaller than the diameter of a human hair, and are
diverse in shape and complexity. Pictures of viruses resemble something out of
science fiction, with polygonal (i.e., strange, many-sided shaped) heads and little
jointed "legs" attached to tails, while others look like round popcorn.
Figure 7: Viruses come in many shapes.
Adenoviruses can cause diseases in humans
and animals. Bacteriophage infect bacteria.
Human immunodeficiency virus (HIV) causes
a disease called Acquired Immunodeficiency
Syndrome (AIDS) in humans.
Figure 8: An electron
micrograph of T4
bacteriophage.
Viruses are composed of:
 Nucleic acid: a set of genetic material packaged in a protein shell,
either DNA or RNA.
 Capsid: a structure that surrounds the DNA or RNA to protect it.
 Lipid membrane: a structure that surrounds the capsid (found only in
some viruses, including influenza; these types of viruses are called
enveloped viruses as opposed to naked viruses, which don’t have lipid
membranes).
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Figure 9: A drawing
of the human
immunodeficiency
virus (HIV) showing
its structure. Note
how the capsid
encases the nucleic
acid, and the lipid
membrane encases
the capsid.
Viral life cycle
Believe it or not, viruses are not ‘alive’. They lack both metabolism and the ability
to reproduce (i.e., produce more viruses) independently of another species.
(Metabolism refers to all the chemical processes that occur in a living cell or
organism that are needed for life). So, a virus must have a host cell (i.e., bacteria,
plant or animal) in which to live and make more viruses. Regardless of the type of
host cell, all viruses follow the same basic steps known as the lytic cycle (Figure
10):
1. The virus attaches to a host cell. Viruses have some type of protein on
the outside of the capsid or envelope that "recognize" the proper host
cells.
2. The virus injects its genetic material into the cell.
3. The viruses ‘hijack’ the cell’s replication machinery (i.e., the parts of
the cell that allows it to make new cells) to produce multiple viral
progeny.
4. The new viruses are assembled into the host
5. The viruses are released in the environment.
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Figure 10: Lytic cycle of the viruses.
(Adapted from http://science.howstuffworks.com/virus-human.htm).
Once inside the host cell, some viruses do not reproduce right away. Instead, they
combine their genetic material into the host cell's genetic material (i.e., so the cell
carries it own DNA along with the virus’s genetic information). When the host cell
reproduces, it also copies the viral genetic material along with its own (so each new
cell made has the host DNA + the virus’s genetic material). This happens without
any new viruses being produced until the cell receives a special signal (e.g., a signal
from the environment) that triggers the production of viruses. The viral genetic
instructions will then take over the host's machinery and make new viruses as
described above. This cycle, called the lysogenic cycle, is shown in the figure below
(Figure 11).
Marine Viruses: Who said viruses were bad?
Viruses are usually considered as bad. However, what we are only beginning to
realize is that viruses may play an absolutely critical role in the world ecosystem,
including the world ocean. Believe it or not, viruses are the most abundant group of
organisms in the oceans! In every millilitre of seawater there 10-100 million
viruses. Viruses from the world ocean are not a stable entity; they are sensitive to
a variety of environmental stresses, such as ultraviolet radiation (like from the
sun), which lead to their inactivation and destruction. They can only survive for a
few hours to a few days. To maintain the abundance of the viral population, viruses
must replicate and, in doing so, continually destroy many of their natural hosts,
primarily bacteria and phytoplankton (plankton are tiny organisms that drift
through the ocean; phytoplankton are plankton that use photosynthesis).
Oceanographers believe that on average, one billion viruses per litre are produced
and destroyed every few days! This results in the death of half of the ocean’s
bacteria and phytoplankton every few days!
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Figure 11: In the lysogenic cycle, the virus reproduces by first injecting its
genetic material, indicated by the red line, into the host cell's genetic instructions
(Adapted from http://science.howstuffworks.com/virus-human.htm)
The presence of viruses in the oceans can also influence the genetic diversity and
population sizes of the plankton community in many ways. Perhaps most
importantly, they can have the effect of maintaining species diversity in the ocean
environment by "killing the winner". What this means is that as the concentration
of a particular planktonic host increases, the viruses prone to infecting this
species will rapidly propagate throughout the host population, killing much of the
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population. This prevents a single species from dominating and permits the coexistence of species. For example, blue, green, and red bacteria co-habit in the
same environment. Blue bacteria however, have a greater ability to use nutrients
than the others. Therefore, the concentration of the blue bacteria would increase
until the point at which it dominates the environment. This could not only have the
result of reducing the size of the other two bacterial species, but may actually
result in their extinction. However, the presence of the virus helps to regulate the
proportion of blue, red and green bacteria in the environment, and keeps the ‘loser’
in the race.
Prions
Short for proteinaceous infectious particle, prions are only made of protein (so,
unlike bacteria and viruses, they do not contain any genetic (DNA or RNA)
information). Prions are similar to normal proteins found in the host organism, but
they are abnormally shaped and they can take the normal proteins in the host cell
and cause them to take on the abnormal shape, just like the prion.
As prions have only recently been discovered by scientists, it is still unclear just
how prions cause these diseases or how someone cathc these diseases.
Figure 12:
How prions
make new
prions.
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Prions cause a class of diseases called the transmissible spongiform
encephalopathy diseases (TSEs). “Encephalopathy” means a diease of the brain
and “spongiform” refers to the fact that the brain tissue ends up with large holes
in it, resembling a sponge. :
Examples of TSEs include:



Figure 13: A tissue section taken
from the brain of a cow affected with
BSE. Note the vacuoles (small holes in
the tissue which gives the tissue a
spongelike appearance). (Photo by Dr.
Al Jenny. Source:
http://www.aphis.usda.gov/lpa/issues/
bse/bse_photogallery.html)


scrapie (occurs in sheep)
kuru (occurred in the Foré tribe
in Papua New Guinea, who passed
on the disease through
canibalism)
bovine spongiform
encephalopathy (BSE or mad
cow disease; occurs in cows)
Creutzfeldt-Jakob disease
(occurs in humans)
variant Creutzfeldt-Jakob
Disease (vCJD) (occurs in
humans; is thought to be caused
by consuming prions from cows
with BSE
There are no treatments avaialble for TSEs and they can be fatal.
ANIMAL ANATOMY
Multicellular organisms, as the name suggests, are made of more than one (and
often many millions) cell. These cells are organised into tissues (a group of cells
that perform a particular function in an organism; e.g., connective tissue, muscle
tissue, bone, nervous tissue), those tissues are organized into organs (a group of
tissues that perform a particular function) and those organs are organized into
organ systems (a group of organs that work together to perform a particular
function, e.g., cardiovascular system, reproductive system, skeletal system). There
are many different organ systems in animals and we will be looking at two of them –
the respiratory system and the digestive system.
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The Respiratory System: A Comparative Approach
All animals need oxygen from the environment to help produce the fuel for the
different processes of living (e.g., running, learning, digesting). During the
production of the body’s fuel, carbon dioxide is produced as a waste product as
oxygen is used up. Therefore, animals must always obtain fresh oxygen and get rid
of carbon dioxide for the processes to be maintained. This is the primary purpose
of respiratory system: to release carbon dioxide and absorb oxygen.
In this section we are going to take a comparative approach to looking at the
respiratory system, which means that we are going to look at the strategies that
different animals use to breathe in different environments. We are going to start
by looking at the basic building blocks of the respiratory system for mammals.
Respiratory system building blocks
The mammalian respiratory system begins at the trachea, a stiff tube reinforced
by cartilage rings, which splits into two bronchi (singular: bronchus). You can feel
the cartilage rings in your trachea. Run your fingers along your throat. Can you feel
the ridges? Those ridges are
the
cartilage
rings!
The
bronchiole
bronchus branches many times
to form smaller tubes called
bronchioles. These bronchioles
trachea
bronchi
form a complex network of
lungs
millions of little tubes that
alveoli
lead to sacs called alveoli
thoracic cavity
(singular:
alveolus).
This
complex network forms the
ribs
lungs, which are protected by
diaphragm
the rib cage in the thoracic
cavity. A large dome-shaped
muscle called the diaphragm Figure 14: Mammaliam respiratory organs.
separates the thoracic cavity Adapted from Randall et al. (1997)
from the abdominal cavity
where the stomach and intestines are found.
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The process by which air moves in and out of the lungs is called ventilation. The
main muscle responsible for ventilation is the diaphragm (has your music teacher
ever told you to breath from your diaphragm??). Other muscles that assist with
ventilation are called the intercostal muscles and they are found between the ribs.
When the diaphragm contracts, it changes its shape from “dome-like” to flat. The
change in shape increases the space in the thoracic cavity that causes air to rush
in via the trachea (through the mouth or nose) to fill the lungs. This phase of
ventilation is inhalation. When the diaphragm is flat, it pushes all the organs in the
abdomen down so that the stomach sticks out. You can try this yourself by taking a
deep breath and imagining you are filling your lungs completely full. If you put your
hands on your stomach, you can see how far it moves out and in during every
breath.
The second phase of ventilation is the relaxation of the diaphragm that causes it
to return to its dome shape. The relaxation causes the muscle to move up and this
movement plus contraction of the intercostal muscles causes the space in the
thoracic cavity to get smaller so air is forced out of the lungs via the trachea (via
the mouth or nose). This phase is called exhalation. This type of ventilation, where
air leaves the lungs by the same way it entered, is called tidal ventilation (it moves
in and out, like the tides) and is not used by all animals.
Gas exchange
Ventilation is the means by which oxygen is brought into the body from the
environment and carbon dioxide is expelled. The blood is the primary method of
transportation within the body, so in the lungs there are lots of tiny blood vessels,
called capillaries, located in the alveoli. Both
oxygen and carbon dioxide are gases that dissolve
LUNGS
into our blood and cells so that they can be
transported around the body.
Blood carries
oxygen from
lungs to cells
Blood carries
carbon dioxide
from the cells
to the lungs
CELLS
Figure 15: Path that oxygen and
carbon dioxide follow in the body
1
First, let’s trace the path a molecule of oxygen
takes from the environment. When an oxygen
molecule is inhaled, it moves in through the mouth
or nose, passes through the trachea, bronchi and
bronchioles and into an alveolus. In an alveolus, the
oxygen is dissolved into the fluid surface lining of
the alveolus and diffuses1 into the blood in the
Diffusion is the movement of molecules from an area of high concentration to an area of low concentration.
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capillary. In the lungs, there is a high concentration of oxygen, so the oxygen
moves into the blood where there is a low concentration of oxygen. In the blood, a
special molecule called haemoglobin, which carries the oxygen molecule until it
reaches its destination, picks up the oxygen.
When the oxygen molecules reaches the cell where it is going to be used, the
haemoglobin molecule releases the oxygen molecules and it diffuses into the cell
where there is a low concentration of oxygen. The cell uses the oxygen and
produces carbon dioxide as a waste product.
Let us now follow the carbon dioxide molecule as it leaves the body. Because there
is a higher concentration of carbon dioxide in the cell compared to the blood, the
carbon dioxide diffuses into the blood. The carbon dioxide dissolves into the blood
and is carried to the lungs. The lungs have a low concentration of carbon dioxide
compared to the blood, so carbon dioxide diffuses into the lungs. During
exhalation, the carbon dioxide molecules leave the body by passing out of the
alveolus, bronchioles, bronchi, and trachea to the environment via the nose or
mouth.
This process of absorbing oxygen and releasing carbon dioxide is called gas
exchange. Gas exchange remains basically the same for all animals.
Interesting air breathers
This section has so far described the typical respiratory system of mammals (one
group of animals). We are now going to look at the interesting differences between
other animals that breathe air and mammals.
Birds
Mammals are the only animals
that
have
muscular
diaphragms which means that
birds, reptiles and frog have
to inflate their lungs using
different methods. The lungs
of birds are organized very
differently. Look at the
diagram very carefully. You
can see that the lungs of the
bird are surrounded by air
air entering lung
air leaving lung
Front air sacs
Lung
to mouth
Rear air sacs
Figure 16: Bird respiratory organs. Blue arrows show fresh
entering the lung and red arrows show air leaving. Adapted
from Randall et al. (1997)
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sacs, which collect the air as it moves through the respiratory system but do not
exchange oxygen or carbon dioxide. The gas exchange takes place as the air is
pushed through the lung.
Birds do not use tidal ventilation like mammals, reptiles and frogs. Their ventilation
is unidirectional (one direction) so that fresh air being inhaled never mixes with
the old air being exhaled. During inhalation, intercostal muscles move the rib cage
to make the rear air sacs larger, so air moves through the trachea to the rear air
sacs. At the same time, air in the lung left from the previous breath moves into the
front air sacs. During exhalation, rear air sacs are made smaller by the movement
of the rib cage and the air in the rear air sacs moves into the lungs while the air in
the front air sacs leaves the bird via the trachea.
This system is designed so that the bird absorbs more oxygen out of the air than a
mammal can because there is fresh air in the lung during both inhalation and
exhalation. The air sacs are also advantageous because they make the bird less
dense, which makes it easier to fly.
Reptiles
The respiratory system of reptiles is very similar to mammals except that reptiles
do not have a diaphragm, therefore they evolved different ways of inflating their
lungs. Different reptiles have different strategies. Lizards use their intercostal
muscles to rotate the rib cage in a way that makes the thoracic cavity larger so
that air moves into the lungs.
Crocodiles have a large muscle that connects their pelvic (hip) bones to their liver.
This
muscle
is
called
the
diaphragmaticus
and
when
it
contracts, it pulls the liver toward
their tail. This movement causes the
Lung
TA
thoracic cavity to get bigger and so
air moves into the lungs. When the
diaphragmaticus relaxes and the
OA
intercostal muscles contract, the liver
moves back into its place and pushes
up on the lungs, forcing air out of the
Figure 17: Arrangement of the transverse
crocodiles.
abdominis (TA) and oblique abdominis (OA), the
ventilatory muscles in turtles. Adapted from
Landberg et al. (2003).
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Turtles are particularly challenged because their rib cage is fused to the shell, so
instead they use limb movement to help inflate and deflate their lungs. They also
have a large muscle called the transverse abdominis (TA) that wraps around the
rear portion of the lungs. The TA contracts, resulting in exhalation by pushing up
on the lungs and forcing the air out. The oblique abdominis (OA) muscles located at
the back of the bottom shell cause inhalation when they contract because they
flatten and make the space in the body cavity larger and air moves into the lungs.
Reptile ventilation is different from mammals since the ventilation cycle starts
with exhalation (exhale, inhale, hold breath, repeat) instead of inhalation (inhale,
exhale, pause with lung empty, repeat).
Frogs
Frogs have two compartments where air
moves in their respiratory system and the
airflow between these two compartments
is controlled by valves, which are flaps of
tissues controlled by muscles to be opened
or closed. The first set of valves is the
nares, which are the paired openings on
the nose of the frog. The nares lead to the
buccal (or mouth) cavity. The buccal
cavity and lungs are separated by another
valve called the glottis.
nares
buccal cavity
glottis
lung
Figure 18: The respiratory organs of
frogs. Adapted from Randall et al. (1997).
Ventilation in frogs occurs in this sequence: the lung is full and when the glottis
opens, the air in the lungs moves into the buccal cavity and through the nares into
the environment. This is exhalation (frogs also start with exhalation). To inhale,
the glottis is closed and the nares are opened causing air to flow into the buccal
cavity. Then the nares close and the glottis opens and the air moves into the lungs.
The lungs are now full and the cycle starts again.
Breathing water
Since all animals have evolved from aquatic animals, all animals once breathed
water. The organization of the respiratory system in fish is very different than
for terrestrial animals, however all the important functions must be maintained.
Study Table 2 to see which organs in fish perform the same functions as the
organs in mammals.
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Table 2: Comparison of respiratory organs between mammals and fish.
Mammalian organ
1.
Trachea
Function
Fish organ
Passageway for air/water
Mouth & pharynx
2.
Lungs
i) Bronchi – bronchioles
ii) Alveoli
Gas exchange organ
Support for gas exchange surface
Actual gas exchange site
Gill arches
Gill filaments
Gill lamellae
3.
Location of the gas exchange organ
Operculum
Inhalation and exhalation
Muscles in mouth
and operculum
Thoracic cavity
4.
Diaphragm &
intercostal muscles
A
Operculum
Gill arches
B
Mouth
Pharynx
Operculum
Gill filaments
View from top of head
Figure 19: A. The location
of the gill arches in the
head of a fish. B. The fish
respiratory system. The
blue arrows show the flow
of water. (Adapted from
Randall et al., 1997).
The fish gas exchange organs are the gills,
therefore the fish must push water across the gill
arches so that oxygen can be absorbed from the
water by the gill lamellae. To create water flow
over the gills, the mouth and pharynx expand so
the space increases and water is sucked in. Muscles
in the operculum, the bony covering over the gills
behind the eye, move it in and out so water passes
over the gill filaments and gill lamellae and out the
operculum into the environment. Ventilation in fish
is unidirectional.
Fish that are very active (like sharks) use a type of
ventilation called ram ventilation by swimming with
their mouths open. The forward motion of their
body forces water to move over the gill arches so
that oxygen and carbon dioxide can be exchanged.
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The Digestive System: A Comparative Approach
All animals need nutrients from their environment; nutrients provide
energy and material to build new cells and tissues, and vitamins and
minerals that play many roles in body. Different types of animals
have different ways of obtaining nutrients and in this section we are
going to explore some of those ways!
Flatworms posses a simple gastrovascular cavity (Figure 19), which
has one opening through which both food enters and waste exits.
Flatworms take food in through their mouth by contracting the
muscles in the upper end of their gut to suck food in during feeding.
Their gut is branched and this allows food to be digested and
absorbed and then waste is ejected through the same opening as food
was initially taken in.
Figure 20:
Diagram of a
flatworm
Tapeworms (Figure 20) don’t have a digestive
system at all! Since tapeworms live inside the
digestive tract of other animals, they just wait
until the host animal digests the food and then
they can absorb the
nutrients directly.
Figure 20: A tapeworm
Many animals, including humans, have a tubular gut,
with a mouth (for taking food in) at one end and an
anus (for excreting wastes) at the other end.
Different sections of the tubular gut play different
roles in the digestive and absorptive process. Parts
of the human digestive tract include:


Buccal cavity (or mouth): the opening of the
digestive tract where food enters; food is
broken up here by the teeth
Esophagus: a tube through which the food
Figure 21: The human digestive
tract.
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


passes from the mouth to the stomach. Muscular contractions (called
peristalsis) push the food through the esophagus.
Stomach: a muscular organ where food is stored and digested by churning
(physical digestion) and by hydrochloric acid and the enzyme pepsin
(chemical digestion) before it is passed along to the rest of the digestive
tract
Intestine: a long tube through which the food passes and where further
digestion, as well as absorption of nutrients, occurs
o The small intestine: it is called the “small” intestine because its
diameter is smaller than that of the large intestine. The small
intestine is actually quite long and contains three sections
 Duodenum: further digestion of food occurs here
 Jejunum: absorption of nutrients occurs here
 Ileum: also functions in absorption (especially the absorption of
vitamin B12 and of bile salts)
o The large intestine: has a larger diameter than the small intestine and
consists of three parts:
 Caecum: a pouch at the beginning of the large intestine which is
attached to the ileum; there are a number of bacteria present
in the caecum which serve to breakdown fibre, which cannot be
broken down by human enzymes
 Colon: absorption of water takes place here
 Rectum: stores fecal waste before excretion
Anus: the opening at the end of the digestive tract through which fecal
waste is excreted.
Humans are known as monogastric animals because they only have one (“mono”)
stomach.
Ruminants
Ruminants are animals that digest their food in two steps:
1. eating food and regurgitating (i.e., bringing the food back up from the gut
into the mouth) it in a partially digested form (known as the cud)
2. chewing and re-swallowing the cud (this process is called rumination)
Examples of ruminants include cows, sheep, goats, llamas, camels and giraffes.
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The ruminant stomach is made up of four compartments:
1. rumen: the first and largest
chamber of the stomach; contains
microorganisms (like “good”
bacteria) which digest cellulose (a
fibre found in many plants which
mammals do not have the
necessary enzymes to digest on
their own)
2. reticulum: the second chamber of
the stomach; like the rumen,
contains microorganisms which
Figure 22: The stomach of a ruminant
digest cellulose
animal consists of four chambers: the
3. omasum: the next chamber of the
rumen, the reticulum, the omasum and
stomach; water is absorbed from
the abomuasum.
the partially digested food
mixture here
4. abomasums: this compartment is analogous to the stomach of
monogastric animals (i.e., it secretes hydrochloride acid and digestive
enzymes) and is sometimes referred to as the glandular stomach.
The ruminant stomach is quite large, taking up 3/4ths of the abdominal cavity!
The way that ruminant digestion works is as follows:
1. food is mixed with saliva
and enters the rumen
2. in both the rumen and the
reticulum the food/saliva
mixture separates into
layers of solids and liquids
3. the solid layer clumps
together to form the cud,
which is regurgitated and
chewed – this increases
the surface area of the
food so that the
Figure 23: The digestive tract of a ruminant
microorganisms can gain
animal.
access to more of the
food in order to digest it once it is returned to the stomach
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4. once the food has been sufficiently digested, it passes into the omasum,
where the water is absorbed, resulting in a more concentrated mixture
5. the food passes into the abomasums, where digestion similar to that which
occurs in monogastric animals takes place
6. the food then passes into the intestine where absorption occurs just as it
does in monogastric animals
Birds
Unlike mammals, birds do not have teeth,
so they cannot masticate (chew) their
food. The physical breakdown of their
food is accomplished by the beak and the
gizzard (a muscular compartment that
contains small stones; muscular
contraction of the gizzard grinds the food
together with the stones, resulting in the
physical breakdown of the food). The
gizzard (sometimes referred to as the
muscular stomach) is found after the
stomach (sometimes referred to as the
glandular stomach or proventriculus) and
the food is passed back and forth between
the glandular stomach and the gizzard,
resulting in a repeated cycle of physical
and chemical digestion.
Figure 24: The digestive tract of a
bird.
In addition to the stomach and gizzard, most (but not all) birds have a crop
(depending on the species, the crop can be either a widening of the esophagus, or 1
or 2 esophageal pouches). The crop can store food before it enters the stomach.
The small and large intestines of birds are similar to those of mammals. At the
end of the digestive tract is the cloaca (a tubular structure that serves as a
shared opening for the digestive, reproductive and urinary systems).
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ECOLOGY
Ecology is the study of interactions of organisms with their environment – including
both the physical environment and other organisms in that environment.
The interactions between two different organisms can result in benefit, harm or no
effect on each of the organisms. Different types of interactions that organisms
can have with one another are presented in Table 3.
Table 3: Different types of ecological interactions
Effect on Organism #2
Benefit
Effect on
Organism #1
Harm
No Effect
Benefit
Harm
No Effect
Mutalism
Predation or
parasitism
Commensalism
Competition
Amensalism
Amensalism
--
Predation or
parasitism
Commensalism
In the situation where one organism benefits by harming another organism, we
have a case of either a predator-prey relationship (e.g., when a lion eats a gazelle)
or host-parasite relationship (e.g., when a tapeworm lives inside the digestive
tract of a human, “stealing” the nutrients from the person). Predators are
organisms that feed on other organisms, whereas parasites are a special type of
predator that live on the inside (endoparasites) or the outside (ectoparasites) of
the host’s body. A parasite that kills its host is called a parasitoid.
When both of the organisms are mutually harmful to one another, we have a case
of competition (e.g., two species of insects trying to live off of the same plants,
but there are not enough of those plants to feed both species).
When both of the organisms benefit from their relationship, it is called mutualism
(e.g., when an insect pollinates a flower, the insect benefits by getting food from
the flower and the flower benefits because its pollen is spread around, allowing the
plant to reproduce).
When one organism benefits and the other organism is unaffected, the interaction
is called commensalism (e.g., plants that grow on trees causing neither harm nor
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benefit to the tree. Plants that grown on other plants are called epiphytic plants)
and when one organism is harmed and the other organism is unaffected, the
interaction is called amensalism (e.g., the Black walnut tree secretes a chemical
that often kills neighboring plants. The Black walnut tree does not gain anything by
doing this).
Ecosystems
The term ecosystem refers to the organisms living within a given area + the
physical environment in which they live and interact. Scientists who study
ecosystems are interested in, among other things, the flow of energy through an
ecosystem. To do so, they group organisms by their source of energy, with
organisms that share a common source of energy being referred to as a trophic
level (see Table 4).
Table 4: Trophic levels
Trophic Level
Source of Energy
Examples
Primary producers
Use photosynthesis to capture Plants, photosynthetic
energy from the sun
bacteria
Herbivores
Eating primary producers
Cows, rabbits, deer,
grasshoppers
Primary carnivores
Eating herbivores
Spiders, wolves
Secondary carnivores Eating carnivores
Tuna fish, falcons, killer
whales
Omnivores
Eating organisms from the
Humans, crabs, robins,
other trophic levels (primary
bears
producers, herbivores and/or
carnivores)
Detritivores
Scavenge dead bodies and
Vultures, fungi, worms,
waste products of other
many bacteria
organisms
A food chain is a set of linkages representing a linear series in which a primary
producer is consumed by a herbivore, which is consumed by a carnivore, etc., as
seen in Figure 25.
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Figure 25: An example of a food chain
Tertiary Consumers
Secondary Consumers
Primary Consumers
Primary Producers
In reality, food chains are usually interconnected into food webs as seen in Figure
261.
Figure 26: An example of a food web
(Source: U. S. Department of Agriculture . Adapted from http://soils.usda.gov/sqi/concepts/soil_biology/images/A-3.jpg)
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References
Farmer, C. G. and D. R. Carrier. 2000. Pelvic aspiration in the American alligator
(Alligator mississippiensis). J. Exp. Biol. 203: 1679-1687.
Landberg, T., Mailhot, J. D. and E. L. Brainerd. 2003. Lung ventilation during
treadmill locomotion in a terrestrial turtle, Terrapene carolina. J. Exp. Biol. 206:
3391 – 3404.
Randall, D., Burggren, W. and K. French. 1997. Eckert Animal Physiology. W. H.
Freeman and Company: New York. Pp 727.
Purves WK, Orians GH, Heller HC. LIFE: The Science of Biology, 4th ed. Sinauer
Associates, Sunderland, Massachusetts, 1995.
Websites
http://science.howstuffworks.com/virus-human.htm
http://www.path.ox.ac.uk/dg/vwork.html
http://www.virology.net/Big_Virology/BVHomePage.html
http://science-education.nih.gov/nihHTML/ose/snapshots/multimedia/ritn/prions/prions1.html
http://arbl.cvmbs.colostate.edu/hbooks/pathphys/digestion/index.html
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