BP004 - Earth and Life Science

EARTH AND LIFE SCIENCE
INTRODUCTION TO EARTH AND LIFE SCIENCE
The study of the earth and living and non-living organisms encompass
this module. Earth and life science is an interesting topic, not least
because it affects us all. The strudy of the earth and the living things
within it is important if you want to understand how the environment
works, as well as plants and animals.
Welcome to the Earth and Life Science module. This is your

introduction to the module where I hope you can get to appreciate why
you need to study this and what knowing these concepts can do for
you.
Origin and Structure of the Earth

The Earth and the Solar System need to be defined in order to
understand the basis of the topic. The creation of the earth is thought to
be directly linked with the creation of the sun. When the sun was
created, the cloud of dust and gases that were left over formed the
inside of the earth, which stayed cool at 2000 F. As time passed, the
elements in the solid center of the earth started to decay. In the
beginning the center of the earth was composed of iron and silicates,
along with materials that were radioactive. These radioactive
materials, as they decayed, emitted heat. Principally, these radioactive
materials are composed of uranium, potassium, and thorium. The heat
that was released melted the silicates and iron. Since iron is heavier, it
sank towards the center. This became the core. Then, a layer of rock
formed around the core. There were depressions on the surface, and
these are where water from the inside of the earth accumulated.
Key Characteristics of the Earth’s Structure
• There are two magnetic fields in the earth which repels solar wind
and protects the earth from solar radiation
• The atmosphere of the earth is stratified, which means that it is
made up of mainly nitrogen and oxygen
• The eath is made up of a variety of minerals, melts, fluids, gases,
and volatiles, which were all left behind after the solar system was
created.
• The earth has layers: a crust, a mantle, and a metallic core
• The earth can be divided into an outer lithosphere and a plastic
asthenosphere.
Introduction to Earth and Life Science 1

X.X Earth and Life Science
The Subsystems of the Earth

The earth has subsystems that consist of the geosphere,
hydrosphere, atmosphere, and biosphere. Each of these spheres
are important for the survival of animals and plants on earth.
The atmosphere is the layer of air that surrounds the eath. It
protects the earth from solar rays. It also circulates the air and
gases that plants and animals need to survive.
The biosphere is made up of living organisms, such as plants and
animals. It is important to note that all the biospheres interact with
each other. For instance, plants and animals (biosphere) interact
with the atmosphere.
The geosphere or also called the lithosphere, is made up of the
physical earth, such as rocks, magma, and soil. The geosphere
extends from the center of the earth to the dust in the atmosphere,
and evens includes the sand in the ocean.
The hydrosphere, on the other hand, is made up of all the water
held on earth. It includes the water molecules in the air, icebergs
and glaciers, lakes, rivers, groundwater, and oceans.
The Atmosphere
Divided into 6 layers according to altitude
Exosphere: (500 km above the eath), this is where the
atmosphere merges with space.
Thermosphere: (90 km above the earth), this is where the
space shuttles orbit.
Mesosphere: (50-90 km above the eath), this is where
meteors burn.
Stratosphere: (12-50 km above the earth), this is where
the air is stable and is good for planes and jets to fly in.
Tropopause: (11-12 km above the earth).
Troposphere (0-11 km above the eath), the is the “mixing
layer,” all the weather is limited to this layer.
The Geosphere
The crust is the outermost “skin” of the earth and has
various thicknesses. The thickest is under the mountain
ranges, and the thinnest is under the mid-ocean ridges.
The Mohorivicic discontinuity or “Moho” is the lower
boundary. It separates the crust from the upper mantle.
It was discovered in 1909 by Andrija Mohorovicic.
It is also marked by a change in velocity of seismic
waves.
There are two types of crust: the continental crust and the
oceanic crust.
The crust is composed of just 8 elements
Oxygen is the most abundant element in the crust
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The mantle is a solid rock layer between the core and the
crust
It is composed of a rock called peridotite
It also convects: the cool mantle sinks and the hot mantle
rises.
Three subdivisions of the mantle: upper, transitional, and
lower
The core is an iron-rich sphere with a radius of 3,471
km.
The outer core is made of liquid iron, nickel, and sulfur
and it s 2,255 km thick.
The flow in the outer core creates the earth’s magnetic
field.
The inner core is made of solid nickel, iron alloy
It has a radius of 1,220 km.
Formation of the Universe and Solar System

The universe and the solar system were formed about 4.6 billion years
ago. However, scientists are not completely sure about how this
happened. It is important to understand this formation in order to
understand how the universe functions and what we need to know
about it.
Formation of the Sun and the Solar System
How the sun was formed:
1. There was a spinning disk in space.
2. As gas collected in the center of this spinning disk, a

“protosun” was created.
3. Molecules in the protosun collided with each other, which

caused heat to form.
4. This raised temperatures to 10,000,000 C.
5. The heat and violent clashes between molecules allowed the

creation of nuclear reactions, which turned the protosun into a
star.
How the planets were formed:

1. In the disk that surrounded the protosun, a process called

accretion formed the planets, comets, moons, and asteroids.
2. Small particles crashed together to form larger and larger

particles, eventually reaching the size of planetesimals, which
are several kilometers big.
3. Since these planetesimals were big enough to have their own

gravity, they caused even more collisions around them.
4. In the planetesimals near the sun, the water evaporated and

gasses were swept to the outside and only the heavier materials
could become solids. Young planets were formed from these
materials.
5. Farther away from the sun, the temperature was cooler. The
amount of ice here allowed for larger bodies to form, which
created the core of the planets, such as Saturn and Jupiter.
Formation of the Universe
The formation of the universe is a question that has sparked

debate and controversy. Today, there are no concrete
conclusions as to how the universe came to be. However, there
are several theories about how the universe was born, and we
shall discuss these here.
The Big Bang Theory
Since the early part of the 1900s, one explanation about the
birth of the universe has prevailed, and this is the Big Bang
Theory. Proponents of this theory have maintained that,
between 13 billion and 15 billion years ago, all the matter
found in the universe today was found in a small space, a tiny
contact point. Indeed, according to this theory, matter and
energy were the same back then. Adherents of the Big Bang
Theory believed that, from this small but extremely dense ball
of matter/energy, expansion came about after an explosion.
Seconds after the explosion, the fireball that emerged ejected
matter/energy at high velocities, which approached the speed
of light. At some time later, matter and energy separated from
each other. All the elements of the universe today developed
from that original explosion. Moreover, proponents of the Big
Bang Theory believe that the explosive energy that was present
back then is still retained today by the stars and galaxies. The
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explosion back then still causes the expansion of the universe

today, with stars and galaxies moving farther and farther away
from each other. The supposition of this movement came in
1929 when the astronomer Edwin Hubble, who was then
conducting astronomical projects at the Mount Wilson
Observatory in California, announced that all of the galaxies
that he was studying are movig further and further away from
us, at speeds that amount of several thousand miles per second.
The Steady State Theory
Although the Big Bang Theory is the most popular theory to

date, it is not the only theory. A competing hypothesis arose in
the 1940s, in the form of the Steady State Theory. The scientist
who proposed this hypothesis was Fred Hoyle, who believed
the universe was governed by two principles: the cosmological
principle and the perfect cosmological principle. The former is
the idea that the universe is uniform in space, while the latter is
the idea that the universe is unchanging in time. Under this
theory, stars and galaxies change, but the universe remains the
same as a whole.
The Steady State Theory also predicts that the universe is

expanding, but it also predicts that new matter is being created
enough to fill the empty spaces left behind by the universe’s
expansion. According to the Steady State Theory, matter
cannot be created nor destroyed, but only transformed into new
forms- such as energy or as a different form of matter. Under
this theory, the amount of new matter formed is very small-
one atom every billion years. This theory, however, fails in one
significant way: the average age of stars should be
approximately the same if matter is continuously created
everywhere. This has been found to be false by astronomers.
The Plasma Universe
Individuals who do not subscribe to either the Big Bang Theory

or the Steady State Theory are formulating other views of the
creation of the universe. Hannes Alfven, a nobel laureate,
created a new model, since he is a plasma physicist. The theory
first states that it has been observed that 99% of the observable
universe is made of plasma, which is where the term Plasma
Universe is derived from. Sometimes called the fourth state of
matter, plasma is an ionized gas that conducts electricity. The
theory also discounts the Big Bang Theory and states that the

universe is crisscrossed by electromagnetic fields and electric

currents. Under this vew, the influence of an electromagnetic
force has caused the universes to have existed forever.
Therefore, the universe has not beginning and no end. In the
Plasma Universe, the galaxies take as long as 100 billion years
to come together. The evidence from the Plasma Universe does
not come from direct observations of the sky; rather they come
from laboratory experiments.
The Earth’s Internal Structure

The size of the earth is about 12,750 kilometers in diameter, and this
was known by the Ancient Greeks. However, it was not until the end
of the 20th century that scientists were able to be sure that the planet is
made up of three layers: the crust, the mantle, and the core.
The crust, or the outer layer, is thinner than the mantle and the core.
Underneath the oceans, the crust varies in thickness, with a thickness
of only just 5 km. The thickness of the crust that exists underneath the
continents is greater, which averages around 30 kilometers deep.
Under the larger mountain ranges, such as those under the Sierra
Nevada or the Alps, the thickness can extend up to 100 kilometers
deep. The crust of the earth is brittle and is liable to breaking.
Below the crust, the mantle is found. It is a hot, dense layer of semi-
solid rock. The mantle is approximately 2,900 kilometers deep. This
layer of the earth contains iron, calcium, and magenisum, and these
exist in greater quantities than in the crust. The mantle is also denser
and hotter compared to the crust because matter is heated by the
pressure and temperature inside the earth.
At the center of the earth is the core. The core is denser than the
mantle because it is composed of an iron-nickel alloy, which is
metallic rather than being stony. The core is made up of two distinct
layers: the liquid outer core and a solid inner core. The liquid outer
core is 2,200 kilometers thick, while the solid inner core is 1,250
kilometers thick. As the earth rotates on its axis, the liquid outer core
spins, which creates the earth’s magnetic field.
The inner structure of the earth influences plate tectonics. The deep
mantle is hotter compared to the upper part of the mantle. These two
layers of the mantle together form the lithosphere. Scientists believe
that, beneath this layer, exists the asthenosphere. The asthenosphere is
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composed of semi-solid, hot material, which flows and softens after

being subjected to high pressure and temperature. The lithosphere is
thought to be located above the asthenosphere, and the movement of
the lithosphere influences plate tectonics.
Glossary
Accretion: the process wherein particles are accumulated into a larger object.
Nuclear reactions: the collision between two nuclei
Planetesimal: an object that was created from rock, dust, and other
materials.
Plate tectonics: the theory that the outer shell of the earth is divided
into several plates that move over the mantle.
Protosun: the ball of energy that preceded the sun; became the sun.
Radioactive: the ability of the nucleus of an unstable atom to lose

energy by producing radiation
Silicates: a salt whose anion contains both oxygen and silicon.
References
Bryson, B. (2004). A Short History of Nearly Everything. Broadway
Books.
Fishman, D. (n.d.). The origin of the universe. Retrieved from

http://www.scholastic.com/teachers/article/origin-universe
USGS. (n.d.). Inside the earth. Retrieved from

http://pubs.usgs.gov/gip/dynamic/inside.html
Videos and Resources

Creation of the Universe

Compositional and Mechanical Layers of the Earth
The Big Bang Theory
An Introduction to Modern Cosmology
Theory of the Earth
The Earth's Mantle
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Earth Materials and Processes
In the earlier module, we learned about the physical structure of the

earth. In this module, we will examine the processes that the various
components of the earth undergo. The materials that comprise the
earth are inherent to the earth’s structure and as elements that facilitate
these processes. Geology, the study of the landscape, includes
variables such as rocks and minerals. Rocks are being formed all
around us, all the time. However, geological timescales are very
different from the timescales of the earth, and can span thousands of
years.
Rocks and Minerals

Rocks are formed from distinct grains that come together. These
distinct grains are called mineral grains, and most rocks are commonly
aggregates of these grains. Igneous rocks form by crystallization and
are usually composed of several kinds of minerals. Sedimentary rocks,
on the other hand, are composed usually of one kind of mineral. This
reflects processes in the rock cycle that favor the mineral’s inclusion.
Thus, the assembly of minerals in rock is not at all random, but the
result of the original rock-forming processes.
Minerals are defined as “a naturally occurring chemical element or

compound, possessing a definite crystalline structure based on an
ordered in ternal arrangement of constituent atoms, and with a
chemical composition that may be expressed in terms of a unique
chemical formula.”
More than 2000 types of minerals are now known, and new ones are
being discovered on a daily basis. These minerals are classified
according to chemical composition and atomic structure. However, the
majority of rocks are formed from one or more of a small group of
minerals, just comprising over a dozen.
Silicate minerals has a structure based on the silicate unit, which can
be represented as part of a tetrahedral building block. Six major groups
of silicate minerals have been identified, based on the way that the
silicate units are joined together. Minerals make up rocks, and silicates
crystallize in order to form rocks. When tabulating the composition of
minerals and rocks, it is common to denote the elements as oxides,
although these elements should not be taken to mean as oxides in the
chemical sense.
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Each rock is made up of one or more silicate minerals. Each

rock, in addition to this, is made up of a distinctive mineral
composition. For instance, peridotites contain olivine and
pyroxene. In contrast to this, olivine is never found in granites.
The main factor that determines whether a mineral is present
after the cooling process is the crystallization temperature.
Each mineral is characterized by a different crystallization
temperature. It is now prudent to discuss the different types of
rocks that are found on the earth.
Igneous Rocks
Igneous rocks are the starting points in the rock cycle. That is, the
materials that make up the other two types of rocks, the sedimentary
and metamorphic rocks, are derived from a source that is igneous.
Igneous rocks are found on the earth’s mantle. It can be said that 70%
of the earth’s mass and 80% of the earth’s volume consists of mantle
rocks. Igneous rocks are derived from the convection in the earth’s
mantle, and the source of heat energy for this convection is found in
the radioactive isotopes of potassium, uranium, and thorium. The types
of rocks that contribute to the amount of energy in terms of heat
energy per unit mass are granites. Peridotites do not contribut much
heat. Therefore, the former makes up much of the crustal rocks. The
internal heat of the earth may have come from the radioactive decay of
potassium.
One obvious consequence of the heat in the earth’s interior is the

presence of volcanoes on the earth’s surface. Volcanic rocks are
products of volacanoes and they have three important characteristics:
1) they crystallize in the surface of the earth; 2) they are commonly
fine-grained; and 3) they rest on top of older rocks rather than cut
across them. Volcanic rocks are an example of igneous rocks, which
are formed from an exothermic process. These rocks start out in the
liquid state and then become solid.
Sedimentary Rocks
While igneous rocks are created from the cooling of magma,

sedimentary rocks are classified as secondary rocks because they come
from igneous rocks. They are also secondary because they come from
the aggregation of pebbles and sand that have been compacted over
time to form rocks. In sedimentary rock, there are three types of
grains: coarse, medium, and fine. These grains are classified
depending on the size of the grains.
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Sedimentary rocks are also classified into three types: clastic,

chemical, and organic (or biogenic). Clastic rocks are basic
sedimentary rocks and they have been created from “clasts” which are
little pieces of rocks that have been compacted and cemented to
become larger pieces. On the other hand, chemical rocks form when
water evaporates. In other words, these rocks were created from
chemical precipitation. Lastly, organic rocks are rocks that contain
shell fragments or fossils.
Examples of sedimentary rocks are: sandstone, shale, limestone, and

conglomerate.
In response to environmental differences, the silicate minerals in

igneous rocks undergo changes. These changes lead to their total or
partial breakdown. The process of breaking down is called weathering,
and it is this process that eventually results in the formation of
sedimentary rocks. This is one part of the rock cycle. There are two
types of weathering: physical and chemical. Physical weathering is
also called mechanical disaggregation and chemical weathering is also
known as chemical decomposition. While physical weathering
produces sedimentary rocks like sand, chemical weathering produces
residual minerals. In addition to this, sediments may be transported by
wind, ice, and water.
Metaphormic Rocks
When rocks are subjected to mechanical forces as well as to extreme

physical conditions, such as temperature, they become metamorphic
rocks. This group of rocks include all other types of rocks, namely,
igneous and sedimentary. Metamorphism occurs when the rocks are in
the solid state. The transition between metamorphic rocks and igneous
rocks are marked by the melting point of the rock. Below this melting
temperature, the rock will become metamorphic.
The mechanical deformation of rocks concerns tectonic processes. The

word tectonic means the mechanical processes by which rocks are
build up into complexities. There are two types of metamorphism:
contact metamorphism and regional metamorphism. The latter applies
to large sections of rock while the former applies to small sections of
contact.
Examples of metamorphic rocks are: slate, diamonds
Exogenic and Endogenic Processes
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Rocks that have broken or are weak undergo exogenic processes-

erosion, transportation, and deposition. A fragment of rock broken
(weathered) from a larger mass will be removed from that mass
(eroded), moved (transported), and set down (deposited) in a new
location. The weathering of rocks usually occurs with the aid of
geomorphic agents, such as ice, wind, and snow. Sometimes, however,
the only factor that causes weathering is gravity itself. For instance,
rocks may slide down a slope due to gravity, and this process is known
as mass wasting. The rate of exogenic processes depend on factors
such as the resistance of rocks to erosion and weathering and the
amount of relief and climate.
On the other hand, the endogenic processes also occur, which uses
heat from within the earth. Endogenic processes are also called
hypogene processes. In other words, when a process originates from
within the earth’s crust, it is an endogenous process. These processes
are governed by the forces within the earth and are not very much
affected by external sources. These processes also cause phenomena
such as earthquakes, volcanic activity, metamorphism, and the
formation of ocean troughs and continents. These processes are mostly
caused by the thermal energy of the crust and the mantle. The thermal
energy in the mantle and the crust is derived from the decay of
radioactive material and the gravitational differentiation in the mantle.
Earthquakes are a form of energy of wave motion that is transmitted

through the surface layers of the earth. It ranges from a faint tremor to
a wild motion. Earthquakes are due mostly to the dislocation of rocks
underneath the surface.
Tectonic movements are movements of the tectonic plates. They may

be folded, thrust over one another, or broken up. Tectonic movements
give rise to mountains, oceans, ridges, troughs, and other land forms.
When the process results in building up a surface, it is termed as
distrophism.
Volcanism, on the other hand, is the process by which matter is

transported to the surface of the earth and then erupted. Volcanism is
the process wherein the magmatic materials are effused towards the
surface of the earth through volcanic structures. When the magma does
not reach the surface, they are called intrusives or plutons.
Deformation of the Crust
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Plate tectonics is concerned with the movement of the continents.

Proposed by Wegener, continental drift is the theory that continents
are moving. Continents are moving due to the movemen of tectonic
plates on the earth’s surface, or across the ocean bed.
The evidence supporting continental drift is now extensive. Along the

shores of different continents, similar plant and animal fossils have
been found, suggesting that these continents were once joined
together. One example is the fossil of the Mesosaurus, which was
found in both Brazil and Africa. Another form of evidence is that of
paleomagnetism, which is the process by which the earth’s magnetic
fields move. Based on basaltic rocks, scientists at the time did not
know how to account for paleomagnetism. The magnetic field
orientation of rcoks of the same age did not point to the same pole.
The common magnetic northo pole could only be established if the
continents were once in different positions than they are today. Using
rocks with different ages, they reconstructed the location of the
continents during the past periods in geologic history.
The deformation of the earth’s crust is the result of forces that are
strong enough to move ocean sediments to an elevation that is many
thousands of meters above sea level. The deformation of rock involves
changes in the volume and/or shape of these substances. Changes in
volume and shape occur when strain and stress causes rocks to fold,
buckle, or fracture. A fold is a bend in the rock that is the response to
compressive forces. On the other hand, a fault forms when the internal
stresses in the rock cause fractures. The fault can be defined as
displacement of a rock that was once connected along a fault plane.
History of the Earth

The magnetic field polarity of the earth changes. As a result, the
magnetic field of the eath shows normal and reversed polarity. The
normal polarity is from the south pole to the north pole, while reverse
polarity is from the north pole to the south pole. The polarity changes
are key indicators of seafloor spreading. Seafloor spreading thus
occurs in the ranges of the ocean where volcanic activity gradually
moves away from the ridge. This phenomenon helps explain the
continental drift in the the plate tectonics theory. The divergence of the
ocean plates causes tensional stress, which in turn causes fractures to
occur in the lithosphere. Then, basaltic magma rises up from these
fractures, and then this cools on the floor of the ocean and causes the
formation of new seafloor. New rocks will be found nearer the
spreading zone, while older rocks will be found farther away.
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The oldest rocks in the earth include both the sediments, which are
water-lain, and the ancient oceanic crust. Thus, oceans have been
forming ever since the beginning of the geologic period. From the
present oceans, no oceanic crust is known to be older than 180 Ma.
The evolution of the ocean basin starts from a rift, which then reaches
a maximum size. It then shrinks and then closes completely.
Stages of Ocean Basin Evolution
1. Embryonic
2. Young
3. Mature
4. Declining
5. Terminal
6. Relict scar
Formation of Stratified Rocks and the Geologic Time Scale
The stratification of sedimentary and igneous rocks occurs on the

Earth’s surface. The layers may be from several millimeters to several
meters in thickness. These layers also vary much in shape.
Stratification planes are the names given to the separation between
individual layers of rocks. The stratification of rocks may occur due to
the changes in composition or texture of the rocks during deposition,
or may also result from changes in deposition. Thus, a certain strata of
rocks may appear to be made of both fine and coarse particles. In the
layers that have been deformed, it is possible to make inferences about
the geologic events that permitted these events.
Thus, the history of the earth has been recorded in stratified rocks. The
geologic time scale is the temporal framework that is composed of the
arrangement of stratified rocks. In order to find out the age of the
rocks, and thus the geologic time scale, geologists rely on two
methods: relative and absolute dating. The latter establishes how many
years ago a certain event took place. The most important aspect of
absolute dating is based on the decay of radioactive elements in the
rocks. On the other hand, relative dating is able to place the events in
their proper order, but cannot ascertain the exact number of years ago
when the event took place.
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In order to date the rocks, marker fossils are used. Marker fossils, or
index fossils, are able to indicate the types of organisms that existed in
a certain time period. They serve as guides to the age of the rocks in
which they are preserved. Since the geologic time scale is an important
consideration when dating the earth, it is also important for
understanding the history of the earth. Organisms that only existed for
a certain period and found in rocks can determine the history of the
evolution of organisms on earth. Moreover, the earth’s history in terms
of animal and plant life can be deduced from the history found within
rocks by showing the time period in which they occurred.
Glossary
Basaltic rock: fine-grained, dark-colored igneous rock
Basaltic magma: molten rocks that are rich in magnesium and iron, and lack
silica
Exogenic: coming from outside a system
Endogenic: coming from inside a system
References
Bryson, Bill. (2004). A Short History of Nearly Everything. New York:
Broadway Books.
Tarbuck, E.J. & Lutgens, F.K. (2002). Earth: An Introduction to

Physical Geology. New Jersey: Prentice Hall.

Geologic Time
Rock Cycle and Types of Rocks
Origins of Oceans
Crustal Deformation and Mountain Building
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Geodynamics from the Top
Geology
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Manual Title 9
Natural Hazards, Mitigation, and

Adaptation
This module is concerned with the natural phenomena that you

observe around you. Storms, earthquakes, landslides, and maybe even
volcanic eruptions, are part of this. The earth is a complex system and
it is dynamic. There are movements on the earth’s surface that cause
these hazards to occur. These hazards are dangerous for human life, as
well as structures on the surface of the earth. In this module, we will
learn about the various hazards that occur as a result of forces on the
earth’s surface.
Geologic Processes and Hazards

As was mentioned, the earth is a dynamic planet. The very forces that
created the earth still act at or beneath its surface. The movements of
plates on the earth’s surface, coupled with local concentrations of heat,
provide a continuing source of hazards for the people and the
structures that they build. Even with the present state of technology
today, geologic hazards often cannot be predicted or prevented with
precision. The exeception to this are landslides, which are preventable.
Areas prone to such hazards can be identified through earthquake fault
lines, coastal areas susceptible to tsunamis, and areas near active
volcanoes.
Estimates of whether a certain hazard will occur are probabilistic,

because it is based on both the magnitude of the event as well as its
occurrence in time and space. Other measures, such as duration, speed
of onset, geographical dispersion, and frequency can be identified with
even less precision. Nevertheless, appropriate measures for mitigating
these hazards can be taken.
Earthquakes and Landslides
Earthquakes are caused by strain energy underneath a fault line within

the earth’s crust. When this strain energy is released, the result is an
earthquake. There are three effects of earthquakes: ground shaking,
surface faulting, and earthquake-induced ground failure, which is
composed of landslides and liquefaction.
Ground shaking, or ground motion, is the primary cause of the partial

or total collapse of structures on the earth’s surface. It is the vibration
Natural Hazards, Mitigation, and Adaptation 1

of the ground caused by seismic waves. Four types of seismic waves

are propagated on the earth’s surface during an earthquake, each with
different effects on structures. The sound wave, or P wave, is the first
wave to reach structures, and it causes buildings to vibrate. The second
wave is the S wave, which causes the earth to move at right angles
towards the direction of the wave. It also causes structures to move
from side to side. Two low frequency waves also cause minor
vibrations. Buildings must be constructed to withstand these vibrations
in order to prevent them from being destroyed.
Surface faulting, on the other hand, is the tearing or offset of the

ground surface caused by the differential movement that occurs along
a fault line. The effect of surface faulting is generally caused by
earthquakes that register as 5.5 or more on the Richter Scale. The
displacement ranges from a few millimeters to several meters. The
damage caused by surface faulting increases with increasing
displacement. Buildings are susceptible to surface faulting, in addition
to roads, bridges, railroads, tunnels, and pipelines. The most effective
way to prevent damage from surface faulting is to restrain from
construction along fault lines.
Earthquake-induced ground failure occurs in a variety of forms.

Earthquake-induced landslides occur through a broad range of
mechanisms. They occur in land that is sloped steeply, and land that is
flat. The principal criteria for classifying landslides are the types of
materials and the types of movement. The types of landslides that
occur can be in the form of slides, falls, flows, spreads, or a
combination of these. On the other hand, liquefaction due to ground
failure can be classified into two types: rapid earth flow and earth
lateral spreads. Rapid earth flows are the most dangerous types of
liquefaction. During this phenomenon, large masses of soil can move
from a few meters to a few kilometers. Earth lateral spreads are the
movement of surface blocks brough about by the liquefaction of
subsurface layers. Liquefaction can be mitigated through appropriate
engineering design and ground-stabilization techniques.
Human activities that trigger landslides include deforestation and

mining. The lack of trees allows water to flow freely down from the
mountains in cases of rains and storms. Water carries with it soil,
which can engulf homes and other structures. The best way to lessen
the chances of a landslide in the community is to prevent the
deforestation of forests.
Coping with Earthquakes
2
There are practical ways of coping with hazards brought about by

earthquakes. One of these is to build structures with construction
standards that are compatible with the degree of ground shaking. The
second is to adopt ordinances that require investigating seismic sites
and geologic sites for hazards. Easements can also be established that
are set apart from active fault lines. Whenever an earthquake occurs, it
is pertinent to stay away from electric lines, tall buildings, and
structues that may collapse. Trees should also be avoided.
Volcanic Eruptions
Volcanic eruptions are the spewing forth of lava from active

volcanoes. They also consist of tephra falls, ballistic projectiles, lahars,
lava flows, and pyroclastic phenomena. Tephra falls include rocks and
blobs of lava that are ejected from within a volcano into the
atmosphere. These also form deposits as the debris falls back onto the
surface of the earth. Tephra falls can cause damage to structures and
property due to the falling fragments. These fragments cause a layer
which covers the ground, and this produces a fine film of fine-grained
particles in the air. The accumulation of tephra causes buildings to
collapse due to their weight. They can also kill vegetation.
Pyroclastic phenomena, on the other hand, are masses of hot, dry

pyroclastic material built into masses. They are also hot gases that
move quickly along the ground surface.
Lahars and floods are a flowing slurry of volcanic debris and water
that comes from within a volcano. The eruption of a volcano that is
covered in snow can melt enough snow that it will cause a lahar. Due
to their high density and velocity, lahars can destroy structures in their
path. These include roads, bridges, crops, and even whole towns. This
can then result to flooding when the water overflows from damaged
dams and because of their capacity to carry water.
Volcanic eruptions can be mapped. These zones, which are typically

located within a certain radius of a volcano, will show areas which are
susceptible to damage due to a volcanic eruption. Called zonation
maps, these maps can show the anticipated scales of future damage.
The mitigation of volcanic hazards primary involves hazard

assessment and land-use planning. There are other mitigation
practices, such as establishing monitoring and warning systems,
protective measures, evacuation measures, relief and rehabilitation
programs, and insurance programs.

Hydrometeorological Phenomena and Hazards

Floods
One of the most common hydrometeorological hazards is flooding.

They are common and very costly for the community. Conditions that
may cause flooding include rains that last for several days and water
that seeps into the ground. Flash floods, on the other hand, occur due
to the sudden overflowing of rivers along a stream or a low-lying area.
There are several types of floods: flash floods, river floods, coastal
floods, urban floods, ice jams, and glacial lake outbursts flood. The
characteristics of floods vary. First, the depth of water brought about
the flood will have different effects on buildings and vegetation.
Secondly, the duration of floods will determine the damage to
structures. The velocity of the flood may create erosive forces,
especially if the velocity is high. Hydrodynamic pressures caused by
the velocity of the water, and these destroy foundations of construction
or agricultural activities. The frequency of occurrence is measured
over a period of time. Sesonality, on the other hand, is when the floods
are most likely to strike, and can have devastating effects on crops and
structures.
Flood preparedness and mitigation have been around for centuries. The
first way to mitigate the effects of floods is to properly regulate and
enforce rules related to developmental activities. These activities are
primarily located near flood plains of rivers. Encroachments to water
flows in rivers are also causes of floods, and should be regulated as
well. Effective steps are needed to regulated unplanned growth in the
flood plains.
Capacity development is composed of flood education. These

activities target groups for development. They also include developing
the capacity of individuals, such as professional training, research, and
development with respect to the management of flood.
Flood response is an effective measue to preven the large loss of lives

associated with rising water levels. There should be evacuation
measures, as well as warning signs that will mitigate floods. There are
also structural measures, such as the construction of embankments that
are designed to minimize the effects of floods. Dams, reservoirs, and
other mechanisms for storage of water are also effective means to
4
contain floods. De-silting and dredging of rivers is another approach to

minimize the effects of flooding.
Cyclones
The tropical cyclone is another phenomenon that occurs within the

earth’s atmosphere. Cyclones are termed as such when their winds
equal or exceed “gale force,” which is a minimum of 62kmph. These
are intense areas of the earth’s atmosphere that coincide with system
and extreme weather events. A cyclone is characterized by a center
that is large and of low pressure. It also has numerous thunderstorms
that produce flooding rain and strong winds. When moist air rises,
cyclones feed on the air, which results in the condensation of water
vapor in the air moist air. The term “tropical” refers to the geographic
origin of these systems, since they form almost exclusively in certain
parts of the globe. The term “cyclone” on the other hand, refers to their
counter-clockwise movement from the Northern Hemisphere, and the
clockwise rotation in the Southern Hemisphere. Depending on its
strength, a cyclone may be termed as a hurricane, tropical storm,
tropical depression, cyclonic storm, or simply cyclone.
Cyclones, aside from producing heavy rains and winds, can also
produce high waves and storm surges which are damaging. These
phenomena develop over large bodies of water, subsequently losing
their strength as they move over land. Thus, coastal regions receive
much of the damage from cyclones, while regions inland are safe from
their effects. Although they have devastating effects on people and
structures, cyclones are also helpful in maintaining the earth’s
troposphere, maintaining a relatively stable and warm temperature
worldwide.
Cyclones are known to cause severe damage due to strong winds.

These winds damage installations, buildings, houses, and
communication systems. This results in the loss of property and life.
On the other hand, torrential flooding and inland flooding, also cause
major damages. Torrential rains are those that fall more than
30cm/hour. Rain is a serious hazard that is caused by cyclones, as
people lose shelter due to it. A storm surge is an abnormal rise of sea
water near coastal areas and is caused by a severe cyclone.
In order to avoid damages due to cyclones, individuals must listen to

weather reports regularly. Safe shelters in an area must be identified.
These are shelters where people can evacuate to in cases of extreme
destruction. Remaining indoors while the cyclone is active is another
safety measure. Emergency kits must also be acquired, which contain

first aid for wounds, and enough supplies to last until the cyclone is
over.
Tornadoes
Tornadoes are rotary storms that appear as a whirling and advancing

funnel of wind extending downward from a cloud. Tornadoes can
occur in any part of the world. They are, however, uncommon in the
Arctic region, since no cumulo-nimbus clouds are formed there. They
are also not likely to occur in the equatorial zone because the cumulo-
nimbus clouds in these areas do not have all the characteristics that are
needed to form tornadoes. The region that is most frequently hit by
tornadoes is the Midwestern United States, from Texas to Iowa. These
areas are sometimes termed as “Tornado Alley.”
Tornadoes are also very small as compared to cyclones. They are

rarely more than a few hundred meters in diameter. However, they
sometimes reach 3km in diameter. The lifespan of a tornado is usually
not more than a few hours. The velocity of the wind during a tornado
can be very high, and the strongest wind ever recorded is observed in
Texas in 1958, where the velocity reached 125m/s.
Additionally, the high destructive force of a tornado is conditioned by

a sharp difference in pressure between the center of the vortex and the
circumference of the tornado. While a tornado is passing, the air
pressure can suddenly drop by 100-200 hPa in a span of a few minutes.
This may cause buildings to explode because of the difference in air
pressure inside the enclosed space and outside it. Hail, or the ice, is
another consequence produced by a tornado. The total impact of a
tornado surpasses all other natural disasters in terms of the destruction
caused.
Due to the unpredictable nature of tornadoes, only a general forecast

can be created. Tornado warnings on a particular day when a tornado
is imminent are usually very inaccurate. Safety measures during
tornadoes include creating an emergency supply kit, with food, water,
and first aid materials. Taking shelter indoors should be done when a
tornado is approaching. Avoid windows, and protection should be
sought by getting underneath furniture that is large and solid. Mobile
homes and automobiles should also be avoided. Those that are caught
outside should lie flat on the the ground and wait for the tornado to
pass.
Marine and Coastal Processes and Their Effects
6
Coastal areas, which are boundaries between water and land, are
characterized both by the dynamic power of the sea and the wind, and
by the geologic nature of land, which is fragile and often unstable. As
a result of this dual nature, coastal areas are constantly changing as
they are struggling to maintain an equilibrium between many naturally
opposing forces. The risks of living in coastal areas are primarily for
those who are living near an earthquake fault, river flood plane, or near
a volcano. Since coastal areas are attractive places to live in, the
natural equilibrium of these areas are further disturbed, which has led
to a coastal crisis.
Coastal erosion affects about 90% of the world’s coasts and occurs at
varying rates. Coastal erosion gives rise to increased storm activity and
rising sea levels. There are five main processes by which coastal
erosion occurs: corrasion, abrasion, hydraulic action, attrition, and
corrosion/solution. Corrasion is when the waves acquire materials
from the beach and then hurl them at the base of a cliff. On the other
hand, abrasion occurs when waves, which contain sand and other
fragments erode the headland or the shoreline. This is also known as
the “sandpaper effect.” Hydraulic action is when the waves hit the base
of a cliff, subsequently compressing them into cracks. Attrition is
when the waves cause rocks and pebbles to collide with each other and
break up. Corrosion is when the cliff eroes as a result of the acids in
the sea.
Submersion, on the other hand, is the portion of coastal erosion which

is sustainable. This occurs when rocks and other sediments move from
the beach’s visible portion to the nearshore region which is
submerged. The reverse of this process, which is the recovery process,
is known as accretion.
Saltwater intrusion is the movement of salt water, or saline water, into

freshwater aquifiers. This can lead to the contamination of drinking
water and other consequences. Saltwater intrusion can occur naturally,
to some degree, in the majority of coastal aquifiers. This is due to the
hydraulic connection between seawater and groundwater. Human
activities, such as groundwater pumping from freshwater wells in
coastal areas, can increase the saltware intrusion.
Tides
The moon and the sun have gravitational pulls on the ocean, which
created oscillations called tides. As the earth spins, the position of the
moon overhead sweeps across all the latitudes. The gravity from the
moon, when it is overhead, produces a high tide. This may also happen

on the opposite side of the earth at the same time as water is “pulled
away” from the sides of the planet, and this is where low tides occur.
In every 24-hour period, there are two low tides and two high tides.
When the sun and moon are lined up together, and the moon is closest
to the earth, the high tides are maximum (spring tides). When the
moon and the sun are at 90 degrees from each other with regards to the
position of the earth, then the low tides are at their minimum (neap
tides).
Waves
Waves are considered to be disturbances in the water caused by the

water energy that is passing through the water. In open ocean basins,
the source of this energy is wind. The energy from the wind is
transferred to the water as wind blows across it. The waves’
characteristics are geometrically described. These are: 1) the amplitude
or the wave height; 2) the wave length; and 3) the wave period. The
wave height is the vertical distance between the top of the wave and its
trough. The wave length refers to the horizontal distance between
successive troughs or crests of the wave. The wave period refers to the
number of waves that occur in a given period of time.
Overall, these characteristics are determined by the duration of the

time that the wind is blowing, the wind speed, and the “fetch,” or the
distance across the open sea that the wind has travelled. The wave’s
height and its steepness vary according the amount of energy that the
wind transfers to it.
Sea-Level Changes
Sea-level changes typically occur as a result of increases in water

temperature, which increases its volume. The effect of sea-level
changes can be local or global. They are local when the water mass is
relatively contained, and they are global if a large portion of the
ocean’s water mass is impacted by warming. Conversely, as the
temperature of the seas go down, this results in reductions of sea water
volume, giving rise to lower sea levels. Mathematicians and
geoscientists have tried to theorize models that cause sea level
changes, but so far no one theory is able to explain the whole
phenomenon. However, what is certain is that a rise in temperature
causes the sea level to rise owing to changes in the volume of the sea
water. The effect of a small rise in temeperature can extrapolate to
changes in sea levels over the entire globe. This extrapolation, when
considered over time, can produce large increases in sea levels. As
8
such, scientists believe that the recent rise in sea level is caused by
global warming.
Crustal Movements
The real cause of crustal activity can be ascertained from the

movement of the crust and the crustal structure. However, there are
very few studies that refer to the relationship between crustal
movement and crustal structure. Real-time observations of the crustal
movement have been generated by observations by geologists. The
evidence for crustal movement, which is the most obvious, are
earthquakes. During an earthquake, the movement of the crust occurs
along the faults. Volcanic eruptions also involve movements of the
crust, as do displaced structures. Bench marks are metal plaques set in
the soil that give the exact locations of the elevation points. These
marks are used as reference points in geological surveys and
measurements of elevations of bench marks reveal that large areas of
land are moving upward or downward.
The causes of crustal movement include the action of unbalanced

forces acting on the earth’s surface. These forces include gravity, the
expansion and contraction of rocks, the forces produced by the rotation
of the earth, and by the density currents found in the mantle of the
earth. These many forces are called stress. On the other hand, tension
pulls the rock into two different directions, causing it to break apart or
stretching it. Compression consists of forces acting towards each other,
which pushes or squeezes rocks together. Finally, shear stresses may
act away or toward each other, causing the rock to twist and tear.
Glossary
Include list of words (arranged alphabetically) with their corresponding
meaning as used or referred to in the module.
References
Devoy, R.J.N. (2012). Sea Surface Studies: A Global View. Springer
Science & Business Media.
Kotlyakov, V.M. (2010). Natural Disasters-Volume 1. EOLSS

Publishers.

OAS.org. (n.d.). Chapter 11-Geologic Hazards. Retrieved from

http://www.oas.org/dsd/publications/unit/oea66e/ch11.htm

Top Ten Natural Disasters
Disaster Preparedness: Natural Disasters
10 Signs that Global Warming is No Longer a Debate
Disaster Risk Management and Climate Change Adaptation in Europe

and Central Asia
Centers for Disease Control and Prevention Emergency Preparedness

and Response
Disaster Preparedness
10
Introduction to Life Science
The study of life is an interesting journey. It allows us to understand

the basis for all living things on earth. Life science is a fundamental
part of learning about organisms, including ourselves. It is thus
imperative that we learn how we came about, and the basic units of life
that are present in our lives.
The Historical Development of the Concept of Life

There are two biographies of life. The first is ontogenic, synthetic, and
developmental. This is based on the properties of cells and their
ecological (biogeomechanical) consequnces. The second is the
historical-collective, populational, diachronic, and evolutionary
process. The two main pillars that sustain life are metabolism and
genetics. Each living thing on earth uses external sources of energy to
fight the disorder and to maintain equilibrium. Organisms also use
external energy sources in order to fight against death. Molecular
machines and membranes are located as part of the frontier between
inside and outside. They also manage flows of energy and matter that
would benefit the cell. In current life forms, these mechanisms are
dependent on digital genetic records. The change, acquisition, and loss
of fragments of information from cells underlie the evolutionary
process. The historical persistence of these records of genes is
absolutely dependent on the ecological and metabolic abilities of
organisms. Thus, the fundamental question emerges: how did life
come to be on earth? Which came first, the hereditary properties of
living matter or their autopoietic properties?
What is Life?
The definition of what constitutes life is a hard question. Howeever,

life can be loosely defined as “a living being is any autonomous
system with open-ended evolutionary capacities.” The term autonomy
refers to the organism’s relationship with its environment, as well as
the mutal modifications of both, as well as the capacity of the
organism to use matter and energy to create its own components. This
means that living things can self-construct, through which they are
able to build an identity that is separate from the environment. In the
simplest case, a living organism is a cell. On the other hand, the term
“open-ended evolution” refers to the capacity of living things to
explore novel functions and relationships with their surroundings,
Introduction to Life Science 1

X.X Module Title
including other living things. It also pertains to their ability to adapt to

situations in a way that is almost unlimited.
There is a range of physical conditions that are compatible with

life. Wherever there is an energy source that can be used (visible-light
protons, certain chemical reactions that are inorganic, or organic
matter), as well as liquid water, biological activity can be found. At a
molecular level, living organisms also show a striking biochemical
unity. The same basic cellular organization, the repeated use of genetic
matter in the form of DNA, the genetic code that is universal, and the
variations that are found in the same bioenergetics mechanisms (i.e.
chemiosmotic energy currency and chemical currency). Thus, the
explanation for all these suppositions on terrestrial life is that they
come from a common ancestor, which was observed by Charles
Darwin.
The Origin of Life
How should the study of the primordial steps of the evolution of life
proceed? Using a top-down strategy, all organisms that are known
are compared in order for the reconstruction of the metabolic and
genetic makeup of the universal “cenancestor” proposed by
Darwin. Thus, in the universal sense, there are two branches to the
tree of life. These are the bacteria and the Archaea. The Eucarya
domain is considered to originate from prokaryotic partners, and
is a chimera. On the other hand, the bottom-up approach starts
with planetary, cosmological, and geological information, as well
as information from other sources that can be used to reconstruct
the ambient, which are the chemical inventories and processes that
are involved in the origin of life.
In the 1920s, Aleksandr I. Oparin fathered the notion that the origin of
life has unfolded based on the physiochemical processes that
occur on earth. However, the importance of Oparin’s theories are
not in the facts that he presented, but rather on the intellectual idea
that historical hypotheses can be tested, and even simple artificial
life forms created. For instance, in 1953, the Urey-Miller
experiment became the start of the prebiotic chemistry program.
Since then, many chemical reactions, such as the synthesis of
amino acids and nucleic acid bases, have been proposed. The
Urey-Miller experiment provided experimental evidence for
Oparin’s theory. Oparin’s theory is popularly known as the
“primordial soup theory,” referring to the acquatic origins of
organisms.
2
The following steps comprise the Oparin’s theory:
1. The atmosphere of the early earth was chemically-reducing.
2. This type of atmosphere, which was exposed to various forms

of energy, was able to produce simple organic compounds
(monomers).
3. These compounds accumulated in a “soup” which may have

been accumulated in various locations.
4. Through further transformation, the more complex organic

compounds (polymers), and ultimately, life, developed.
Following the scenario proposed by Oparin, prebiotic organic

molecules, which may either be terrestrial or extraterrestrial in
origin, were built up from the oceans. This promoted the
proliferation of organisms that can survive in aerobic
environments. In this scenario, then, life started as heterotrophic
and anoxygenic cells. On the other hand, Gunter Wachtershauser
proposed that the origin of life was both autotrophic and
thermophilic. He suggested that pyrite was the energy source, as
well as the electron source, of all living matter. Although his
theory may be viable, evidence is still lacking as to the
autotrophic origins of life.
That being said, there are several standpoints that have been debated
upon concerning the origin of life.
Heterotrophic vs. Autotrophic Origins
The standpoint in this case is that either life started out as a simple
system that took advantage of the environment, as proposed by Oparin,
or self-sustained systems emerged early on, as proposed by
Wachtershauser. Upon considering the chart of the autotrophic
evolution, then Oparin’s theory is more plausible, as conferred by
experts.
Replicators or Metabolism First
The principal debate here is whether genes, or genetic material,

emerged first (as proposed by Henry Muller), or whether proteins
emerged first (as proposed by Leonard Troland). Many authors believe
that the origin of life emerged as the first replicators, or the first
molecules that copied themselves. There are several supporting
experiments that gave rise to evidence that genetic materials came

X.X Module Title
first. One of these experiments was created by Tom Cech and Sydney
Altman, who discovered catalytic RNA. Catalytic RNA causes the
formation of proteins from genetic materials. However, those that
contest the replicators theory contest that there is no way to efficiently
use energy without the necessary proteins. Thus, several researchers,
including Wachtershauser, have advocated for the emergence of
primitive, self-catalytic metabolic networks as the primary step
towards the creation or synthesis of replicators. Those prebiotic
processes, which are self-organized, would have provided a useful
scaffolding for the emergence of genetics.
Early or Late Cellularization
The debate surrounding the origin of life includes whether the

formation of compartments was a late or early phenomenon. This
debate is closely related to the debate between whether genetic
material or proteins came first. Those that regard the early emergence
of replicators have regarded the cell as physical compartment in which
polymers are segregated. However, ample evidence from biochemistry
has shown that the cells is not simply a compartment that is enclosed
by a semi-permeable membrane. Instead, the cell’s interior is a
physically and chemically different environment from the outside
because of the presence of active phospholipid membranes and their
protein machines. Thus, the essence of bioenergetics lies in the
disposition, which is asymmetric, or the molecular machines on the
membranes of cells and the corresponding chemical messengers
allowing coupling between energy sources and metabolic networks. It
is worth noting that this debate has spurred the bottom-up strategy for
the chemical synthesis of life.
Unifying Themes in the Study of Life

The study of life is rife with themes that are common to all living
things. These themes are important for characterizing what living
things are, and can help in the study of their origins as well as their
characteristics. Evolution is the mechanism by which an organism
adapts to its environment. Biology is the scientific study of life. Life is
recognized through a set of characteristics.
Theme 1: New Properties Emerge at Successive Levels of

Biological Organization
The study of life can be as great as on a global scale, to as small as the

study of cellular organisms. Reductionism is the approach of breaking
4
down complex systems into simpler systems that are more manageable
for study. For instance, the molecular structure of DNA can be broken
down in order to understand the chemical basis of inheritance.
Emergent Properties are properties that are new, and that emerge at
each level of organization. These properties are absent from the
preceding level. Systems biology is a system that combines
compenents that function together. This type of biology attempts to
model the dynamic behavior of whole biological system, which are
based on the study of the interactions between the parts of the system.
Structure and Function is a major theme in biology. That is, the

organism’s form must fit its function. For instance, a hummingbird’s
wings are design to beat rapidly and to set it to fly. Analyzing the
structure of organisms gives clues as to how it works. Conversely,
analyzing its function can give rise to clues about how it is
constructed.
The Cell is the basic unit of life structure and function. This is the
lowest level of biological organization and can perform all the
activities required for it to survive. Understanding how cells work is a
major focus of research endeavors in biology. There are two main cell
types: eukaryotic and prokaryotic. Eukaryotic cells contain organelles
in their cytoplasm. Prokaryotic cells, on the other hand, is a simpler
cell and do not contain organelles in their cytoplasms.
Theme 2: Life’s Processes Involve the Expression and

Transmission of Genetic Information
The division of cells to form new cells is the basic foundation for the
growth and reproduction of all organisms. In the dividing cell,
deoxyribonucleic acid (DNA) is replicated and then partitioned
between two resulting daughter cells.
DNA is where genes are found. Genes are the basic units of inheritance
that transmits the genetic information from parents to offsprings. DNA
controls the development and maintenance of the whole organism. It is
also responsible, albeit indirectly, for everything that the organism
does. DNA is the storage space for genetic information. It is composed
of nucleic acids, which are building blocks for genes. These nucleic
acids are: guanine (G), adenine (A), thymine (T), and cytosine (C).
DNA also controls the production of proteins through an intermediate
molecule. This intermediate molecule is known as ribonucleic acid
(RNA). The process of transcribing genetic information to proteins is

X.X Module Title
known as gene expression. However, not all RNA are transcribed into
proteins.
Genomics is the large-scale study of DNA sequences. The entire

“library” of genes in an organism is termed as it genome. The new area
of genomics is concerned with studying the whole sets of genes of a
species. Proteomics, on the other hand, is the study of proteins and
their properties.
Theme 3: Life Requires the Transmission and

Transformation of Energy and Matter
A fundamental characteristic of all living things is that they use energy

to carry out their activities, and to sustain them. Growing and moving
requires work, and this work requires energy. Living organisms
function to transform the types of enegery. For instance, solar energy
is transformed to chemical energy (sugar) through the process of
photosynthesis. The flow of energy in living things starts with
producers (plants) to consumers (animals), and then to decomposition
(bacteria and fungi).
Theme 4: From Ecosystems to Molecules, Interactions are

Important in Biological Systems
Ecosystem encompasses an organism’s interaction with the physical

environment and other organisms. At the level of the ecosystem, each
organism interacts with other organisms. In addition to this, organisms
also interact with other factors of the physical environment.
Molecules interact with organisms. The regulation of biological

processes is important for the operation of living systems. The
chemical processes of the cells are mediated by active proteins called
enzymes. The chemical pathway contains several steps, and each step
is controlled by an enzyme. Biological processes regulate themselves
through a mechanism called feedback regulation. Negative feedback
occurs when the accumulation of the end product halts the chemical
process. On the other hand, positive feedback occurs when the product
speeds up its own production.
Theme 5: Evolution is the Core Theme of Biology
Organisms exhibit the diversity as well as the unity of evolution.

Living organisms have shared traits (unity). Yet, each organism is
suited to its own environment (diversity). All organisms are descended
from a common ancestor. Charles Darwin proposed the theory of
evolution, after observing animals from his boat, the SS Beagle.
6
Glossary
Anoxygenic: does not use oxygen
Autotophic: an organism that is capable of synthesizing its own food using

light or chemical energy
Bioenergetics: the study of transformation of energy in all living things
Chemiosmotic energy: energy derived from the movement of ions across a

selectively permeable membrane
Diachronic: concerned with the development of an organism, or language.
Heterotrophic: Organisms that use energy from sunlight or inorganic

compounds to produce organic compounds
Polymers: repeating units of monomers
Thermophilic: drawn towards heat
Ontogenic: concerned with the origin and development of an organism.
References
Dawkins, R. (1996). The Blind Watchmaker. W.W. Norton & Company.
Reece, J.B., Cain, M.L., Wasserman, S.A…& Jackson, R.B. (2013). Campbell Biology 9th ed.
Pearson.
Pereto, J. (2005). Controversies on the origin of life. International Microbiology, 8, 23-31.
Videoes and Resources

Origin of Life- How Life Started on Earth
What was the Miller-Urey Experiment?
Origins of Life- Abiogenesis

X.X Module Title
Themes in the Study of Life
Molecular Cell Biology
Ten Themes Unify the Study of Life
8
Bioenergetics
In the previous module, we learned about the origin of life, as well as

the theories that support certain hypothesis. Now, it is time to delve
deeper into the processes that perpetuate life. It is important to
understand how these processes occur at both a cellular and
organismic level. Learning these processes will arm you with the
knowledge needed to understand broader and deeper studies of life.
Bioenergetics concerns itself with studying the transfer of energy; that
is, how energy is converted into matter and other forms of energy.
The Cell as the Basic Unit of Life

The cell is the basic unit of life. Organisms may either be unicellular
(composed of one cell alone), or multicellular. Cells comprise both
animals and plants, although there are differences with regards to each.
However, the cell is the smallest unit of life. Cells may come together
to form tissues, which can come together to form organs. Organs make
up the human body, as well as the bodies of plants and animals.
The study of the cell is not possible without a microscope. Anton van
Leewenhoek constructed the first simple microscope. He was able to
study the structure of bacteria, protozoa, spermatozoa, and red blood
cells. Robert Hooke, in 1665, coined the term “cell” that he used to
designate the small, honey-comb like structures that he was able to
view on a cork bottle. He was impressed with the little structures, as
they reminded him of rooms in a monastery. In 1838, Matthios
Schleiden proposed that all plants are made up of cells. Then, 1839,
Theodore Schwann proposed that all animals were also made up of
cells. Together, Schleiden and Schwann studied a wide variety of plant
and animal tissues, and proposed the Cell Theory in 1839. The theory
essentially stated that all organisms are made up of cells. However, the
theory was rewritten by Rudolf Virchow in 1858. In the succeeding
theory, Virchow wrote that, aside from all living things being made up
of cells, all cells arise from pre-existing cells. In 1861, Schulze found
that cells were not empty, as Hooke thought, but that they contained
material known as protoplasm.
It was during the 1950s that scientists were able to classify cells
according to eukaryotic cells and prokaryotic cells; with the latter
lacking a nucleus. Another important difference between prokrayotes
and eukaryotes is that prokaryotic cells do not have any intracellular
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components. Prokaryotic cells include bacteria and blue-green algae,

while eukaryotic cells include plants, animals, fungi, and protozoa.
Modern Cell Theory
Biologists today have made additions to the cell theory, which now
states:
1) All organisms are made up of cells;
2) New cells arise from pre-existing cells;
3) The cell is the structural and functional unit of all living things;
4) The cell contains genetic information that is passed from cell to

cell during cell division; and
5) All cells are basically the same in chemical composition and

metabolic activities.
The Structure of the Cell
Both prokaryotic and eukaryotic cells posses a plasma membrane and

a cytoplasm. The plasma membrane is the outermost surface of the cell
and it separates the cell from its environment. The cytoplasm is the
aqueous content of the cell, in which the cell’s organelles are
suspended.
2
The plasma membrane is semi-permeable membrane that is present in

all cells. The plasma membrane is composed of carbohydrates,
proteins, phospholipids, and cholesterol. The plasma membrane
contains a lipid bilayer, which is termed as such because it contains
two layers of fat cells organized into two sheets. It is typically about
five nanometers thick and the surrounds all cells, providing the
membrane structure. The structure of the lipid bilayer explains its
function as a barrier. Lipids are fats, such as oils, that are insoluble in
water. There are two important regions of a lipid that are crucial for
the lipid bilayer. Each lipid molecule contains a hydrophilic region
(the polar head region) and a hydrophobic region (the non-polar tail
region). The hydrophilic region is attracted to water conditions while
the hydrophobic region is repelled from these conditions. Since lipid
molecules contain both regions, they are termed as amphipathic
molecules. The most abundant types of lipids found in the plasma
membrane are phospholipids. It has two nonpolar fatty acid chain
groups and a tail. The tail is composed of a string of carbons and
hydrogens. Due to its double-bond structure, the tail has a kink.
The bilayer is where the lipids organize themselves to hide their

hydrophobic region and to expose their hydrophilic regions. The
organization as such is a spontaneous process, which does not require
energy. The most important property of the lipid bilayer is that it is a
highly impermeable structure. This means that molecules cannot freely
pass across the lipid bilayer. Only water and gas can pass through. It
also means that large molecules and small polar molecules cannot
cross the bilayer, and thus, the cell membrane, without being assisted
by other structures. Another important characteristic of the lipid
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bilayer is its fluidity. The fluidity of the bilayer allows proteins to

move within it. The fluidity of the bilayer is also important because it
allows membrane transport. Fluidity is dependent on the temperature
as well as the specific structure of the fatty acid chains. Due to these
two properties, the lipid bilayer was summarized by Singer and
Nicholson (1974) as the Fluid Mosaic Model.
On the other hand, cells also contain a cytoplasm, which is where

organelles are suspended. The cytoplasm contains living components,
which are cell organelles, and non-living components, which are
ergastic subsances and cytoskeletal elements. Without the organelles,
the cytoplasm is termed as cytosol. It is a jelly-like, semi-fluid matrix
that is found between the nuclear membrane and the cell membrane.
The cytoplasm often comprises up to 50% of the cell’s volume. Aside
from providing structural support for the cell, the cytoplasm is also
where protein synthesis occurs.
The cytoskeleton is another cell component that gives the cell its
structure. It also allows the cell to adapt. Thus, cells can reorganize
their cytoskeletal components in order to change their shapes. The
cytoskeleton also has ‘tracks’ where it allows organelles to move
around the cell. The cytoskeleton can also move entire cells in multi-
cellular organisms. Therefore, the cytoskeleton is involved in
intercellular communication. The cytoskeleton is composed of three
different types of protein filaments: intermediate filaments,
microtubules, and actin. Briefly, actin is the main component of actin
filaments. They are double-stranded, thin, and flexible structures. It is
also the most abundant protein in eukaryotic cells. Microtubules are
long, cylindrical structures composed of tubulin. They are organized
around a centrosome. These filaments provide tracks upon which
organelles can move inside the cells. Intermediate filaments are rope-
like and fibrous. They have a diameter of approximately 10
nanometers. These filaments, however, are not found in all animal
cells, but only in those where they function to form the nuclear lamina.
The nucleus of the cell is one of the largest organelles found in cells. It
also plays an important biological role. It comprises close to 10% of
the cell’s volume and it is found near the center of eukaryotic cells.
The importance of the nucleus lies in its function as the storage space
for DNA. The cell nucleus is composed of two layers which form an
envelope around the cell and only allows selected molecules to enter
and leave the cell. The DNA that is found in cells is packaged in
chromosomes. The nucleus directly comes into contact with the
endoplasmic reticulum. It is also the site of DNA and RNA synthesis.
4
The mitochondria, on the other hand, is a double-membrane structure

that is highly specialized. It generates adenosine triphosphate (ATP),
which provides organisms with energy. The outer membrane of the
mitochondria is smooth, while the inner membrane produces finger-
like infoldings called cristae. The inside of the mitochondria is filled
with the homogenous, granular mitochondrial matrix. This matrix has
mitochondrial DNA, RNA, lipids, proteins, enzymes, and 70s
ribosomes.
The endoplasmic reticulum is a network of tubular structures found in

the cystoplasm and is bound by a membrane. It extends from the
nuclear membrane to the cell membrane. The endoplasmic reticulum
exists as oval vesicles, unbranched tubules, and flattened sacs called
cisternae. There are two types of endoplasmic reticulum: smooth and
rough. The former does not contain ribosomes, while the latter
contains 80s ribosomes. The function of the endoplasmic reticulum is
that it helps in intracellular transportation. It also provides mechanical
support for the cytoplasmic matrix, and it helps in the formation of the
Golgi complex and nuclear membrane. It is also the storehouse of
lipids, carbohydrates, and metabolic wastes.
Golgi bodies (Golgi complex) are a group of curved, flattened, plate-

like cisternae. The cisternae produce a netwrork of tubules from the
periphery. These tubules also end in vesicles. The Golgi complex is
also known as the packaging center of the cell. These bodies package
proteins, carbohydrates, etc. in their vesicles. They also produce
enzymes called lysosomes, which are “suicide bags” of the cell and
result in cell death. They secrete enzymes, hormones, and material
from the cell wall.
Plastids are found in plant cells and euglenoids. They are classified
based on the type of pigment that they contain. Chromoplasts contain
carotenoids. Leucoplasts store food materials and are colorless.
Chloroplasts are green in color and function in photosynthesis.
Vacuoles are single-membrane bound sacs that are present in the

cytoplasm. Plant cells have large vacuoles and animal cells have small
vacuoles. The tonoplast is the term for the membrane of the vacuoles.
It is filled with cell sap, which is watery. The cell sap has sugars, salts,
pigments, and enzymes. There are four types of vacuoles: contractile
vacuoles, food vacuoles, gas vacuoles, and storage vacuoles.
Ribosomes produce proteins in cells. These are granular,

nonmembraneous structures inside the cells. They are present in the
cytoplasm, mitochondria, and chloroplast. Eukaryotes have 80s
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ribosomes in the cytoplasm and 70s ribosomes in the plastids and

mitochondria. Centrosomes form spindles during cell division. They
are surrounded by a denser type of cytosol called the centrosphere.
Centrosomes have two cylindrical structures called centrioles at the
center.
Photosynthesis
Photosynthesis is the process by which plants that contain chlorophyll
covert energy from the sun into photochemical energy. This energy is
stored in the form of carbohydrates. Carbohydrates provide food for
man and other heterotrophic organisms. Aside from this,
photosynthesis also produces oxygen as a by-product that is essential
for all life on earth. The photosynthetic activity from previous eras in
geology have provided us with large deposits of fuel. Lately, however,
the by-products produced through photosynthesis is undergoing
scrutiny, in part because it is in danger of being inadequate for animal
and human survival. Thus, understanding the process of
photosynthesis will help us gain an underastanding of how its efficieny
can be improved, and in devising artificial sources of photochemical
energy based on it. In addition to this, many biochemical processes,
such as electron transport, can be understood through photosynthesis.
In the photosynthetic activity of green plants, CO2, H2O, and light

energy react with each other, producing O2 and carbohydrates (CH2O)
as its products.
6
Molecules of pigment, especially chrolophyll, various enzymes, and

electron carriers act in a manner that is catalytic in this reaction. The
overall bioenergetics of this reaction can be summarized as follows: C,
H, and O in CO2 and H2O are converted from a very stable
arrangement of atoms to less stable arrangement of the same electrons
and nuclei (CH2O + O2). In order for this process to occur, light energy
is needed. The total energy stored is 112kcal/mole difference. The
difference is supplied by the energy from light. Photosynthesis is
considered as an oxidation-reduction reaction.
In addition to green plants, certain kinds of bacteria (e.g. purple and

green) are capable of photosynthesis. Photosynthetic bacteria are
different from plants in that they are not capable of oxidizing H2O.
Consequently, no oxygen is involved in the photosynthesis of bacteria.
Primary Events in Photosynthesis
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Light absorption is the first step in photosynthesis. There are three

main groups of pigments involved in light absorption: chlorophylls,
phycobilins, and carotenoids. These pigments function as a means for
plants to absorb light through the visible sprectrum. The energy is then
transferred to reaction centers, where it is used for photochemical
reactions. The bulk of the pigments involved in absorbing light are
called light-harvesting pigments.
There are two kinds of chlorophyll in plants and green algae:

chlorophyll A (Chl a) and chlorophyll b (Chl b). These pigments are
soluble in organic solvents. On the other hand, carotenoids are yellow
and orange pigments that are found in almost all photosynthetic
organisms. They are also soluble in organic solvents. There are two
kinds of carotenoids: carotenes, of which beta-carotene is the most
common, and carotenols, or alcohols. Phycobilins are water-soluble
pigments, which are present in blue and red algae. They are open-
chain tetraphyroles. There are also two kinds of phycobilins:
phycocyanins, which are primarily found in blue-green algae, and
phycoerythrins, which are found in red algae.
Light emission is the second step in photosynthesis. The Chl a

molecule becomes excited due to direct light absorption. These
molecules undergo fluorescence. After fluorescence, delayed light
emission occurs. Photosynthetic organisms emit light for short periods
of time.
The third step is energy transfer and migration. Through a maze of

several hundred Chl a molecules, energy migration occurs until the
energy reaches the reaction center where it can be converted into
chemical energy. There are two processes in energy transfer and
migration: heterogenous, when the energy is transferred to other Chl a
molecules, and homogenous, when energy is transferred through the
same kinds of molecules.
The fourth step is the reaction at reaction centers. This is the process
by which energy reaches reaction centers and is converted into
chemical energy. This reaction produces an oxidizing and reducing
equivalent. The primary electron in this process is reduced and the
reaction center undergoes oxidation. In turn, this receives an electron
from the primary electron donor. This transfer of electrons is
summarized in the Calvin cycle. After electrons are transferred, the
products of oxygen and carbohydrates are created.
8
Glossary
Cisternae: comprise the Golgi bodies
Chl a: chlorophyll A
References
Reece, J.B., Urry, L.A., Cain, M.L…& Jackson, R.B. (2013).
Campbell Biology 10th ed. Pearson.

Cell Organelles
Mitosis
Photosynthesis
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Chapter 10: Photosynthesis
Molecular Cell Biology
Cell Structure and Function
10
MODULE OF INSTRUCTION
Perpetuation of Life
Plant and animal reproduction, as well as all movements and functions
of living things, require energy to proceed. In the previous module, we
learned about bioenergetics, and we focused on how plants create
photochemical energy from sunlight. We also learned extensively
about the parts of the cell, the basic unit of living things, as well as
their functions. In this module, we will learn about how life continues
through reproduction. We will also learn about how hereditary
materials are passed from parents to offspirings. Finally, we will also
delve into genetic engineering in order to understand genetically
modified organisms (GMOs) and their implications for our lives today.
Plant Reproduction
The reproduction of plants is important for the propagation of life on
earth. Plants reproduce through three types: asexual, sexual, and
vegetative.
Asexual Reproduction
In the asexual mode of reproduction, offsprings are produced from the
vegetative unit produced by a parent without any fusion of sex cells or
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gametes. In addition to this, only a single parent is involved and the
offspring produced are genetically identical to the parent. There are
also several types of asexual reproduction.
Fission can be seen in unicellular organisms such as yeast or bacteria.
The content of the parent cell divides into 2, 4, or 8 daughter cells.
Accordingly, fission may be called binary (2) or multiple (4 or more).
Each daughter cell that is newly formed grows into a new organism.
Budding is bud-like growth formed on one side of the parent cell. As
soon as the bud separates from the parent cell, it becomes a whole new
organism (e.g. yeast).
Fragmentation occurs in filamentous algae. It occurs as a result of
accidentally breaking off a filament into many fragments. Each new
fragment may give rise to a new organism through cell division (e.g.
Spirogyra).
Spore formation occurs in lower plants, such as pteridophytes and
byrophytes. During this type of asexual reproduction, special
reproductive units develop asexually on the body of the parent. These
special reproductive units are called spores. These are microscopic
units and are covered by protective wall. Once spores reach an
2
environment that is conducive to growth, they develop into new plant
bodies (e.g. bread moulds, mosses, ferns).
Vegetative Reproduction
Vegetative reproduction involves the formation of new plants from a
somatic, or vegetative cell, or buds or organs of the plant. Here, a
vegeatitive part of the plant, such as the root, stem, leaf, or bud, is
detached from the body of the parent and grows into a daughter plant
that is independent. It is similar to asexual reproduction in that it only
requires mitotic division. Thus, no gametic fusion occurs and daughter
plants are exact genetic copies of their parents.
Sexual Reproduction
Sexual reproduction involves the fusion of female and male
reproductive cells (gametes). These gametes are haploid, which means
that they contain only half the genetic material (chromosomes) for a
new organism to exist. The fusion of gametes is also called
fertilization and it results in the production of diploid zygote. When
the zygote undergoes further development, it gives rise to a new
individual that is diploid. At the beginning stages of sexual
reproduction, meiosis occurs. The offsprings are not genetically
identical to their parents.
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Reproduction in Lower Plants
Two representative plants that are considered lower plants are
Spirogyra (multicellular) and Chlamydomonas (unicellular).
The unicellular algae, Chlamydomonas, is a haploid, unicellular algae
that is found in freshwater ponds. The plant’s body is pear-shaped, and
there are two flagella attached to the narrow end. Flagella are filaments
found in flagilates. A large chloroplast is present. Towards the center
of the organism, a nucleus is present. The chloroplast contains a single
pyrenoid. The organism may undergo sexual or asexual reproduction.
When it undergoes asexual reproduction, it is through zoospores.
Consequently, its flagellae is lost and the organism becomes non-
motile. The protoplasm divides mitotically and forms 4-8 zoospores.
Each zoospore develops a cell wall and it also grows into an adult cell.
The parent cell, however, does not exist anymore.
During sexual reproduction of the Chlamydomonas, the cell again
becomes non-motile by losing its flagella. The protoplasm also divides
mitotically into 2,4,8,16, and 132 daughter cells. Each daughter cell
then develops its own flagella and is released to the water by the
rupture of the mother cell wall. Each daughter cell acts as a gamete.
The gamete is morphologically identical (isogamous). Two gametes
released from the mother cell fuse together. The contents of the
4
gametes then fuse and form a zygote (diploid). This is the only stage in
the organim’s life cycle that is diploid. The zygotes then develop a
thick wall around itself (zygospores). Then, the zoospore grows into a
new organism.
On the other hand, Spirogyra is a free-floating algae found in
freshwater ponds. The body contains a row of rectangular cells that are
joined end to end (filamentous alga). Each cell has a sparial ribbon-
shaped chloroplast that contains many pyrenoids. The nucleus is
present in the cental vacuole with support from cytoplasmic strands. It
undergoes two types of reproduction: vegetative reproduction by
fragmentation and sexual reproduction.
Vegetative reproduction by fragmentation occurs first when filaments
break into smaller fragments. Then, each fragment grows into a new
organism by cell division.
On the other hand, sexual reproduction occurs in the organism.
Scalariform conjugation, which is when filaments conjugate to form a
ladder-like appearance, start when two filaments lie very close to each
other. The cells of the two filaments connect with each other through a
conjugation tube. The contents of the cytoplasm of each cell rounds of
to act as a separate gameter. The gamete from one cell (male) passes
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into the conjugation tube towards the other cell (female). The contents
of these two gametes fuse to form a diploid zygote.
Reproduction in Angiosperms (Flowering Plants)
Angiosperms may reproduce vegetatively or sexually. Sexual
reproduction occurs by the fusion of male and female gametes that are
present in the flower. Thus, the plant’s basic reproductive unit is the
flower. Angiosperms can be classified according to the following:
Annuals: these plants live for only one year. The plants that
produce seeds and flowers within just one season are termed as
annuals (e.g. peas).
Biennials: plants that live for two seasons, and complete their
life cycles within these two seasons. During the first year, the
plant is in a vegetative state. In the second year, the plants
produce flowers, fruits, or seeds and then they perish (e.g.
radish).
Perennials: plants that live for several years. The vegetative
state of these plants may last from one year to several years. In
the year following their vegetative state, they produce flowers,
seeds, or fruits (e.g. mangoes).
6
Monocarpic: perennial plants that reproduce only once during
their lifetime and then die (e.g. bamboo).
Initiation of Flowering
When the plant’s seed germinates, plantlets emerge from it. The
young plant grows and continues to grow until it has a definites
shape and size. The plant’s vegetative parts (root, stem, leaves)
must be well-developed. This phase in the plant’s life cycle is
known as the young of juvenile phase.
After the plant completes vegetative growth, the plant then enters
into the reproductive phase, or the adult phase. A vegetative shoot
apex then tranforms into a floral apex, a reproductive part, and
starts bearing flowers. The flowering stage may last from several
days to several years.
A juvenile shoot has a soft stem, and only bears a few leaves. The
size and shape of the leaves remain the same. It does not respond
to stimuli nor does it produce flowers. On the other hand, an adult
shoot has well-developed stems and leaves. The size and shape of
the leaves change. It also responds to stimuli and can produce
flowers.
Factors Affecting Flowering
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The plant’s flowering is affected by light (photoperiodism) and by
temperature (vernalisation). Vernasilation is when low
temperatures occur, and this stimulates the early formation of
flowers. On the other hand, photoperiodism is the response of the
plant to the duration of dark and light per day. This determines its
growth and flowering.
The sex of a flower may be bisexual, which means that they have
both carpels and stamens, or unisexual (having only a staminate or
pistillate). The sexual determination of flowers may vary in
dioceious species. However, sex determination may have a
chromosomal basis. The plants may also exhibit different levels of
substances required for growth. For instance, Cucumis, which bear
male flowers, have high levels of gibberellin as compared to those
that bear only female flowers. Gibberellin is a plant hormone that
assists in growth and reproduction. When gibberellin is applied
externally, the production of male flowers may be induced even in
plants that are genetically female. Conversely, treating male plants
with ethylene or auxin may induce the development of functional
female flowers. The latter response has been seen in Cannabis.
Parts of a Flower
8
A typical flower consists of four whorls which are located on a
stalk (thalamus). Sepals comprise the calyx. Petals comprise the
corolla. Additionally, stames comprise the androecium and pistils
(gynoecium) consists of carpels. The two outer whorls are known
as non-essential or accessory whorls because they do not play a
part in the plant’s reproduction, although they aid indirectly. The
two inner whorls, the androecium (male reproductive organ) and
the gynoecium (female reproductive organ) are termed as essential
whorls because they are the main components of the plant’s
reproduction.
Stamen, Microsporagia, and Pollen Grain
The plant’s stamen consists of an anther that contains
microsporagia, or four pollen sacs. These supported by a slender
filament. Each sporangium contains masses of large cells. These
cells show a prominent nucleus and abundant cytoplasm. These
cells are also known as the sporangeous or the microspore mother
cells. Each microsporangium is madeup of a distinct layers of cells
when mature. The outer most layer is the epidermis. It has a middle
layer of cells with thin walls. The innermost layer is the tapetum,
which consists of large cells. The tapetum nourishes the
developing grains of pollen.
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Microspore mother cells undergo meiosis. Each mother cell
produces four haploid microspores (diploid pollen grains) that are
arranged in a tetrad.
The Development of the Male Gametophyte
The wall of the microspore consists of two principal layers. The
outer layer is the exine and thin spaces (germ pores). The exine is
made up of a durable substance called sporopollenin. The pollen
tube grows out of the pollen grain through the germ pores. The
inner layer is the cellulosic wall (the intine). The microspore
moves towards the periphery. The cell then divides into a small
generative cell and a large vegetative cell. At this stage, the pollens
are released by the rupture of the stodium dehiscence of the anther.
The pollen grain itself is not a male gamete. Rather, it produces the
male gamete and is therefore a male gametophyte.
The Development of the Female Gametophyte
The main part of the ovule is bounded by two coverings
(integuments). These integuments leave behind a small aperture, or
opening. The ovule is attached to the ovary via a stalk, known as
the furniclus. The basal part of this structure is the chalaza.
10
The female gamete’s gynoecium (pistil) represents its reproductive
part. Each pistil is composed of a stigma, ovary, and style. The
ovary contains one or more ovules (megasporangia), which act as
future seeds. An ovule develops as a type of projection from the
placenta in the ovary. It consists of integuments and nuclei. As the
ovule grows, it becomes raised on the stalk, termed as furniculus.
This is attached to the placenta on the other end.
Within the nucleus, a single hypodermal cell becomes larger and it
becomes the megaspore mother cell. This cell undergoes meiotic
division, and then gives rise to four haploid megaspore cells.
Usually, three of the megaspores degenerate, while one remains as
the functional megaspore. Thus, 8 nuclei are formed as a result of
this division. The enlarged structure, shaped like an oval and with
8 nuclei, is known as the embryo sac. The nuclei then migrate and
form three groups. Cell membranes and nuclei develop around the
nuclei, except the two at the center of the sac, which is now termed
as the central cell.
Vegetative Reproduction in Angiosperms
The natural method of the vegetative reproduction of angiosperms
starts with the underground modification of stems, such as ing
ginger, potato, onion, and corn. These are provided with buds
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which develop into a new plant and are therefore used to carry out
vegetative propagation of the plant in the filed. Plants with
subaerial modification, such as chrysanthemum and pistia, are also
used for vegetative propagation. Artificial methods of vegetative
reproduction include the use of cuttings, layering, and aerial
layering.
Animal Reproduction
Animal reproduction is the process by which animals propagate on
earth and it is also the process through which genetic materials are
transferred to offspring. Animals, like plants, may reproduce through
asexual or sexual means. Asexual reproduction is primarily employed
by turnicates, protists, and cnidaria. However, it may also occur in the
more complex animal species. Indeed, the formation of identical twins
by the separation of two identicall cells in the early embryo is a form
of asexual reproduction. Through mitosis, genetically identical cells
are produced from one parent cell. This permits asexual reproduction
to occur in protists by the organism’s division, called fission. Cnidaria
commonly reproduce by budding, which is when a part of the parent’s
body is separated from the rest and differentiates into a new organism.
The new organism may become independent, or it may remain
attached to the parent organism, forming a colony.
12
Sexual reproduction occurs when a new individual is formed from the
union of two sex cells, or gametes. Gamates include the sperm and the
egg. The union of these two produces a fertilized egg, or zygot.
Through mitotic division, the zygote develops into a new organism.
The zygote and the cells that it forms are diploid. This means that they
contain both members of each pair of homologous chromosoms. The
gametes are formed in the sex organs, or gonads (the testes and the
ovaries), and are haploid. The process of sperm formation
(spermatogenesis) and egg formation (oogenesis) are also included in
the study of the reproduction of animals.
Different Approaches to Sex
Virgin birth, or parthenogenesis, is common in many species of
arthropods. Some species are exclusively parthenogenic (all female),
while others switch between generation. Another variation in the
reproductive strategies used by animals is hermaphroditism. This is the
case when one individual has both testes and ovaries. Tapeworms are
hermaphroditic, and it is able to fertilize itself. However, most
hermaphroditic animals require another organism to reproduce, such as
in the case of two earthworms. There are also some deep sea fish
which are hermaphrodites, meaning that they are both male and female
at the same time. Numerous species of fish can change their sex, a
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process which is called sequential hermaphroditism. The change from
female to male is protogyny, while the change from male to female is
protandry.
Sex Determination
In fish, there are conditions which cause changes in sex. In mammals,
however, sex is already determined early in embryonic development.
The reproductive systems of both males and females (humans) are
identical during the first 40 days of embryonic development. During
this time, the cells that will give rise to either ova or sperm move from
the yolk sac to the embryonic gonads. These gonads can become testes
in males and ovaries in females. For this reason, embryonic gonads are
said to be indifferent. If the embryo is a male, it will posses a Y
chromosome. If the embryo is a female, it will have no Y
chromosomes. Recent evidence suggests that the sex-determining gene
(SRY) appears to have been highly conserved during the evolution of
vertebrate groups. Once the testes are formed in the embryo, they
secrete testosterone and other hormones that will promote the
development of the external genitalia of the male, as well as accessory
reproductive organs. In other words, all embryos are females until they
are masculanized by testosterone.
Fertilization and Development
14
There are two types of fertilization: internal and external. External
fertilization commonly occurs among organisms in the ocean, where
water allows for the rapid dispersion of sperm or ova towards others of
the same species. On the other hand, internal fertilization is common
in terrestrial animals. Internal fertilization is the introduction of the
male gamete into the female’s reproductive tract. Vertebrates that
practice internal fertilization have three strategies:
Oviparity, which is found in some amphibians, fish, and some
reptiles, is when the eggs are deposited outside the mother’s
body after fertilization.
Ovoviviparity is commonly found in mollies, guppies, and
mosquito fish. The fertilized eggs are retained within the
mother in order to complete their development. The embryos
still take all of their nourishment from the egg yolk. The young
are thus fully developed when they hatch.
Viviparity is found in almost all mammals. The young develop
within the mother and takes its nourishment directly from their
mother’s blood, as opposed to egg yolks.
Reproduction in Fish and Amphibians
Manual Title 15
X.X Module Title
In most species of bony fish (teleosts), the fertilization of eggs
occurs externally. The eggs contain only enough yolk to sustain the
developing embryo until it is ready to tach. The development of
fish is rapid, and the young are able to find their own food source
from a very young age. Although thousands of eggs are fertilized
during a mating period, most of the eggs perish. In most
cartilaginous fish, however, most fertilization is internal. The male
introduces sperm into the female by means of a modified pelvic
fin. In these vertebrates, the development of the young is
viviparous.
Amphibians use external fertilization in most cases. In these
organisms, gametes from the males and females are released
through the cloaca. Most amphibian eggs develop in the water. The
time required for amphibians to develop is much longer than fish.
However, amphibian eggs do not have a lot of yolk. Instead, the
process of amphibian development is divided into embryonic,
larval, and adult stages.
Reproduction in Reptiles and Birds
Most reptiles and birds are oviparous. That is, after their eggs have
been fertilized, they are deposited outside of the mother’s body in
order to complete their development. As with most animals that
16
fertilize internally, male reptiles have a penis that they use to
introduce male gametes into the female’s reproductive tract. The
shells of reptile eggs are leathery, and this allows for better
withdstanding of environmental conditions.
All birds practice internal fertilization, although most birds lack a
penis. In some of the larger birds (e.g. ostriches, geese, and swans),
the male cloaca can extend to form a false penis. As the eggs
passes through the oviduct, the glands secrete the egg whites and
the hard shells that distinguish bird eggs from reptilian eggs. Most
birds are also homeotherms, meaning that they keep a stable body
temperature. Thus, they often incubate their eggs after laying them
to keep them warm. The young that emerges from bird eggs do not
develop rapidly, and they need to be assisted and fed by their
parents until they are ready to be independent.
Bird and reptile eggs show the stark evidence for adaptation to
land. These eggs are termed as amniotic eggs because the embryo
that develops within the cavity filled with fluid is surrounded by a
membrane called an amnion. The amnion is an extra-embryonic
membrane and develop outside of the body of the embryo. Other
extra-embyronic membranes include the chorion, the yolk sac, and
the allantois.
Manual Title 17
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Reproduction in Mammals
The reproductive cycles of mammals differ greatly. Some are
seasonal breeders that reproduce only once a year. Other have
shorter reproductive cycles. Among those that have short
reproductive cycles, females usually undergo the reproductive
cycle, while males are more constant in their reproductive activity.
Ovulation in females is the cyclic release of an egg from the ovary.
Most mammals are fertile only at the time of ovulation. The period
of sexual receptivity is called estrus, and the reproductive cycle is
therefore called an estrous cycle.
The estrous cycle of most mammals change according to the
secretion of follicle-stimulating hormone (FSH) and luteinizing
hormone (LH). These are secreted by the anterior pituitary gland
and cause changes in egg cell development and hormone secretion
in the ovaries. Like other mammals, humans and apes have an
estrous cycle. However, unlike other mammals, humans and apes
can mate anytime during their reproductive cycle. The most
primitive mammals, the monotremes, are oviparous. The
marsupials (e.g. kangaroos) give birth to offspring that are already
completely developed. The placental mammals retain their young
for a much longer period within the mother’s uterus. The fetuses
18
are nourished by the placenta, which is derived from the chorion
and the uterine lining of the mother. The fetus derives its nutrients
from the mother’s blood, since fetal and maternal blood vessels are
in close proximity.
Overview of Genetics
The most fundamental characteristic of all living things is the ability to
reproduce. All organisms gain their genetic material from their
parents. Genetic information determines their structures and functions
by directly influencing the synthesis of proteins.
Genes and Chromosomes
Gregor Mendel deduced the classical principles of genetics in 1865.
He based his deductions on the results of breeding experiments with
peas. Characteristics of the peas, such as seed color, could be predicted
by Mendel through the determination of a pair of inherited factors.
These inherited factors are now called genes. One gene copy, which ci
termed as an allele, specifies a certain trait that is inherited from each
parent. A gene is said to be dominant if it contains alleles for two
colors, and only one color shows. For instance, breeding yellow and
green peas yields yellow peas. In this case, the yellow is said to be
dominant gene while green is said to be recessive. If Y designates
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yellow and y designates green, then the genetic composition
(genotype) of the peas is Yy, and their physical appearance
(phenotype) is yellow. Mendelian genetics is the term for the
deductions of Mendel.
Shortly after, the role of chromosomes as carriers of genes was
proposed. It was also realized that higher animals and plants have
diploid cells, which contain two copies of each chromosome. Cell
division in the form of meiosis involves the daughter cell inheriting
only one member of each chromosome pair. Consequently, the sperm
and egg are haploid cells at fertilization, and this creates diploid
organisms.
20
Experiments on the fruit fly, Drosophila melanogaster,
established most of the principles of genetics today. The
fundamentals of genetic linkage, mutation, and the
relationships between chromosomes and genes were
elucidated. Genetic alterations were observed in Drosophila
in the 1900s. These involved readily observable traits, such
as eye color and wing shape. This experiment showed that
there are traits which are inherited in pairs, which are said
to be linked genes.
Chromosomes exchange materials during meiosis, leading to the
linked genes’ recombination. The frequency of recombination between
two linked genes depends on their distance from each other on the
chromosome. Thus, the frequency with which different genese
recombine can be used for mapping their positions on chromosomes,
which is known as genetic mapping.
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X.X Module Title
Genes and Enzymes
The first evidence for the existence of enzymes came in 1909, through
the study of the disease called phenylketoneuria. The disease results
from a genetic defect that results in problems with the metabolism of
phenylalanine, an amino acid. This defect was hypothesized to result
from a lack of enzymes needed to catalyze the metabolic reaction.
Subsequently, this led to the suggestion that genes also specify the
synthesis of enzymes.
Understanding the chromosomal basis of heredity and the relationship
between enzymes and genes did not itself provide a molecular
22
explanation for the gene. Chromosomes, aside from containing DNA,
also contain proteins.
The structure of DNA is three-dimensional. We owe our understanding
of this structure to James Watson and Francis Crick, who formed the
basis for present-day molecular biology. DNA is a polymer composed
of four nucleic acid bases: adenine (A), guanine (G), cytosine (C), and
thymine (T). The former two are purines, while the latter two are
pyrimidines. These bases are linked to phosphorylated sugars. The
central model of the DNA is that it is double-helix with a sugar-
phosphate backbone on the outside of the molecule. On the inside,
bases are held together by hydrogen bonds that are formed between
purines and pyrimidines on opposite chains. The amount of adenine is
always equal to the amount of thymine, and the amount of guanine to
that of cytosine. Due to this specific base pairing, two strands of DNA
are complementary: each strand contains the bases that are required to
specify the sequence of the other strand.
Replication of DNA
The discovery of complementary base pairing between DNA strands
suggest that there is a molecular solution to the problem of how
genetic material directs its own replication. Two strands of DNA can
separate to serve as templates for a new strand. This would be
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X.X Module Title
specified by base pairing. This process is called semiconservative
replication, because one strand is conserved in the progeny DNA
molecule. The enzyme that catalyzes DNA replication is DNA
polymerase. The replication of DNA can either be bidirectional, going
both forwards and backwards, or unidirectional, going only one
direction. DNA polymerase adds nucleotides to the DNA chain in a
specific direction, which is from 5’ to 3’.
DNA Transcription and Translation
Protein synthesis is directed by genes. When genes are defective, they
produce defective proteins and this results in abnormalities such as
albinism. There are two basic steps to the synthesis of protein. The
first is the transcription of genes, which produces a messenger RNA
(mRNA) molecule. The second step to protein synthesis is translation.
24
This is the portion of protein synthesis in which the mRNA molecule
is translated into proteins.
During transcription, the sequence of nucleotides in a gene in the DNA
is copied to the corresponding sequence of nucleotides in mRNA.
During translation, the sequence of nucleotides in the mRNA
determines the sequence of amino acids in the proteins.
DNA transcription is mediated by RNA polymerase. It separates the
two strands of the double helix and constructs an mRNA molecule by
adding nucleotides one at a time. The base-pairing rule summarizes
which nucleotides pair with each other. Guanine pairs with cytosine,
while adenine pairs with thymine.
DNA translation determines the sequence of amino acids in the
protein. The cell uses transfer RNA (tRNA) the bring the correct
amino acid for each codon in the mRNA. Each tRNA has three
nucleotides that form an anti-codon. The three nucleotides in the anti-
codon are complementary to the three nucleotides in the mRNA codon
for a specific amino acid. Amino acids are the building blocks of
proteins.
Manual Title 25
Genetics
Genetics is the study of heredity. In the previous module, we delved

into a brief overview of genes and how protein synthesis ensues from
DNA replication, translation, and transcription. In this module, we will
look at genetics on a much deeper level, in order to understand the
genetic basis of life on earth. The study of genetics is important. For
instance, have you ever wondered why your hair is black, and not
blond? It all comes down to the genes that you inherited from your
parents. Genetics will help explain these, and more.
The Structure and Function of DNA

A DNA molecule is composed of two long, polynucleotide chains.
These chains are, in themselves, composed of four types of nucleotide
subunits. Each of these two chains is known as a DNA chain, or a
DNA strand. Between the base portions of the nucleotides are
hydrogen bonds, which hold them together. Nucleotides are composed
of a five-carbon sugar to which one or more phosphate groups are
attached. There is also a nitrogen-containing base. Thus, in the case of
the nucleotides in DNA, the sugar comprising the nucleotides is
deoxyribose, which is then attached to a single phosphate group
(hence, DNA designates deoxyribonucleic acid). These bases may
either by adenine (A), guanine (G), cytosine (C), or thymine (T). A
covalent bond links the nucleotides together in a chain through the
sugars and phosphates. This forms a backbone of alternating sugar-
phosphate-sugar-phosphate. In each of the four types of subunits, only
the bases differ.
Genetics 1
The way in which nucleotides are linked together gives the DNA
strand polarity. The chain can be thought of as having sugars as block
with the knob that is protruding (the 5’ phosphate) on one side and a
hold (the 3’ hydroxyl) on the other. Each completed chain is formed
by interlocking knobs with holds. Thus, all subunits will line up in the
2
same direction. Moreover, the two ends of the chain will be easy to
distinguish. This is because one has a hole (the 3’ hydroxyl) and a
knob (the 5’ phosphate) at its end. This polarity in the DNA strand is
indicated by referring to one end as the 3’end and the other end as the
5’end.
The three-dimensional structure of the DNA strand, which is the

double-helix, arises from the structural and chemical features of its
two polynucleotide chains. Since these chains are held together by
hydrogen bonds, all the bases are on the inside of the double helix, and
the sugar-phosphate backbones are on the outside. In each case, the
two-ring base, which is bulkier and a purine, is paired with a single-
ring base, which is a pyrimidine. Thus, A always pairs with T, and C
anlways pairs with G. This is termed as complementary base-pairing
and it enables the the arrangement of the interior of the double-helix to
be energetically favorable. In this arrangement, the widths of the base
pairs are equal, thus holding the sugar-phosphate backbone at an equal
distance from another along the DNA molecule. The double-helix
turns once every ten base pairs.
Genetics 3
The members of each base pair can fit together within the double helix
only if the two strands of the helix are antiparallel. Thus means that
the polarity of one strand is opposite of the polarity of the other strand.
A consequence of this base pairing is that each DNA strand has bases
which are exactly complementary to the strands on the opposite base.
It is worth noting that a fifth base, which is a 5-methyl cytosine, occurs

in smaller amounts in certain organisms. In addition to this, a sixth
base, which is a 5-hydroxyl-methyl-cytosine, is found instead of
cytosine in phages. Additionally, the complementary base-pairing in
the DNA’s double structure allows for information to be copied with
no loss of information. During replication, the strands separate and
each serves as a template for assembling the subunits of its
complements in the right order. This produces two DNA copies with
4
the same sequence. Thus, when a cell divides into two, each is
endowed with the same information.
The information encoded into DNA is expressed by cells primarily by

the synthesis of amino acids in proteins, which have specific
sequences. The sequence of bases in the DNA encodes the sequences
of amino acids in the many different kinds of proteins. Each gene was
found to encode a polypeptide chain that the nucleotide sequence
determined, which was the determination of the sequence of amino
acids. The code for the sequence of amino acids is known as codon
which consists of three nucleotides. It was also discovered that the
code relating the nucleotide sequence to the amino acid sequence is
nearly universal among all organisms. Eventually, this discovery made
possible the use of a convenient organism (such as bacteria) to express
and produce the protein of another.
The genetic information in DNA is not decoded directly to produce

proteins. Instead, the DNA segments encoding a polypeptide chain is
first copied selectively into single-stranded polymer called the
messenger RNA (mRNA). The mRNA copies are then used to direct
the synthesis of proteins. The lifetime of mRNA molecules is
generally short, so that when the production of mRNA ceases, then the
production of protein ceases shortly after as well.
DNA Transcription
The central dogma of biology describes how genetic information from
from DNA to the RNA to protein is conveyed. In a nutshell, the central
dogma of biology conveys that DNA is where hereditary information
is found, and this information is converted through transcription to
RNA, one type of which is translated into protein. The process of
transcription is the process by which RNA polymerase enzymes and
Genetics 5
other proteins for transcription and other enzymes use the DNA strand
as a template to synthesize an RNA strand that is complementary. The
translation process, on the other hand, is the process by which the
mRNA is used to direct the synthesis of proteins.
In contrast the bacterial transcription, which uses a single RNA

polymerase core enzyme and several alternative sigma subunits to
transcribe all genes, eukaryotes have multiple RNA polymerases that
are specialized for the transcription of different types of genes. The
archaeal and eukaryotic RNA polymerases account for the
transcription of most genes that produce polypeptides that share a
common structure that is different from bacterial RNA polymerase.
Transcription in eukaryotes and archaea proceed through four stages,
the same with bacteria. These stages are: promoter recognition,
transcription initiation, transcript elongation, and transcript
termination. However, several factors make transcription more
complex in archaea and eukaryotes.
First, eukaryotic consensus sequences and promoters are more diverse

than those found in E. coli, and eukaryotes have three different RNA
polymerases that have the ability to recognize different promoters,
transcribe different genes, and produce different types of RNAs.
Secondly, the molecular apparatus that is assembled at promoters is
much more complex in archaea and eukaryotes than in bacteria. Thus,
the eukaryotic genes contain exons and introns, which thus requires
post-transcriptional processing of mRNA. Finally, eukaryotic DNA is
associated with a large amount of protein to form chromatin.
Chromatin has a role that is central to the regulation of eukaryotic

transcription. In eukaryotic genomes, chromatic is a dynamic and
permanent feature. The state of chromatic controls whether DNA is
accessible for transcription, because they either block or permit the
6
RNA polymerase and other transcription patterns from accessing

promoters.
Eukaryotic and Archaeal RNA Polymerases
There are three different types of RNA polymerases that transcribe

different types of RNA. RNA polymerase I (RNA pol I) is responsible
for transcribing three ribosomal RNA genes. RNA polymerase II
(RNA pol II) is responsible for transcribing mRNA, as well as most
nuclear RNA genes. RNA polymerase III (RNA pol III) is responsible
for transcribing most transfer RNA (tRNA) genes, one ribosomal RNA
gene, and small nuclear RNA genes. RNA pol II and RNA pol III are
responsible for miRNA and siRNA synthesis. RNA polymerase has a
similar overall molecular complexity that it shares with bacteria.
RNA polymerase II transcribes the polypeptide-coding gene into

mRNA. These genes have promoters that are diverse and numerous.
There are three types of investigations that help researchers to identify
and characterize the promoters of genes that code for polypeptides.
First, promoters are identified based on which proteins are associated
with RNA pol II that are bound to DNA during transcription.
Secondly, promoter sequences from different genes are compared to
evaluate their differences and similarities. Third, mutations that alter
the transcription of genes are examined in order to identify how base-
pair changes in the DNA affect transcription.
Genetics 7
The most common promoter in the eukaryotic cell is called the TATA
box. It is also known as the Goldberg-Hogness box, and is located at a
position that is approximately -25 relative to the site where
transcription starts. It is part of three consensus segments. It consists of
the 6 base pairs (6bp) and has the TATAAA sequence. It is the most
strongly conserved promoter in eukarotic cells. There are two other
consensus sequences. The CAAT box is the usually located near -80
when it is found in the promoter. Upstream, the GC-rich box, that has
a consensus sequence of GGGCGG, is located in the -90 or more
upstream of where transcription will start. All of these consensus
8
sequences play an important role in the binding of transcription

factors, which is a group of transcriptional proteins.
Promoter Recognition
Transcriptional factors (TF) aid in the binding of RNA pol II to the

promoter consensus sequences in eukaryotes. The TF ptoteins bind to
the regulatory sequences in the promoter and initiates transcription by
interaction with RNA polymerase. The TF that influence the
transcription of mRNA, and therefore interact with RNA pol II, are
designated as TFIL.
In most eukaryotic promoters, the principal binding site for TF during

promoter recognition is the TATA box. At the TATA box, TFIID,
which is a multi-subunit protein that contains the TATA-binding
protein (TBP) and subunits of a protein called the TBP-associated
factor (TAF), binds the TATA sequence. The TFIID that is bound to
the TATA box forms the initial committed complex. This joins RNA
polymerase to form the minimal initiation complex, which in turn is
joined by the TFIIE and TFIIH to form the preinitiation complex
(PIC). The complete initiation complex contains 6 proteins that are
commonly known as general transcription factors. Once the initiation
complex has been assembled, it directs RNA polymerase II to the +1
nucleotide on the template strand. This begins the assembly of the
mRNA.
Enhancers and Silencers
Alone, promoters are not enough to initiate the transcription of

eukaryotic genes. Other regulatory sequences are needed in order to
complete the initiation of transcription. Enhancer sequences are an
important group DNA of regulatory sequences that increase the level
of transcription of specific genes. Enhancer sequences function to bind
Genetics 9
specific proteins that can interact the the proteins bound at the gene
promoter sites. Together, the promoters and enhancers drive the
transcription of certain genes. In most cases, enhancers are located
upstream of the genes that they will regulate; however, they can be
found downstream as well. Some enhancers are close to the genes that
they regulate, but others are located several thousand base pairs away.
Enhancers function to bind activator proteins and other coactivator

proteins in order to form a “protein bridge” that bends the DNA. It
also links the complete initiation complex at the promoter site to the
activator-coactivator complex at the enhancer.
There are also silencer sequences, which also regulate the transcription
of genes. These are DNA elements that can act at a distance from the
target genes to repress their transcription. They bind transcription
factors called repressor proteins. These two induce bends in the DNA,
similar to what can be seen when activators and coactivators bind to
enhancers. The exception, however, is that the consequence of
reducing the transcription of target genes is part of the function of
silencers. Just as with enhancers, silencers can either be located
upstream or downstream from a target gene, and can also be
locatedseveral thousand base pairs away from it. Thus, enhancers and
silencers operate using similar mechanisms but with opposite effects
on gene transcription.
RNA Polymerase I Promoters
RNA polymerase I transcribes the genes for rRNA. It uses a

mechanism for transcription similar to that used by RNA pol II. RNA
pol I is the most specialized eukaryotic RNA polymerase, since it can
only transcribe a limited number of genes. Following the initial
binding of the transcription factors, it is to recruited upstream
10
promoter elements. It also transcribes ribosomal RNA, rRNA. rRNA is

found in the nucleolus (plural, nucleoli). Promoters recoganized by
RNA pol I contain two similar functional sequences that are located
near the start of transcription. The first is the core element, which
stretches from -45 to +20 and the bridging start of transcription. The
second is the upstream control element, which spans -100 to -150
nucleotides. The core element is needed for the initiation of
transcription, while the upstream control element functions to increase
the transcription of genes. Both of these elements are rich in G and C.
A second protein complex, which is the sigma-like factor 1 (SL1)
binds the core element. This complex then returns the RNA pol I to the
core element in order to initiate the transcription of rRNA genes.
RNA Polymerase III Promoters
RNA pol III is primarily responsible for the transcription of tRNA

genes. However, it also transcribes one rRNA and other RNA-
encoding genes. Small nuclear RNA genes contain three upstream
elements. On the other hand, the gene for 5s rRNA and tRNA each
contain two internal promoter elements, which are downstream from
the start of the transcription.
The upstream elements of small nuclear RNA genes are the TATA
box, a promoter-specific element (PSE), and an octamer (OCT). A
small number of transcription factors, such as TFIII, bind to the
elements. They also recruit the RNA pol III, which initiates
transcription using a similar mechanism as that of other polymerases.
The genes for the 5s rRNA and tRNA have internal promoter elements
called internal control regions (ICRs). ICRs are short DNA sequences,
which are designated as either box A and box B, or box A and box C.
These are located upstream of the start of transcription, between
nucleotides +55 and +80. To initiate transcription, either box B or box
Genetics 11
C are bound by TFIIIC to box A. In the final step for initiation, RNA
pol III binds to transcriptions factor complex and overlaps the +1
nucleotide. With the RNA polymerase correctly positions,
transcription commences at 55 bp (base pairs) upstream of the
beginning of box A, at the +1 nucleotide.
Termination in RNA Polymerase or III Transcription
Each of the RNA polymerases utilizes a different mechanism to

terminate transcription. The RNA pol III transcribes a terminator
sequence that creates a sequence of nucleotides in the transcript. The
RNA pol sequences does not contain an inverted repeat, so that no
stem-loop structure forms at the 3’end of RNA. The transcription by
RNA pol I is terminated at the 17-bp consensus sequence. This
sequences binds to the transcription-terminating factor I (TTFI).
DNA Translation
Ribosomes are complexes made of both RNA and protein. They bind
to an mRNA strand and progressively move from the 5’ to 3’. They
pick up aminoacyl-tRNAs, checking to see if they are complementary
to the RNA tri-nucleotide being “read” at the moment. These
nucleotides are added to the polypeptide chain if they are correct and
complementary. The part of the ribosomes that is composed of RNA is
generated by RNA pol I and RNA pol III in eukaryotes.
The eukaryotic rRNA molecules are also cleaved from the larger
transcripts after transcription. This processing, as well as the ensuing
assembly of the large and small ribosomal subunits, are carried out in
the nucleolus. The nucleolus is a region of the nucleus that is
specialized for ribosome production. It also contains high
concentrations of rRNA, ribosomal proteins, RNA pol I and RNA pol
12
III. In contrast to this, RNA pol II is found all throughout the nucleus.
The 40s ribosome has 1 rRNA and 33 proteins. The 60s ribosomal unit
has three rRNA molecules and 50 proteins. The smaller subunit is
responsible for finding the initiation site (start site) and positioning the
ribosome on the mRNA. The larger subunit contains the sites for
docking the incoming amioacyl-tRNAs. The larger subunit also
contains the catalytic component, which is essential for attaching
amino acids through peptide bonds.
Eukaryotic Translation
Genetics 13
Eukaryotic translation is similar to that in prokaryotes. The initiation

process is more complex, but the termination and elongation processes
are the same. For eukaryotes, each mRNA encodes one and only one
gene. The start codon is AUG, which is a regular methionine.
Therefore, in contrast to prokaryotes, the Shine-Dalgarno sequence is
not needed. The small ribosomal subunit is accompanied by eIF-3,
eIF-2, and Met-tRNAi, which are initiation factors. Meanwhile, the
14
eIF-4A, -4B, -4E, and -4G hinds to the 5’ end of the mRNA which is
the methyguanosine cap. The small subunit complex and the
eIF4/mRNA cap-binding complex interact to form the 43S complex,
which then begins the scanning the mRNA strand for the start codon,
AUG.
Once the 43S scanning complex has found the AUG codon, the
initiation factors are dropped off and the larg ribosomal subunit
arrives. The large ribosomal subunt is bound to eIF-6. eIF-6 prevents it
from binding with other small subunits, and its removal is needed
before these can bind.
During the elongation phase of translation, several tRNAs carrying

amino acids bind to the ribosome as it moves along the mRNA and the
amino acids are linked together by peptide bonds. During the
termination phase of translation, the ribosomal subunits release both
the mRNA and the newly formed protein. Translation occurs only in
the cytoplasm, in contrast to replication and transcription, which
occurs in the nucleus.
Steps in Protein Synthesis
1. A promoter binds to the DNA and opens it up at a particular

site.
2. The RNA polymerase unzips the molecule.
3. The 3’to 5’ DNA strands serves as the template for the addition
of new nucleotides.
4. The genetic code of DNA is transcribed into the mRNA (A, U,
C, G).
5. The mRNA detaches from the DNA and is spliced by the
spliceosome before leaving the nucleus.
Genetics 15
6. The newly spliced mRNA goes to the ribosomes in the

cytoplasm.
7. The mRNA attaches to the ribosomes and the ribosome moves
down with the mRNA, reading the nitrogenous bases.
8. Three nucleotids on the mRNA constitute a codon.
9. tRNA is involved in the next stage, which is translation.
10. The initiator codon (AUG) binds to the P side of the ribosome.
AUG helps align the tRNA, the mRNA, and the ribosome and
signals the beginning of the gene to be expressed.
11. tRNA carries amino acides. Each tRNA has an anticodon that
binds to a complementary condon on the mRNA.
12. A second tRNA molecule binds to the second codon of the
mRNA and a di-peptide is formed.
13. The first tRNA is then released from the ribosome’s E site.
14. The process continues until a stop codon is encountered (UAA,
UGA, or UAG).
15. The codons from the mRNA have now been translated into a
polypeptide (protein).
16. The mRNA, polypeptide, tRNA, and ribosome disassemble.
Ovierview of Genetic Engineering

The term “biotechnology” was coined by Karl Erekcy, who was a
Hungarian engineer. At the time, biotechnology included all the
processes by which products were obtained from raw materials with
the help of living organisms. Nowadays, biotechnology is defined as
“any technological application that uses biological systems, living
organisms, or derivatives thereof, to make or modify products or
processes for specific use.”
16
However, decades ago, the simple biotechnology used in earlier times

became much more complex. Genes were discovered and today, the
following are techniques used for the purpose of biotechnology:
Gene isolation coding for a protein of interest.

Cloning (which is the transfer of this gene into an appropriate
reproduction host).
Improving gene expression by the use of stronger promoters.
Together, all these techniques are known as recombinant DNA
technology.
Recombinant DNA technology allowed for protein engineering. There

are also several techniques used in this regard:
Mutagenesis that is used to cause changes in the specific

locations or regions of a gene to produce a new gene
product.
Expression of a gene that has been altered in order to
produce a stable protein.
Characterization of the structure and function of the protein
produced.
Selection of new gene locations or regions to modify for
further improvement as a result of this characterization.
Biotechnology has important commercial implications, since small

numbers of proteins can now be produced in quantitu. More
importantly, however, the production of transgenic animals and plants
that contain genetic material from other organisms that have novel
characteristics and traits is also based on the techniques outlined
above. All these approaches produce genetically-modified organisms
(GMOs), and are strictly regulatrd by biosafety laws and guidelines.
Genetics 17
An Overview of the Applications of Biotechnology
Biotechnology can be used to develop alternative sources of fuels. An

example of this is the conversion of maize starch into ethanol by yeast.
This can subsequently be used to produce gasohol (gasoline-ethanol
mix). Bacteria are also used to sludge and decompose landfills that
contain wastes. Microorganisms can also be used to convert biomass
into feed stock, and they can also be used for manufacturing
biodegradable plastics. Other organisms, mammals include, are used
as bioreactors for producing chemical compounds that are extracted
from them and processed as drugs and other products. Biotechnology
is used to create products from plants and animals.
In the area of health and medicine, biotechnology is used to

manufacture vaccines and other medicine. Through the use of gene
therapy, scientists are making efforts to cure genetic diseases. They are
doing this by attempting to replace defective genes with the correct
version. Aside from this, biotechnology also has applications in
agriculture and other industries.
Recombinant DNA Technology
Following the elucidation of the genetic code and DNA structure, it

became clear that may biological secrets are hidden in the sequence of
bases in DNA. A new era of DNA analysis and manipulation thus
arose. Key to this progress was the discovery of two types of enzymes
that made DNA cloning possible. In this sense, DNA cloning refers to
the isolation and amplification of defined pieces of DNA. One type of
enzyme, called restriction enzymes, cuts the DNA from any organism
at specific sequences of a few nucleotides. This generates sequences
that can be reproduced from the set of fragments. These enzymes
occur naturally in some bacteria, where they serve as defense
18
mechanisms against viruses that infect bacteria (bacteriophages). The

other enzyme, called DNA ligases, can covalently join DNA fragments
at their ends, which have been created by restriction enzymes. Thus,
DNA ligases can insert DNA restriction fragments into DNA
molecules that are replicating, such as plasmids (bacterial, circular
DNA molecules). This process results in recombinant DNA molecules.
All the descendants from this cell are called clones, and they carry the
same recombinant DNA molecule. Once a clone has been isolated,
unlimited quantities of the DNA sequence can be prepared. In case
that the DNA molecule contains sequences for proteins, it can be
inserted into an organism to create proteins in that organism. These
proteins are called recombinant proteins.
Genetic Engineering and Recombinant DNA Technology
The terms genetic engineering and recombinant DNA designate the

techniques in which DNA may be cut, rejoined, its sequence
determined, or the sequence of a segment altered to suit an intended
use. The study of genetic engeering began with the use of phages,
through which variant DNA sequences can be gathered for th study of
altered genes or proteins. Of course, the most interesting aspect of
genetic engineering is the “engineering” that it makes possible. A
simple application of the technology is the efficient and economical
synthesis of proteins that have traditionally been difficult or
impossible to purify from their natural sources. These proteins may be
in the form of antigens used for immunization purposes, enzymes for
chemical processs, or specialized proteins for therapeutic purposes.
Cloned DNA sequences can also be used to detect chromosomal
defects for genetic studies. The following are the steps to genetic
engineering:
Genetics 19
The DNA for study should be free from contaminants and it

should be isolated.
It should be possible to cut this DNA reproducibly at specific
sites so that fragments can be produced containing genes or
parts of genes.
It should be possible to rejoin the DNA fragments in order to
form hybrid DNA molecules.
Vectors, such as bacteriophages, should exist wherein
fragments can be joined and then introduced to cells by the
process called transformation.
Vectors need to have two properties: first, they must provide
for autonomous DNA replication of the vector in the cells.
Secondly, they must permit selective growth of only those cells
with vectors.
Genetic engineering is used to create GMOs. Examples of GMOs are

plants that have been genetically engineered to withstand pests.
Another example is plants that have been genetically engineered to
produce more fruit. GMOs will be discussed at length at a later
module.
Glossary
Include list of words (arranged alphabetically) with their corresponding
meaning as used or referred to in the module.

DNA Replication
20
Understanding the Central Dogma of Biology
DNA Cloning and Recombination
DNA, RNA, replication, translation, and transcription
DNA Replication I: Enzymes and Mechanism
Biotechnology and Its Applications
References
Schleif, R. (1993). Genetics and molecular biology (No. Ed. 2). Johns
Hopkins University Press.
Genetics 21
Animal Survival
In this module, we will explore the various ways in which animals

survive. That is, we will understand the role of nutrition and food in
the body, as well as how these nutrients enter the organs and allow
animals to fend off death and starvation. After this module, you are
expected to understand how animals survive through feeding and
nutrition, as well as the various biological processes involved in
transporting nutrients into cells, ultimately leading to animal survival.
Animal Diets
The activities of cells, tissues, organs, and the entire organism depends
on the nutrients available for it to function. Cells function in concert
with one another to bring nutrients to the organs, allowing them to
function in keeping the entire organism alive. The energy gained from
feeding, which is often converted to ATP, powers the processes that
are needed for DNA replication and cell division. In turn, these
processes allow for the supply of proteins needed by the animal to
renew tissues and to function, including the energy for motion.
Animals ingest nutrients, such as proteins and carbohydrates, for use
in cell respiration and energy storage.
In addition to providing the fuel essential for ATP production, an

organism’s diet must provide for the raw materials needed for
biosynthesis. In order to build complex molecules that it needs to grow
and maintain itself, as well as to reproduce, animals must obtain two
types of organic precursors from its diet. Animals need a source of
organic carbon (such as sugars) and source of nitrogen (such as amino
acids that are produced from the breakdown of protein). Starting with
these raw materials, animal systems can create a wide variety of
organic molecules.
The materials that an animal needs but cannot synthesize on its own
care called essential nutrients. These nutrients are taken from dietary
sources and include both preassembled organic molecules and
minerals. Some essential nutrients are needed by all animal species,
while others are only needed by some species. For instance, vitamin c
(ascorbic acid) is vital for primates and humans, whereas it is not for
most other animals. Overall, a complete diet satisfies all the nutritional
requirements of animals that provides for three nutritional needs:
organic building blocks for carbohydrates and other macromolecules,
essential nutrients, and cellular processes.
Animal Survival 1
Essential Nutrients
There are four classes of essential nutrients: essential fatty acids,

essential amino acids, minerals, and vitamins.
Essential amino acids are important for protein production. Animals

require 20 types of amino acids for this. The majority of animal
species can synthesize about half of these amino acids, as long as
organic nitrogen is included in their diets. The other amino acids,
however, must be obtained from the diet in a preassembled form called
essential amino acids. Most animals, including humans, need eight
essential amino acids from their diets. It should be noted that infants
need histidine, a ninth amino acid.
A diet that provides insufficient amounts of one or more amino acids

causes protein deficiency. Protein deficiency is the most common type
of nutritional deficiency in humans. Children are often the victims of
protein deficiency. These children often have impaired mental and
physical development. Proteins in animal products, such as meat, eggs,
and cheese, are termed as complete because they provide all the
essential amino acids in their proper proportions. In contrast to this,
most proteins derived from plants are incomplete, because they are
deficient in one or more amino acids. For instance, corn (maize) is
deficient in lysine and tryptophan, wheras beans are deficient in
methionine. To prevent protein deficiency, vegetarian diets must often
include a variety of proteins that, together, provide all the essential
amino acids.
Essential fatty acids are also needed by animals since these are fatty
acids that they cannot synthesize. Essential fatty acids are unsaturated,
which means that they contain one or more double bonds. For
instance, humans require linoleic acids to synthesize the phospholipids
in cellular membranes. Since vegetables, seeds, and grains provide
almost all of the essential fatty acids, deficiencies of these are rare.
Vitamins are organic molecules that need to be acquired from the diet
in very small amounts. For instance, vitamin B2 is converted by the
body to FAD, which is a coenzyme used in metabolic processes,
including cellular respiration. Thirtheen essential vitamins for humans
have been identified: vitamin B (thiamine), vitamin B2 (riboflavin),
Niacin (B3), vitamin B6 (pyridoxine), vitamin B5 (panthothenic acid),
vitamin B9 (folic acid/folacin), vitamin B12, biotin, vitamic C
(ascorbic acid), vitam A (retinol), vitamin D, vitamin E (tocopherol),
and vitamin K (phylloquinone).
2
There are two kinds of vitamins: water-soluble and fat-soluble. The

water-soluble vitamins include the B complex. These are compounds
that primarily function as coenzymes and vitamin C, which is needed
for the production of connective tissue. Among fat-soluble vitamins
are vitamin A, which is included in the visual pigments of the eye, and
vitamin K, which is essential for blood clotting. Vitamin D, on the
other hand, is needed for calcium absorption and bone formation. The
dietary requirements for vitamin D vary because this can be
synthesized from exposure to sunlight.
People will poorly balanced diets will benefit from vitamin

supplements. However, excessive consumption of fat-soluble vitamins
is harmful because there are stored in the body as fat. The
overconsumption of these vitamins can lead to the accumulation of
toxic levels in the body.
Minerals are inorganic nutrients. Examples include zinc and

potassium, and these are generally required in small amounts, from
less than 1 mg to 2,500 mg per day. The requirements for minerals
vary among species. For instance, humans and other vertebrates
require large amounts of calcium and phosphorous for maintaining and
building bone. Additionally, calcium is essential for nerve function
and the conduction of nerve impulses to muscles. Phosphorous is a
component of ATP and nucleic acids. Iron is a component of
cytochromes, and it functions in cellular respiration. It is also
component of hemoglobin, which is the oxygen-binding protein of red
blood cells. Many minerals are cofactors that are built into the
structure of enzymes. For instance, magnesium is present in the
enzymes that split ATP to produce ADP. The synthesis of thyroid
hormones requires iodine, and thyroid hormones regulate the
metabolic rate. Chloride, sodium, and potassium ions are important in
the functioning of nerve and maintaining the osmotic balance between
the surrounding body fluid and cells.
The following is the list of minerals required by humans: calcium

(Ca), phosphorous (P), sulfure (S), potassium (K), chlorine (Cl),
sodium (Na), magnesium (Mg), iron (Fe), fluorine (F), zinc (Zn),
copper (Cu), Manganese (Mn), iodine (I), cobalt (Co), selenium (Se),
chromium (Cr), and molybdenum (Mo). Ingesting large amounts of
these minerals can upset the homeostatic balance and cause toxic side
effects. For instance, excessive iron intake leads to liver damage,
which affects as much as 10% of the population in Arfica. Excess
sodium can lead to high blood pressure, and this is a particular
problem in the United States.
Animal Survival 3
Dietary Deficiences
Diets that fail to meet the basic dietary requirements can lead to
malnourishment or undernourishment. Undernourishment is the result
of a diet that supplies less than the chemical energy that the body
requires. On the other hand, malnourishment is the long-term absence
from the diet of one or more essential nutrients. Both of these are
detrimental to survival.
Undernourishment causes a series of events to occur. First, the body

uses up the stored carbohydrates and fats. The body begins breaking
down its own proteins as sources of fuel. The muscles then begin to
decrease in size and the brain may become protein-deficient. If the
energy intake is less than the energy expenditure, the organism will
eventually die. Additionally, even if an animal that is seriously
undernourished survives, the damages caused by undernourishment
may be irreversible. Undernourishment may also occur in populations
that are supplied well with food. These occur in the cases of eating
disorder, such as anorexia nervosa.
Malnourishment has the following possible effects: deformities,

disease, and even death. For instance, cattle may develop fragile bones
if they gaze on plants that lack phosphorous. There are gazing animals
that make up for the lack of nutrients by gazing on sources of salt or
other minerals. Among populations that rely mainly on rice,
individuals are afflicted with vitamin A deficiency, which causes death
or blindness. In order to overcome this problem, scientists have
engineered a type of rice can synthesize beta-carotene, an orange-
colored source of vitamin A that is found in carrots. This “Golden
Rice” has potential benefits for 1-2 million young children worldwide
that die every year from vitamin A deficiency.
Food Processing
There are various mechanisms by which animals process food. Food
processing can be divided into four stages: ingestion, digestion,
absorption, and elimination. The first stage, ingestion, is the act of
eating. Food can be acquired in both liquid and solid forms. The
strategies for extracting food also vary among animals. In digestion,
the second stage of food processing, food is broken down into
molecules that are small enough for the body to absorb. This stage is
necessary because animals cannot directly absorb fats, proteins, and
carbohydrates. They also cannot directly absorb nucleic acids and
phospholipids in food. One problem is that these molecules are too
4
large to cross the cellular membranes of the animal. In addition, not all
large molecules in food are identical to those that the animal needs for
its functions and tissues. When large molecules are broken down into
their components, the animal can use these small molecules to create
large molecules. For example, humans convert proteins in their food to
the same amino acids from which they assemble proteins for their
specific species.
Chemical digestion by enzymes reverses the process of breaking down

bonds with the addition of water. The process of splitting is called
enzymatic hydrolysis. A variety of enzymes catalyze the digestion of
large molecules that are acquired from food. Polysaccharides and
disaccharides are split into simple sugars. Proteins are broken down
into amino acids, and nucleic acids are broken down into nucleotides.
Enzymatic hydrolysis also relases fatty acids and other components
from fats and phospholipids. This chemical digestion is preceded by
mechanical digestion (such as chewing). Mechanical digestion breaks
down food into small particles, increasing the surface area that is
available for chemical digestion.
The last two stages of food processing occur after food is digested.
The third stage, absorption, is when the animal’s cells take up small
molecules, such as amino acids and simple sugars. Elimination
completes the process as undigested material passes out of the
digestive system.
Digestive Components
The evolutionary adaptaion found across species is the processing of

food in specialized compartments. Such components can be
intracellular or extracellular.
Intracellular digestion occurs when food vacuoles (cellular organelles

in which hydrolytic enzymes break down food) digest food molecules.
Vacuoles are the simplest digestive compartments. The hydrolysis of
food inside vacuoles is called intracellular digestion. It begins after a
cell engulfs solid food by phagocytosis (cell eating) or liquid by
pinocytosis (cell drinking). Newly fomed food vacuoles fuse with
lysosomes, which are organelles that contain hydrolytic enzymes. The
fusion of these organelles brings food together with the enzymes,
allowing digestion to occur within the cellular compartment. There are
animals, such as sponges, that digest their food purely through
intracellular digestion.
Animal Survival 5
Extracellular digestion occurs in comparments that are continuous

with the outside of the animal’s body. Having more than one
extracellular compartment for digestion allows animals to consume
much larger sources of food than is allowed by phagocytosis.
Many animals that have simple body plans have digestive

compartment with only one opening. This pouch, which is called a
gastrovascular cavity, functions in digestion as well as the distribution
of nutrients throughout the body. The carnivorous cnidarians provide
an excellent example of how a gastrovascular cavity works. A hydra
(cnidarian) uses its tentacles to stuff food into its gastrovascular cavity.
The specialized glands of the hydra’s gastrodermis, the tissue that lines
the cavity, then secrete digestive enzymes that break down the prey
into tiny pieces. Other cells in the gastrodermis engulf these food
particles, and the hydrolysis of the food particles occurs intracellularly.
In contrast with cnidarians, most animals, and humans, have a

digestive tube that extands between two openings, a mouth and an
anus. Such a tube is called the complete digestive tract, or the
alimentary canal. Since the food moves in only one direction, the tubes
can be organized into specialized compartments that carry out
digestion and nutrient absorption in a stepwise fashion. An animal
with an alimentary canal can ingest food while previous meals are still
being digested. This is difficult for animals with a gastrovascular
cavity.
Organs Specialized for Food Processing (Mammalian)

The mammalian digestive system can be used as a representative
example of animal digestion, since most animals have an alimentary
canal. In mammals, the digestive system is composed of various
accessory glands that secrete digestive juices, as well as the alimentary
canal. The accessory glands of the mammalian digestive system
consist of three pairs of salivary glands, the pancreas, the liver, and the
gallbladder.
Food is pushed along the alimentary canal by movements called

peristalsis, which are waves of relaxation and contraction in the
smooth muscles lining the alimentary canal. Thus, peristalsis allows us
to process and digest food even while we’re lying down. At some of
the junctions between specialized compartments, the muscular layer
forms ring-like valves called sphincters. Sphincters act like
drawstrings that regulate the passage of materials between
compartments.
6
The Oral Cavity, Pharynx, and the Esophagus
Ingestion and the initial steps of digestion occur in the mouth, or oral
cavity. Mechanical digestion begins as teeth cut, smash, and grind
food, which makes food easier to swallow and increases its surface
area. Meanwhile, the presence of food stimulates a nervous reflex that
causes the salivary glands to secrete saliva through ducts in the oral
cavity. Salive may be released before food enters the mouth, triggered
by the smell of food, or other stimuli.
Saliva initiates chemical digestion while also protecting the oral

cavity. Amylase, an enzyme in saliva, hydrolyzes starch (a glucose
polymer from plants) and glycogen (a glucose polymer from animals).
Mucin, which is a slippery glycoprotein (a carbohydrate-protein
complex) found in saliva, protects the lining of the mouth from
abrasion. Mucin also lubricates food, making it easier to swallow.
Additional components of saliva include buffers, which prevent tooth
decay by neutralizing acids and antibacterial agents.
The tongue assists digesting my moving food to enable it further

passage down the alimentary canal. After food is deemed to be
acceptable for swallowing, the tongue moves to manipulate food,
shaping it into a ball called a bolus.
The pharynx, or the throat region, opens to two passageways: the

trachea (windpipe) and the esophagus. The esophagus connects to the
stomach, whereas the trachea leads to the lungs. Thus, swallowing
food must be carefully choreographed in order to prevent the food
from entering the lungs and blocking the airway. Whenever an animal
swallows, a cartilaginous flap, called the epiglottis, prevents food from
entering the trachea by covering the glottis. The glottis consists of the
vocal chords and the openings between them. Guided by the
movement of the larynx, the upper part of the respiratory tract, the
bolus is directed into the entrance of the esophagus. If the swallowing
reflex fails, choking may ensue, which is a blockage of the trachea.
The esophagus contains both smooth and striated muscles. The striated
muscle is found at the top of the esophagus and is active in
swallowing. Smooth muscle, on the other hand, functions in
peristalsis. The rhythmic cycles of contraction direct food to the
stomach.
Digestion in the Stomach
The stomach is located below the diaphragm in the upper abdominal

cavity. There are a few nutrients that are absorbed from the stomach
Animal Survival 7
into the bloodstream, but the main function of the stomach is to store
food and to continue digestion. It has folds and an elastic wall, and can
accommodate about 2L of food. The stomach secretes a digestive fluid
called gastric juice. It mixes this secretion with the food through a
churning motion. The mixture of ingested food and digestive juice is
called chyme.
Two components of gastric juice carry out chemical digestion. The

first is hydrochloric acid (HCl). The function of HCl is that it disrupts
the extracellular matrix that binds together plant and meat material.
The concentration of HCl is so high that the pH of gastric juice is
about 2. It is acidic enough to dissolve iron nails. The low pH is
necessary for killing most types of bacteria and also unfolding
proteins, increasing the exposure of their peptide bonds. The exposed
bonds are attacked by the second component of gastric juice, which is
a protein-digesting enzyme called pepsin. Pepsin is a protease and it
works best in an environment that is strongly acidic. It cleaves proteins
into smaller polypeptides by cleaving peptide bonds. The digestion of
protein into amino acids occurs in the small intestine.
The ingredients of gastric juice are kept inactive until they are released
into the cavity of the stomach, called a lumen. The components of
gastric juice are produced by cells in the gastric glands of the stomach.
HCl is secreted by parietal cells, which secrete hydrogen and chloride
ions. The parietal cells use an ATP-driven pump to expel hydrogen
into the stomach cavity at very high concentrations. There, the
hydrogen atoms combine with chloride ions that diffuse towards the
lumen through specific membrane channels. Meanwhile, chief cells
release pepsin into the lumen. Pepsin is relased in its inactive form,
pepsinogen. HCl converts pepsinogen into pepsin by exposing its
active site by clipping off a portion of the molecule. Through these
processes, HCl and pepsin form in the stomach cavity, and not in the
cells of the gastric glands. Pepsin itself can also clip pepsinogen. Thus,
the presence of pepsin generates more pepsin within the lumen.
The stomach lining protects itself from the acidity of the gastric juice
by secreting mucus. Mucus is a mixture of glycoproteins, cells, salts,
and water. In addition to this, cell division adds a new epithelial layer
every three days, replacing the cells damaged by gastric juices.
Despite these defenses, however, gastric ulcers may appear, which are
eroded portions of the stomach lining. The bacteria, Helicobacter
pylori, may infect the stomach and cause ulcers.
Chemical digestion by gastric juices is accompanied by the churning

of the stomach. This coordinated series of muscle contractions and
8
relaxations mixes the stomach contents every 20 seconds. As a result

of this churning motion, swallowed food become nutrient-rich and
acidic, which is chyme. Most of the time, the stomach is closed off at
both ends. The sphincter between the esophagus and the stomach
opens only when a bolus arrives. Sometimes, however, a person
experiences acid reflux, which is when a backflow of chyme enters
into the lower end of the esophagus. The burning sensation is caused
by the acidity of the chyme, which is incompatible with the basic (non-
acidic) nature of the esophagus. The sphincter that is located where the
stomach opens into the small intestine regulates the passage of chyme
into the small intestine. The mixture of acid, enzyme, and food
typically leaves the stomach about 2-6 hours after each meal.
Digestion in the Small Intestine
Most enzymatic hydrolysis of macromolecules from food occurs in the

small intestine. The small intestine is the longest compartment of the
alimentary canal, as it is over 6 meters long. The small diameter of the
small intestine gives it its name. The first part of the small intestine is
known as the duodenum, which is a major crossroad in digestion. It is
here that chyme mixes with digestive juices from the pancreas, liver,
and gallbladder. Hormones released by the stomach and duodenum
control the digestive secretions into the alimentary canal.
The pancreas aids chemical digestion by producing an alkaline

solution that is rich in bicarbonate, as well as severel enzymes. The
bicarbonate neutralizes the acidity of the chyme and acts as a buffer.
Among the pancreatic enzymes are trypsin and chemotrypsin, which
are also proteases that are secreted into the duodenum in an inactive
form. They are only activated when they are located in the
extracellular space within the duodenum.
The digestion of fats and other lipids begins in the small intestine. This
digestion relies on the presence of bile, which is a mixture of
substances that are made in the liver. Bile contains bile salts, which act
as detergents (emulsifiers) that help in digesting and absorbing lipids.
Bile is stored and concentrated in the gallbladder. The liver has many
vital function aside from the production of bile. It also breaks down
toxins that enter the body, such as alcohol. Bile is also important for
the destruction of red blood cells that are no longer functional.
The epithelial lining of the duodenum is the source of several digestive

enzymes. Some of these enzymes are bound to the cells of the
duodenum, while others are secreted into the lumen of the small
intestine. During enzymatic hydrolysis, peristalsis moves the mixture
Animal Survival 9
of chyme and digestive juices along the small intestine. Most of the
digestive processes are completed in the duodenum. The remaining
parts of the small intestine, the jejunum and ileum, function mainly in
the absorption of water and nutrients.
To reach body tissues, nutrients in the lumen must first cross the lining
of the alimentary canal. Most of this absorption occurs in the small
intestine. The surface area of the small intestine is roughly 300 m 2.
Large folds in the small intestine have finger-like projections called
villi. In turn, each epithelial cell of the villus has many microscopic
appendages, called microvilli. The microvilli give the epithelial lining
a brush-like appearance, which is reflected in the name brush border.
The large surface area created by the microvilli allows for more
capacity for nutrient absorption.
Depending on the nutrient, transport across the epithelial cells can

either be passive or active. For instance, fructose (a sugar), moves by
facilitated diffusion down its concentration gradient into the epithelial
cells. From there, fructose exits the basal surface and is absorbed into
microscopic blood vessels (capillaries) at the core of each villus. Other
nutrients, such as amino acids, vitamins, and most glucose molecules
move against their concentration gradient. The latter, which is active
transport, allows much more absorption of nutrients than would be
possible with passive diffusion alone.
Although many nutrients leave the intestine through the bloodstream,

some products of fat (triglyceride) digestion takes a different path.
After being absorbed by epithelial cells, fatty acids and
monoglycerides (glycerol joined to a single fatty acid chain) are
recombined into triglycerides into those cells. These fats are then
coated with cholesterol, phospholipids, and proteins. They then form
chylomicrons, which are fat-soluble globules. These globules are too
big to pass through the capillaries. Instead, they are transported to a
lacteal, which is a vessel at the core of each villus. Lacteals are part of
the lymphatic system of vertebrates that are filled with a clear fluid
called lymph. Starting at the lacteals, lymph containing chylomicrocs
passes into the larger vessels of the lymphatic system. These
eventually pass to the large veins that return blood to the heart.
In contrast with the lacteals, capillaries and veins that carry blood rich
in nutrients and away from the villi all converge into the hepatic portal
vein. This vein leads directly to the liver. From the liver, blood travels
to the heart and other organs. This arrangement has two major
functions: 1) it allows the liver to regulate the distribution of nutrients
10
to other parts of the body; and 2) it allows the liver to remove toxins
before they are circulated into the rest of the body.
Absorption in the Large Intestine
The alimentary canal ends with the large intestine. The parts of the
large intestine are the colon, cecum, and the rectum. The small
intestine connects to the large intestine at a T-shaped junction, where
sphincter controls the movement of material. One arm of the T is a
1.5m- long colon, which leads to the anus and the rectum. The other
arm forms a pouch called the cecum. The cecum is integral for
fermenting ingested material. This is especially so in animals that
ingest large amounts of plant material. Humans have a small cecum
compared to other mammals. A finger-like extension of the human
cecum, the appendix, has a small and dispensible role in immunity.
A major function of the colon is to recover any liquid that has entered
the alimentary canal as solvents of digestive juices. About 7L of fluid
are secreted into the cavity of the alimentary canal per day. Together,
the small intestine and the colon absorb about 90% of the water that
enters the alimentary canal. There is no biological mechanism for the
active transport of water, thus, the absorption of water occurs in the
colon by osmosis. This results when ions, in particular sodium, are
pumped out of the lumen.
The feces, which are the wastes of the digestive system, become
increasingly solid as they are moved along the colon by peristalsis. To
travel the length of the colon, it takes about 12-24 hours for the
material to pass through. If the colon is irritated, by a bacteria or virus,
for instance, less water may be absorbed than normal. This results in
diarrhea. The opposite problem, which is constipation, occurs when
the feces move too slowly along the length of the colon. Therefore, an
excess of water becomes reabsorbed, leading to the compaction of
feces.
In the human colon, a rich flora of bacteria can be found. They

comprise about 1/3 of the weight of feces. On important inhabitant of
the colon is Escherichia coli. Since E. coli is so common in the
digestive system, it is an indicator of the level of contamination of
lakes and other bodies of water by human feces. As by-products of
their metabolism, many bacteria produce gases, including methane and
hydrogen sulfide, which has an offensive odor. Some of the bacteria
may also produce vitamins, such as vitamin K, biotin, and several B
vitamins, including folic acid. These vitamins, which are absorbed into
the blood stream, supplement the daily intake of vitamins.
Animal Survival 11
Besides bacteria, feces also conatin cellulose fiber, which is an

undigested material. Although fiber has no caloric value for humans, it
helps move feces along the colon. The last portion of the colon is the
rectum, where feces are stored until they can be eliminated. Between
the anus and the rectum and two sphincters. The inner sphincter is
involuntary, while the outer sphincter is voluntary. Periodically, the
contractions of the sphincter produce the urge to defecate.
Homeostatic Mechanisms
The energy from food balances the expenditure of energy for
metabolism, activity, and storage. Homeostatic mechanisms are
integral for maintaining homeostatis, which is a balance that allows
animals and other organisms to survive in an environment which is in
constant entropy.
Energy Sources and Stores
Animals make use of certain sources of fuel before others when they
derive energy from their diets. Nearly of the ATP in animal
metabolism is based on the oxidation of energy-rich organic
molecules, such as carbohydrates, proteins, and fats, in cellular
respiration. Although all of these substances can be used as fuel, most
animals only utilize proteins after they have used up their stores of
carbohydrates. Fats are rich in energy. Oxidizing a gram of fat releases
about twice the energy that is released from oxidizing a gram of
protein or carbohydrates.
When an animal takes in more energy-rich molecules than it breaks

down, the result is that excess energy is converted to storage
molecules. In humans, the primary storage sites are the muscle cells
and the liver. Excess energy is stored there in the form of glycogen, a
polymer that is composed of many units of glucose. When fewer
calories are taken in than is expended, the result is the oxidation of
glycogen. The hormones insulin and glucagon maintain glucose
homeostatis by regulating glycogen synthesis and breakdown.
Adipose (fat) cells represent a second site for the storage of energy in
the body. If glycogen storage sites are full, and there is still excess
energy ingested, the excess is usually stored as fat. When more energy
is required than is acquired from the animal’s diet, then the body
expends liver glycogen first and then draws on muscle glycogen and
then fat. Most healthy people have enough fat stores to sustain them
for weeks even in the absence of food.
12
Overnourishment and Obesity
The consumption of more calories than the body needs is termed as

overnourishment. It causes obesity, which is the excess accumulation
of fat. Obesity, in turn, contributes to a number of health problems.
The most prominent health problem caused by obesity is diabetes
mellitus type II. It also contributes to cancer of the colon, breast, and
cardiovascular diseases that lead to strokes and heart attacks.
Researchers have discovered several homeostatic mechanisms that

regulate body weight. Operating as feedback circuits, these
mechanisms control the metabolism and storage of body fat. Several
hormones that regulate short-term and long-term appetite by affecting
a “satiety center” in the brain help control appetite. A network of
neurons integrates and relays information from the digestive system to
regulate the release of these hormones. Our understanding of the
satiety pathway has been greatly helped by the study of mice that are
chronically obese.
Mice with mutations in the ob or db gene eat more, thus, becoming

obese. Cloning of the ob gene led to the demonstrates that it produces
a hormone that is now called leptin. The db gene, on the other hand,
encodes the leptin receptor. The leptin receptor and leptin play key
roles in the circuitry that regulates appetite over the long-term. Leptin
is a product of adipose cells. Thus, the amount of leptin increases as
the volume of body fat increases. This cues the brain the suppress
appetite. Conversely, the loss of body fat decreases the amount of
leptin the body, and this signals the brain the increase appetite. By this
way, the feedback signals provided by leptin maintain body fat levels
within a set range. Leptin also has a role in how the nervous system
develops. In addition, most people who are obese have abnormally
high levels of leptin, which somehow fails to elicit a response from the
brain to decrease appetite.
Animal Survival 13
Glossary
Alimentary canal: the digestive tract
Homeostasis: regulatory mechanisms of the body keep the body in

equilibrium
Peristalsis: the movement of the smooth muscles of the digestive tract to

move food downwards.

Digesting Food
Absorption
Insulin and the Regulation of Glucose in the Blood
Malnutrition
Types of Malnutrition
Making Sense of Digestive Enzymes
References
Reece, J.B., Urry, L.A., Cain, M.L…& Jackson, R.B. (2013).
Campbell Biology 10th ed. Pearson.
14
How Plants Survive
This module will introduce you to the function and form of plants. It
will also focus on how plants develop and grow. An understanding of
plant form and function is integral to understanding the natural world
since plants are essential for the survival of all life on earth. As
members of the biosphere, plants govern the oxygen exchange on the
planet, and are thus important subjects for study.
Plant Structure
Plants have structural adaptations to their environment. However, in
addition to this, plants have developed a specific morphology, or
external form, that they accumulated through natural selection. For
instance, cacti have become so specialized for the desert environment
that their leaves have become spines, and their stems are little more
than photosynthetic organs. The adaption of leaf morphology has
added to the success of cacti in the desert environment because the
surface areas of their leaves are reduced, which means that they lose
less water. Both genetic and environmental factors influence form in
both plants and animals. However, the effect of the environment in
greater in plants. Consequently, the morphology of plants vary widely
among species compares to animals.
Plant Organs, Tissues, and Cells
Like animals, plants have organs composed of different tissues, which

are, in turn, composed of different types of cells. A tissue is a group of
cells with a common structure, function, or both. An organ consists of
several types of tissues that, together, carry out particular functions for
the organism.
The three basic plant organs are roots, stems, and leaves. The basic
morphology of most vascular plants reflect their evolutionary history
as terrestrial organisms that inhabit and draw resources from below
ground and above ground. Plants need to absorb water and minerals
from below the ground surface and CO2 and light from above the
ground. The ability to acquire these resources resulted in three distinct
organs which are morphological features- leaves, stems, and roots.
These organs form a shoot system and a root system, with the former
consisting of stems and leaves. With very few exceptions, angiosperns
and other vascular plants rely on both these systems for survival.
How Plants Survive 1

Roots are usually non-photosynthetic and they starve unless

photosynthates, which are sugars and carbohydrates imported from the
shoot system, arrive at the roots. Conversely, the shoot system depends
on the water and minerals that roots absorb from the soil.
Roots
Roots are multicellular organs that anchor vascular plants in the soil.
They also absorb water and minerals, and they often store
carbohydrates. Most eudicots and gymnosperms have taproot systems.
A taproot system consists of a main vertical root, the taproot, that
develops from the embryonic root. The taproot gives rise to lateral
roots, which are also called branch roots. In many angiosperms, the
taproot stores carbohydrates and sugars that the plant will consume
during flowering and fruit production. For this reason, many crops,
such as carrots and beets, are harvested before they flower. Taproot
systems generally penetrate deep into the soil and are well-adapted to
accessing sources of water that are far from the ground surface.
In seedless vascular plants, as well as in most monocots, such as

grasses, the embryonic root dies and does not give rise to the main
root. Instead, many small roots grow from the stem. These roots are
said to be adventitious, which is a term that describes a plant organ
that grows in an unusual location, such as roots arising from stems and
leaves. Each small root forms its own lateral roots. The result is a
fibrous root system. This is generally a mat of thin roots spreading out
below the soil surface, and no root functions as the main root. Fibrous
root systems usually do not penetrate the ground deeply and are
therefore best for shallow soils or regions where rainfall is light and
does not moisten the soil much below the surface layer. Most grasses
have this type of root system, which does not penetrate far underneath
the soil surface. These shallow roots hold the topsoil in place, which
means that they make excellent ground cover for preventing soil
erosion.
Although the entire root system helps anchor the plant into the soil,
most plants absorb minerals and water primarily near the tips of roots.
This is where vast numbers of root hairs are located, and these increase
the surface area of roots enormously. Root hairs are short-lived and
constantly being replaced. A root hair is a thin, tubular extension of a
root epidermal cell. It should not be confused with a lateral root, which
is a multicellular organ. Despite their large surface area, root hairs
contribute little to the anchoring of plants to the soil. Many plants have
modified roots. Some of these arise from roots, while others are
2
adventitious, developing from stems. In rare cases, roots may also

develop from leaves.
Stems
A stem is an organ that consists of alternating systems of nodes. These

are the points at which leaves are attached, and internodes, which are
the segments of stem between the nodes. In the upper angle formed by
the leaf and stem (axil) is an axillary bud. The axillary bud is a
structure that can form a lateral shoot, commonly called a branch.
Most axillary buds of a young shoot are dormant. Thus, the elongation
of a young shoot is usually concentrated near the shoot tip. This
consists of an apical bud, or terminal bud, with developing leaves and
compact series of internodes and nodes.
The proximity of the axillary buds to the apical buds is partly

responsible for their dormancy. The inhibition of axillary buds by an
apical bud is called apical dominance. Through the concentration of
resources on elongation, the evolutionary adaptation of the apical
dominance increases the plant’s exposure to light. If an animal, for
instance, eats the end of the shoots, the axillary buds break their
dormancy, and they start growing. A growing axillary bud gives rise to
a lateral shoot, complete with its own apical buds, axillary buds, and
leaves. This is the reason why pruning trees and shrubs will increase
the number of leaves. Some plants have stems that have additional
functions, such as for food storage and asexual reproduction. These
modified stems, which include rhizomes, bulbs, stolons, and tubers,
are often mistaken for roots.
Leaves
In most vascular plants, the main photosynthetic organ is the leaf.

However, green stems may also perform photosynthetic functions.
Leaves vary extensively in their morphology, but generally consist of a
flattened blade and a stake, which is the petiole, and which joins the
leaf to the stem at a node. Grasses and many other monocots lack
petioles. Instead, the base of the leaf forms a sheath that envelops the
stem.
Monocots and eudicots differ in the arrangement of veins, which is the

vascular issue of leaves. Most monocots have parallel major veins that
run the length of the blade. Eudicots generally have a branched
network of major veins.

In identifying angiosperms according to structure, taxonomists

generally rely on the floral morphology, but they also use variations in
leaf morphology. Many leaves are compound or doubly compound.
This structural adaptation may enable large leaves to withstand strong
winds with less tearing. It may also confine some pathogens that
invade the leaf to a single leaflet, rather than allowing them to spread
to the entire leaf. Almost all leaves are specialized for photosynthesis.
However, some species have leaves that allow them to perform special
functions, such as protection, support, or reproduction.
Dermal, Vascular, and Ground Tissue
Each of the three plant organs have dermal, vascular, and ground
tissues. These three categories of tissues form a tissue system, which is
a functional unit connecting all of the organs of the plant. Although
each tissue system is continuous throughout the plant, specific
characteristics of the tissues and their spatial relationships to one
another vary in different organs.
The dermal tissue system is the outer protective layer of the plant, or
the covering. It forms the first line of defense against pathogens and
physical damage. In plants that are not woody, it is usually a single
tissue called an epidermis, which is a layer of tightly packed cells. In
leaves and most stems, the cuticle, which is a waxy coating on the
epidermal surface, helps prevent the loss of water. In woody plants, the
protective tissue is called a periderm. This replaces the epidermis in
the older regions of the stems and roots. In addition to protecting the
plant from pathogens and water loss, the epidermis has specialized
characteristics in each organ. For instance, a root hair is an extension
of an epidermal cell near the tip of the root. Trichomes which are
hairlike outgrowths of the shoot epidermis, reduce water loss and
reflect excess light. They can also provide defense against insects by
secreting stickly fluids and toxic compounds. For example, trichomes
on aromatic leaves such as mint secret oils that protect plants from
herbivores.
The vascular tissue system carries the long-distance transport of

materials between the shoot and root systems. The two types of
vascular tissue are xylem and phloem. The xylem transports water and
dissolved minerals. The phloem transports sugars (usually from the
leaves) to where they are needed (usually the roots and other sites of
growth). The vascular tissue of a root or shoot system is collectively
called a stele. The arrangement of the stele varies, depending on the
organ and the species. In angiosperms, for examples, the root stele is a
solid vascular cylinder of phloem and xylem, whereas the stele of
4
leaves and stems consists of vascular bundles, which are separate

strands composed of either phloem or xylem. Both the xylem and the
phloem consist of differentiated cell types for transport or support.
Tissues that are neither dermal nor vascular are part of the ground
tissue system. Ground tissue that is internal to the vascular tissue is
called pith. Ground tissue that is external to the vascular tissue is
called cortex. The ground tissue system is not just a filler. It includes
cells that are specialized for functions such as storage, photosynthesis,
and transport.
Common Types of Plant Cells
Cells in plants are specialized according to structure and function.

Cellular differentiation may consist of changes in the both the
cytoplasm and its organelles in the cell wall.
Parenchyma cells have primary walls that are relatively thin and
flexible, and most of them lack secondary walls. Parenchyma cells
generally lack a central vacuole when they are maure. These cells are
the least specialized structurally. Parenchyma cells perform most of
the metabolic functions of the plant. They synthesize and store various
organic products. For instance, photosynthesis occurs in the
chloroplasts of parenchyma cells in the leaf. Some parenchyma cells in
the roots and stems have plastids which store starch. The fleshy tissue
of most fruits is composed of parenchyma cells. Most parenchyma
cells retain the ability to divide and differentiate into other types of
plant cells under particular conditions. For instance, during wound
repair, parenchyma cells can differentiate. Thus, it is possible for
scientists to grow an entire plant from a single parenchyma cell.
Collenchyma cells are grouped either into cylinders or strands that

help support the young parts of the plant shoot. These cells have thick
primary walls, thicker than parenchyma cells, although the walls are
unevenly thickened. Young stems and petioles often have collenchyma
cells just below their epidermis. They also lack secondary walls.
Lignin, which is a hardening agent, is often absent from their primary
walls. Therefore, these cells are able to provide support without
restricting the growth of the plant. During maturity, these cells are
living and flexible, allowing them to elongate the leaves and stems that
they support.
Sclerenchyma cells, on the other hand, also function as supporting

elements in the plant. However, they have thick secondary walls that
are strengthened by lignin. They are much more rigid than

collenchyma cells. Mature sclerenchyma cells cannot elongate, and

they are found in regions of the plant that have stopped growing.
Sclerenchyma cells are also specialized for support and are dead at
maturity. However, they produce secondary walls before the
protoplasts (the living the part of the cell) dies. The remaining walls
serve as skeletons, which can support the plant for hundreds of years.
There are two types of sclerenchyme cells: sclereids and fibers. Both
of these are specialized for support and transport. Sclereids are shorter
than fibers and irregular in shape. They have thick, lignified secondary
walls. Sclereids allow the shells of nuts to be hard. Fibers are usually
arranged into threads. They are long, slender, and tapered.
Water-Conducting Cells of the Xylem
There are two types of water conducting cells: tracheids and vessel
elements. Both of these cell types are tubular and elongated. They are
also dead at maturity. Tracheids are found in the xylem of nearly all
vascular plants. In addition to tracheids, most angiosperms, as well as
a few gymnosperms, have vessel elements. When the living contents
of the plant’s tracheids and vessel elements disintegrate, the thickened
walls of the cells remain behind. These form a living conduit through
which water can flow. The secondary walls of tracheids and vessel
elements are often interrupted by pits, which are thinner regions where
only primary walls are present. Thus, water can migrate laterally
through pits.
Tracheids are long, thin cells with tapered ends. Water moves from
cell to cell mainly through pits, where it does not have to cross thick
secondary walls. The secondary walls of tracheids are hardened
through lignin, and this prevents the collapse of the cell during water
transport.
Vessel elements are generally wider, shorter, and thin-walled. They are
also less tapered that tracheids. They are aligned from end-to-end,
forming long micropipes called vessels. The end walls of the vessel
elements have perforation plates that enable water to flow freely
through the vessels.
Sugar-Conducting Cells of the Phloem
Unliked the water-conducting cells of the xylem, the sugar-conducing

cells of the phloem are alive at functional maturity. In seedless
vascular plants and gymnosperms, sugars and other nutrients are
transported through long, narrow cells called sieve cells. In the phloem
of angiosperms, these nutrients are transported through sieve tubes,
6
which consist of chains of cells called sieve-tube elements, or sieve-

tube members.
Although alive, sieve-tube elements lack ribosomes, a nucleus, a

distinct vacuole, and cytoskeletal elements. The reduction in the
contents of the cells allows nutrients to pass through the cell more
easily. The end walls between sieve-tube elements are called sieve
plates, which have pores that facilitate the flow of fluid form cell to
cell along the sieve tube. Alongside each sieve-tube element is
nonconducting cells called a companion cell. This is connected to the
sieve-tube elements by numerous channels, the plasmodesmata. The
nucleus and ribosomes of the companion cell not serve not only the
cell itself, but also the nearby sieve-tube element. In some plants, the
companion cells in leaves also help load sugars into the sieve-tube
elements, and then the sugars are transported to other regions of the
plant.
Plant Growth and Development

In contrast to animals, which only grow during the embryonic and
juvenile periods, plants grow throughout their life, which is termed as
indeterminate growth. At any given time, a plant has parts that are
mature, embryonic, or developing. Except for plants that are in their
dormant periods, most plants grow continuously. Some plants organs
undergo determinate growth, such as most leaves, thorns, and flowers.
That is, they stop growing once they reach a certain size.
Although plants continue to grow throughout their lives, they also die.
As was discussed in previous chapters, plants may be annuals, biennals
or perennials.
Plants are capable of indeterminate growth because they have

perpetually embryonic tissues called meristems. These two main types
of meristems: apical meristems and lateral meristems. Apical
meristems are located at the tips of roots and shoots and in the axillary
buds of shoots. They provide additional cells that allow the plant to
grow in length, in a process known as primary growth. Primary growth
allows roots to extend through soil and shoots to increase their
exposure to light. The herbaceous, or non-woody, plants, primary
growth produces most, if not all, of the plant body. Woody plants,
however, also grow in girth and in parts of stems and roots that no
longer grow in length. This growth in thickness, known as secondary
growth, is caused by the activity of lateral meristems, which are called
the vascular cambium and the cork cambium. These cylindes of
dividing cells extend along the length of stems and roots. The vascular

cambium adds layers of vascular tissue called secondary xylem (wood)

and secondary phloem. The cork cambium, on the other hand, replaces
the epidermis with a thicker, tougher, epiderm.
The cells within the meristems divide relatively often, generating

additional cells. Some of these new cells remain in the meristem and
produce more cells, while other differentiate and are incorporated into
tissues and organs of growing plants. Cells that remain as sources of
new cells are called initials. The new cells that are displaced from the
meristem are called derivatives, since they continue to divide until the
cells they produce become specialized within developing tissues.
Primary Growth in Roots and Shoots
Primary growth is a growth in length, produced by apical meristems.

The primary plant body is the result of this growth. In herbaceous
plants, it is usually the entire plant. In woody plants, it consists of only
the youngest parts, which are not yet woody. Although apical
meristems lengthen both shoots and roots, there are differences in the
primary growth of these two systems.
Primary Growth of Roots
The tip of the root is covered by a root cap, which protects the delicate
apical meristem as the root pushes through the abrasive soil during
primary growth. The root cap also secretes a polysaccharide slime that
lubricates the soil around the tip of the root. Growth occurs behind the
tip in three zones of cells. These cells are at successive stages of
primary growth. Away from the tip, they are zones of cells division,
elongation, and differentiation.
8
There are no sharp boundaries between the three zones, and they grade
together. The zone of cell division includes its derivatives and root
apical meristem. In this region, new root cells are produced. Behind
the tip of the root is the zone of elongation. This is where root cells
elongate. Sometimes, these cells elongate to more than 10 times their
length. In this zone, cell elongation allows the tip to penetrate farther
into the soil. Even before the root cells start lengthening, they may
begin specializing in structure and function. In the zone of
differentiation, which is the zone of maturation, cells complete the
differentiation process and become specific cell types.
The primary growth of a root is when its epidermis is produced, as

well as the ground tissue and vascular tissue. In most roots, the stele is
a vascular cylinder. It is a solid core of xylem and phloem.
In the roots of most eudicots, the xylem has a star-like appearance. The
phloem occurs the indentations between the arms of the star. In
monocots, the central core is composed of parenchyma cells. This core
surrounded by a ring of xylem and then a ring of phloem. This central
region is called a pith, but it is different from a stem pith.
The ground tissue of roots, which consists mostly of parenchyma cells,

fills the cortex. The cortex is the region between the vascular cylinder
and the epidermis. The ground tissue has cells that store carbohydrates.

Their plasma membranes allow for the absorption of water and

minerals. The cortex has an innermost layer called the endodermis.
This is a cylinder that is one cell thick and forms the boundary with the
vascular bundle.
Lateral roots come from the pericycle, which is the outermost layer in
the vascular cylinder. It is adjacent to, and just inside, the endodermis.
A lateral root pushes through the epidermis and the cortex until it
emerges from the main root. The lateral root cannot come from near
the root’s surface because the vascular system must be continuous with
vascular cylinder at the center of the established root.
Primary Growth of Shoots
A dome-shaped mass of dividing cells at the shoot tip is the shoot

apical meristem. Finger-like projections along the sides of the apical
meristem are where leaves develop, the leaf primordia. Axillary buds
develop from islands of merismatic cells left by the apical meristem at
the bases of the leaf primordia. These buds can form lateral roots at
some later time.
10
The internodes are shaped close together within leaf primordia because
the internodes are very short. Most of the elongation of the shoot is
due to the lengthening of the internode cells underneath the shoot tip.
In grasses, and other plants, some of the leaf cells are produced by
areas of merismatic tissue that is separated from the apical meristem.
These areas are called the intercalary meristems, and remain at the
base of leaf blades and stem internodes. This type of morphological
feature helps grasses tolerate grazing because the elevated part of the
leaf blade can be removed without interfering with growth.
The Tissue Organization of Stems
As part of the continuous dermal tissue system, the epidermis covers

the stem. As vascular bundles, vascular tissue runs the length of the
stem. Unlike lateral roots, which arise from the vascular tissue deep
within a root and thus disrupt the vascular cambium, cortex, and
epidermis as they emerge, lateral roots develop from axillary bud
meristems on the surface of the stem. These lateral roots do not disrupt
other tissues. The stem’s vascular bundles converge with the root’s
vascular cylinder in a zone of transition near the surface of the soil.
In most eudicot species, the vascular tissue is composed of vascular

bundles that are arranged in a ring. The xylem contained within each

vascular bundle is situated beside the pith, and the phloem in each
bundle is situated beside the cortex. In most monoct stems, the
vascular bundles are scattered throughout the ground tissue. They do
no form rings. In the stems of both eudicots and monocots, the ground
tissue consists mainly of parenchymal cells. However, collenchyma
cells underneath the epidermis strengthen many stems. Sclerenchyma
cells, especially fiber cells, also provide support in parts of the stem
that have stopped elongating.
Tissue Elongation of Leaves
The epidermal barrier of leaves is interrupted by stomata, which allow

gas exchange between the surrounding air and the photosynthetic cells
inside the leaf. Stomata also function to regulate the CO2 uptake for
photosynthesis and they are major avenues for the evaporative loss of
water. The stomatal complex is composed of the pore flanked by two
guard cells, and the latter regulate the opening and closing of the pore.
Sandwiched between the upper and lower epidermal layers is the

ground tissue of the leaf, the mesophyll. Mesophyll contain mainly
parenchymal cells that are specialized for photosynthesis. The leaves
of many eudicots have two areas: the spongy mesophyll and the
palisade mesophyll. The palisade mesophyll consists of one or more
layers of elongated parenchyma cells located on the upper part of the
leaf. On the other hand, the spongy mesophyll is located below the
palisade mesophyll. The parenchyma cells of the spongy mesophyll
are loosely arranged and contain a labyrinth of spaces through which
CO2 and oxygen circulate. The air spaces are large near the somata,
where gas exchange with the environment occurs.
12
The vascular tissue of each leaf is continuous with the vascular tissue
of the stem. Connections from the vascular bundles in the stem, leaf
traces, pass through petioles and into the leaves. In the vascular bundle
are veins, which branch out. This network brings the xylem and
phloem near the photosynthetic tissue. The photosynthetic tissue
receives water and minerals, and brings the products of photosynthesis
to the phloem. The vascular structure also reinforces the shape of the
leaf. Each vein is enclosed by a bundle sheath, consisting of one or
more layers of cells, which are usually parenchyma cells. Unlike stems
and roots, leaves rarely undergo secondary growth.
Secondary Growth
The secondary plant body consists of the tissue produced by the

vascular cambium and the cork cambium. The former adds secondary
xylem and secondary phloem, increasing the vascular flow and support
for the shoot system. On the other hand, the cork cambium produces a
tough, thick covering that consists mainly of cells with wax that
protect the stem from water loss and from invasion by insects, fungi,
and bacteria. Monocots rarely have secondary growth, unlike eudicots
and gymnosperms. Primary growth and secondary growth occur
simultenously.
The vascular cambium is a cylinder of merismatic cells, and it is often

only one cell thick. It increases in circumference and also adds layers
of secondary xylem to its interior and secondary phloem to its exterior.
Each layer has a larger diameter than the previous layer. In this way,
the vascular cambium thickens stems and roots.

In woody plants, the vascular cambium consists of a continuous

cylinder of undifferentiated parenchyma cells, which are located
outside the pith, and primary xylem. The inside of the cortex has the
primary phloem. In a woody root, the vascular cambium forms the
exterior of the primary xylem and the interior of the primary phloem
and the pericycle.
As merismatic cells divide, they increase the circumference of the

vascular cambium. They also add secondary xylem to the inside of the
cambium and secondary phloem to its outside. Some initials are
elongated and are oriented with their long axis parallel to the axis of
the stem and root. They produce cells, such as the tracheids, vessel
elements, fibers of the xylem, as well as companion cells. The other
initials are shorter and are oriented perpendicular to the axis of the root
or stem. The produce vascular rays, which are radial files of cells that
connect the secondary xylem with the secondary phloem. These rays
move water and nutrients between the secondary xylem and the
phloem. They also store carbohydrates and aid in wound repair.
As secondary growth continues over many years, layers of secondary

xylem, which is wood, accumulates. This consists mainly of tracheids,
vessel elements, and fibers. Gymnosperms only have tracheids,
whereas angiosperms have both tracheids and vessel elements. The
walls of secondary xylem have lignin, which makes them hard. As the
tree grows, the older layers of secondary xylem no longer transports
minerals and water (which is a solution called xylem sap). These
layers are called heartwood because they are closer to the core of the
stem or root. The newest, and outermost layers of the secondary xylem
still transport xylem sap, and are therefore known as sapwood. Since
each new layer of secondary xylem is larger in circumference than the
previous one, growth enables the xylem to transport more xylem sap
each year, which supports an increasing number of leaves. Only the
youngest secondary phloem, which is closest to the vascular cambium,
functions in sugar transport. The older secondary phloem is sloughed
off, which is why secondary phloem does not accumulate as
extensively as secondary xylem.
The Cork Cambium and the Production of Periderm
During the first few stages of secondary growth, the epidermis is

pushed outward, causing it to dry, split, and fall of the root or stem. It
is replaced by two tissues produced by the first cork cambium, which
is a layer of dividing cells that arises in the outer cortex of the stems
and in the outer layer of the pericycle in roots. One of these tissues,
which is called the phelloderm, is a thin layer of parenchymal cells
14
that forms to the interior of the cork cambium. The other group of cells
form to the exterior of the cork cambium. As these cells mature, they
deposit suberin, which is a waxy material. The cork tissue functions as
a barrier that prevents the stem or root from water loss, pathogens, and
physical damage. Each cork cambium and the tissue it produces
comprises a layer of the periderm.
Most of the periderm is impermeable to water due to the presence of

suberin, unlike the epidermis. In most plants, therefore, water and
minerals are absorbed mostly in the younger parts of the plant. The
older parts of the roots anchor the plant and transport water and solutes
between the soil and the shoots. Located on the periderm are small,
raised areas called lenticels. It enables plants with woody stems to
exchange gases with the environment. Lenticels often appear as slits.
The thickening of a stem or root often splits the first cork cambium.
The first cork cambium often differentiates into cork cells and loses its
merismatic activity. A new cork cambium forms on the inside,
resulting in another layer of periderm. The bark contains all the tissues
that are external to the vascular cambium. Its components are, from the
inside, the secondary phloem, the most recent periderm, and all the
older layers of periderm.
Glossary
Dicots: dicotyledons, where embryonic seeds have two cotyledons.
Monocots: monocotyledons, or flowering plants (angiosperms) which contain

only one cotyledon.

Plant Parts and Functions
Plant Nutrition and Transport
Plant Tissues
Plant Anatomy
Practical Plant Anatomy
Water Transport in Plants: Anatomy and Physiology

References
Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P.
V., & Jackson, R. B. (2011). Campbell biology (p. 379). Boston:
Pearson.
16
The Process of Evolution
In this module, we will examine how animals and plants to came to be

in their present forms and functions. Evolutionary adaptations are
crucial for the survival of species, with natural selection spurring on
the evolutionary process.
The Darwinian Concept of Evolution
Classification of Species and Scala Naturae
Several Greek philosophers, long before Darwin was born, suggested

that life might have changed gradually over time. What compelled
Charles Darwin to revise his view on evolution? The answer is that
much of his propositions were based on the work of many individuals.
However, one philosopher, who was greatly influential in Western
philosophy, held the view that species were fixed. Aristotle postulated
that there were certain “affinities” between species. He concluded that
life forms could be arranged in a scale, or a ladder, of increasing
complexity, which he termed scala naturae. Each form, perfect and
permanent, had its place in the ladder.
These ideas were also found in the Old Testament account of creation,
which holds that specific species were individually designed by God,
and therefore, perfect (creationism). In the 1700s, this was interpreted
by scientists as marks of God’s work, that species were so perfectly
adapted to their environments.
One such scientist was Carolus Linnaeus, who developed the binomial
system of naming species. For instance, humans are designated as
homo sapiens. In contrast to the linear hierarchy of scala naturae,
Linnaeus developed a nested classification system, which was used to
group organisms into specific categories. However, he did not ascribe
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these classifications to evolutionary adaptations. Rather, he ascribed

them to God’s creative powers.
Ideas About Change
Many scientists drew their work from the remains of living things,
which are fossils. Most fossils have been found in sedimentary rocks
formed from mud and sand that settle into the bottom of seas, lakes,
and swamps. New layers of sediments form over older ones and
compress them into superimposed layers of rocks called strata. At the
time the layers were formed, the fossils were deposited in the rocks.
Thus, the fossils provide clues about the organisms that lived during
the time that the strata were formed.
Georges Cuvier largely developed paleontology, which is the study of

fossils. Cuvier observed that there were species that were present in
one layer of rock, but then disappeared in later layers. He then inferred
that extinctions must have been a common occurrence in the history of
life. However, Cuvier opposed the idea of evolution. As explanations
for his observations, he advocated catastrophism. Catastrophism is the
principle that events in the past occurred suddenly and operated under
different mechanisms from those found in the present. He also
speculated that each boundary in the strata represented a single
catastrophe.
In 1975, James Hutton proposed that the geologic features of the Earth
could be explained by gradual mechanisms that were still operating.
The leading geologist during Darwin’s time, Charles Lyell, included
Hutton’s thinking into his principle of uniformitarianism. This
principle stated that the mechanisms of change are constant over time.
Lyell proposed that they very same geologic processes are operating
today, and at the same rate. The ideas of Hutton and Lyell influenced
2
the thinking of Darwin in that if geologic processes were slow, then

the actions that are continuous rather than sudden evens, then the Earth
must be older than what was previously thought.
Lamarck’s Hypothesis of Evolution
Several naturalists, during the 18th century, suggested that life evolved
as environments change. However, only one of Darwin’s predecessors
proposed how life changes over time. French biologist, Jean-Baptiste
Lamarck proposed a mechanism for evolution, which was later found
to be incorrect. Lamarck published his hypothesis in 1809, the year
that Darwin was born. By the comparison of living things and fossils,
he found what appeared to be several lines of descent. Each
chronological order of species led to the subsequent species that was
alive at the time. He explained this occurrence using two principles.
The first was use and disuse, the idea that parts of the body that are
commonly used become larger and stronger and parts of the body that
are no longer being used shrink and become weaker. The second
principle was the inheritance of acquired characteristics, which stated
that an organism could pass the modifications to its offspring. He also
thought that organisms had an inner drive to evolve. Darwin rejected
this idea. However, he thought that variations were introduced into
species through the inheritance of modified characteristics. Today,
however, Lamarck’s hypothesis has been rejected, as there is no
genetic mechanism that would allow inheritance in the way that
Lamarck proposed.
Darwin’s Research
Darwin left England on the Beagle on December 1831. He spent most

of his time on shore, collecting and observing thousands of plants and
animals. He noted their characteristics that made them well-suited to
the environment. In addition to this, he also spent much of the time
thinking about geology. He read Lyell’s Principles of Geology. When
the Beagle stopped at Galapagos, his interest in geology was further
enhanced. He was fascinated by the unique organisms that he found
there.
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During the voyage on the Beagle, Darwin was able to observe that
there were many examples of adaptations. These are characteristics
that enable organisms to thrive in the environment that they are in.
Later, he perceived adaptations to the environment and the origin of
new species as closely related processes. By the 1840s, the hypotheses
of Darwin were published in a paper. He anticipated that there would
be uproar about the implications of his proposal, but he continued on
his pursuit.
The Origin of Species
Darwin’s book, The Origin of Species, had two main ideas: that
descent with modifications explains life’s unity and diversity and that
natural selection brings about the match between organisms and their
environment.
Descent with modification summarized Darwin’s view of life. He

perceived unity in life, which he attributed to the descent of all
organisms from a common ancestor in the past. He also believed that
these ancestors also acquired diverse modifications, or adaptations,
that fit them to specific ways of life. Darwin viewed the history of life
as like that of a tree, with multiple branches coming from a common
trunk.
Natural selection was proposed by Darwin as a mechanism to explain

the observable patterns of evolution. He observed that humans have
modified species over time through selective breeding to produce
desired traits. He called this artificial selection. As a result of artificial
selection, animals and crops bear little resemblance to their wild
ancestors.
Darwin also perceived that there was an important connection between

the capacity of organisms to overreproduce and natural selection. He
4
realized that all species held the capacity to overreproduce. He was

influenced by the works of Thomas Malthus, who contended that all
suffering, such as disease, war, and famine, were caused by the
explosion of populations and the limited resources found on Earth.
Aside from this, Darwin also observed that an organism’s traits can
influence not only its own performance, but also how well its
offsprings cope with environmental changes. Organisms with offspring
that are able to obtain food or withstand physical conditions are able to
survive and reproduce, thus producing more offspring. Thus, natural
selection is imposed by factors such as predators and environmental
conditions, which can increase the favorable traits in a population.
A Summary of Natural Selection
Natural selection is the process by which organisms that have certain

heritable characteristics survive and reproduce at a higher rate than
other individuals.
Over time, natural selection can increase the match between organisms
and their environment.
If an environment changes, or if organisms move to a new

environment, natural selection may result in adaptations to these new
conditions, sometimes giving rise to new species in the process.
An important point to note is that individuals do not evolve, rather,

populations evolve. A second important point is that natural selection
can only diminish or amplify heritable traits. Thus, although an
organism may acquire modifications over its lifetime, these may not be
heritable traits. Third, a trait that is favorable in one environment may
be unfavorable in another. Natural selection is always operating, but
which traits are favorable depend on the context of the environment.
Evidence for Evolution
The evidence for evolution is overwhelming. The first such evidence is

the direct observations of evolutionary change. Predators are potent
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forces shaping the adaptations of their prey. The predator is more

likely to feed on prey organisms that are less able to avoid detection,
escape, or defend themselves. As a result, prey individuals are less
likely to reproduce and pass their traits onto their offspring that are
individuals who whose traits allow them to evade predators.
Consider the example of the evolution of drug-resistant HIV. HIV is

the virus that causes AIDS. Researchers have developed numerous
drugs to combat this pathogen, but using these medications selects
viruses which are resistant to them. Those that survive the early doses
may reproduce, passing on the alleles that enable them to resist the
drug. In this way, the frequency of resistant viruses increases rapidly
in the population. A drug does not create resistant pathogens; rather it
selects for resistant individuals that are already present in the
population. Thus, natural selection is a process of editing rather than a
creating mechanism. Second, natural selection depends on time and
place. It favors those characteristics in a genetically viable population
that provide advantages in the local, current environment.
The fossil record is the second evidence for evolution. Fossil records
show that present-day organisms differ significantly from organisms
that existed before. Many species have also become extinct. Fossils
show the evolutionary changes that have occurred over time in various
groups of organisms.
Over longer time scales, fossils are able to document the origins of
major new groups of organisms. An example of this is the fossil record
of early cetaceans, which is the mammalian order to includes whales,
dolphins, and porpoises. The early cetaceans lived about 60 million
years ago. Fossil records indicate that, prior to that time period, most
mammals were terrestrial. However, fossils were recovered in
Pakistan, Egypt, and North America that document the transition from
6
life on land to life in the sea. Collectively, these and other early fossils
document the formation of new species and the origin of a major group
of mammals, the cetaceans. In addition to providing evidence for the
pattern of evolution, fossil records can also be used to test the
evolutionary hypotheses. For instance, based on anatomical data,
scientists believe that early land vertebrates evolved from a group of
fishes. They also believe that early amphibians also evolved from
descendants of land vertebrates. If these relationships were correct, we
would predict that the earliest fossils of fishes would be older than the
earliest fossils of amphibians. These predictions can be tested using
radioactive dating techniques.
Homology is the third evidence for evolution. Homology is the

analysis of similarities between organisms. As a remodeling process,
evolution would predict that similar species would share similar
features. For example, the forelimbs of all mammals, including
humans and cats, show the same arrangement of bones from the
shoulder to the tips of the digits, even though they have very different
functions. These striking anatomical similarities would not be there if
they had arisen anew in each species. Rather, the underlying skeletal
structures of arms, flippers, and wings of different mammal are
homologous structures that show the variations in a common theme,
and also that that these animals have a common ancestor.
The early stages of development in different animals reveals additional

anatomical homologies not visible in adult organisms. For instance, at
some point in their development, all vertebrates have a tail located
posterior (behind) the anus, as well as structures called pharyngeal
(throat) pouches. These throat pouches are homologous and ultimately
develop into structures with very different functions. Some of the most
interesting homologies refer to the leftover, or marginal, structures
which are of little importance to the organism. These structures, called
vesitigial structures, are remnants of important features that were
functional in the ancestors of the organism. For instance, the skeleton
of some snakes retain vestiges of the pelvis and legs of walking
ancestors.
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At the molecular level, biologists also observe similarities among

organisms. All forms of life use the same genetic language, which is
DNA and RNA, and the genetic code is essentially universal. Thus, it
is likely that all species descended from a common ancestor that used
this genetic code. For instance, humans and bacteria share genes that
are inherited from a shared distant ancestor. Like other structures,
these genes have different functions in different organisms.
The pattern of descent from common ancestors is often represented

using an evolutionary tree, which is a diagram that reflects the
evolutionary relationships among groups of organisms. Evolutionary
trees are hypotheses that summarize our current understanding of the
patterns of descent.
Convergent evolution also occurs. This is when distantly related

organisms resemble one another for a different reason. Convergent
evolution is the independent evolution of similar features in different
lineages. For instance, marsupials are found in Australia and are
distinct from another group of mammals, the eutherians. Some
marsupials have members that look like eutherians.
A fifth type of evidence for evolution is biogeography. Biogeography

is the geographic distribution of species. The geographic distribution
of organisms is influences by many factors. One of these is continental
drift, which is the slow movement of the earth’s continents over time.
About 250 million years ago, these movements united all the
continents on earth into a single large continent, known as Pangaea.
Roughly 200 million years ago, this large mass of land began to break
apart. Around 20 million years ago, the continents as we know them
today were in their present locations.
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The Evolution of Populations

The smallest scale of evolution is called microevolution. These are
changes in allele frequencies in specific populations over generations.
There are three main mechanisms that cause allele frequencies to
change: natural selection, genetic drift (chance events that later allele
frequencies), and gene flow (the transfer of alleles between
populations). However, only natural selection is consistent in
improving the match between the organisms and their environment.
Genetic Variation Through Mutation and Sexual Reproduction
Phenotype is the product of an inherited genotype and many

environmental influences. For instance, bodybuilders may get larger
but they do not pass on their large muscles to their offsprings. Only the
genetic part of variations can have evolutionary consequences.
Characters that vary within a population may be quantitative or

discrete. Discrete characters occur on an either-or basis. For instance,
Mendel’s peas may either be green or yellow. The majority of discrete
characters are determined by a single gene locus with different alleles
that produce distinct phenotyoes. However, the majority of heritable
variation involves quantitative characters, which vary along a
continuum in a population. Heritable quantitative variation usually
results from the influence of two or more genes on a single phenotypic
character.
Biologists can measure that genetic variation in a population at both

the molecular level of DNA (nucleotide variability) and whole-gene
level (gene variability). Gene variability can be quantified as average
hetetozygosity. This is the average percentage of loci that are
heterozygous. Average heterozygosity is often surveyed by using gel
electrophoresis to meaure the products of genes. On the other hand,
nucleotide variability is measured by comparing the DNA sequences
of two individuals in a population and then averaging the data from
these comparisons. For instance, the genome of Drosophila
melanogaster has 180 million nucloetides, and the sequence of any
two fruit flies differs by an average of 1.8 million nucleotides.
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In addition to the genetic variability in populations, scientists are also

able to observe geographic variation, which is the difference in the
genetic composition of separate populations. Geographic variations
also occur as a cline, which is a graded change in character along a
geographic axis. Some clines are produced by a gradation in an
environmental variable. Selection, however, can only operate as
multiple alleles exist for a given gene locus.
Mutation is the ultimate source of new alleles. Mutation is the change

in nucleotide sequence of an organism’s DNA. It is not possible to
predict with accuracy which segments of DNA will be altered or in
what way. In multicellular organisms, only mutations in cell lines that
produce gametes can be passed on to the offspring. This is not as
limiting as it sounds, especially in plants and fungi, since they have
many different cell lines that produce gametes. However, in most
animals, mutations occur in somatic cells and are lost when the
individual dies.
A point mutation is a difference in a gene in as little as one base pair in

a gene, and it can have a significant effect on the organism’s
phenotype. Organisms reflect thousands of previous selections, thus,
their phenotype is generally closely matched to their environment. As
a result of this close match, any mutation in their genes is unlikely to
provide any benefit. Sometimes, it can even be harmful. However,
much of the genes in eukaryotic organisms do no code for proteins.
Point mutations in these non-coding regions are harmless. In addition,
because the genetic code is redundant, a point mutation in a gene that
encodes a protein will have no effect on the protein’s function if the
composition of the amino acid is not changed. Moreover, if there is a
change in amino acid, this may not necessarily affect the protein’s
shape and function. However, on rare occasions, a mutant allele may
10
actually make the organism better suited to its environment, which

enhances its reproductive success.
Chromosomal changes that disrupt, delete, or rearrange many loci at

once are almost sure to be harmful. However, when large-scale
mutations such as this occur, but they leave genes intact, their effect on
the organism may be neutral. In rare cases, chromosomal
rearrangements may be beneficial. An important source of variation
begins when genes are duplicated due to errors in meiosis, slippage
during DNA replication, or the activities of transposable elements. The
duplication of smaller pieces of DNA may not be harmful. Gene
duplications, in addition, do not have severe effects that persist over
generations, allowing mutations to accumulate. The result is that the
genome becomes expanded with new loci that may take on new
functions.
Mutation rates tend to be low in animals and plants, averaging about

one mutation every 100,000 genes per generation. Mutation rates are
even lower in prokaryotes. However, prokaryotes generally have short
generation spans, so mutations can quicly generate genetic variation in
populations of these organisms. Viruses are also another group of
organisms where generation spans are short.
Genetic Drift
Chance events can cause allele frequencies to fluctuate unpredictably
from one generation to the next, especially in small populations. This
is known as genetic drift. Certain circumstances can result in genetic
drift having significant effects on a population. Two examples are the
founder effect and the bottleneck effect.
The Founder Effect
When a small group from a population becomes separated from the

main population, they may establish a new population whose gene
pool differs from the main population. This is known as the founder
effect. The founder effect might occur, for instance, when members of
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population are blown by the wind to a new island. Genetic drift, in

which chance events alter the allele frequencies, occur in such a case
because the wind transported individuals to another location, leaving
the rest of the population behind. The founder effect accounts for the
relatively high frequency of certain inherited disorders among isolated
human populations.
The Bottleneck Effect
A sudden change in the environment, such as a fire or a flood, may

drastically reduce the size of the population. A drastic drop in the
population can cause the bottleneck effect, which is termed that way
because the population has gone through a restrictive event. By chance
alone, certain alleles may be overrepresented in survivors, others may
be underrepresented, and some may be absent altogether. Ongoing
genetic drift is most likely to have a substantial effect on the gene pool
unless the population becomes large enough for chance events to have
less of an effect. However, a population that has gone through a
bottleneck may have little genetic variation even if the population
increases in size for a long time. Human actions create severe
bottlenecks for some species, such as when humans cause forest fires
or flooding in a certain area.
Effects of Genetic Drift
1. Genetic drift is significant in small populations.
2. Genetic drift can cause allele frequencies to change at random.
3. Genetic drift can lead to a loss of genetic variation within

populations.
4. Genetic drift can cause harmful alleles to become fixed.
12
Gene Flow
Allele frequencies can also change by gene flow, which is the transfer
of alleles into or out of a population due to the movement of fertile
individuals or their gametes. Since alleles are exchanged among
populations, gene flow tends to reduce the genetic variations between
populations. If it is extensive enough, gene flow can result in
neighboring populations combining into a single population with a
common gene pool.
When neighboring populations live in different environments, alleles

transferred by gene flow may prevent a population from fully adapting
to its environment. There are instances when beneficial alleles are
transferred very widerly. For instance, gene flow has allowed the
spread of insecticide-resistant alleles in the mosquito Culex pipiens. C.
pipiens is a vector for malaria and the West Nile virus. Gene flow, like
mutations, can introduce new alleles into a population. However, since
gene flow can occur at a higher rate than mutation, gene flow is more
likely.
Three Aspects in Evolutionary Thinking
The last 35 years have seen a widening inquiry into evolution.

Evolution is now recognized that there is more to studying
evolutionary change than studying the evolution of populations. Three
aspects of evolutionary thinking are, in particular, important.
The first is that phenotypic evolution comes from evolutionary change

in the process of development that transforms a single-celled fertilized
cell into an adult organism. Although under genetic control, the
process of development is so complex that it cannot be understood by
studying the DNA sequences alone. Rather, the understanding of how
phenotypes evolve, and the extent to which evolution is directed and
constrained by developmental systems, requires detailed embyrologcal
and molecular knowledge.
Second, the understanding of evolution necessitates the understanding

of history. Paleontology is the study of direct evidence from the past.
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In recent years, interest has been renewed in the field because of new
findings and discoveries. There are also new theories, such as those of
mass extinction, punctuated equilibrium and stasis, and species
selection. Initially crictial in the acceptance and development of
evolutionary theory, paleontology has once again become an integral
part of evolutionary biology. Concurrently, a more important
revolution has taken place over the last 30 years. This emphasizes the
historical perspective that is based on the information on phylogenetic
relationships. That is, the tree of life, which is the pattern of descent
and relationships among species. The tree of life is critical to
understanding the aspects of evolution from above the population
level.
Finally, life is organized as a hierarchy. That is, genes are found

individuals, and individuals are found within populations, and
populations within species, and species within clades (a clade consists
of an ancestral species and its descendants). Population genetics
concerns itself with what happens within a population, however,
evolutionary change can occur on all levels. There is a possibility that
some genes are particularly adept at mutating to multiply the number
of copies of that gene within a genome. This may occur such that
genes may multiply within a genome even if it poses no benefit to the
organism. Just as selection among individuals can lead to evolutionary
change, selection among individuals at other levels (species, genes)
can lead to evolutionary change. This will occur as long as entities
have heritable traits that are transmitted to offspring. Thus, evolution
occurs at multiple levels of the hierarchy of life.
Another concept on evolution is that differences among populations

may also reflect changes in response to the environment. This does not
reflect genetic differentiation however, if these responses are
constantly retained, they may be transmitted to the next generation.
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Thus, these nongenetic differences may lead to selective, divergent

pressures on traits that are genetically determined. This promotes
evolutionary divergence among populations. One example of this
concerns behavior, which is a response to the environment. Learned
behaviors that are transmitted from one generation to the next, which
are often called culture or traditions, can occur in animals as well as
humans. These behavioral differences would not reflect differences at
the genetic level, but they might set the stage for genetic divergence in
traits relating to these behaviors. For instance, chimpanzees that use
certain tools more than others may evolve into animals that are suited
to the use of these tools, thereby supporting the underlying behavioral
pattern.
Evolution, Humans, and Society
Evolution has important implications for us in many ways. Humans

have used the principles of evolution to alter species to serve their
purposes. Conversely, wild species are responding to environmental
changes caused by humans. They may adapt to our efforts to control
them and responde to new opportunities. Thus, the knowledge of
evolution is important for our knowledge of artificial selection and to
fight our evolutionary enemies. There are diverse areas where
evolution is relevant to society. These include criminal forensics and
medicine. They also include important pursuits such as the creation of
novel molecules in laboratories.
Beyond a focus that is purely utilitarian, an understanding of evolution

can tell us about ourselves. Through evolutionary biology, we can
understand where we came from, where we might be heading to, and it
may even shed light on what it means to be human.
Glossary
Heterozygosity: refers to two different alleles in a single gene locus
Homologous: two structures that may seem alike, or look alike
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Mechanisms of Evolution
What is the Evidence for Evolution?
Genetic Variation, Gene Flow, and New Species
Population Genetics
Population Genetics: A Concise Guide
Misconceptions About Evolution
References
Ferrell, V. (2001). Evolution Handbook. Altmont: Evolution Facts,
Inc.
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Ecology
Ecosystems, and their ecology, are essential matters of study as they

are pertinent to understanding life on earth. Ecology is a broad and
diverse field of study that concerns itself with the relationship between
organisms and their environment, as well as the relationships between
one environment and another. In this module, we will discuss the
principles of ecology in order to gain an understanding of how systems
work to keep and maintain the balance in the world today.
History of the Ecosystem Concept

One of the basic distinctions between autecology and synecology is
that autecology is considered the ecology of the individual organism
and populations. Autecology is mostly concerned with the biological
organisms themselves. Synecology, on the other hand, concerns itself
with the ecology of relationships among organisms and populations.
This is mostly concerned with the communication of material,
information, and energy of the entire system of components. In order
to study an ecosystem, one must have knowledge of the individual
parts. Thus, it is dependent on the fieldwork and experiments grounded
in autecology, but the focus is much more on how these parts interact
and relate to, and influence one another including the physical
environmental resources on which life depends. Therefore, ecosystem
ecology is the implementation of synecology.
The environment’s systems concepts have long played a role in the

development of ecology as a discipline, but these came to a head in the
early 20th century. During this period, two dominant and competing
ecological paradigms were the organismic and the individualistic
views. The organismic approach held that ecosystems and
communities were discernible objects that had an inherent and
organized complexity resulting in a cybernetic and self-governing
system, which is akin to the ways through which an organism regulates
itself.
On the other hand, the individualistic approach held that communities

had observer dependent boundaries and internal development was
stochastic and individual. In this paradigm, the internal relations were
synergistic, but not cybernetic since the individual parts functioned
independently. The organismic paradigm grew out of the
Ecology 1
understanding of whole systems, such as lakes and oceans, and also

from the discussions involving how communities changed over time
during the recession. These ideas were influenced by philosophers
during the time, such as Jan Smuts. There were both holists and
reductionists in this regard. The dialogue between them affected the
main currents of ecological thought during this period. It was, in part,
resolved by the introduction of the concept of ‘ecosystem,’ which is
aboth systemic and physical in nature.
The term ecosystem arose from this dialogue. It was first used by
Arthur Tansely and 1935, in a paper he published in the journal
Ecology. Tansley himself brought a systems perspective. The
underpinnings of the ecosystem have now become established.
However, the introduction of the term was theoretical, lacking
guidance as to how it might be useful as a field of study. A clear
application of the ecosystem concept was Lindeman’s study of Cedar
Bog Lake in Wisconsin. In addition to constructing the food cycle of
the aquatic system, Lindeman developed a metric, which is now called
the Lindeman efficiency. This metric was used to assess the efficiency
of energy movement from one trophic level to the next based on the
ecological feeding relations.
Defining an Ecosystem
2
As a unit of study, an ecosystem must be a bounded system. It can

range in scale from a puddle, to a lake, to a watershed, to a biome. The
scale of the ecosystem is defined more by the functioning of the
system rather than a checklist of constituent parts. The scale of the
analysis should also be determined by the problem being addressed.
Although individuals perish over time and even populations cannot
live indefinitely, every ecosystem contains the ecological community
necessary to sustain life. This includes the producers, the consumers,
the decomposers, and the physical environment for oikos. It is this
feature of the ecosystem that makes them the basic unit for sustaining
life over the long-term. The two main features of the ecosystem, which
are energy flow and nutrient biogeochemical cycling, comprise the
major areas of ecosystem ecology research.
Energy Flow in Ecosystems

The recognition that an ecosystem is an open system is the starting
point of its thermodynamic assessment. The ecosystem receives
energy and matter input from outside its border and transfers output
back to this environment. Thus, every ecosystem must have a
boundary and must be embedded in an environment that provides low
entropy energy input and can receive high entroy energy output. In
addition to the external sources of energy, there is another internal
environment with which organisms interact.
Patten proposed that there are two environments. One is external and
mostly unknowable (other than the input-output interactions) and the
second is internal and measurable (i.e. external to the specific
organismal component within system boundary).
Energy flow in the ecosystem begins with the capture of solar

radiation by photosynthetic processes in primary producers. Note,
however, that there are also chemoautotrophs that are able to capture
energy even without light. However, these chemoautotrophs contribute
negligible energy flux to the overall energy balance of the global
ecology.
Energy + 6CO2 + 6H2O C6H12O6 + 6O2
The accumulated organic matter, which starts out as sugars, then

combine with other elements to produce more complex molecules.
This represents the gross primary production in the system, some of
which is used for the growth and respiration of the primary producer.
Ecology 3
The remaining energy, or net primary production, is available for the

rest of the ecosystem consumers, including decomposers. Secondary
production refers to the energetic availability of heterotrophic
organisms, which accounts for the energy uptake by heterotrophs, and
the energy used for their maintenance. Primary producers support the
overall ecosystem production. Additionally, ecosystem respiration
includes the metabolic activity of all the ecosystem biota. In this
manner, plants provide the essential base for all food webs.
The movement of energy goes through a network of dependencies,

which is known as the food web. In a simplified food chain, the
trophic concept is used to assess the distance away from the original
energy importation. However, in reality, the multiple feeding pathways
found in ecological food webs make discrete trophic levels a
convenient, yet inaccurate, simplification. Elton found that the number
of organisms decreases as one moves up from the food chain, from
primary producers to herbivores, carnivores, and the top carnivores.
Thus, Elton proposed a pyramid of numbers. One can control the
variation of an individual’s body size by controlling for the biomass at
each trophic level, resulting in a pyramid of biomass.
4
The trophic pyramid is satisfying view of interactions since, according

to the second law of energy, energy must be lost at each
transformational step. In addition to this, energy is used at each trophic
level for the maintenance at that level. Under this paradigm, the
trophic levels cap out at five or six level. Fractional trophic levels have
been employed to account for organisms that feed at each different
trophic levels. However, these do not account for the role of detritus
and decomposition, which extends the feeding pathways to higher
numbers.
Energy sources flowing through the ecosystem are necessary to

maintain all development and growth activities. Organisms follow a
linear life history pattern and while the timelines vary from species to
species, early stage energy availability is generally used for growth,
what later energy surplus is used for reproduction or maintenance. A
similar pattern is observed in ecosystem growth and development. The
biomass and physical structure of the ecosystem is buit by net primary
production. The additional photosynthetic material allows for the input
of energy until saturation is reached at about 80% of the available solar
radiation. At this point, the overall growth of the ecosystem begins to
level off because although gross primary production is high, the
overall system supports more and more nonphotosynthetic organisms.
When the average gross production is utilized to support and maintain
Ecology 5
the existing structure, net production is zero and the system has
reached a steady state regarding the growth of biomass. However, the
ecosystem continues to grow in terms of information capacity and
network organization. In addition to being in a dynamic steady state, it
does not persist indefinitely because disturbances occur which sets the
system to a previous successive state. In this manner, the disturbances
allow the ecosystem to develop along a different path.
Biogeochemical Cycles
Understanding how chemical elements are necessary for life is another
major focus of ecosystem ecology. The biosphere actively interacts
with the three abiotic spheres (hydrosphere, atmosphere, and
lithosphere) to provide the available concentration of each chemical
element for life. This interaction has a significant impact on the
relative distribution of these elements. The products of photosynthesis,
which are simple sugars, are the bases for organic matter. Thus,
oxygen, hydrogen, and carbon dominate the composition of life.
Oxygen is available in the lithosphere and hydrogen in the
hydrosphere. However, carbon is quite scarce in the environment. A
hallmark of life is the disproportionate amount of carbon in the
biomass. There are about 20 elements used regularly in living
organisms, of which 9 are called macronutrients and are major
components of organic matter (hydrogen, oxygen, carbon, nitrogen,
calcium, potassium, silicon, magnesium, and phosphorous). Some of
these elements are easily available from the abiotic environment, in
which case conserving them through cycling is not important.
However, those that are scarce, such as phosphorous and nitrogen,
must be used many times before they are released from the system.
These biogeochemical cycles provide the foundation to understand
how human modification leads to eutriphica (N and P cycles) and
global climate change (C cycles). Therefore, much effort has been
made to study and understand these cycles, especially that of carbon,
nitrogen, and phosphorous.
Fundamental Laws in Ecology

There are, tentatively, 8 laws of ecology. However, it is pertinent to
split them into 10 because of the intricacies of each. Here, the 10 laws
of ecology will be presented.
6
1. All ecosystems are open systems embedded in an environment

from which they receive energy (matter) input and discharge
energy (matter) output.
-This first law is a prerequisite to ecological processes. If

ecosystems could be isolated, then they would be at
thermodynamic equilibrium without life and without gradients.
The first law is rooted in Prigogine’s law of thermodynamics.
The openness explains why systems can be maintained far
from thermodynamic equilibrium without violating the second
law of thermodynamics.
2. Ecosystems have many levels of organization and operate

hierarchically.
-The law is based on differences in scale of interactions. The

distance between components becomes essential because it
takes time for events and signals to propagate. Ecological
complexity makes it necessary to distinguish between different
levels and with different local interactions.
3. Thermodynamically, carbon-based life has a viability domain

determined to be between 250 and 250 K.
- It is within the temperature range of 250 to 350 K that there is

a good balance between the opposing ordering and disordering
processes: decomposition of organic matter and building of
biochemically important compounds. The process rates are too slow
at lower temperatures. At higher temperatures, the enzymes that
catalyze the processes are destroyed. At increasing temperatures, as
well, the order creating processes increase, but the cost of
maintaining the structure in the face of disordering processes also
increases.
4. Mass, including biomass, and energy are conserved.
- This principle is used principally in ecological modeling.
5. The carbon based life on earth has a characteristic basic

biochemistry which all organisms share.
-It implies that many similar biochemical compounds can be found

in all living things. All living things have largely the same
Ecology 7
composition, which can be represented using around 25 elements.

This principle also allows one to identify stoichiometric chemistry.
6. No ecological identity exists in isolation but is connected to

others.
-The theoretical minimum unit for any ecosystem is two

populations. One population fixes energy and the other decomposes
and cycles waste. In reality, however, ecosystems are composed of
complex interactions at all levels. These interactions provide
environmental niche in which each component acts. The network
also has a synergistic effect on its components. The ecosystem is
more than the sum of its parts.
7. All ecosystem processes are irreversible (this is the most useful

way to express the second law of thermodynamics).
-Living organisms need energy to maintain, grow, and develop. This

energy is as heat to the environment, and cannot be recovered again
as usable energy. Thus, evolution can also be understood in the
context of this principle that is rooted in the second law of
thermodynamics. Evolution is a stepwise development to based on
previously achieved solutions to survive in a dynamic and changing
world. Due to the genetic and structural encapsulations of these
solutions, evolution has produced more and more complex
solutions.
8. Biological processes used captured energy (input) to move further

from thermodynamic equilibrium and maintain a state of low
entropy and high energy relative to its surrounding and to
thermodynamic equilibrium.
-This principle is another way of showing that ecosystems grow and

expand. It has been shown that eco exergy of an ecosystem
corresponds to the amount of energy that is needed to break down
the system.
9. After the initial intake of energy across a boundary, ecosystem

growth and development is possible by 1) an increase of physical
structure (biomass); 2) an increase of the network (more cycling); or
3) an increase of information embodies in the system.
-All three of these growth and development forms imply that the
system is moving away from thermodynamic equilibrium and all
8
three are associated with an increase of 1) the eco exergy stored in

the ecosystem, 2) the energy flow in the ecosystem (power), and 3)
the ascendency. When cycling increases, the space-time
differentiation, the energy use efficiency, and the eco exergy storage
capacity all increase. When information increases, the animal gets
bigger, the feedback control becomes more effective, which implies
that specific respiration decreases.
10. An ecosystem receiving solar radiation will attempt to maximize

eco exergy storage or maximize power such that if more than one
possibility is offered, then in the long run the one which moves
energy furthest from thermodynamic equilibrium will be selected.
-The eco exergy storage and energy flow increase during all three
growth and development forms. When an ecosystem evolves, it can
apply all three forms in a continuous Darwinian selection process.
The nested space-time differentiation in organisms optimizes the
thermodynamic efficiency as expressed in this law, because it
allows the organism to simultaneously exploit equilibrium and non-
equilibrium energy transfer with minimum dissipation.
Population Coherence
In evolutionary biology, cost and benefit are measured in terms of
fitness. While mutation and natural selection represent the main forces
of evolutionary dynamics, cooperation is a fundamental principle that
is required for every level of biological organization. For instance,
individual cells rely on cooperation among their components.
Multicellular organisms exist because their cells exhibit cooperation.
Social insects, such as bees, are masters of cooperation. Whenever
evolution constructs something new, such as human language or
multicellularity, cooperation is needed. Thus, evolutionary
construction is based on cooperation. There are five rules for
cooperation.
1. Kin Selection
-Kin selection occurs when cooperation favors those from the

same family lineage. Kin selection is also more likely to work
in small groups, rather than large groups, unless highly inbred.
2. Direct Reciprocity
Ecology 9
- All strategies of direct reciprocity can lead to evolution of

cooperation if the fundamental inequality is fulfilled.
3. Indirect reciprocity
-Whereas direct reciprocity indicates that species will do for

others as others will do for them, indirect reciprocity suggests that
what one species does for another, then the other will do for others as
well.
4. Graph selection
-The traditional evolutionary game dynamics suggests that

populations are well-mixed. This means that interactions between any
two individuals in a population is equally likely to happen. More
realistically, however, the interactions between individuals are
governed by spatial effects or social networks. Games, that are
presented on graphs, grew out of the tradition of evolutionary game
theory and spatial models in population genetics.
5. Group Selection
-Group selection is a powerful mechanism that promotes

cooperation. It only occurs, however, when all its basic requirements
are fulfilled in a particular situation.
Predator-Prey Interactions
A widespread population process, predation has evolved many times.
It can affect the distribution, abundance, and dynamics of species in
ecoystems. Predator-prey interactions have an inherent tendency to
fluctuate and show oscillary behavior. If predators are initially rare,
then the size of the prey population can increase. As prey population
increases, the predator population also begins to increase, which in
turn leads to a decrease in prey populations. As prey becomes scarce,
they the numbers of predators also decreases, and the cycle stars again.
Behavior and Patch Dynamics
Predators do not automatically respond to changes in prey density, nor

do they immediately convert prey to new predators. It takes time to
find, subdue, and consume prey. These behaviors require the
investment of time and energetic resources, and the foraging activities
10
of predators for prey have important consequences for the population

dynamics at a variety of different temporal and spatial scales.
For prey that are distributed in patches, patterns of distribution of

parasitism by insect parasitoids have been observed. The proportion of
hosts that have been parasitized can be a positive function, a negative
function, or independent of host density.
Intraspecific Competition
Individuals of the same species have very similar requirements for
their survival, growth, and reproduction. However, their combined
demand for resources may exceed the available supply. The
individuals then compete for the resource. Thus, some individuals
become deprived of resources.
In many cases, competing individuals do not interact with each other

directly. Instead, individuals respond to the level of resource, which
has been depleted by the presence of other individuals. For instance,
grasshopers compete with one another for a plant. In such cases,
competition may be described as exploitation, in that each individual is
affected by the amont of resource that remains after that resource has
been exploited by others. Exploitation can occur if the resource that is
needed is of limited supply.
In many other cases, competition takes the form of interference. Here,

individuals interact directly with each other. Thus, one individual can
actually prevent another individual from accessing a resource. For
instance, this can be seen among animals who defend their own
territories, and among the sessile animals and plants that live on rocky
shores. Thus, interference competition may occur for a resource of real
value, such as space. In this case, interference is accompanied by a
degree of exploitation, or for a surrogate resource (territory, ownership
of a harem), which is only valuable because of the access it provides to
real resource (food, females). With exploitation, the intensity of
competition is closely linked to the level of resource present and the
level required. On the other hand, with interference, intensity might be
high even when the level of the real resource is not limiting.
Another case is of one-sided competition. Whether they compete

through exploitation or interference, individuals within a species have
Ecology 11
many fundamental features in common, using the same resources and

reacting in a similar way to similar conditions. Nonetheless,
intraspecific competition may be one-sided. For instance, a plant may
shade another plant, causing it to die. Hence, the ultimate effect of
competition is far from being the same for every individual. Weak
competitors may make only small contributions to the next generation,
or no contribution at all.
Species Interactions
Individuals from different species can compete with each other. There
are two general points when considering interspecies competition.
First, careful, separate, ecological attention must be paid to both the
ecological and the evolutionary effects of interspecific competition.
The ecological effects are, broadly, that species may be eliminated
from a habitat by competition from individuals of other species. Or, if
competing species coexist, that at least one individual from the species
undergoes deprivation. The evolutionary effects appear to be that
species differ more from one another that they would otherwise do.
Thus, they compete less.
The second point is that there are important and profound difficulties
in invoking competition as an explanation for observed patterns, and
especially invoking it as an evolutionary explanation.
There are two types of interspecific competition: symmetric and

assymetric. Asymmetric competition occurs when the effects of the
competition are not the same for both species. On a broad front, it
shows that highly asymmetric cases of interspecific competition
gradually outnumber symmetric cases. The fundamental point,
however, is that there is a continuum linking the perfectly competitive
cases to strongly asymmetric ones. Asymmtric competition results
from the differential ability of species to occupy higher positions in the
competitive hierarchy. In plants, for instance, this may result in height
differences, when one species is able to gain access to more light
12
compared to another. Asymmetric competition is also more likely

when the body sizes of species differ greatly.
Similary, the competition for one resource may influence the

competition for another resource. Examples are found among rooted
plants. If one species invades the canopy of another and deprives it of
light, the suppressed species will suffer directly from the decreased
light energy available. Therefore, they will also be less able to exploit
the water and nutrients in the soil. This, in turn, will reduce the rate at
which leaves and shoots grow. Therefore, when plant species compete,
repercussions flow backwards and forwards between roots and shoots.
The niche of a species without competition from other species is its

fundamental niche. On the other hand, the niche of a species in the
presence of competitors is its realized niche. The nature of the realized
niche is determined by the characteristics of the competing species that
are present. This can be summarized in the Competitive Exclusion
Principle, which states: 1) if two competing species coexist in a stable
environment, then they do so as a result of niche differentiation (i.e.
differentiation of their realized niches). If, however, such
differentiation does not occur, then one competing species will
eliminate or exclude the other. Thus, exclusion occurs when the
realized niche for a superior competitor completely fills those parts of
the inferior competitio’s fundamental niche that are provided by the
habitat.
There is also the phenomenon of mutual antagonism. Mutual

antagonism can be seen in beetles, in which adult beetles may
sometimes cannibalize their own species. They also ate beetles from
other species. The important note here is that the beetles ate
Ecology 13
individuals from other species more than they ate their own species.
Thus, a crucial mechanism for the interaction of these competing
species is reciprocal predation, and each species was more affected by
interspecific competition rather than intraspecific competition. Mutual
antagonism is strongest when the number of one species is greater than
the other.
The Nature of Predation

Predation is the consumption of one organism (prey) by another
organism (predator). In this relationship, the prey is alive when the
predator first attacks it. Thus, detrivory, the consumption of dead
matter, is excluded from the predator-prey relationship. Nevertheless,
the prey-predator relationship encompasses a wide variety of
relationships and interactions, with a wide variety of predators.
There are two main ways through which predators can be classified.
Neither one of these ways is perfect, but they are useful. The most
obvious classification is taxonomic. That is, carnivores consume
animals, herbivores consume plants and omnivores consume both.
An alternative way of classification is the functional classification.

Here, there are four types of predators. There are true predators,
parasitoids, grazers, and parasites (which are divisible into
macroparasites and microparasites).
True predators kill their prey immediately after attacking them. During
the lifetime of the true predator, it consumes several of many different
prey organisms, often consuming the prey in its entirety. The most
obvious true predators are lions, tigers, etc. However, rodents, ants,
and even plankton-consuming whales are also true predators.
Grazers, on the other hand, attack a large number of prey during their
lifetime. However, they do not consume their prey in its entirety, but
only parts of it. Their effect on the prey organism is rarely lethal in the
short-term, although it is typically harmful. The most obvious grazers
are sheep, cattle, and cows. However, flies that bite vertebrate prey,
and leeches that suck their blood, are also grazers. Thus, grazers are
not limited to herbivores.
Parasites, like grazers, consume parts of their prey. Like grazers, they
are harmful, but they are not lethal in the short-term. Unlike grazers,
however, parasites only attack one or very few individuals during their
14
lifetime. Thus, there is an intimate relationship between parasites and

their hosts that is not seen in true predators and grazers. Measles virus,
tapeworms, liver flukes, and tuberculosis bacterium are all examples
of parasites. There are also many fungi, plants, and microorganisms
that act as parasites on plants, called plant pathogens. In addition,
many herbivores can be thought of as parasites. For instance, aphids
extract sap from plants with which they enter into intimate contact.
Even caterpillars can be thought of as parasites, as they often rely on
just one plant.
Parasitoids are a group of insects that belong mainly to the order

Hymenoptera, but it also includes individuals from Diptera. These
individuals are free-living as adults. However, they lay their eggs in,
on, or near other insects. The larval parasitoid develops either inside
its host or on its host. At first, it does little harm, but it eventually
consumes the host and therefore kills it. Thus, an adult parasitoid
emerges from a host. Often, just one parasitoid develops from one
host, but there are instances wherein several parasitoids develop from
one host. The rate of predation of parasitoid is dependent on the rate at
which the adult females lay eggs. Each egg, therefore, is an attack on
the host, even though it is the larva that emerges from the egg that
does the killing. Parasitoids seem to be of very little importance.
However, they account for 10% of the world’s species. Parasitoids
maya also be attacked by other parasitoids.
Human-Caused Changes on the Earth’s Ecosystem

Humans have effects on the earth’s ecosystems. Humans transform
land surfaces, add or remove species, and alter the biogeochemical
cycles. There are human activities that have direct impacts on the
earth’s ecosystem, such as land use changes and management. Other
activities, however, are indirect, such as atmospheric changes and
changes in hydrology. At least some of these anthropogenic activities
affect all the ecosystems on earth.
The most substantial and direct effect of human activities that alter
ecosystems is the conversion of land for production of food, fiber, and
other goods used by humans. About 50% of the ice-free land on earth
has been altered by human activities. Agricultural fields and urban
areas cover 10-15% of land areas, whereas pastures cover 6-8% of the
land. Even more land is used for grazing and forestry. All portions of
the earth, except the most extreme environments, can experience
human impact.
Ecology 15
Marine and freshwater ecosystems are also altered by human activities.

For instance, half of all the world’s accessible run-offs are used by
humans. In addition to this, humans use about 8% of the primary
production of the oceas. Commercial fishing reduces the size and
abundance of target species. It also alters the population characteristics
of species that are incidentally caught in the fishery. About 22% of all
marine fisheries are over-explooted or already depleted. Many coastal
areas are also being exploited. Nutrient enrichment of these areas has
led to the increased production of algae and created anaerobic
conditions in which fish cannot survive. This nutrient enrichment is
due largely to the transport of agricultural fertilizers and from human
sewage and livestock sewage.
Land use change causes a loss of habitat. It is the primary driving force
for the extinction of species and the loss of biological diversity. There
is also a time lag between ecosystem changes and species loss, which
makes it likely that species will continue to be driven to extinction
even when land use change have stabilized. Homogeneity of the
earth’s biota is also being caused by the transport of species around the
world. The frequency of these invasions is increasing, in large part due
to the globalization of the world’s economy. International commerce
breaks down biogeographic barriers, through both purposeful trade of
live organisms and inadvertent introductions. The former selects
species which are more likely to grow and reproduce in the new
environment. Many of these biological invasions are irreversible
because it is too expensive and difficult to remove species that have
invaded. Some of these species incur large economic losses or cause
damages to human health. Others alter to balance of ecosystems,
leading to further losses of species.
Human activities have also altered biogeochemical cycles in many

ways. Usage of fossil fuels and the intensification and expansion or
agriculture have altered the carbon cycles, nitrogen cycles, and sulfur
cycles on a global scale. These changes in biogeochemical cycles alter
ecosystems and they also influence unmanaged ecosystems through
changes in lateral fluxes of nutrients and other materials through
surface waters and the atmosphere. Land use changes, which include
the intensive use of fertilizers and deforestations, have increased the
concentration of atmospheric gases that influence the climate. Land
transformations cause runoff and erosion of sediments that lead to
significant changes in lakes, rivers, and oceans.
16
Glossary
Autecology: the study of organisms or a particular species
Exergy: the available energy that can be used
Synecology: the study of whole communities of plants or animals
Mutual antagonism: occurs when interspecific competition has effects that

outweigh those of intraspecific competition
Thermodynamic equilibrium: the state at which an object with higher

temperatures transfers heat to an object with lower temperature, thereby
reaching a temperature equilibrium.

Energy Flow in Ecosystems
Nutrient Cycling
Ecosystem Ecology
Principles of Terrestrial Ecosystem Ecology
Biodiversity, Ecosystems, and Ecosystems Services
Human Domination of Earth's Ecosystems
References
Gotelli, N. J. (1995). A primer of
ecology. Sinauer Associates
Incorporated.
Ecology 17
Introduction to Genetic Engineering
Genetic engineering has been widely used to manipulate protein

expression in plants and animals. The applications of genetic
engineering are wide and the potential of this technology is greatly
beneficial to humans. Genetic engineering has been used in the
propagation of insulin, in vaccines, in crops, and for many other
purposes. For this reason, it is important to understand the basics of
genetic engineering because it will become more prominent in the
years to come.
Defining Genetic Engineering

The availability of techniques and methods is where scientific progress
rests on. Over the past 35 years, advancements in science have been
demonstrated by genetic engineering. The field of genetic engineering
has grown so rapidly that in many laboratories all over the world, the
isolation of a DNA fragments from the genome of an organism is
widely practiced. The technology of genetic engineering is now widely
used in forensics, paternity disputes, medical diagnoses, genome
sequencing and mapping, and the biotechnology industry. Gene
manipulation is striking in that it can easily be done in a wide range of
laboratories and is accessible to many scientists.
The term genetic engineering is often thought to rather trivial or

emotive, yet it is probably the label that most people would recognize.
There are several other terms that can be used to describe the
technology, such as gene manipulation, gene cloning, recombinant
DNA technology, genetic modification and new genetics.
Although there are many complex and diverse techniques involved in

genetic enginerring, the basic principles are simple. The premise on
which the technology rests is that genetic information, encoded by
DNA and arranged in the form of genes, is a resource that can be
manipulated in various ways to achieve certain goals in both applied
and pure science. There are many ways in which genetic engineering
can be of value, including the following:
Basic research on the structure and function of genes
Production of useful proteins by novel methods
Generation of transgenic plants and animals
Introduction to Genetic Engineering 1

Medical diagnoses and treatment
Genome analysis by DNA sequencing
The mainstay of genetic manipulation is the ability to isolate a

single DNA sequence from the genome. This is the essence of gene
cloning and can be considered as a series of four steps. Successful
completion of these steps provides the genetic engineer with a
specific DNA sequence, which may then be used for a variety of
purposes. Gene cloning can be thought of as molecular agriculture,
enabling the production of large amouns of a particular DNA
sequence. The ability to isolate a particular gene sequence is a
major aspect of gene manipulation. The four steps to genetic
engineering are:
Generation of DNA fragments
Joining to a vector or carrier molecule
Introduction into a host cell for amplification
Selection of required sequence
One aspect of new genetics is that there are concerns being raised
about the applications of the technology. The term genethics has been
coined to mean the ethical problems that exist in modern genetics.
These concerns are also likely to increase in number and complexity as
genetic engineering ensues. The use of transgenic plants, gene therapy,
investigation of the human genome, and many other topics are of
concern. These concerns are not just concerns for the scientists, but for
the population as a whole. Recent developments, for instance, in
genetically modified foods have raised public backlash against the
technology. Additional developments in the cloning of organisms, and
in areas such as in vitro fertilization and xenotransplantation, raise
further questions.
The Process of Genetic Engineering

Many of the procedures used in genetic engineering can be carried
out in a basic laboratory. However, large-scale applications, such
as production-scale biotechnology, require major facilities and
investment. The requirements for genetic engeering can be
summarized as follows: general laboratory facilities, cell culture
and containment, and processing and analysis.
2
General facilities include aspects such as laboratory layout and

furnishings, as well as the provision of essential services such as
water, electrical power, gas, compressed air, vacuum lines,
drainage, and so on.
Cell culture and containment are facilities that are important for
growing cell lines and organisms required for research. Most labs
have facilities for growing bacterial cells, with the need for
equipment such as autoclaves, incubators (static and rotary),
centrifuges, and protective cabinets in which manipulation can be
carried out. Mammalian cell culture requires more sophisticated
facilities. Plant and algal cultures require the use of lighting in
culture cabinets. In many cases, some form of physical
containment is required to prevent the escape of organisms during
manipulation. The overall type of containment depends on the
vector and host being used. Biological containment necessitates
that the host does not survive outside of containment.
The overall containment requirements will be specified by national

bodies that regulate gene manipulation, and these will apply to
both bacterial and mammalian culture facilities. Thus, cloning E.
coli may require simple facilities, whereas cloning using
mammalian cells may require more stringent safety requirements.
For the processing and analysis of cells and cellular components,

such as DNA, there are a variety of equipment that needs to be
used.

Isolation of DNA and RNA

Every gene manipulation experiment requires a source of nucleic
acids, either in the form of RNA or DNA. It is therefore important
that reliable methods for isolating these genetic components be
available for genetic engineering. There are three basic requiments:
1) opening the cells in the sample to expose the nucleic acid for
further processing; 2) separation of the nucleic acid from other
cellular components; and 3) recovery of the nucleic acid in purified
form. Several techniques may be used, ranging from simple to
complex.
The first step in the isolation protocol is the disruption fo the

starting material. The starting material may be viral, bacterial,
plant, or animal. The method used to disrupt the starting material
should be as gentle as possible, preferably involving the enzymatic
degradation of the cell wall and the detergent lysis of cell
membranes. If rougher methods are used, the danger of shearing
large DNA molecules will arise.
Following cell disruption, most of the methods used in DNA and

RNA isolation involve a deproteinization stage. This can be
achieved by one or more extractions using phenol/chloroform or
phenol. Protein molecules partition into the phenol phase and
accumulate at the interface after the emulsification and
centrifugation phases. The nucleic acids remain mostly in the
upper aqueous phase and may be precipitated from the solution by
issuing ethanol or isopropanol.
If DNA preparation is needed, the enzyme ribonuclease (RNase)

can be used to digest the DNA in preparation. If mRNA is needed
for cDNA synthesis, further purification can be performed using
affinity chromatography. This type of chromatography uses the
oligo(dT)-cellulose to bind the poly(A) tails of the eukaryotic
mRNAs. This enables the removal of contaminants, which are
chiefly DNA, rRNA, and tRNA.
The technique of gradient centrifugation is usually used to prepare

the DNA, in particular, plasmid DNA (pDNA). In this technique, a
caesium chloride (CsCl) solution containing the DNA prepraration
is spun at high speeds using an ultracentrifuge. Over a long period,
which takes up to 48 hours, a density gradient is formed and the
pDNA forms a band at one position in the centrifuge ube. The
band may be taken off and the CsCl removed by dialysis, resulting
to a pure preparation of pDNA.
4
Handling and Quantification of Nucleic Acids

During a cloning experiment, it is often necessary to use small
amounts of nucleic aicds. It is obviously impossible to handle these
amounts directly, because they are so small, so most of the
measurements that are done involve the use of aquaeous solutions
of DNA and RNA. The concentration of nucleic acids can be
determined by measuring the absorbance at 260 nm, using a
sprectrophotometer. An A260 of 1.0 is equivalent to a concentration
of 50 g ml-1 for double-stranded DNA or 40 g ml-1 for single
stranded DNA or RNA. If the A280 is determined, ratio indicates if
there are contaminants present, such as residual protein or phenol.
The A260/A280 ratio should be around 1.8 for pure DNA or 2.0 for
pure RNA preparations.
In addition to spectrophotometric methods, the concentration of

DNA may be estimated by monitoring the fluorescence of bound
ethidium bromide. This dye, which is toxic and carcinogenic, binds
between DNA bases (intercalates) and fluoresces orange when
illuminated with ultraviolet light. By comparing the fluorescence
of the samples with that of a series of standards, an estimate of the
concentration of nucleic acids may be obtained. This method can
detect as little is 1-5 ng of DNA and can be used when
spectrophotometric measurements are not possible due to
ultraviotet-absorbing contaminants. When the concentration of the

solution has been determined, it is easy to dispense the liquid with

accuracy to obtain small amounts of nucleic acids.
In a variety of applications, the precipitation of nucleic acids is

essential. The two most commonly used precipitants are
isopropanol and ethanol, with the latter being preferred. When
added to a DNA solution in a ratio, by volume, of 2:1 in the
presence of 0.2 M salt, ethanol causes the nucleic acids to come
out of the solution. After precipitation, nucleic acids can be
recoved through centrifugation, which causes a pellet of nucleic
acid to form at the bottom of the test tude. The pellet can then be
dried and the nucleic acid resuspended in the buffer needed for the
next stage of the experiment.
Labelling of Nucleic Acids

A major problem in genetic engineering, and specifically in DNA
or RNA isolation, is that there is a need to keep track of small
amounts of nucleic acids. This can be done using tracers.
Radioactive tracers have been used extensively in biochemistry

and molecular biology for a long time, and procedures are now
well-established. The most common radioactive isotopes used are
tritium, carbon-14, sulphur-35, and phosphorous-32. Tritium and
carbon-14 are low-energy emitters, with sulphur-35 being medium-
energy emitter, and phosphorous-32 being a high-energy emitter.
Thus, phosphorous-32 is more hazardous than the other radioactive
isotopes and special care must be taken during its use. Due to the
hazards of working with radioactive dyes, alternative methods such
as enzyme-linked labels and fluorescent dyes have also been used.
However, radioactive tracing is still the preferred choice.
Radiolabelling is often used to describe the technique.
One way of tracing RNA and DNA samples is to label the nucleic
acids with a radioactive molecule (usually deoxynucleoside
triphosphate, labelled with tritium or phosphorous-32). This is
done so that portions of each reaction may be counted in a
scintillation counter to determine the amount of nucleic acid
present. This is usually done using calculations that involve taking
into account the radioactivity present in the sample.
Radiolabelling may also be used in the production of highly

reactive nucleic acids that are used for hybridization experiments.
These molecules are known as radioactive probes and have a large
number of uses. The difference between labelling for hybridization
6
and for tracing purposes is that labelling for probes is largely one
of specific activity. That is, the measure of how radioactive the
whole molecule is. For tracing purposes, the activity is not as
specific and high specificity is not needed.
Gel Electrophoresis
To the genetic engineer, the technique of gel electrophoresis is
vital. It represents a way through which nucleic acids may be
visualized directly. The method relies on the fact that nucleic acids
are polyanionic at neutral pH; that is, they carry multiple negative
charges because of the presence of the phosphate groups on the
phosphodiester backbone of nucleic acid strands. Thus, the
molecules will migate towards the positive pole of an electrode
when placed in an electric field. The mobility of the DNA
fragments depends on the fragment length. The technique is carried
out using a gel matrix, which separates the nucleic acid according
to their size.

The type of matrix used for electrophoresis has important for the
degree of separation achieved. This is dependent on the porosity of
the matrix. Two types of gel are commonly used: agarose and
polyacrylamide. Agarose is extracted from seaweed and can be
purchased as a dry powder that is then melted in buffer at an
appropriate concentration, and the agarose sets to form a gel.
Agarose gel electrophoresis is usually run using the submerged
agarose gel electrophoresis technique (SAGE). Polyacrylamid gel
electrophoresis (PAGE) is sometimes used to separate small
nucleic acid molecules, in applications such as DNA sequencing.
The pore size of polyacrylamide gel is small.
Electrophoresis is carried out by placing the nucleic acids in the

gel and applying a potential difference across it. The potential
difference is maintained until a marker dye reaches the end of the
gel. The marker dye is usually bromophenol blue. The nucleic
acids are usually stained using ethidium bromide and visualized
under ultraviolet light. These nucleic acids show up as bands,
which can then be photographed. The data from gel electrophoresis
can be used to estimate the size of the fragments through
calibration. This technique is particularly useful in restriction
mapping.
DNA Sequencing
A central part of modern molecular biology is the ability to
determine the sequence of genes.
By definition, the determination of the sequence of a fragment of

DNA requires that bases are identified in a sequential manner. This
also enables the identification of processive bases. There are three
main requirements for this to be achieved:
DNA fragments need to be prepared in a form suitable for

sequencing
The technique used must achieve the aim of presenting each

base in turn in a form suitable for identification
The detection method must permit rapid and accurate

identification of the bases
The preparation and generation of DNA fragments in fairly simple.

The fragments are often cloned sequences that are presented for
sequencing in a suitable vector. Much more difficult, however, is
8
the identification of the position of the fragment within the

genome.
The sequencing protocol is more of a technical endeavor rather

than an experimental one. There are several variants of the
procedure, but the most widely used techniques are based on the
enzymatic method. Whatever the method, the desired result is to
generate a series of overlapping fragments that terminate at
different bases and differ in length by one nucleotide. This is
known as a set of nested fragments. Assuming that the technique
has generated a set of nested fragments, the detection step is the
final stage of the sequencing protocol. Usually, this involves the
separation of the fragments using a polyacrylamide gel.
There are two main methods for sequencing DNA. The first
method, developed by Allan Maxam and Walter Gilbert, uses
chemicals that cleave the DNA at certain positions, generating a s
set of fragments that differ by one nucleotide. The same result is

also generated in the same way by the second method, developed

by Fred Sanger and Alan Coulson. This involves the enzymatic
synthesis of DNA strands that terminate in a modified nucleotide.
The analysis of fragments is the same for both methods, which
involves gel electrophoresis and autoradiography. The enzymatic
method has now completely replaced the chemical method.
In the Sanger-Coulson method, enzymes are used to sequence

DNA. A copy of the DNA to be sequenced as made by the Klenow
fragment of RNA polymerase. The template for this reaction is a
single-stranded DNA. A primer must be used to provide the 3’
terminus for DNA polymerase to begin synthesizing the copy. The
production of nested fragments is achieved by the incorporation of
a modified dNTP in each reaction. These dNTPs lack a hydroxyl
group at the 3’ position of deoxyribose, which is necessary for
chain elongation to proceed. Such modified dNTPs are known as
dideoxynucleoside triphosphates (ddNTPs). The four ddNTPs (A,
G, T, and C forms) are included in a series of four reactions, each
of which contains the normal dNTPs. The concentration of the
dideoxy form is such that it will be incorporated into the growing
DNA strand infrequently. Each reaction thus produces a set of
fragments terminated at a specific nucleotide, and the four
reactions thenn provide nested fragments. The DNA chain is then
labelled using a radioactive dNTP in the reaction mixture.
Electrophoresis and Reading of Sequences

The separation of DNA fragments created during sequencing
reactions is achieved by PAGE. A single gel system is usually used
for standard laboratory procedures. The gel usually contains 6-20%
polyacrylamide and 7 M urea. The latter acts as a denaturing agent
to reduce the effects of DNA secondary structure. This is important
because fragments are being separated that differ in length by only
one nucleotide. The gels are very tin (0.5 mm or less) and are run
at high-power settings. These settings cause them to heat up to 60-
70 C. This also helps to maintain the conditions necessary for
denaturing. After the gel has been run, it is removed from the
apparatus and may be dried onto a paper sheet to facilitate
handling. It is then exposed to x-ray film. The emissions from the
radioactive label sensitize the silver grains, which turn black when
the film is developed and fixed. The result is an autoradiograph.
The sequence is read from the smallest sequence upwards. Using
this method, sequences of up to several hundred bases may be read
from single gels. The sequence data are then compiled and studied
using a computer. The computer can perform analyses such as
10
translation into amino acid sequences and identification of

restriction sites, regions of sequence homology, and other
structural characteristics, such as promoters and control regions.
Recombinant DNA
The production of recombinant DNA cannot be done directly.
Thus, a vector is used. A vector used is often a plasmid, which is a
small, circular piece of DNA found in bacterial cells. First,
plasmids are isolated. Using restriction enzymes, they are cut open
and the new gene or DNA fragment is inserted with the aid of
ligases. Thus, recombinant DNA is formed, which is the DNA
from different organisms joined in a single molecule.
Bacterial plasmid is the vector most commonly used. Plasmids

used in genetic engineering are said to be under relaxed control.
That is, their replication is totally independent of chromosomal
replication. These plasmids may be present in copies of 10-700 per
cell. The most popular plasmid is pUC18. However, bacterial
plasmids cannot accept DNA fragments that are longer than 5000
base pairs. Thus, they are restricted to cloning smaller DNA
fragments.
For lager DNA fragments, specially developed bacteriophage

lambda chromosome can incorporate up to 15-60 kilobases of
DNA fragments. A central 1/3 of its genome is normally not
required for phage infection and therefore can be replaced by
foreign DNA. The chimeric phase DNA can be introduced into the
host cells by infecting them with phages. On the other hand,

cosmids are vectors that combined the features of both plasmids

and bacteriophages. It can accommodate DNA fragments up to 50
kilobase pairs long. Since cosmids have no phage DNA, they
reproduce as plasmids upon introduction into host cells by phage
infection. Yeast artificial chromosome (YAC) is a specially
constructed linear yeast chromosome that can incorporate DNA
strands of up to 1 million base pairs.
DNA Insertion
The simplest methods for the insertion of recombinant DNA into
cells are transformation and transfection. In the context of cloning
E. coli cells, transformation refers to the uptake of plasmid DNA,
and transfection refers to the process of uptake of phage.
In order for transformation of E. coli cells to occur, the host cells

must be made competent. This is achieved by soaking the cells in
an ice-cold solution of calcium chloride. Then, the cells are mixed
with plasmid DNA, incubating on ice for 20-30 minutes. This
enables the DNA to enter into the cells. The transformed cells are
usually then incubated in a nutrient broth at 37 C for 60-90 minutes
12
to enable the plasmids to become established and to allow for the

phenotypic expression of their traits. The cells can then be plated
out onto selective media for propagation of the cells harboding the
plasmid DNA. Transformation is an inefficient process in that only
a small amount of competent cells become transformed. On the
other hand, transfection occurs using the same protocols, except
that plasmids are replaced by phage DNA. Once recombinant DNA
is present, the vector used will propagate, resulting in clones of the
recombinant DNA.
Plant Transformation
Genetic transformation, which can sometimes be hereditary, is a
change in the genome of an organism or a cell brought about by
the uptake of foreign DNA. A wide variety of gene transfer events
comprise transformation. Transformation can be characterized by
the stability of transformation, the subcellular component that has
been transformed, and whether the transferred DNA is integrated
in a stable manner into the host genome.
There are a number of definitions of transformation. Stable

transformation pertains to the stable maintenance of genes inside
the host organism. Transient expression, on the other hand, is when
the foreign DNA can be detected in the organism for the first few
day, and then ceases to be replicated. This type of expression is
typical for non-integrated, chromosomal DNA. Integrative
transformation is when the gene is covalently integrated into the
host cell and the gene is inherited by the offspring. Nuclear
transformation is when the gene is transferred into the nucleus of
the cell and is confirmed by cellular fractionation. Organellar
transformation is a transfer into the plastid or mitochondria f the
cell, as confirmed using cellular fractionation. Lastly, episomal
transformation is when viral genomes are introduced into the host
genome. It is also stable over several generations in most cases.
Whole plants can be regenerated from single events. Plant

transformation is based on two events: 1) successful introduction
of foreign DNA into host cells; and 2) subsequent development of
a complete plant derived from the transformed cells. In vitro
regeneration is the technique of developing plant organs or
plantlets that have been isolated from the mother plant and
cultivated using media in a laboratory. Regeneration occurs via
organogenesis (the initiation of adventitious roots from plant tissue
or cells), or embryogenesis (formation of plants from somatic cells
through a pathway resembling normal embryogenesis from the

zygote. Both of these processes can be initiated either directly

(from merismatic cells) of after the formation of a callus (mass of
undiffertiated parenchymal cells introduced by wounding or
hormone treatment).
There is a large variety of gene delivery methods that scientists use

in order to transform plants. These methods range from being
simple, to complex, and to experimental.
Agrobacterium is a well-established transformation vector for

many dicots and several monocots. It is also a promising vector for
gymnosperms. In this technique, Ti or Ri-derived plasmic vectors
are used. Another technique is the direct transfer of DNA to
protoplasts, which is also a well-established technique with a wide
host range. The plasma membrane is permealized (made
permeable) by DNA chemical agents or electroporation.
Microprojectile bombardment is a widely used technique for
transforming plant cells by the introduction of DNA via coated
particles.
Micro-injection is an effective gene delivery method allowing the

visual DNA targeting to cell type and intracellular compartment.
Macro-injection is a simple approach that is used to deliver DNA
to floral tissue using a hypodermic needle. Impregnation with
whiskers, is the suspension of plant cells mixed with DNA and
micron-sized whiskers. Laser perforations is composed of transient
expression observed from cells targeted with a laser microbeam in
DNA solution. Impregnation of tissues is the transient and stable
expression from tissue bathed in DNA solution or infiltrated under
vacuum. Floral dip is used for transformation and expression
following the dipping of floral buds in DNA solution. Pollen tube
pathway, on the other hand, is the germ line transformation by
treating pollen or carpels with DNA and the procedure remains
controversial. Lastly, ultrasonication is a stable transformation
using explants in the presence of DNA.
The application of transformed plants is one of the hallmarks of

biotechnology and genetic engineering. The main focus of plant
transformation is to make them herbicide tolerant. In addition,
resistances to antibiotic stresses, such as drought, or improved
nutritional content are being investigated. Another application is
the production of medically valuable proteins or chemicals
(biopharmaceuticals), or the production of edible plants containing
vaccines. Gene stacking became popular in recent years. Gene
14
stacking is the introduction and targeting of several traits in one

species.
Animal Transformation
The field of animal breeding today is influenced by the application
and development of biotechnology. The common goal of all efforts
in this field is genetic progress within a population. Genetic
progress is defined as the improvement of genetic resources and,
ultimately, the phenotype outcome. Genetic progress is influenced
by several factors: the accuracy of the candidates chosen for
breeding; the additive genetic variation within population;
selection intensity (the proportion of the population selected for
further breeding); and the generation interval (the age of breeding).
The first three factord need to be increased in order to increase
genetic progress. On the other hand, the last factor, which is
generational, needs to be decreased.
Techniques that are available for biotechnology vary, but they can
be divided into two groups. The first group includes all
technologies that interfere with reproduction efficiency (e.g.
artificial insemination, embryo transfer (ET), embryo sexing,
multiple ovulation, ova pick-up and cloning, among others. The
second group of application is based on the molecular
determination of genetic variability and the identification of
genetically valuable traits and characteristics. This includes the
identification and characterization of quantitative trait loci (QTL),
as well as the use of molecular markers for improved selection
process. Quantitative traits are phenotypic characteristics that show
a distribution of expression degree within a population (usually
expressed by a normal distribution) and that are based on the
interaction of at least two genes (known as polygenic inheritance).
An example of this is human skin color, which is determined by a
number of genes. A QTL is a DNA sequence that is related to a
certain quantitative trait. Knowledge of loci respoinsible for a
certain quantitative trait and underlying genes can help select
individuals for further breeding, or to start genetic engineering of
the selected trait.
Transgenic animals are animals that carry a specific and deliberate

modification of its genome, which is analogous to the transgenic
plant. To establish a transgenic animal, foreign DNA constructs
need to be introduced into the genome of the animal using
recombinant DNA technology. The DNA construct should be
stable enough that it can be passed on to the next generation.

Heritability of genetic modification can be achieved by creating an

animal that carries the modification of in the genome of its germ
line. Thus, all offspring derived from this animal will be
completely transgenic as they will carry the foreign DNA in their
germ cell lines and somatic cells.
Transgenic animals can be created for a number of applications.

Examples are to gain an understanding of its genetic code and the
functions of genes. They can also be used to study gene control in
organisms and to build genetic disease models. They can improve
the production traits of animals and to produce new animals.
There are a number of ways to create transgenic animals. One of

these is micro-injection, which was discussed above. It is based on
the procedure of injecting foreign DNA into a fertilized zygote.
The construct integrates randomly into the host’s genome.
Subsequently, the zygote continues embryonic development. The
embryo is then transferred to foster mother and develops into a
transgenic animal.
Embryonic stem (ES) cell technology has also been developed,

partly to overcome the low-yield problem of micro-injection. ES
are derived from embryos at an early age in embryonic
development. Pluripotency is the ability of these cells to
differentiate into any of the cell types and tissues found in the adult
organism. This technique allows for gene targeting. In addition,
genes can be introduced, removed or replaced (knock-ins and
knock-outs).
Somatic cell nuclear transfer (SCNT) is the current method of

choice for producing transgenic animals. It is also known as
somatic cell cloning and initially gained importance for the
possibility of cloning animals in theoretically unlimited numbers.
It can also be used to produce transgenic animals, with genetic
manipulation as an added benefit. The insertion of a transgene
construct into a specific, pre-determined DNA site of the host
genome is known as gene targeting. The process of contructing of
the transgene is more complex that random gene insertion, as is the
case when micro-injection is used.
Artificial chromosome transfer is another technique that uses

artificial chromosomes. Artificial chromosomes posses a
centromere, telomere and origins of replication, which are
sequences that are responsible for their stable maintenance within
16
the cell. Artificial chromosomes have the benefit of being able to

carry large fragments of DNA.
Sperm-mediated DNA transfer uses sperm as a vector to deliver

transgene DNA to the oocyte during the process of fertilization.
Viral-vector mediated DNA transfer can accomplish transgenesis

by using virus-derived vectors. These vectors are specifically
based on the retrovirus class of lentiviruses. Genes that are
essential for viral replication are deleted from the viral genome.
The capacity for integration of the viral genome into the host cell is
maintained. Parts of the vector that have been deleted can then be
occupied by the transgene of interest. Viruses that carry the
modified vector are then produced in vitro and subsequently
injected into the perivitelline space of the zygote. This results in
the infection of the zygote and the integration of the viral genome
into the host genome.
Applications for Transgenic Animals

Almost three decades ago, the first transgenic mice were produced.
Since then, a lot of techonologies have been developed for efficient
transgenesis. There are two main interests with regard to the
production of transanimals. The first is to improve intrinsic traits,
such as milk production and disease resistance. The second is the
production of animals that produce novel products, such as
proteins needed for medicine and pharmaceuticals.
Engineering transgenic animals usually focuses on improved meat

production, improved carcass quality, and enhanced milk
production. The main goal for transgenic animal development
concerning milk production are increased milk production higher
nutrient content, or milk containing novel substances. For insatce,
most milk proteins are caseins, and transgenic cattle have extra
copies of casein genes. This results in elevated casein levels in
proteins.
Experiments in cattle ar focused on the myostatin gene, which is a

negative regulator of muscle mass, resulting a high increase in
muscle mass in animals that have modified or deleted myostatin
genes.
Animal pharming is the term given to the use of animals for the
production of pharmaceutical products. The costs for producing
transgenic animals are high, but it is a worthwhile investment for

the pharmaceutical company, which is a multibillion dollar

industry. Since the production of human proteins mostly cannot be
carried out in microorganisms, the production of
biopharmaceuticals in transgenic animal bioreactors is a feasible
alternative. Pharmaceutical proteins and other compounds can be
produced from a variety of body fluids, such as milk, urine, blood,
chicken egg whites, and so on. Nevertheless, milk is the preferred
medium due to its large production volume.
Transgenic animals may also produce humal polyclonal antibodies.

Antibodies are the fastest growing set of new biopharmaceuticals,
which are used for cancer therapy, autoimmune diseases,
transplantations, infections, and immune deficiencies. This
possibility is currently being investigated.
The introduction of genes into organisms may also increase disease

resistance. These genes can target specific areas of the host’s
immune system. Diseases that are being investigated include
bovine spongiform encephalopathy (BSE) and brucellosis.
Aside from those mentioned above, other applications for

biotechnology include the production of vaccines, the diagnosis
and cure of genetic diseases, DNA testing for paternity purposes,
and nutrition physiology. The latter refers to the use of specific
enzyme to modify foods and thus improve the nutrient availability
and uptake by the animal. Prebiotics (substances that simulate
microbial growth) and probiotics (live microorganisms) as
additives in feed can increase nutritional content of food.
Glossary
Autoclaves: used to sterilize equipment
dNTP: nucleoside triphosphate
Radioactive tracers: used to label nucleic acids

Coding Life: The Future of Genetic Engineering
Basics of Recombinant DNA Technology
18
Genetic Engineering Benefits: Applications in Medicine
DNA Cloning
Recombinant DNA Technology and Molecular Cloning
Gene Cloning & DNA Analysis: An Introduction
References
Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P.
V., & Jackson, R. B. (2011). Campbell biology (p. 379). Boston:
Pearson.

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EARTH AND LIFE SCIENCE

INTRODUCTION TO EARTH AND LIFE SCIENCE

Welcome to the Earth and Life Science module. This is your

Origin and Structure of the Earth

Key Characteristics of the Earth’s Structure

Introduction to Earth and Life Science 1

The Subsystems of the Earth

Formation of the Universe and Solar System

Formation of the Sun and the Solar System

How the sun was formed:

1. There was a spinning disk in space.

2. As gas collected in the center of this spinning disk, a

3. Molecules in the protosun collided with each other, which

4. This raised temperatures to 10,000,000 C.

5. The heat and violent clashes between molecules allowed the

How the planets were formed:

Introduction to Earth and Life Science 3

1. In the disk that surrounded the protosun, a process called

2. Small particles crashed together to form larger and larger

3. Since these planetesimals were big enough to have their own

4. In the planetesimals near the sun, the water evaporated and

Formation of the Universe

The formation of the universe is a question that has sparked

The Big Bang Theory

explosion back then still causes the expansion of the universe

The Steady State Theory

Although the Big Bang Theory is the most popular theory to

The Steady State Theory also predicts that the universe is

The Plasma Universe

Individuals who do not subscribe to either the Big Bang Theory

Introduction to Earth and Life Science 5

universe is crisscrossed by electromagnetic fields and electric

The Earth’s Internal Structure

composed of semi-solid, hot material, which flows and softens after

Nuclear reactions: the collision between two nuclei

Radioactive: the ability of the nucleus of an unstable atom to lose

Silicates: a salt whose anion contains both oxygen and silicon.

Fishman, D. (n.d.). The origin of the universe. Retrieved from

USGS. (n.d.). Inside the earth. Retrieved from

Videos and Resources

Introduction to Earth and Life Science 7

Compositional and Mechanical Layers of the Earth

The Big Bang Theory

An Introduction to Modern Cosmology

Theory of the Earth

The Earth's Mantle

Earth Materials and Processes

In the earlier module, we learned about the physical structure of the

Rocks and Minerals

Minerals are defined as “a naturally occurring chemical element or

Each rock is made up of one or more silicate minerals. Each

One obvious consequence of the heat in the earth’s interior is the

While igneous rocks are created from the cooling of magma,

Sedimentary rocks are also classified into three types: clastic,

Examples of sedimentary rocks are: sandstone, shale, limestone, and

In response to environmental differences, the silicate minerals in

When rocks are subjected to mechanical forces as well as to extreme

The mechanical deformation of rocks concerns tectonic processes. The

Examples of metamorphic rocks are: slate, diamonds

Exogenic and Endogenic Processes