Module For General Biology (Biol. 1012) : Ministry of Science and Higher Education-Ethiopia
Module For General Biology (Biol. 1012) : Ministry of Science and Higher Education-Ethiopia
Module For General Biology (Biol. 1012) : Ministry of Science and Higher Education-Ethiopia
Module Writers
Tegenu Gelana (PhD) …………… Addis Ababa University
Baye Sitotaw (PhD) ………………. Bahir Dar University
Zufan Bedewi (PhD) …………… Hawasa University
Kedir Arebo (PhD) ……………… Defense University
Mulugeta Desta (PhD) ………….... Haramaya University
Samuel Getachew (MSc) ………… Mizan-Tepi University
Abiyu Enyew (Ass. Prof) ……….... University of Gondar
Wondimu Ersino (MSc) …………. Wachamo University
November, 2019
Addis Ababa
1
Preface
The primary goal of this module is to provide the basic information about general biology.
Biology is an introductory college text that covers the concepts and principles from the
structure and function of the cell to the organization of the biosphere. It draws up on the entire
world of living things to bring out an evolutionary theme that is introduced from the start.
The writing style and clarity of this module make it appropriate for use by liberal students; it
gives an opportunity for the reader participate in scientific analysis, as notable practical‘s/
investigations are mentioned, and significant experiments and laboratory works are fully
explained. These all are also followed by self-testing questions, which encourage students to
use scientific methodology in order to think critically.
Team members
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Table of Contents
Preface .................................................................................................................................... 2
Module Objectives .................................................................................................................. 7
Acknowledgements ................................................................................................................. 8
Unit ............................................................................................................................................. 9
1. Introduction ............................................................................................................................ 9
1.1 The meaning and scope of biology .............................................................................. 9
1.2 The origin and nature of life ...................................................................................... 10
1.3 Scientific methods ..................................................................................................... 12
Unit ........................................................................................................................................... 15
2. Biological Molecules ............................................................................................................ 15
1.4 Carbohydrates ............................................................................................................ 15
1.5 Lipids ......................................................................................................................... 20
1.6 Proteins ...................................................................................................................... 22
1.7 Nucleic acids .............................................................................................................. 23
1.8 Vitamins ..................................................................................................................... 25
1.9 Water.......................................................................................................................... 25
1.10 Minerals ..................................................................................................................... 26
Unit ........................................................................................................................................... 28
3. The cellular basis of life ....................................................................................................... 28
3.1 The cell theory ................................................................................................................ 28
3.1.1 Cell organelles ............................................................................................................. 29
3.1.2 Structure and function of organelles ............................................................................ 30
3.1.3 Cellular diversity.......................................................................................................... 44
3.1.3.1 Cell Shape ............................................................................................................. 44
3.1.3.2 Cell Size ................................................................................................................ 45
3.1.4 Transport across the cell membranes ....................................................................... 45
Unit 4 ........................................................................................................................................ 55
Cellular Metabolism and Metabolic Disorders ........................................................................ 55
4.1 Cellular metabolism ........................................................................................................ 55
4.1.1 Enzymes and their role in metabolism ..................................................................... 57
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4.1.2 Chemical nature and classification of enzymes ....................................................... 58
4.1.3 Mechanisms of enzyme action ................................................................................. 60
4.1.4 Factors affecting enzymatic activities ...................................................................... 61
4.1.5 Enzyme inhibitors .................................................................................................... 63
4.2 Bioenergetics and biosynthesis ....................................................................................... 65
4.2.1 Cellular respiration ................................................................................................... 65
4.2.2 Biosynthesis ............................................................................................................. 75
4.2.2.1The photosynthetic apparatus................................................................................. 78
4.2.2.2 The photosynthetic process ................................................................................... 81
4.3 Metabolic disorders, diagnosis and treatments ............................................................... 85
4.3.1. Risk factors of metabolic disorders ......................................................................... 86
4.3.2 Diagnosis of metabolic disorders ............................................................................. 87
4.3.3 Treatments of metabolic disorders ........................................................................... 87
Unit 5 ........................................................................................................................................ 89
Genetics and Evolution ............................................................................................................ 89
5.1 Basic Principles of Mendelian genetics and patterns of inheritance .............................. 91
5.2 Molecular genetics and inheritance ................................................................................ 93
5.2.1 DNA, Gene, Chromosomes and Cell division ......................................................... 93
5.3 Protein synthesis ............................................................................................................. 99
5.1.2 ABO blood groups and Rh Factors ........................................................................ 107
5.4 Introduction to Evolution .............................................................................................. 111
5.4.1 Theories on the origin of life on Earth ....................................................................... 111
5.4.2 Theories of Evolution ................................................................................................ 114
Unit 6 ...................................................................................................................................... 117
Infectious diseases and Immunity .......................................................................................... 117
6.1 Principles of infectious diseases ................................................................................... 118
6.2 Types of infectious disease and their causative agent ............................................... 122
6.2.1 Bacteria .................................................................................................................. 122
6.2.2 Viruses ................................................................................................................... 123
6.2.3 Fungi ................................................................................................................. 125
6.2.3 Protozoa ............................................................................................................ 126
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6.2.4 Helminths ......................................................................................................... 126
6.2.6. Prions .................................................................................................................... 127
6.3 Modes of transmission .............................................................................................. 128
6.4. Host defenses against infectious diseases ................................................................ 129
6.5. Adverse immune reactions (responses) .................................................................... 136
6.5.1. Hypersensitivity reactions ..................................................................................... 137
6.5.2. Autoimmunity and autoimmune disease ............................................................... 142
6.5.3. Immune Deficiencies ............................................................................................ 145
6.6. Tumor Immunolology .............................................................................................. 146
6.6.1. Evidence for immune reactivity to tumor ............................................................. 147
6.6.2. Tumor associated antigens .................................................................................... 148
Unit 7............................................................................................................................... 149
Taxonomy of organisms ......................................................................................................... 149
7.1 Early Attempts to Classify Organisms ......................................................................... 151
7.2 Modern Views of Classification (Schemes of Classification) ...................................... 153
7.3 Domains of Life and the Hierarchical System of Classification .................................. 156
7.4 Binomial Nomenclature ................................................................................................ 160
7.4.1. The Purpose of giving names to organisms .......................................................... 160
7.5 Operative Principles of Nomenclature .......................................................................... 163
Unit 8 ...................................................................................................................................... 165
Ecology and Conservation of Natural Resources (3 Hrs) ...................................................... 165
8.1 Definition of ecological terms and Basic concepts of Ecology .................................... 165
8.2 Branches of ecology...................................................................................................... 168
8.3 Aquatic and terrestrial ecosystems ............................................................................... 170
8.4 Energy flow through ecosystems .................................................................................. 177
8.4.1 The food chains .......................................................................................................... 177
8.5 Cycling of Materials (Nutrients) ................................................................................... 183
8.6 Conservation of natural resources................................................................................. 189
8.6.1 Principles of conservation of natural resources ......................................................... 189
8.7 Environmental pollution and public health ................................................................... 191
Unit 9 ...................................................................................................................................... 209
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Introduction to Botany and Zoology ...................................................................................... 209
9.1 Introduction to Botany .................................................................................................. 209
9.1.1 Algology................................................................................................................. 209
9.1.2 Bryology and Pteridology ...................................................................................... 211
9.1.3 Seed plants ............................................................................................................. 213
9.2 Introduction to zoology................................................................................................. 215
9.2.1 Invertebrates ........................................................................................................... 215
9.2.1.1 General Characteristics of Invertebrates ............................................................. 215
9.2.1.2 Classification of Invertebrates ............................................................................ 216
9.2.1.3 Services Provided by Invertebrates ..................................................................... 222
9.2.2 Subphylum Vertebrates .......................................................................................... 224
9.2.2.1 Classification of Vertebrates ............................................................................... 224
Unit 10 .................................................................................................................................... 233
Applications of Biological Sciences....................................................................................... 233
10.1 Application of Biology in medicine and other health sciences (Fast diagnosis tools,
drug and vaccine production, gene therapy, immuno-diagnosis, immunotherapy,
transplantation, medicinal plants, etc) ................................................................................ 233
10.2 The application of Biology in technology .................................................................. 235
10.3 Application of Biology in agriculture (soil fertility, tissue culture, animal breeding and
transgenic animals, plant disease and pest management) ................................................... 236
10.4 Application of Biology in industries (Food, brewery, pharmaceuticals, tannery and
textile, single cell production, preservation) ....................................................................... 239
10.5 Application of Biology in waste treatments and recycling (Bioenergy, bioremediation,
water treatment, biomining) ................................................................................................ 240
10.6 Application of Biology in forensic Science ................................................................ 240
10.7 Biological warfare....................................................................................................... 240
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Module Objectives
At the end of the course, the student will be able to:
Explain the scope of biology and molecular basis of life
Describe life activities from the cellular point of view
Manipulate basic biological tool, record data and draw conclusions
Develop scientific attitude, skill and conduct biological experiments using
scientific procedures
Outline basic processes of energy transduction and synthesis of intermediate or
final products in living cells
Understand the basic concepts of genetics and inheritance
Understand the concepts of infection and immunity
Classify organisms based on their cellular organization and complexity
Explain components, processes and interrelationships within a given ecosystem
Know the general features of invertebrate and vertebrate animals
Appreciate the practical uses of biological knowledge and its application in the
wider society
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Acknowledgements
The module writing team would like to thank Dr. Eba Mijena, Director General for Academic
and Research; Ministry of Science and Higher Education (MoSHE), for his guidance in the
write up. The team would also like to extend our deepest gratitude to all who had direct and
indirect participation in writing of this module.
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Unit
1. Introduction
Dear learner! Welcome to this module which deals about the course, General Biology (Biol.
1012). This module chapter is primarily intended for natural science students to familiarize with
basic concepts of biological science, the nature and origin of life, scientific methods and the
subject matter of biology. I hope you will find it interesting!
Learning Objectives: After completing this chapter, you will be expected to:
Biological Sciences is the study of life and living organisms. It is also called as ―Biology‖.
The Greek word ‗bio‘ means life and ‗logos‘ means study of. In the late 1700s Pierre-Antoine
de Monet and Jean-Baptiste de Lamarck coined the term biology. Earlier study of living
things was restricted to the pure Science like Botany and Zoology that together comprise the
Biology, but as the time passed new branches evolved. New technologies developed in pure
subjects as well as in applied fields, which gave rise to a very broad concept of science called
Biological Sciences. Biological Sciences is an extensive study covering the minute workings
of chemical substances inside living cells to the broad scale concepts of ecosystems and
global environmental changes.
It is also concerned with the physical characteristics and behaviors of organisms living today
and long ago. How they came into existence and what relation they possess with each other
and their environments? Intimate study of details of the human brain, the composition of our
genes, and even the functioning of our reproductive system are dealt in Biological sciences.
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Therefore, Biology is the science of Living Things. That is why Biology is sometimes known
as Life Science.
The life sciences can be defined as ―a systematic study of living beings or study of nature‖.
Teaching of life Science basically deals with providing information about the latest
developments in the field of Biological sciences all over the world.
One of the biggest and most important of emergent phenomena is that of the origin or
emergence of life. The mystery of life's origin is still a big debating issue in science. The
question ―what is life?‖ is so hard to answer; we really want to know much more than what it
is, we want to know why it is, ―we are really asking, in physical terms, why a specific material
system is an organism and not something else‖. To answer this why question we need to
understand how life might have originated. There are a number of theories about the origin of
life. The next few sections give emphasis on these different theories about the origin of life.
The evolution of life on earth has involved the following sequence of events. The first living
things to appear were the simplest creatures, single-celled organisms. From these came more
complex, multi-cellular organisms. Becoming more complex meant more than just an increase
in cell number but more cells showed cellular specialization, where certain cells within the
multi-cellular organism carried out specific tasks. Millions, even billions of years of changes
of organisms led to the living things we now call plants and animals.
Since this basic sequence of events is in accord with that agreed upon by most geologists,
paleontologists, biologists, and even theologians, one might conclude that Moses, Aristotle,
and Darwin were all keen observers and naturalists who were able to logically assess the most
probable creation story. Scientists generally concur that the time from the formation of our
solar system until now has been on the order of some 4.5 billion years. Those who believe the
world as we know it was created in six days are often called creationists. Their method of
inquiry is based on the belief that the Bible is to be accepted as a completely accurate
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accounting of all about which it speaks. Scientists, on the other hand, utilize what they call the
scientific method, which allows them to test hypotheses and theories and to develop concepts
and ideas.
Several attempts have been made from time to time to explain the origin of life on earth. As a
result, there are several theories which offer their own explanation on the possible mechanism
of origin of life. Following are some of them:
1. Theory of Special Creation: according to this theory, all the different forms of life that
occur today on planet earth have been created by God, the almighty.
Theory of Spontaneous Generation: this theory assumed that living organisms could arise
suddenly and spontaneously from any kind of non-living matter. One of the firm believers in
spontaneous generation was Aristotle, the Greek philosopher (384-322 BC).
3. Cosmozoic Theory (Theory of Panspermia): according to this theory, life has reached this
planet Earth from other heavenly bodies such as meteorites, in the form of highly resistance
spores of some organisms. This idea was proposed by Richter in 1865 and supported by
Arrhenius (1908) and other contemporary scientists. The theory did not gain any support. This
theory lacks evidence, hence it was discarded.
Life is defined as a "condition" that distinguishes animals and plants from inorganic materials
and dead organisms.
Life is comprised of processes and is a maintained state.
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The most sophisticated form of life is man as a result of this we focuses upon the
nature of the life and death of man.
Man demonstrates three lives or aspects of life: Life of the body (physical), life of the mind
and life of the spirit.
Physical life is basic existence
Mind contributes effectiveness and scope
Spiritual entity contributes maximum living.
Physiology: The existence of life physical is demonstrated by the presence of functions.
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The scientific method is a process for experimentation that is used to explore
observations and answer questions. It is an empirical method of acquiring knowledge. It is
also the technique used in the construction and testing of a scientific hypothesis.
The scientific method has five basic steps, plus one feedback step:
Make an observation.
Ask a question.
Form a hypothesis, or testable explanation.
Make a prediction based on the hypothesis.
Test the prediction.
Iterate: use the results to make new hypotheses or predictions.
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Summary of the scientific method
Step 1: Observe behavior or other phenomena
Step 2: Form a tentative answer or explanation (a hypothesis (guess a reason)
Step 3: Use your hypothesis to generate a testable prediction
Step 4: Make systematic, planned observations (data collection)
Step 5: Results and Discussion Use the observations to evaluate (support, refute, or
refine) the original hypothesis
Step 6: Conclusion
Step 7: Recommendation
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Unit
2. Biological Molecules
Biological molecules are often referred to as the molecules of life (bio-molecules) that are
basically found in a living cell and categorized as organic and inorganic molecules in general.
Each member of the groups is vital for every single organism on Earth. The organic
biomolecules are proteins, carbohydrates, lipids and nucleic acids. Without any of these four
molecules, a cell and organism would not be able to live. They are important either
structurally or functionally for cells and, in most cases, they are important in both ways. the
most commonly known inorganic molecules are water and minerals, which are still important
for the normal functioning of the cell.
Learning Objectives: After completing this chapter you will be expected to:
1.4 Carbohydrates
Self-test:
1. What are the elemental compositions of carbohydrates?
2. Why cells rely on carbohydrates as a major source of energy compared to other
biomolecules?
3. What are the additional importance’s of carbohydrates besides their role as energy source?
A carbohydrate molecule is made of atoms of carbon, hydrogen and oxygen. They are an
important source of energy and they also provide structural support for cells and help with
communication between cells (cell-cell recognition). They are found in the form of either a
sugar or many sugars linked together, called saccharides. Based on the number sugar units
they contain, they are categorized into three, as follows.
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A single sugar molecule containing carbohydrate is known as a monosaccharides,
while two and many having are regarded as disaccharides and polysaccharides,
respectively.
Each of the sugar molecules are bonded together through the glycosidic linkage/s. The
three different types of carbohydrates are all important for different reasons
Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these
compounds on hydrolysis. Example: Glucose is an aldehyde while fructose is a ketone.
Monosaccharides - simple sugars with multiple OH groups. Based on number of carbons (3, 4,
5, 6), a monosaccharide is a triose, tetrose, pentose or hexose.
Disaccharides - 2 monosaccharides covalently linked
Oligosaccharides - a few monosaccharides covalently linked.
Polysaccharides - polymers consisting of chains of monosaccharide or disaccharide
6 CH2OH 6 CH2OH
6 CH2OH 6 CH2OH
5 O 5 O
H 5 H H 5
H
H O H H O H
H H
H 1 4 H 1
4
4 OH HH 1 4 OH
OH
H
H 1
OH
OHOH OO OH
OH
3 3 2 2 33 2
HH OH
OH maltose HH OH
OH
maltose
Fig: 2.2. A structure of maltose (disaccharide)
Monosaccharides
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Monosaccharides containing the aldehyde group are classified as aldoses, and those with a
ketone group are classified as ketoses. Aldoses are reducing sugars; ketoses are non-reducing
sugars. This is important in understanding the reaction of sugars with Benedict's reagent.
However, in water pentoses and hexoses exist mainly in the cyclic form, and it is in this form
that they combine to form larger saccharide molecules.
Glucose
Glucose is the most important carbohydrate fuel in human cells. Its concentration in the blood
is about 1 gdm-3. The small size and solubility in water of glucose molecules allows them to
pass through the cell membrane into the cell. Energy is released when the molecules are
metabolized.
Two glucose molecules react to form the dissacharide maltose. Starch and cellulose are
polysaccharides made of glucose units.
Galactose
Galactose molecules look very similar to glucose molecules. They can also exist in α and β
forms. Galactose reacts with glucose to make the dissacharide lactose. However, glucose and
galactose cannot be easily converted into one another. Galactose cannot play the same part in
respiration as glucose. This comparison of glucose and galactose shows why the precise
arrangement of atoms in a molecule (shown by the displayed formula) is so important.
Fructose
Fructose, glucose and galactose are all hexoses. However, whereas glucose and galactose are
aldoses (reducing sugars), fructose is a ketose (a non-reducing sugar). It also has a five-atom
ring rather than a six-atom ring. Fructose reacts with glucose to make the dissacharide
sucrose.
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Disaccharides
Monosaccharides are rare in nature. Most sugars found in nature are disaccharides. These
form when two monosaccharides react. Disaccharides are soluble in water, but they are too
big to pass through the cell membrane by diffusion. They are broken down in the small
intestine during digestion to give the smaller monosaccharides that pass into the blood and
through cell membranes into cells.
This is a hydrolysis reaction and is the reverse of a condensation reaction and it releases
energy.
A condensation reaction takes place by releasing water. This process requires energy. A
glycosidic bond forms and holds the two monosaccharide units together. The three most
important disaccharides are sucrose, lactose and maltose. They are formed from the a forms
of the appropriate monosaccharides. Sucrose is a non-reducing sugar. Lactose and maltose are
reducing sugars.
Monosaccharides are used very quickly by cells. However, a cell may not need all the energy
immediately and it may need to store it. Monosaccharides are converted into disaccharides in
the cell by condensation reactions. Further condensation reactions result in the formation of
polysaccharides. These are giant molecules which, importantly, are too big to escape from the
cell. These are broken down by hydrolysis into monosaccharides when energy is needed by
the cell.
Polysaccharides
Monosaccharides can undergo a series of condensation reactions, adding one unit after
another to the chain until very large molecules (polysaccharides) are formed. This is called
condensation polymerisation, and the building blocks are called monomers. The properties
of a polysaccharide molecule depend on:
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The extent of any branching (addition of units to the side of the chain rather than one
of its ends)
Any folding which results in a more compact molecule
Whether the chain is 'straight' or 'coiled'
Starch
Starch is often produced in plants as a way of storing energy. It exists in two forms: amylose
and amylopectin. Both are made from α-glucose. Amylose is an unbranched polymer of α-
glucose. The molecules coil into a helical structure. It forms a colloidal suspension in hot
water. Amylopectin is a branched polymer of α-glucose. It is completely insoluble in water.
Glycogen
Glycogen is amylopectin with very short distances between the branching side-chains. Starch
from plants is hydrolysed in the body to produce glucose. Glucose passes into the cell and is
used in metabolism. Inside the cell, glucose can be polymerised to make glycogen which acts
as a carbohydrate energy store.
Cellulose
Cellulose is a third polymer made from glucose. But this time it's made from β-glucose
molecules and the polymer molecules are 'straight'. Cellulose serves a very different purpose
in nature to starch and glycogen. It makes up the cell walls in plant cells. These are much
tougher than cell membranes. This toughness is due to the arrangement of glucose units in the
polymer chain and the hydrogen-bonding between neighboring chains. Cellulose is not
hydrolysed easily and, therefore, cannot be digested so it is not a source of energy for humans.
The stomachs of Herbivores contain a specific enzyme called cellulase which enables them to
digest cellulose.
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Summary of carbohydrates
1.5 Lipids
Self-test:
1. What are lipids?
2. What is the difference between saturated and unsaturated?
3. What are the physiological and structural roles of lipids for life forms?
Lipids are a highly variable group of molecules that include fats, oils, waxes and some
steroids. They are esters of fatty acids and alcohol (glycerol or chains of alcohols). Fatty acids
are made mostly from chains of carbon and hydrogen and they bond to a range of other types
of atoms to form many different lipids. The primary function of lipids is to store energy.
A lipid called a triglyceride is a fat if it is solid at room temperature and oil if it is liquid at
room temperature. In addition, triglycerides are stored in the fat cells, also called adipocytes
or lipocytes, and are responsible in storing fats and lipids which will facilitate energy store in
animals‘ body. Fat cells are categorized in white fat cells and brown fat cells. The different is
made from their ways of storing lipids. White fat cells store one large lipid drop while brown
fat cells store smaller and multiple droplets of lipids spreading in the whole body of the cell.
Various types of lipids occur in the human body, namely 1) triacylglycerol, 2) cholesterol, and
3) polar lipids, which include phospholipids, glycolipids and sphingolipids. Plant leaves are
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coated with lipids called waxes to prevent water loss, and the honeycomb in a beehive is made
of beeswax.
The basic structure of a lipid includes fatty acid tails as shown in Figure 2.3. Each tail is a
chain of carbon atoms bonded to hydrogen and other carbon atoms by single or double bonds.
Lipids that have tail chains with only single bonds between the carbon atoms are called
saturated fats because no more hydrogens can bond to the tail. Lipids that have at least one
double bond between carbon atoms in the tail chain can accommodate at least one more
hydrogen and are called unsaturated fats. Fats with more than one double bond in the tail are
called polyunsaturated fats.
Properties of lipids
• Insoluble in water
• Longer chains
More hydrophobic, less soluble
• Double bonds increase solubility
• Melting points:
Depend on chain length and saturation
Double bonds lead acyl chain disorder and low melting temperatures
Unsaturated fatty acids are solid at room temperature.
Importance of lipids
As the main component of cell membranes (phospholipids)
Insulation of heat and water,
Storing energy, protection and cellular communication.
Activity
1. What are the elemental compositions of lipids?
2. Why lipids act as major source of energy?
3. What are the major classes of lipids?
4. Jot down the importance of cholesterol?
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1.6 Proteins
Self-test:
1. Comment on the following statements (answer by saying true or false for each statement
and then elaborate)
a) All proteins are enzymes
b) Enzymes initiate a chemical reaction
c) Chemical reactions cannot take place in the body without enzymes
2. What are the elemental compositions of proteins?
3. What are the physiological and structural roles of proteins?
4. Compare protein with nucleic acid
5. How is the primary structure of a protein determined?
A protein is a compound made of small carbon compounds called amino acids. Amino acids
are small compounds that are made of carbon, nitrogen, oxygen, hydrogen, and sometimes
sulfur. All amino acids share the same general structure.
Amino acids have a central carbon atom like the one shown in Fig. 2.3. Recall that carbon can
form four covalent bonds. One of those bonds is with hydrogen. The other three bonds are
with an amino group (–NH2), a carboxyl group (–COOH), and a variable group (–R). The
variable group makes each amino acid different. There are 20 different variable groups, and
proteins are made of different combinations of all 20 different amino acids. Several covalent
bonds called peptide bonds join amino acids together to form proteins, which are also shown
in Fig. 2.3. A peptide forms between the amino group of one amino acid and the carboxyl
group of another.
Based on the variable groups contained in the different amino acids, proteins can have up to
four levels of structure. The number of amino acids in a chain and the order in which the
amino acids are joined define the protein‘s primary structure. After an amino acid chain is
formed, it folds into a unique three-dimensional shape, which is the protein‘s secondary
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structure. A protein might contain many helices, pleats, and folds. The tertiary structure of
many proteins is globular, such as the hemoglobin protein, but some proteins form long fibers.
Some proteins form a fourth level of structure by combining with other proteins.
Proteins make up about 15 percent of your total body mass and are involved in nearly every
function of your body. For example, your muscles, skin, and hair all are made of proteins.
Your cells contain about 10,000 different proteins that provide structural support, transport
substances inside the cell and between cells, communicate signals within the cell and between
cells, speed up chemical reactions, and control cell growth.
Nucleic acids are complex macromolecules that store and transmit genetic information.
Nucleic acids are made of smaller repeating subunits called nucleotides. Nucleotides are
composed of carbon, nitrogen, oxygen, phosphorus, and hydrogen atoms. There are six major
nucleotides, all of which have three units a phosphate, a nitrogenous base, and a ribose sugar,
as shown in Fig. 2.5
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Fig. 2.5. Basic structure of nucleotide
There are two types of nucleic acids in living organisms: deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). In nucleic acids such as DNA and RNA, the sugar of one nucleotide
bonds to the phosphate of another nucleotide. There are five different bases found in
nucleotide subunits that make up DNA and RNA, Adenine, Cytosine, Guanine, Thymine and
Uracil. Each of these nitrogenous base that sticks out from the chain is available for hydrogen
bonding with other bases in other nucleic acids.
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1.8 Vitamins
Self-test:
1. What are vitamins?
2. What are the roles of vitamins in maintaining homeostasis?
3. What are the water soluble and fat soluble vitamins?
Vitamins are organic compounds that are needed in small amounts for metabolic activities.
Many vitamins help enzymes function well. Vitamin D is made by cells in your skin. Some B
vitamins and vitamin K are produced by bacteria living in the large intestine. Sufficient
quantities of most vitamins cannot be made by the body, but a well-balanced diet can provide
the vitamins that are needed. Some vitamins that are fat-soluble can be stored in small
quantities in the liver and fatty tissues of the body. Other vitamins are water-soluble and
cannot be stored in the body. Foods providing an adequate level of these vitamins should be
included in a person‘s diet on a regular basis.
1.9 Water
Self-test:
What are the physical and chemical properties of water, and their roles in maintaining
homeostasis?
Water molecules are formed by covalent bonds that link two hydrogen (H) atoms to one oxygen
(O) atom, and each water molecule has the same structure. It is one of the most plentiful and
essential of compounds, which is a tasteless and odorless, existing in gaseous, liquid, and solid
states. It has the important ability to dissolve and as a media for transportation of many other
substances. In reality, the versatility of water as a solvent is essential to living organisms, as well.
Water molecules have an unequal distribution of charges and are called polar molecules, meaning
that they have oppositely charged regions.
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1.10 Minerals
Self-test:
1. What are minerals?
2. What are the roles of minerals in maintaining homeostasis?
Minerals are inorganic compounds used by the body as building material, and they are
involved with metabolic functions. For example, the mineral iron is needed to make
hemoglobin and it binds to hemoglobin in red blood cells and is delivered to body cells as
blood circulates in the body. Calcium, and other minerals, is an important component of bones
and is involved with muscle and nerve functions and they serve as cofactors for enzymes.
Magnesium is an important component of the green pigment, chlorophyll, involved in
photosynthesis.
Activity
1. Explain why raw edible oil is added on dishes of raw vegetables before consumption?
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Chapter Review Questions
1. Explain if an unknown substance found on a meteorite is determined to contain no
trace of carbon, can scientists conclude that there is life at the meteorite's origin?
2. List and compare the four types of biological macromolecules.
3. Identify the components of carbohydrates and proteins.
4. Discuss the importance of amino acid order to a protein‘s function.
5. Given the large number of proteins in the body, explain why the shape of an enzyme is
important to its function.
6. Compare and contrast the functions of carbohydrates, lipids, proteins, and nucleic
acids.
7. State why the polarity of water molecules makes water a good solvent.
8. Given the large number of proteins in the body, explain why the shape of an enzyme is
important to its function?
27
Unit
3. The cellular basis of life
Learning Objectives: Upon successful completion of this unit, you should be able to:
Self-Test:
1. State the cellular basis of life and cell theory
2. Identify the different types of organelles, their structure and functions
3. Why is homogenization important in cell study?
In the late 1600s, an English scientist named Robert Hook was the first to observe plant cells
with a crude microscope. Then, almost a century and a half later, in the 1830‘s two German
scientists proposed that all living things are composed of cells (their names were Mathias
Schleiden and Theodore Schwann). A German pathologist, Rudolph Virchow extended this
idea by contending that cells arise only from other cells.
28
The nucleus: an organelle that controls cellular activities. Typically the nucleus
resides near the cells center.
29
There are two kinds of cell organelles on the basis membrane covering, membranous and
non-membranous organelles. Endoplasmic reticulum (Rough and Smooth), Golgi bodies,
mitochondria, chloroplasts, nucleus, lysosomes, peroxisomes and vacuoles are membranous
whereas, non-membrane bound cell organelles are ribosomes (70s and 80s), centrosomes, cilia
and flagella, microtubules, basal bodies and microfilaments.
30
The Nuclear envelope
surrounds nuclear material
consists of outer and inner membrane
perforated at intervals by nuclear pores
Through this pores most ions and water soluble molecules to transfer b/n nucleus and
cytoplasm
Chromatin: The term chromatin means "colored material" and refers to the fact that this
material is easily stained for viewing with microscope, and it is composed mainly of coils
DNA bound to basic protein called his tones. The DNA is so long that it has to be packed in
an organization manner or it would get entangled like unraveled ball of string.
Nucleoli: The nuclei of most cells contain one or more lightly stained structures called
nucleoli that actively engage in synthesizing of ribosomes. The nucleolus, unlike most of the
organelles, does not have a limiting membrane. Instead, it is simply a structure that contains
large amounts of RNA and protein of the type found in ribosomes. The nucleolus becomes
considerably enlarged when a cell is actively synthesizing proteins. The genes of five separate
chromosome pairs synthesize the ribosomal RNA and then store it in the nucleolus.
The Cytoplasm: The cytosol is the material of cell interior not occupied by the nucleus,
containing a number of distinct, highly organized membrane-enclosed structures- the
organelles- dispersed within a complex jelly like marrow called the cytosol. All cells
contain six main types of organelles- the endoplasmic reticulum, Golgi complex,
lysosomes, peroxisomes, mitochondria, and vacuoles. They are similar in all cells, but
with some variations depending on the cell specialization. Each organelle is a separate
compartment, containing different chemically setting for fulfilling a partial or cellular
function. These organelles occupy about half of the total cell volume. The remaining
part of the cytoplasm is cytosol.
31
reticulum as stacks of flattened sacs. Though different in structure and function, they are
continuous with each other.
The rough Endoplasmic Reticulum: The outer surface of the rough ER contains dark
particles called ribosomes, which are ribosomal RNA protein complexes that produce protein
under the direction of nuclear DNA. Messenger-RNA carries the genetic message from the
nucleus to the ribosomes ―workshop‖ where proteins are synthesized. Some ribosomes are
―free‖ dispersed throughout the cytosol. The rough ER in association with ribosomes produces
and releases a variety of proteins, into the fluid-filled space enclosed by the membrane.
Some proteins for export as secretory products (hormones or enzymes). Other proteins are
transported to sites within the cell for use in the construction of new plasma membrane or new
organelle membrane. Cellular membrane contains predominantly fats and proteins. ER
membrane also contains enzymes required for the synthesis of almost all the lipids needed for
the production of new membranes. These lipids enter the ER lumen along with the proteins.
This structure is well developed in cells producing digestive enzymes or in rapidly growing
cells. Each ribosome is involved in producing only one type of protein. The free ribosomes
synthesize enzyme proteins that are used intra-cellularly within the cytosol.
Smooth Endoplasmic Reticulum: Since it does not have ribosomes, it looks ‗smooth‘ and
does not produce proteins. It serves a variety of other functions that differ in cell types. In
most cells, the smooth ER is sparse and serves in packaging and discharging site for protein
molecules that are to be transported from the ER. All new proteins and fats pass from ER
gathered in the smooth ER. Portions of the smooth ER then ―bud off/pinch off‖, giving rise to
‗transport vesicles‘, they contain the new molecule wrapped in a membrane derived from the
smooth ER membrane. Transport vesicles move to the Golgi complex for further processing
of their cargo. Some specialized cells have an extensive smooth ER, which has additional
functions as follows:
The smooth ER is well developed in cells specialized in lipid metabolism- cells that
synthesize steroid hormones. The membrane wall of the smooth ER contains enzymes
for synthesis of lipids. This is an additional site for synthesis in addition for ER to
keep pace with demands for hormone secretion.
32
In liver cells, the smooth ER contains enzymes involved in detoxifying harmful
endogenous substances produced within the body by metabolism or exogenous
substances entering the body from outside as drugs or other foreign compounds.
The detoxifying enzymes alter toxic substances so that they could be easily eliminated
in the urine. But unfortunately, in some instances the same enzyme transforms
otherwise harmless substance into carcinogens that play a role in cancer development.
The smooth ER has a special role in skeletal muscle cells. They have an elaborate
network of smooth ER, which stores ionic calcium and plays a crucial role in the
process of muscle contraction.
33
the sugar attached to the protein. This is a very elaborate, precisely programmed
activity, specific for each final product.
2. Sorting and directing finished product to their final destination. According to their
function and destination, different types of products are segregated by the Golgi
complex, i.e., molecules that are destined for secretion to the exterior, molecules that
will eventually become part of the plasma membrane, and the molecules that will
become incorporated into other organelles.
3. The smooth ER of the liver and kidney cells are responsible for the detoxification
and inactivation of drugs. Enzymes within the smooth ER can inactivate or
destroy a variety of chemicals including alcohol, pesticides, and carcinogens.
4. In skeletal muscle cells, a modified form of smooth ER stores Ca2+ to be released for
muscle contraction.
Fig: 3.3. Structure of endoplasmic reticulum and its relation with the Golgi apparatus
and the nucleus.
34
internalized within the cell. Lysosomes vary in size and shape, and about 300μm in a cell.
Surrounding membrane confines these enzymes, preventing from destroying the cell that
houses them. Extrinsic material to be attacked by lysosomal enzymes is brought into the
interior of the cell through the process of endocytosis. If the fluid is internalized by
endocytosis, the process is called pinocytosis. Endocytosis is also accomplished by
phagocytosis.
In pinocytosis, ECF and a large molecule such as protein is engulfed. A specific molecule
may bind to surface receptor, triggering pinocytosis- receptor-mediated endocytosis.
Dynamin, a molecule forms rings wrapping around, severing the vesicle from the surface
membrane in pinocytosis.
A lysosome fuses with the membrane of the internalized vesicle and releases its contents of
hydrolytic enzymes into the vesicle. These enzymes safely attack the microbes or other
trapped material within the enclosed confines of the vesicle without
damaging the remainder of the cell.
Lysosomes can take up old organelles such as mitochondria and break down into their
component molecules. Those molecules that can be released are reabsorbed into the cytosol,
and the rest are dumped out of the cell. The process by which worn-out organelles are
digested is called autophagy a human liver cell recycles about half its content every week.
In the inherited condition known as lysosomal storage disease (Tay-Sachs disease)
lysosomes are not effective because they lack specific enzymes. As a result, harmful waste
products accumulate disrupting the normal function of cells, often with fatal results
35
Peroxisome: Peroxisome is membrane-enclosed sacs containing oxidative enzymes and
catalase that detoxify various wastes. Oxidative enzymes need oxygen to remove hydrogen
from specific substance/molecule; such reactions are important in detoxifying various waste
products within the cell or foreign compounds that have entered in, such as ethanol consumed
in alcoholic drinks (in liver and kidneys). The major product generated is hydrogen peroxide;
hydrogen peroxide itself is a powerful oxidant. It also contains catalase, and antioxidant
enzyme decomposing hydrogen peroxide into harmless water and oxygen. This reaction is an
important safety reaction that destroys deadly hydrogen peroxide, at the site of production,
thereby preventing possible devastating escape into the cytosol. It is shorter and smoother
than lysosome and several hundreds may present in one cell.
Peroximal disorders disrupt the normal processing of lipids and can severely disrupt the
normal function of the nervous system by altering the structure of the nerve cell membrane
Mitochondria
Mitochondria are the ‗‘power houses‘‘ of a cell; they extract energy from nutrients in food and
transform it into usable form to energize cell activity. Their number varies depending on the
energy needs of each particular cell types. A single cell may have few hundreds or thousands.
Mitochondria are rod or oval shaped about the size of a bacterium. Each is enclosed by a
double membrane - a smooth outer that surrounds the mitochondria, and an inner membrane
that forms a series of enfolding or shelves called cristae, which project into an inner cavity
filled with a jelly-like matrix (See figure 3.5). These cristae contain proteins that convert
much of the energy in food into a usable form (the electron transport protein). The enfolding
increase the surface area available for keeping these important proteins.
The matrix contains a mixture of hundreds of different dissolved enzymes (Citric acid cycle
enzymes) that are important in preparing nutrient molecules for the final extraction of usable
energy by the cristae proteins.
Carbon-hydrogen bonds in ingested food are the source of energy stored in the chemical
forms. Body cell can extract energy from food nutrients and convert it into energy form that
they can use. The high energy phosphate bonds of ATP contain adenosine with 3 phosphate
groups. When high energy phosphate bond is split, a substantial amount of energy is released.
36
ATP is the universal energy carrier the common energy ―currency‖ of the body. Cells can
―cash in‖ ATP to pay the energy ―price‖ for running the cellular machine. To get immediate
usable energy cells can split terminal phosphate bond of ATP, which yields ADP with
phosphate group attached - plus inorganic phosphate (Pi) plus energy. (See figure 3below).
37
Mitochondria are unusual organelles in two ways:
In the matrix they have their own unique DNA called mitochondrial DNA.
Mitochondria have the ability to replicate themselves even when the cell to which they
belong is not undergoing cell division.
Chloroplasts
Chloroplasts are useful organelles among plastids as they highly participate in the process of
photosynthesis which is a process by which plants synthesize their own food. They are located
in outer surface of the cell to receive enough light. Chloroplasts are green colored due to the
chlorophyll pigments found in its internal parts. Some of important characteristics of plant is
its ability to carry out photosynthesis as the way they use in making their own food and pass
through converting light energy in chemical energy.
Vesicles are membrane bound sacs that are used to store or transport substances around the
cell. Lysosomes are actually Vesicles.
Vacuoles are essentially larger Vesicles, and they are formed by the joining together of many
Vesicles. They are membrane bound organelles that have no specific shape and contain water
with a number of different compounds within it. Their function varies greatly depending on
38
the type of cell they are part of. In plant cells they are important in maintaining Turgor
Pressure.
Cytoskeleton
The cytoskeleton is a complex protein network that act as the ―bone and muscle‖ of the cell.
This necessary intracellular scaffoldings supports and organizes cellular components
arrangements and to control their movements; this provides distinct shape, size to the cell.
This network has at least four distinct elements: Microtubules, Microfilaments, Intermediate
filaments and Microtubular lattice
The different parts of the cytoskeleton are structures linked and functionally coordinated to
provide integration of the cell. The microtubule is the largest of the group; slender, long,
hollow tubes composed of a globular protein molecule (6 nm diameter) tubulin. They provide
asymmetrical shape to the cell, such as a neuron with cell body and long axon. They
coordinate numerous complex cell movements in transport of secretory vesicles from region
to region of the cell, movements of cilia and flagella, distribution of chromosomes during cell
division, microfilaments are important to cellular contractile system and as mechanical
stiffeners. The microfilaments are the smallest of the cytoskeleton composed of protein
molecule actin having a globular shape similar to tubulin. Generally, cytoskeletons
determine/ provide the:
shape of a cell
structural support
organizing its contents
substances movement through cell (cilia, flagella and intracytoplasmic vesicles), and
Contribute to movements of the cell as a whole.
Plasma/cell membrane
The plasma membrane is extremely thin layer of lipids and proteins forming outermost
boundary of living cell and enclosing the intracellular fluid (ICF). It serves as a mechanical
barrier that traps needed molecules within the cell; plasma membrane plays an active role in
determining the composition of cell by selective permeability of substances to pass between
the cell and its ECF environment. There are some differences in the composition of plasma
39
membrane between cell types, which permit the cell to interact in different ways with
essentially the same extracellular fluid (ECF) environment. The plasma membrane is a fluid
lipid bilayer embedded with proteins. It appears as ‗trilaminar’ layer structure having two
dark layers separated by a light middle layer as a result of specific arrangement of the
constituent molecules.
All plasma membrane are made up of lipids and proteins plus small amount of carbohydrates.
Phospholipids are most abundant with a lesser amount of cholesterol. Phospholipids have a
polar charged head having a negatively charged phosphate group and two non-polar
(electrically neutral) fatty acid tails. The polar end is hydrophilic (water loving) because it can
interact with water molecule, which is also polar; the non-polar end is hydrophobic (water
fearing) and will not mix with water. Such two-sided molecule self-assemble into a lipid
bilayer, a double layer of lipid molecules when in contact with water. The hydrophobic tails
bury themselves in the center away from the water, while the hydrophilic heads line up on
both sides in contact with water. The water surface of the layer is exposed to ECF, whereas
the inner layer is in contact with the intracellular fluid (ICF). The lipid is fluid in nature, with
consistency like liquid cooking oil. Cholesterol provides to the fluidity as well as the stability;
cholesterol lies in between the phosphate molecules, preventing the fatty acid chain from
packing together and crystallizing that could decrease fluidity of the membrane. Cholesterol
also exerts a regulatory role on some of the membrane proteins. For fluidity of the membrane,
40
it gives flexibility to the cell to change its shape; transport processes are also dependent on the
fluidity of the lipid bilayer. The membrane proteins are either attached to or inserted within
the lipid bilayer; some extending through the entire membrane thickness; they have polar
region at both ends joined by a non-polar central portion. Other proteins are on either the
outside or inner surface, anchored by interactions with proteins that spans the membrane or by
attachment to the lipid bilayer. On account of membrane fluidity, many proteins float freely,
although the mobility of protein that have special function in a particular area of the
membrane is restricted - this gives ever changing mosaic pattern of the protein embedded in
the lipid layer. Only the outer surface of the plasma membrane contains a small amount of
carbohydrate. Short-chain carbohydrates are bound primarily to membrane proteins and to a
lesser extent to lipids, forming glycoproteins and glycolipids.
The plasma membrane is actually asymmetrical; the two surfaces are not the same;
carbohydrate is only on the outer surface; different amount of different proteins are on the
outer and inner surfaces and even the lipid structures of the outer and inner half is not the
same. The plasma membrane is highly complex, dynamic, regional differentiated structure.
The lipid layer forms the primary barrier to diffusion, whereas proteins perform most of the
specific membrane functions.
Lipid bilayer forms the basic structure of the membrane, is a barrier to passage of water-
soluble substances between the ICF and ECF; and is responsible for the fluidity of the
membrane.
Membrane proteins are variety of different proteins within the plasma membrane; have the
following special functions: 1. some form water-filled passage ways or channels, across the
lipid bilayer; such channels allow ions to pass through without coming in direct contact with
lipid interior. The channels are highly selective; they can selectively attract or repel particular
ions. This selectively attracts or repels particular ions. This selectivity is to specific charged
amino acids group. Number and kind of channels vary in cells. Channels open and close in
response to a controlling mechanism. 2. Other proteins serve as carrier molecule that transport
specific molecule that cannot cross on their own. They differ in cells, e.g., thyroid epithelial
cell possesses carriers for iodine. 3. Many proteins on the outer surface serve as ‗receptor
sites‘ that recognize and bind with specific molecules in the cell environment. This binding
41
triggers a series of membrane and intracellular events that alter the activity of the target cell.
In this way hormones influence specific cell, even though every cell is exposed to the same
chemical messenger via its widespread distribution by the blood 4. Another group of proteins
act as membrane-bound enzymes that control specific chemical reactions on either side of the
plasma membrane e.g., outer layer of the plasma membrane of skeletal muscle contains
enzyme ACh-esterase that destroys the chemical messenger that triggers contraction. 5. Some
proteins are arranged as filaments network/meshwork on the inner side and are secured to
certain internal protein elements of the cytoskeleton. They maintain cell shape. 6. Other
proteins function as cell adhesion molecules (CAMs). These molecules protrude from the
membrane surface that grip each other and grip the connective tissue fibers that interlace
between cells. 7. Some proteins, especially in conjunction with carbohydrate are important in
the cell‘s ability to recognize ‗self‘ and in cell-to-cell interactions.
42
Recognition of ―self‖ and cell-to-cell interactions. Cells recognize each other and form
tissues; complex carbohydrates act as a ―trademark‖ of a particular cell type, for
recognition.
Carbohydrate-containing surface markers are important in growth. Cells do not
overgrow their own territory. Abnormal surface markers present in tumor cells, and
abnormality may underline uncontrolled growth.
Some CAMS have carbohydrate, on the outermost tip where they participate in cell
adhesion activity.
Functions of biological membranes
The phospholipid bilayers provide the basic structure of the membrane and they also restrict
entry and exit of polar molecules and ion. The other molecules in the membrane have a
variety of function:
Channel protein and carrier protein: these proteins are involved in the selective
transport of polar molecule and ion across the membrane
Enzymes: membrane proteins sometimes act as enzymes, For example, the microvilli
on epithelial cells lining some part of the gut contain digestive enzymes in their cell
surface membrane
Receptor molecules: proteins have very specific shapes and this makes them ideal as
receptor molecules for chemical signaling between cells.
o For example, hormones are chemical messengers, which circulate in the blood
but, only bind to specific target cells, which have the correct receptors sites.
Neurotransmitters, the chemicals that enable nerve impules from one nerve cell
to the next, also fit into specific receptor proteins in nerve cells.
Antigens: these act as cell identity markers or ''name tag''. They are glycoproteins that
is proteins with branching carbohydrates side chains like antennae. There is an
enormous number of possible shapes to these side chains, so each type of cell can have
its own specific markers.
This enables cells to recognize other cells, and to behave in an organized way, for
example, during development of tissues and organs in multicellular organisms. It also
means that foreign antigens can be recognized and attacked by the immune system.
43
Glycolipids- also have branching carbohydrate side chain and are involved in cell-cell
recognition. They may act as a receptor sites for chemical signals. With glycoproteins
they also involved in sticking the correct cell together in tissues. Eg. sperm recognition
of ova
Energy Transfer in photosynthesis and respiration proteins take part in the energy
transfer systems that exist in the membranes of chloroplast and mitochondria
respectively.
Cholesterol: acts like a plug, reducing even further the escape or entry of polar
molecules through the membrane.
Cells are found in different organisms, and are very diverse in their size, shape and their
internal structure and this also applies to cells found in the same organism. This diversity is
influenced by their roles and function within organism‘s body.
44
Fig: 3.9. Various types of animal cells (shape)
The plasma membrane is selectively permeable. Lipid-soluble substances and small ions can
passively diffuse through the plasma membrane down their electro-chemical gradients.
Highly lipid-soluble particles are able to dissolve in the lipid bilayer and pass through the
membrane. Uncharged/non-polar molecules oxygen, carbon dioxide and fatty acids are highly
45
lipid-soluble and readily permeate the membrane. Charged particle sodium/potassium ions
and polar molecules such as glucose and proteins have low lipid solubility, but are very
soluble in water. For water-soluble ions of less than 0.8 nm diameters, protein channels serve
as an alternate route for passage. Ions for which specific channels are available can permeate
the plasma membrane. Particles with low lipid-permeability and too large for channels, cannot
permeate the membrane on their own. The phospholipid bilayer is a good barrier around cells,
especially to water soluble molecules. However, for the cell to survive some materials need to
be able to enter and leave the cell. There are 4 basic mechanisms:
1. Diffusion and facilitated diffusion
2. osmosis
3. active transport
4. bulk transport
Two forces are involved in facilitating movement across the plasma membrane:
1. Forces that do not require the cell to expend energy for movement – passive force
2. Forces requiring energy (as ATP) to be expended to transport across the membrane - active
force
Diffusion
Diffusion is the net movement of molecules (or ions) from a region of their high
concentration to a region of their lower concentration. The molecules move down a
concentration gradient. Molecules have kinetic energy, which makes them move about
randomly. All molecules in liquid and gases are in continuous random motion in any direction
as they have more room to move before colliding with another. As a result of this haphazard
movement, the molecules frequently collide bouncing off each other in different directions.
The greater the concentration, the greater the likelihood of collision. Such a difference in
concentration in molecules between two adjacent areas is chemical /concentration gradient.
The net movement of the molecule by diffusion will be from the higher area of concentration
to the area of lower concentration.
Certain additional factors that influence the rate of net diffusion across a membrane are:
46
3. molecular weight of the substance (lighter one diffuses rapidly)
4. distance through which diffusion must take place
N.B:- Increasing all the factors increases rate of net diffusion, except distance - thickness, that
if increased, decreases the rate of diffusion; and molecular weight if increased, decreases rate
of diffusion.
As a result of diffusion molecules reach an equilibrium where they are evenly spread out. This
is when there is no net movement of molecules from either side.
47
Fig:3.12. Diffusion of lipid molecules
Carrier- Mediated Transport
All carrier proteins span the thickness of the plasma membrane and are able to undergo
reversible changes in shape so that specific binding site can alternately be exposed at either
side of the membrane. As the molecule to be transported attaches to a binding site on the
carrier on one side of the membrane, it triggers a change in the carrier shape that causes the
same site to be exposed to the other side of the membrane. Their having movement in this
way, the bound molecule detaches from the carrier. This transport displays three
characteristics:
1. Specificity: each cell possesses protein specified to transport a specific substance or
few closely-related chemical compounds amino acid cannot bind to glucose carrier,
but similar amino acids may use the same carrier. Type of carriers vary in cells. A
number of inherited disorders involve defects in transport system for a particular
substance.
2. Saturation: in a given time only a limited amount of a substance can be transported
via a carrier; limited number of carrier site are available within a particular plasma
membrane for a specific molecule. This limit is known as transport maximum (Tm).
The substance‘s rates of transport across the membrane are directly related to its
concentration. When the Tm is reached, the carrier is saturated, and the rate of
48
transport is maximum. Further increase in the substance concentration is not
accompanied by corresponding increase in the rate of transport. Saturation of carrier is
a critical rate-limiting factor to the transport of selected substances across the plasma
membrane in kidney and the intestine. There is a mechanism to increase the number of
carriers in the plasma membrane.
3. Competition: Several closely related compounds may compete for ride across the
plasma membrane on the same carrier.
Facilitated Diffusion
Facilitated diffusion uses a carrier protein to facilitate the transfer of a particular substance
across the membrane ''downhill'' from higher to lower concentration. This process is passive
and does not require energy because movement occurs naturally down a concentration
gradient. Active transport, on the other hand, requires the carrier to expend energy to transfer
its passenger ''uphill'' against a concentration gradient from an area of lower concentration to
an area of higher concentration. Active transport requires protein carrier to transfer a specific
substance across the membrane, transporting against concentration gradient. Carrier
phophorylation increases the affinity for its passenger. The carrier has ATPase activity
splitting high-energy phosphate from an ATP to yield ADP plus a free Pi. This phosphate
group gets bound to the carrier.
Osmosis
Osmosis is the net diffusion of water down its own concentration gradient. Water can readily
permeate the plasma membrane. The driving force for diffusion of water is its concentration
gradient from area of higher water concentration (low solute) to the area of lower water (high
49
solute) concentration. This net diffusion of water is known as osmosis. Special mechanisms
are used to transport selected molecules unable to cross the plasma membrane on their own.
Active transport
Active transport is energy consuming transport of molecules or ions across a membrane
against its natural tendency to diffuse in the opposite direction. The movement of molecules
in active transport is in one direction only; unlike diffusion that is reversible the energy is
supplied by the broke down of ATP, which energy carrier is made in respiration
The major ions within the cells and their surrounding are sodium (Na+), potassium
(K+) and chloride (Cl-). In recent years it has been shown that the cell surface
membrane of most cell have sodium pump is coupled with a potassium pump that
actively moves potassium ion from outside to inside the cell. The combined pump is
called the sodium pump (Na+-K- pump).
The pump is a carrier protein that spans across the membrane from one side to the other. The
transfer of sodium and potassium across the membrane is brought about by the changes in the
shape of the protein. Note that for every 2K+ions taken into the cell, 3Na+ ions are removed.
Thus a potential difference is built up across the membrane, with the inner side of the
cell being negative. This tends to restrict the entry of negatively charged ions (anions)
such as chloride and favoring diffusion of cations into the cell. This explains why
50
chloride concentration inside red cell is less than the outside despite the fact that
chloride ions can diffuse in and out by facilitated diffusion
Similarly, positively charged ions (cations) tend to be attracted in to cell. Thus both
concentration and charge are important in deciding the direction in which ions cross the
membrane. The pump is essential in controlling the osmotic balance in animal cells
(osmoregulation) . If the pump is inhibited, the cell swells and brusts because of the building-
up of Na+, which results in excess water entering in to the cell by osmosis . The pump is also
important in maintaining electrical activity in nerve and muscle cells and in driving active
transport of some other substances such as sugar and amino acids. In addition, high
concentrations of potassium are needed inside cells for protein synthesis, glycolysis,
photosynthesis and other vital processes.
2. It helps regulate cell volume by controlling the concentration of solutes inside the cell and
thus minimizing osmotic effects that would induce swelling or shrinking of the cell.
51
3. The energy used to run the pump also indirectly serves as the energy source for the co-
transport of glucose and amino acids across the membrane (intestine and kidney cell).
Vesicular Transport The special cell membrane transport system selectively transports ions
and small polar molecules. But large polar molecules and even multimolecular material may
leave or enter the cell, such as hormone secretion or ingestion of invading microbe by
leukocytes. These materials cannot cross the plasma membrane but are to be transferred
between the ICF and ECF not by usual crossing but by wrapped in membrane. This process of
transport into or out of the cell in a membrane-enclosed vesicle is - vesicular transport.
Transport into the cell is termed endocytosis, whereas transport out of the cell is called
exocytosis. In endocytosis, the transported material is wrapped in a piece of the plasma
membrane, thus gaining entrance to the interior of the cell. Endocytosis of fluid is called
pinocytosis cell (drinking), whereas endocytosis of large multimolecular particle is known as
phagocytosis (cell eating).
Endocytosis and exocytosis are active processes involving the bulk transport of materials
through membranes, either in to cells (endocytosis)or out of cells (exocytosis).
52
Endocytosis occurs by an in folding or extension of cell surface membrane to form a vesicle
or vacuole. It is of two types.
Phagocytosis (cell eating) material taken up is in solid form. Cells specializing in the
processes are called phagocytes and are said to be phagocytic. The sac formed during the
uptake is called a phagocytic vacuole.
Pinocytosis (cell drink) material taken up is in liquid form. Vesicles formed are extremely
small, in which case the process is known as micropinocytosis and the vesicles as
micropinocytic vesicles. Pinocytosis is used by the human egg cell to take up nutrients from
the surrounding follicle cells.
Exocytosis is the reverse process of endocytosis. Waste materials such as solid and undigested
remains from phagocytic vacuoles may be removed from cells or useful materials may be
secreted. Secretion of enzymes from the pancreas is achieved in this way. Plant cells use
exocytosis to export the materials needed to form cell wall.
Activity
1. What is autophagy?
2. Describe the change in domination of types of plastids when a banana fruit gets ripened.
3. Describe the different sizes and shapes of cells? Why are so varied?
53
4. Compare and contrast respiration and biosynthesis.
5. write down roles of different components of cell membrane
6. How osmotic condition of the body is kept constant?
7. Which of the means of transport of materials in cells are active and which are passive?
What is the difference?
8. Differentiate endocytosis from exocytosis?
9. Explain the development of cell theory
10. What are the factors affecting the rate of diffusion?
54
Unit 4
Cellular Metabolism and Metabolic Disorders
Learning Objectives:
This chapter deals with the chemical reactions which keep us alive-metabolism. Therefore, at
the end of this chapter students are expected to
define and understand the different types of metabolism and ,metabolic pathways
understand the energy transduction in a cell
describe the nature and role of enzymes in metabolism
describe the main processes in photosynthesis and understand major photosynthetic
apparatus
understand the central metabolic pathways(glycolysis, kreb‘s cycle and electron
transport chain)
know some of the metabolic disorders of public health concern
Living cells are in a constant activity. Macromolecules are assembled and broken down,
substances are transported across cell membranes, and genetic instructions are transmitted. All
of these cellular activities require energy.
Living organisms are unique in that they can extract energy from their environments and use it
to carry out activities such as movement, growth and development, and reproduction. But the
basic question is how living organisms or, their cells extract energy from their environments,
and how cells use this energy to synthesize and assemble the components from which the cells
are made. The answers to these questions lie in the enzyme-mediated chemical reactions that
take place in living matter (metabolism). Hundreds of coordinated, multistep reactions, fueled
by energy obtained from nutrients and/or solar energy, ultimately convert readily available
materials into the molecules required for growth and maintenance.
55
Metabolism is thus the sum of chemical reactions that takes place within each cell of a living
organism and that provides energy for vital processes and synthesizing of new organic
materials. Broadly, these reactions can be divided into catabolic reactions that convert
nutrients to energy and anabolic reactions that lead to the synthesis of larger biomolecules.
In metabolism, a series of chemical reactions in which the product of one reaction is the
substrate for the next reaction is called a metabolic pathway. Catabolic pathways release
energy by breaking down larger molecules into smaller molecules. Anabolic pathways use the
energy released by catabolic pathways to build larger molecules from smaller molecules,
insuring the continual flow of energy within an organism. The reactants and products of these
chemical reactions are metabolites. The major classes of metabolites include proteins,
carbohydrates, nucleotides, lipids, coenzymes, and cofactors. These classes of compounds
encompass an enormous diversity of molecular structures, physicochemical properties,
functions, and abundances. Due to the analytical challenges posed by this diversity, most
studies require division into subsets of metabolites. The most common criteria for this
distinction rely on the hydrophilic (polar) and hydrophobic (nonpolar) nature of metabolites.
Polar metabolites are soluble in aqueous solutions and include most sugars, purines and
pyrimidines, nucleotides and nucleosides, acyl carnitines, organic acids, hydrophilic acids,
amino acids, and phosphorylated compounds. These metabolites include most of the reactants
and products involved in cellular respiration (e.g., glycolysis, the Kreb‘s cycle, or in other
pathways) and in the production of building blocks for synthesis of large biopolymers such as
DNA, RNA, proteins, and oligosaccharides. The nonpolar or hydrophobic metabolites are
commonly lipids. These metabolites function in energy storage, membrane structure, and
signal transduction.
At the cellular level of organization, the main chemical processes of all living matter are
similar, if not identical. This is true for animals, plants, fungi, or bacteria; where variations
occur (such as, the secretion of antibodies by some molds), the variant processes are but
variations on common themes. Thus, all living matter is made up of large molecules called
proteins, which provide support and coordinated movement, as well as storage and transport
of small molecules, and, as catalysts, enable chemical reactions to take place rapidly and
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specifically under mild temperature, relatively low concentration, and neutral conditions (i.e.,
neither acidic nor basic).
The chemical reactions that take place in living cells are similar as well. Green plants use the
energy of sunlight to convert water (H2O) and carbon dioxide (CO2) to carbohydrates (sugars
and starches), other organic (carbon-containing) compounds, and molecular oxygen (O2). The
process of photosynthesis requires energy, in the form of sunlight, to split one water molecule
into one-half of an oxygen molecule (O2; the oxidizing agent) and two hydrogen atoms (H;
the reducing agent), each of which dissociates to one hydrogen ion (H+) and one electron.
Through a series of oxidation-reduction reactions, electrons (denoted e−) are transferred from
a donating molecule (oxidation), in this case water, to an accepting molecule (reduction) by a
series of chemical reactions; this ―reducing power‖ may be coupled ultimately to the reduction
of carbon dioxide to the level of carbohydrate. In effect, carbon dioxide accepts and bonds
with hydrogen, forming carbohydrates (Cn[H2O]n). Living organisms that require oxygen
reverse this process: they consume carbohydrates and other organic materials, using oxygen
synthesized by plants to form water, carbon dioxide, and energy. The process that removes
hydrogen atoms (containing electrons) from the carbohydrates and passes them to the oxygen
is an energy-yielding series of reactions. In plants, all but two of the steps in the process that
converts carbon dioxide to carbohydrates are the same as those steps that synthesize sugars
from simpler starting materials in animals, fungi, and bacteria. Similarly, the series of
reactions that take a given starting material and synthesize certain molecules will be used in
other synthetic pathways are similar, or identical, among all cell types. For instance, from a
metabolic point of view, the cellular processes that take place in a lion are only marginally
different from those that take place in a dandelion.
Self-test
Most chemical reactions within cells do not occur spontaneously. Instead, they need a catalyst to
get them started. Why do you think this is so?
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In many cases, heat may be a catalyst, but this is inefficient because heat cannot be applied to
molecules in a controlled fashion. Thus, most chemical reactions require biological catalyst
called enzymes.
Enzymes are protein catalysts that speed biochemical reactions by facilitating the molecular
rearrangements that support cell function. Enzymes speed up (catalyze) chemical reactions; in
some cases, enzymes can make a chemical reaction millions of times faster than it would have
been without it. Almost all metabolic processes in the cell need enzyme catalysis in order to
occur at rates fast enough to sustain life.
Enzymes bind with particular reactants until the chemical reaction occurs, then free
themselves. Thus, at any given time, the numerous pathways involved in building up and
breaking down cellular components must be monitored and balanced in a coordinated fashion.
To achieve this goal, cells organize reactions into various enzyme-powered pathways.
Enzymes speed up reactions by lowering activation energy. Many enzymes change shape
when substrates bind. This is termed "induced fit", meaning that the precise orientation of the
enzyme required for catalytic activity can be induced by the binding of the substrate.
Many enzymes require the presence of other compounds (cofactors) before their catalytic
activity can be exerted. This entire active complex is referred to as the holoenzyme; i.e.,
apoenzyme (protein portion) plus the cofactor (coenzyme, prosthetic group or metal-ion-
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activator). Thus, on the basis of differences in chemical nature, the enzymes may be described
as follows:
Simple enzymes: Simple enzymes are made up of only protein (polypeptide). They
contain no chemical groups other than amino acid residues. Digestive enzymes such as
pepsin and trypsin are of this nature.
Isoenzymes (Isozymes): At one time it was believed that an organism has only a
single enzyme for a given step of a metabolic reaction. It was later discovered that a
substrate may be acted upon by a number of variants of an enzyme producing the same
product.
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Table 4.1. Major classes of Enzymes
An enzyme attracts substrates to its active site, catalyzes the chemical reaction by which
products are formed, and then allows the products to dissociate (separate from the enzyme
surface). The combination formed by an enzyme and its substrates is called the enzyme–
substrate complex. The substrates are attracted to the active site by electrostatic and
hydrophobic forces, which are called noncovalent bonds because they are physical
attractions and not chemical bonds.
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4.1.4 Factors affecting enzymatic activities
The activity of an enzyme is affected by its environmental conditions such as temperature and
pH. Changing these alter the rate of reaction caused by the enzyme. In nature, organisms
adjust the conditions of their enzymes to produce an optimum rate of reaction, where
necessary, or they may have enzymes which are adapted to function well in extreme
conditions where they live.
Temperature
Increasing temperature increases the kinetic energy that molecules possess. In a fluid, this
means that there are more random collisions between molecules per unit time. Since enzymes
catalyse reactions by randomly colliding with substrate molecules, increasing temperature
increases the rate of reaction, forming more product.
However, increasing temperature also increases the vibrational energy that molecules have,
specifically (in this case enzyme molecules), which puts strain (damage) on the bonds that
hold them together. As temperature increases, more bonds, especially the weaker hydrogen
and ionic bonds, will break as a result of this strain. Breaking bonds within the enzyme will
cause the active site to change shape. This change in shape means that the Active Site is less
complementary to the shape of the Substrate, so that it is less likely to catalyse the reaction.
Eventually, the enzyme will become denatured and will no longer function. The temperature
at which the maximum rate of reaction occurs is called the enzyme‘s Optimum Temperature.
This is different for different enzymes.
Activity
1. Graphically, show the relationship between enzyme activity and temperature.
2. What is the optimum temperature for most enzymes in the human body?
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charges created by the bonds. This interference causes a change in shape of the enzyme, and
importantly, its active site.
Different enzymes have different optimum pH values. This is the pH value at which the bonds
within them are influenced by H+ and OH- ions in such a way that the shape of their active
site is the most complementary to the shape of their substrate. At the optimum pH, the rate of
reaction is at an optimum. Any change in pH above or below the optimum will quickly cause
a decrease in the rate of reaction, since more of the enzyme molecules will have active sites
whose shapes are not (or at least are less) complementary to the shape of their substrate.
Small changes in pH above or below the optimum do not cause a permanent change to the
enzyme, since the bonds can be reformed. However, extreme changes in pH can cause
enzymes to denature and permanently lose their function. Enzymes in different locations of
our body have different optimum pH values since their environmental conditions may be
different. For example, the enzyme pepsin functions best at around pH-2 and is found in the
stomach, which contains hydrochloric acid.
Because enzymes are sensitive to changes in acidity, most living systems are highly buffered;
i.e., they have mechanisms that enable them to maintain a constant acidity.
Activity
What do you know about a buffer and its importance in the body of organisms?
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factor will be limiting the maximum rate of reaction. As a reaction proceeds, the rate of
reaction will decrease, since the substrate will get used up.
Substrate concentration
Increasing substrate concentration increases the rate of reaction. This is because more
substrate molecules will be colliding with enzyme molecules, so more product will be formed.
However, after a certain concentration, any increase will have no effect on the rate of reaction,
since substrate concentration will no longer be the limiting factor. The enzymes will
effectively become saturated, and will be working at their maximum possible rate.
Enzyme concentration
Increasing enzyme concentration will increase the rate of reaction, as more enzymes will be
colliding with substrate molecules. However, this too will only have an effect up to a certain
concentration, where the enzyme concentration is no longer the limiting factor.
Activity
Show graphically the relationships between enzyme activity and substrate
concentration as well as enzyme concentration
Reversible inhibition
Competitive inhibition: occurs when molecules very similar to the substrate molecules bind
to the active site and prevent binding of the actual substrate. Penicillin, for example, is a
competitive inhibitor that blocks the active site of an enzyme that many bacteria use to
construct their cell walls.
Noncompetitive inhibition: occurs when an inhibitor binds to the enzyme at a location other
than the active site. In some cases of noncompetitive inhibition, the inhibitor is thought to
bind to the enzyme in such a way as to physically block the normal active site. In other
instances, the binding of the inhibitor is believed to change the shape of the enzyme molecule,
thereby deforming its active site and preventing it from reacting with its substrate. This latter
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type of noncompetitive inhibition is called allosteric inhibition; the place where the inhibitor
binds to the enzyme is called the allosteric site. Frequently, an end-product of a metabolic
pathway serves as an allosteric inhibitor on an earlier enzyme of the pathway. This inhibition
of an enzyme by a product of its pathway is a form of negative feedback.
Activators: Allosteric control can involve stimulation of enzyme action as well as inhibition.
An activator molecule can be bound to an allosteric site and induce a reaction at the active site
by changing its shape to fit a substrate that could not induce the change by itself. Common
activators include hormones and the products of earlier enzymatic reactions. Allosteric
stimulation and inhibition allow production of energy and materials by the cell when they are
needed and inhibit production when the supply is adequate.
Irreversible inhibition
Irreversible inhibitors usually covalently modify an enzyme, and inhibition can therefore not
be reversed. Irreversible inhibitors often contain reactive functional groups. Irreversible
inhibition is different from reversible enzyme inactivation. Irreversible inhibitors are generally
specific for one class of enzyme and do not inactivate all proteins; they do not function by
destroying protein structure but by specifically altering the active site of their target
Activity
1. Describe other types of inhibition.
2. Relate the concept of irreversible enzyme inhibition to drug discovery and food poisoning.
3. Explain how painkillers like ibuprofen relieved you from pain.
4. What is the difference between endothermic and exothermic reaction?
5. What is meant by a catalyst?
6. Why are several enzymes needed in a typical metabolic path ways?
7. Which of the three (coenzyme, cofactor, apoenzyme) is a protein?
8. Describe three factors that that influences enzymatic activity.
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4.2 Bioenergetics and biosynthesis
Cellular respiration occurs in two main parts: glycolysis and aerobic respiration. The first
stage, glycolysis, is an anaerobic process. Anaerobic metabolic processes do not require
oxygen. Aerobic respiration includes the Krebs cycle and electron transport chain and is an
aerobic process. Aerobic metabolic processes require oxygen.
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important substrates are amino acids, which are obtained either from a protein-rich diet-for
example, during fasting on meat exclusively-or, during starvation, from breakdown of cellular
protein, mainly in skeletal muscle. Gluconeogenesis occurs in the liver and in the kidneys.
Self test
1. Define terms (glycolysis and gluconeogenesis)
2. Why glucose is more preferred by cells for respiration than other carbohydrates/lipids?
3. How is anaerobic respiration differing from aerobic respiration?
4. What are the three basic metabolic stages in respiration?
The first step in the degradation of glucose is glycolysis, which breaks down glucose to
pyruvate. The main purpose of glycolysis is the generation of energy (ATP). A modest
amount of ATP is produced in glycolysis directly, but much more ATP is formed downstream
of glycolysis through the complete oxidation of pyruvate. Glycolysis is the most common
pathway for glucose degradation to pyruvate and is found in animals, plants and
microorganism. This pathway is used by anaerobic as well as aerobic organisms. The process
takes place in the cytoplasm of prokaryotes and eukaryotes and does not require oxygen.
Under aerobic conditions, most of the pyruvate formed in glycolysis undergoes complete
oxidative degradation to CO2 and H2O.
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Activity
1. Which phases are regarded as the preparatory (or investment) phase? Why?
2. What is the purpose of each step?
3. What is the fate of pyruvate?
The first five are preparatory phases or investment phase. Here, glucose is phosphorylated,
rearranged and phosphorylated again, with the two phosphate groups coming from ATP.
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3. The phosphorylation of fructose-6-phosphate to the 1,6-bisphosphate by
phosphofructokinase,
The energy expenditure of another ATP in this step is justified in 2 ways: The
glycolytic process (up to this step) becomes irreversible, and the energy supplied
destabilizes the molecule. Because the reaction catalyzed by Phosphofructokinase
1 (PFK-1) is coupled to the hydrolysis of ATP (an energetically favorable step) it
is, in essence, irreversible, and a different pathway must be used to do the reverse
conversion during gluconeogenesis. This makes the reaction a key regulatory
point. This is also the rate-limiting step.
The second phosphorylation event is necessary to allow the formation of two
charged groups (rather than only one) in the subsequent step of glycolysis,
ensuring the prevention of free diffusion of substrates out of the cell.
The same reaction can also be catalyzed by pyrophosphate-dependent
phosphofructokinase (PFP or PPi-PFK), which is found in most plants, some
bacteria, archea, and protists, but not in animals. This enzyme uses pyrophosphate
(PPi) as a phosphate donor instead of ATP. It is a reversible reaction, increasing
the flexibility of glycolytic metabolism.
4. The cleavage of fructose-1,6-bisphosphate by aldolase. This yields two different
products, dihydroxyacetone phosphate and glyceraldehyde-3-phosphate,
Destabilizing the molecule in the previous reaction allows the hexose ring to be
split by aldolase into two triose sugars: dihydroxyacetone phosphate (a ketose),
and glyceraldehyde 3-phosphate (an aldose). There are two classes of aldolases:
class I aldolases, present in animals and plants, and class II aldolases, present in
fungi and bacteria; the two classes use different mechanisms in cleaving the ketose
ring.
Electrons delocalized in the carbon-carbon bond cleavage associate with the
alcohol group. The resulting carbanion is stabilized by the structure of the
carbanion itself via resonance charge distribution and by the presence of a charged
ion prosthetic group.
5. The isomerization of dihydroxyacetone phosphate to a second molecule of
glyceraldehyde-3-phosphate by triose phosphate isomerase,
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Triosephosphate isomerase rapidly interconvert dihydroxyacetone phosphate with
glyceraldehyde 3-phosphate (GADP) that proceeds further into glycolysis. This is
advantageous, as it directs dihydroxyacetone phosphate down the same pathway as
glyceraldehyde 3-phosphate, simplifying regulation.
Remember!!
The rest five are pay-off phases which are characterized by a net gain of the energy-
rich molecules ATP and NADH. Since glucose leads to two triose sugars in the
preparatory phase, each reaction in the pay-off phase occurs twice per glucose
molecule. This yields 2 NADH molecules and 4 ATP molecules, leading to a net gain
of 2 NADH molecules and 2 ATP molecules from the glycolytic pathway per glucose.
Along the way, the two molecules are rearranged into pyruvate.
6. The dehydrogenation and concomitant phosphorylation of glyceraldehyde-3-phosphate
to 1,3-bis-phosphoglycerate by glyceraldehyde-3-phosphate dehydrogenase,
The aldehyde groups of the triose sugars are oxidised, and inorganic phosphate is
added to them, forming 1, 3-bisphosphoglycerate.
The hydrogen is used to reduce two molecules of NADH, a hydrogen carrier, to
give NADH + H+ for each triose.
Hydrogen atom balance and charge balance are both maintained because the
phosphate (Pi) group actually exists in the form of a hydrogen phosphate anion
(HPO42-), which dissociates to contribute the extra H ion and gives a net charge of
-3 on both sides.
Note that: Arsenate (AsO43−), an anion similar to inorganic phosphate may replace
phosphate as a substrate to form 1-arseno-3-phosphoglycerate. This, however, is unstable and
readily hydrolyzes to form 3-phosphoglycerate, the intermediate in the next step of the
pathway. As a consequence of bypassing this step, the molecule of ATP generated from 1-3
bisphosphoglycerate in the next reaction will not be made, even though the reaction proceeds.
As a result, arsenate is an uncoupler of glycolysis during Arsenic poisoning.
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At this step, glycolysis has reached the break-even point: 2 molecules of ATP were
consumed, and 2 new molecules have now been synthesized. This step, one of the two
substrate-level phosphorylation steps, requires ADP; thus, when the cell has plenty of
ATP (and little ADP), this reaction does not occur. Because ATP decays relatively
quickly when it is not metabolized, this is an important regulatory point in the
glycolytic pathway.
ADP actually exists as ADPMg−, and ATP as ATPMg2−, balancing the charges at -5
both sides.
8. The isomerization of 3-phosphoglycerate to 2-phosphoglycerate by phosphoglycerate
mutase(PGAM),
Note that: PGAM plays an important role in coordinating glycolysis and anabolic activity to
promote cancer cell proliferation. It is suggested that even under aerobic conditions cancer
cells can show a high rate of glycolysis and increased production of lactate, generating ATP
faster than normal cells. However, to obtain sufficient ATP and carbons to generate biomass
[nucleotides, amino acids, lipids and nicotinamide adenine dinucleotide phosphate (NADPH)]
cancer cells must uptake more glucose than normal cells to meet the metabolic requirements
of rapid cell proliferation owing to the low efficiency of glycolysis.
Most, but not all reactions in glycolysis are reversible; this can be indicated by different
arrows (Fig. 4.1). Because it contains several irreversible reactions, the pathway as a whole
is also irreversible. However, alternate routes exist that bypass the irreversible reactions and
allow glucose to be synthesized from pyruvate.
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molecules, such as glycogen or starch. The reverse reaction, breaking down, e.g., glycogen,
produces mainly glucose-6-phosphate; very little free glucose is formed in the reaction. The
glucose-6-phosphate so produced can enter glycolysis after the first control point.
In the second regulated step (the third step of glycolysis), phosphofructokinase converts
fructose-6-phosphate into fructose-1, 6-bisphosphate, which then is converted into
glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. The dihydroxyacetone
phosphate can be removed from glycolysis by conversion into glycerol-3-phosphate, which
can be used to form triglycerides. Conversely, triglycerides can be broken down into fatty
acids and glycerol; the latter, in turn, can be converted into dihydroxyacetone phosphate,
which can enter glycolysis after the second control point.
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Activity
1. Relate regulation of the rate limiting enzymes to homeostasis and biosynthesis?
2. Name and describe diseases related to failure in one or more of the steps of glycolysis?
3. Write the overall reactions of glycolysis.
4. Which of the following are products of cellular respiration?
A. Glucose; B. Pyruvate; C. Carbon dioxide; D. Acetyl CoA E.all except A
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Finally, acetyl CoA and citric acid are generated and the cycle continues.
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Oxaloacetate can also be converted to phosphoenolpyruvate, which is a
precursor of glucose.
Acetyl - CoA is the starting material for fatty acid biosynthesis.
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2. How many ATP molecules are collected during electron transport chain and chemiosmosis
from a single glucose?
4.2.2 Biosynthesis
Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into
more complex products in living organisms. In biosynthesis, simple compounds are modified,
converted into other compounds, or joined together to form macromolecules. This process
often consists of metabolic pathways. Some of these biosynthetic pathways are located within
a single cellular organelle, while others involve enzymes that are located within multiple
cellular organelles. Examples of these biosynthetic pathways include the production of lipid
membrane components and nucleotides. Biosynthesis is usually synonymous with anabolism.
The prerequisite elements for biosynthesis include: precursor compounds, chemical energy (e.g.
ATP), and catalytic enzymes which may require coenzymes (e.g.NADH, NADPH). These
elements create monomers, the building blocks for macromolecules. Some important biological
macromolecules include: proteins, which are composed of amino acid monomers joined via
peptide bonds, and DNA molecules, which are composed of nucleotides joined via
phosphodiester bonds.
Requirements of Biosynthesis
Sometimes all that is required for biosynthesis is for two substances to physically join
together to make a new physical substance, which is called a macromolecule.
A very simplified equation for biosynthesis of one form of macromolecule: two substances
join together to form a new, more complex substance.
i. Photosynthesis
Self-test
1. Define photosynthesis.
2. What is an ultimate source of energy for all life forms?
Energy is transformed all around us every day. Batteries convert chemical energy into electric
energy, and radios convert electric energy into the energy carried by sound waves. Similarly,
some autotrophs convert light energy into chemical energy through photosynthesis.
The importance of photosynthesis
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The processes of all organisms, from bacteria to humans require energy. To get this energy,
many organisms access stored energy by eating food. Carnivores eat other animals and
herbivores eat plants. But where does the stored energy in food originate? All of this energy
can be traced back to the process of photosynthesis and light energy from the sun.
Photosynthesis is essential to all life on earth. It is the only biological process that captures
energy from outer space (sunlight) and converts it into chemical energy in the form of
Glyceraldehyde3-phosphate (G3P), which in turn can be made into sugars and other organic
compounds such as proteins, lipids, and nucleic acids. Plants use these compounds in all of
their metabolic processes; plants do not need to consume other organisms for food because
they build all the molecules they need. Unlike plants, animals need to consume other
organisms to consume the molecules they need for their metabolic processes.
The process of photosynthesis
During photosynthesis, molecules in leaves capture sunlight and energize electrons, which are
then stored in the covalent bonds of carbohydrate molecules. That energy within those
covalent bonds will be released when they are broken during cell respiration. How long
lasting and stable are those covalent bonds? The energy extracted today by the burning of coal
and petroleum products represents sunlight energy captured and stored by photosynthesis
almost 200 million years ago.
Plants, algae, and some bacteria such as cyanobacteria are the only organisms capable of
performing photosynthesis. Because they use light to manufacture their own food, they are
called photoautotrophs (―self-feeders using light‖). Other organisms, such as animals, fungi,
and most other bacteria, are termed heterotrophs (―other feeders‖) because they must rely on
the sugars produced by photosynthetic organisms for their energy needs. A third very
interesting group of bacteria synthesize sugars, not by using sunlight‘s energy, but by
extracting energy from inorganic chemical compounds; hence, they are referred to as
chemoautotrophs.
The importance of photosynthesis is not just that it can capture sunlight‘s energy. A lizard
sunning itself on a cold day can use the sun‘s energy to warm up. Photosynthesis is vital
because it evolved as a way to store the energy in solar radiation (the''photo'' part) as high-
energy electrons in the carbon-carbon bonds of carbohydrate molecules (the ''synthesis'' part).
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Those carbohydrates are the energy source that heterotrophs use to power the synthesis of
ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth‘s ecosystems.
When a top predator, such as a wolf, preys on a deer, the wolf is at the end of an energy path
that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to
vegetation, to deer, and finally to wolf.
During oxygenic photosynthesis, light energy transfers electrons from water (H2O) to carbon
dioxide (CO2), to produce carbohydrates. In this transfer, the CO2 is "reduced," or receives
electrons, and the water becomes "oxidized," or loses electrons. Ultimately, oxygen is
produced along with carbohydrates.
On the other hand, anoxygenic photosynthesis uses electron donors other than water. The
process typically occurs in bacteria such as purple bacteria and green sulfur bacteria, which
are primarily found in various aquatic habitats.
Anoxygenic photosynthesis does not produce oxygen. What is produced depends on the
electron donor. For example, many bacteria use the bad-eggs-smelling gas hydrogen sulfide,
producing solid sulfur as a byproduct.
Though both types of photosynthesis are complex, multistep affairs, the overall process can be
neatly summarized as a chemical equation.
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CO2 + 2H2A + Light Energy → [CH2O] + 2A + H2O
The letter A in the equation is a variable and H2A represents the potential electron donor. For
example, A may represent sulfur in the electron donor hydrogen sulfide (H2S).
Self test
1. What cellular components are essential to photosynthesis?
2. why plant leaves vary in color?
Plastids
Photosynthetic eukaryotic organisms contain organelles called plastids in their cytoplasm.
Plastids generally contain pigments or can store nutrients. Colorless and
nonpigmented leucoplasts store fats and starch, while chromoplasts contain carotenoids
and chloroplasts contain chlorophyll.
Photosynthesis occurs in the chloroplasts; specifically, in the grana and stroma regions. The
grana is the innermost portion of the organelle; a collection of disc-shaped membranes,
stacked into columns like plates. The individual discs are called thylakoids. It is here that the
transfer of electrons takes place. The empty spaces between columns of grana constitute the
stroma.
Chloroplasts are similar to mitochondria, the energy centers of cells, in that they have their
own genome, or collection of genes, contained within circular DNA. These genes encode
proteins essential to the organelle and to photosynthesis. Like mitochondria, chloroplasts are
also thought to have originated from primitive bacterial cells through the process of
endosymbiosis.
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Fig: 4.4. Structure of chloroplast
Pigments
Pigments are molecules that bestow color on plants, algae and bacteria, but they are also
responsible for effectively trapping sunlight. Pigments of different colors absorb different
wavelengths of light. Below are the three main groups.
Chlorophylls: These green-colored pigments are capable of trapping blue and red
light. Chlorophylls have three subtypes, dubbed chlorophyll a, chlorophyll b and
chlorophyll c. There is also a bacterial variant aptly named bacteriochlorophyll, which
absorbs infrared light. This pigment is mainly seen in purple and green bacteria, which
perform anoxygenic photosynthesis.
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Fig: 4.5. Basic structures of major photosynthetic pigments
Antennae
Pigment molecules are associated with proteins, which allow them the flexibility to move
toward light and toward one another. A large collection of 100 to 5,000 pigment molecules
constitutes antennae. These structures effectively capture light energy from the sun, in the
form of photons.
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Ultimately, light energy must be transferred to a pigment-protein complex that can convert it
to chemical energy, in the form of electrons. In plants, for example, light energy is transferred
to chlorophyll pigments. The conversion to chemical energy is accomplished when a
chlorophyll pigment expels an electron, which can then move on to an appropriate recipient.
Reaction centers
The pigments and proteins, which convert light energy to chemical energy and begin the
process of electron transfer, are known as reaction centers.
Light-dependent reactions (also called light reactions): When a photon of light hits the
reaction center, a pigment molecule such as chlorophyll releases an electron.
The released electron manages to escape by traveling through an electron transport chain,
which generates the energy needed to produce ATP (adenosine triphosphate, a source of
chemical energy for cells) and NADPH. The "electron hole" in the original chlorophyll
pigment is filled by taking an electron from water. As a result, oxygen is released into the
atmosphere.
Light-independent reactions (also called dark reactions and known as the Calvin cycle):
Light reactions produce ATP and NADPH, which are the rich energy sources that drive dark
reactions.
Although NADPH and ATP provide cells with large amounts of energy, these molecules are
not stable enough to store chemical energy for long periods of time. Thus, there is a second
phase of photosynthesis called the Calvin cycle in which energy is stored in organic molecules
such as glucose.
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Three chemical reaction steps make up the Calvin cycle: carbon fixation, reduction and
regeneration. These reactions use water and catalysts. The carbon atoms from carbon dioxide
are ''fixed,'' when they are built into organic molecules that ultimately form three-carbon
sugars. These sugars are then used to make glucose or are recycled to initiate the Calvin cycle
again.
In the first step of the Calvin cycle called carbon fixation, six carbon dioxide
(CO) molecules combine with six 5-carbon compounds to form twelve 3-
carbon molecules called 3-phosphoglycerat (3-PGA). The joining of carbon
dioxide with other organic molecules is called carbon fixation.
In the second step, the chemical energy stored in ATP and NADPH is
transferred to the 3-PGA molecules to form high-energy molecules called
glyceraldehyde 3-phosphates (G3P). ATP supplies the phosphate groups for
forming G3P molecules, while NADPH supplies hydrogen ions and electrons.
In the third step, two G3P molecules leave the cycle to be used for the
production of glucose and other organic compounds. In the final step of the
Calvin cycle, an enzyme called rubisco converts the remaining ten G3P
molecules into 5-carbon molecules called ribulose 1, 5-bisphosphates (RuBP).
These molecules combine with new carbon dioxide molecules to continue the
cycle.
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Fig:4.6. Calvin cycle
Because rubisco converts inorganic carbon dioxide molecules into organic molecules that can
be used by the cell, it is considered one of the most important biological enzymes. Plants use
the sugars formed during the Calvin cycle both as a source of energy and as building blocks
for complex carbohydrates, including cellulose, which provides structural support for the
plant.
Alternative Pathways
The environment in which an organism lives can impact the organism‘s ability to carry out
photosynthesis. Environments in which the amount of water or carbon dioxide available is
insufficient can decrease the ability of a photosynthetic organism to convert light energy into
chemical energy. For example, plants in hot, dry environments are subject to excessive water
loss that can lead to decreased photosynthesis. Many plants in extreme climates have altered
native photosynthesis pathways to maximize energy conversion.
C4 plants one adaptive pathway that helps plants maintain photosynthesis while minimizing
water loss is called the C4 pathway. The C4 pathway occurs in plants such as sugar cane and
corn. These plants are called C4 plants because they fix carbon dioxide into four-carbon
compounds instead of three-carbon molecules during the Calvincycle. C4 plants also have
significant structural modifications in the arrangement of cells in the leaves. In general, C4
plants keep their stomata (plant cell pores) closed during hot days, while the four carbon
compounds are transferred to special cells where CO2 enters the Calvin cycle. This allows for
sufficient carbon dioxide uptake, while simultaneously minimizing water loss.
CAM plants another adaptive pathway used by some plants to maximize photosynthetic
activity is called crassulacean acid metabolism (CAM photosynthesis). The CAM pathway
occurs in water conserving plants that live in deserts, salt marshes, and other environments
where access to water is limited. CAM plants, such as cacti, orchids, and the pineapple allow
carbon dioxide to enter the leaves only at night, when the atmosphere is cooler and more
humid. At night, these plants fix carbon dioxide into organic compounds. During the day,
carbon dioxide is released from these compounds and enters the Calvin cycle. This pathway
Also allows for sufficient carbon dioxide uptake, while minimizing water loss.
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Scientific Tips!!
Photosynthesis in the future
Photosynthetic organisms are a possible means to generate clean-burning fuels such as hydrogen or even
methane. Recently, a research group at the University of Turku in Finland, tapped into the ability of green algae
to produce hydrogen. Green algae can produce hydrogen for a few seconds if they are first exposed to dark,
anaerobic (oxygen-free) conditions and then exposed to light. The team devised a way to extend green algae's
hydrogen production for up to three days, as reported in their 2018 study published in the journal Energy and
Environmental Science.
Scientists have also made advances in the field of artificial photosynthesis. A group of researchers from the
University of California, Berkeley, developed an artificial system to capture carbon dioxide using nanowires, or
wires that are a few billionths of a meter in diameter. The wires feed into a system of microbes that reduce
carbon dioxide into fuels or polymers by using energy from sunlight. The team published its design in 2015 in the
journal Nano Letters.
In 2016, members of this same group published a study in the journal Science that described another artificial
photosynthetic system in which specially engineered bacteria were used to create liquid fuels using sunlight,
water and carbon dioxide. In general, plants are only able to harness about one percent of solar energy and use
it to produce organic compounds during photosynthesis. In contrast, the researchers' artificial system was able
to harness 10 percent of solar energy to produce organic compounds.
Continued research of natural processes, such as photosynthesis, aids scientists in developing new ways to
utilize various sources of renewable energy. Seeing as sunlight, plants and bacteria are all ubiquitous, tapping
into the power of photosynthesis is a logical step for creating clean-burning and carbon-neutral fuels.
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4.3 Metabolic disorders, diagnosis and treatments
Self-test
1. What are the risk factors for metabolic disorders?
2. How are metabolic disorders treated?
Metabolism is the breaking down of food to its simpler components: proteins, carbohydrates
(or sugars), and fats. Metabolic disorders occur when these normal processes become
disrupted. Disorders in metabolism can be inherited, in which case they are also known as
inborn errors of metabolism, or they may be acquired during your lifetime.
There are numerous examples of inherited metabolic disorders, which can be classified based
on the type of food-related building block that they affect, including amino acids (the
building block for proteins), carbohydrates, and fatty acids (the building block for fats).
Inherited causes of metabolic disorders include:
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Other causes of metabolic disorders
Metabolic disorders can be due to other factors, such as a combination of inherited and
environmental factors. Some of the conditions that can cause metabolic disorders include:
Alcohol abuse, Diabetes (chronic disease that affects your body‘s ability to use sugar
for energy)
Diuretic abuse, Gout (type of arthritis caused by a buildup of uric acid in the joints)
Ingestion of poison or toxins, including excessive aspirin, bicarbonate, alkali, ethylene
glycol, or methanol
Kidney failure, Pneumonia, respiratory failure, or collapsed lung
Sepsis (life-threatening bacterial blood infection)
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4.3.2 Diagnosis of metabolic disorders
Metabolic syndrome is more effectively diagnosed by testing different blood markers (specific
markers of insulin resistance), obesity (especially abdominal obesity), high blood pressure,
and lipid abnormalities. Specifically, metabolic syndrome is diagnosed if any three of the
following five markers are present:
Elevated waist circumference: 40 inches or more for men; 35 inches or more for
women
Elevated triglycerides: 150 mg/dL or higher
Reduced high-density lipoprotein (HDL) levels (AKA ''good'' cholesterol): less than
40 mg/dL in men; less than 50 mg/dL in women
Elevated blood pressure: 130/85 mm Hg or higher or are already taking blood pressure
medications
Elevated fasting glucose: 100 mg/dL or higher or are already taking glucose-lowering
medications
Acquired metabolic disorder treatment will include normalizing the metabolic balance by both
reversing the cause and administering medications.
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Activity
1. What are the risk factors of metabolic disorders?
2. How are metabolic disorders treated?
3. Write down the common metabolic disorders and their symptoms.
Summary
Phenylketonuria is an example of an inherited metabolic disorder characterized by an
inability to break down one of the building blocks of protein, the amino acid
phenylalanine.
Type I diabetes, a disease in which the pancreas does not create enough insulin to
maintain balanced blood sugar levels, is a metabolic disorder of sugar metabolism.
An example of a metabolic disorder affecting fat metabolism is Gaucher’s disease,
which is characterized by a lack of the of the enzyme glucocerebrosidase.
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Unit 5
Learning Objectives: After completing this chapter, you should be able to:
Self test
1. Define terms ( genetics and evolution)
2. What is the importance of studying genetics?
3. What is the inter-relationship between genetics and evolution?
Genetics forms one of the central pillars of biology and overlaps with many other areas, such
as agriculture, medicine, and biotechnology. Since the start of civilization, humankind has
recognized the influence of heredity and applied its principles to the improvement of
cultivated crops, domestic animals and industrial microbes. Most of the mechanisms of
heredity, however, remained a mystery until the 19th century, when genetics as a systematic
science began.
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Genetics is a field of biology that studies how traits are passed from parents to their offspring.
The passing of traits from parents to offspring is known as heredity; therefore, genetics is the
study of heredity. The basic components of genetics are DNA, RNA, genes, chromosomes and
genetic inheritance. DNA molecules hold all the genetic information for almost all organisms.
It provides cells with the information they need to perform tasks that allow an organism to
grow, survive and reproduce. A gene is one particular section of a DNA molecule that tells a
cell to perform one specific task. Heredity is what makes offspring look like their parents.
During reproduction, DNA is replicated and passed from a parent to their offspring. This
inheritance of genetic material by offspring influences the appearance and behavior of the
offspring. The environment that an organism lives in can also influence how genes are
expressed.
Genes (and, thus, the traits they code for) are passed from parent to offspring. From
generation to generation, well-understood molecular mechanisms reshuffle, duplicate, and
alter genes in a way that produces genetic variation. This variation is the raw material for
evolution.
Activities
Students take an inventory of their own easily-observable genetic traits and compare those
inventories with other students in groups.
Can you think of a trait you have inherited? How about a trait that you have acquired by
learning or tradition?
What inherited traits do you share in common with others? What traits are unique to you?
Learn how common chronic diseases (such as heart disease) run in families and how risk for
developing these diseases is influenced by the combined action of several genes.
Identical twins have exactly the same DNA, but they are not exactly alike. Each twin has his
or her own personality, talents, likes, and dislikes. There are even diseases that appear in one
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twin but not in the other, including arthritis, diabetes, autism, schizophrenia, cancer, and many
others. What do you think is the reason?
It is wondering why you are the only one in your family with your grandfather's nose? The
way in which traits are passed from one generation to the next, and sometimes skip
generations was first explained by Gregor Mendel. By experimenting with pea plant breeding,
Mendel developed three principles of inheritance that described the transmission of genetic
traits, before anyone knew genes existed. Mendel's insight greatly expanded the understanding
of genetic inheritance, and led to the development of new experimental methods.
Traits are passed down in families in different patterns. Pedigrees can illustrate these patterns
by following the history of specific characteristics, or phenotypes, as they appear in a family.
The inheritance pattern in which traits of generation I has passed down through the family tree
is considered dominant, because it is observable in every generation. Thus, every individual
who carries the genetic code for this characteristic will show evidence of the characteristic. A
characteristic may disappear in one generation, only to reappear in a subsequent one. This
pattern of inheritance, in which the parents do not show the phenotype but some of the
children do, is considered recessive.
Mendelian inheritance is a type of biological inheritance that follows the principles originally
proposed by Gregor Mendel in 1865 and 1866. It was re-discovered in 1900 and popularized
by William Bateson. These principles were initially controversial and even rejected by some
scholars. When Mendel's theories were integrated with the Boveri–Sutton chromosome theory
of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics.
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Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book. The
genetic theory of natural selection, putting evolution onto a mathematical footing and forming
the basis for population genetics within the modern evolutionary synthesis.
Gregor Johann Mendel formulated his idea after conducting simple hybridisation experiments
with pea plants (Pisum sativum) he had planted in the garden of his monastery. From these
experiments, he induced two generalizations which later became known as Mendel's
Principles of Heredity or Mendelian inheritance.
Activities
1. Why Mendel choose Pisum sativum for his experimentation?
2. Recall the basic experiments Mendel used to convey his principles of inheritance
3. What were the major conclusions of Mendel's experiment?
Mendel's results were largely ignored by the vast majority. Although they were not
completely unknown to biologists of the time, they were not seen as generally applicable,
even by Mendel himself, who thought they only applied to certain categories of species or
traits. In 1900, however, his work was "re-discovered" by some scientist. Regardless, the "re-
discovery" made Mendelism an important but controversial theory.
Mendel's findings allowed some scientists to predict the expression of traits on the basis of
mathematical probabilities. An important aspect of Mendel's success can be traced to his
decision to start his crosses only with plants he demonstrated were true-breeding. He only
measured discrete (binary) characteristics, such as color, shape, and position of the seeds,
rather than quantitatively variable characteristics. He expressed his results numerically and
subjected them to statistical analysis.
Mendel's conclusions
Five parts of Mendel's discoveries were an important divergence from the common theories at
the time and were the prerequisite for the establishment of his rules.
1. Characters are unitary. That is, they are discrete (purple vs. white, tall vs. dwarf).
2. Genetic characteristics have alternate forms, each inherited from one of two parents.
Today, we call these alleles.
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3. One allele is dominant over the other. The phenotype reflects the dominant allele.
4. Gametes are created by random segregation. Heterozygotic individuals produce
gametes with an equal frequency of the two alleles.
5. Different traits have independent assortment. In modern terms, genes are unlinked
Chromosome is a thread- like structure that is made up of DNA (deoxyribonucleic acid) and
histone (a set of globular (30) proteins). While DNA is the molecule that stores genetic
information whereas histone is the core of a chromosome around which chromosome‘s DNA
wrapped is the loosely organized form of chromosome throughout the nucleus in loops when
the cell is not dividing is called Chromatin. Individual chromosomes are not easily
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distinguished unless condensed. On the condensed organization of chromosome, genes are
inactive while uncondensed or loose organization allows the genes to be active. As a cell
prepares for cell division, the chromatin loops will have duplicated themselves and become
compacted or ―condensed‖ to form a chromosome that is visible under light microscope.
DNA-is made up two strands of polynucleotides joined together and twisted into a double
helix and the strands are anti-parallel to each other. The basic unit of DNA strand is a
nucleotide (monomers of DNA). There are four types of nucleotides:-
Adenine (A) – containing nucleotide
Guanine (G) – containing nucleotide
Cytosine (C) - containing nucleotide
Thymine (T) – containing nucleotide (in DNA, or Uracil (U) nucleotide in RNA)
All nucleotides have: a phosphate group, a pentose sugar (deoxyribose in DNA and ribose
sugar in RNA) and one of four nitrogen bases- adenine, cytosine guanine and either thymine
(DNA) or uracil (RNA).
Bonds between the sugar in one nucleotide and the phosphate group in the next hold the
nucleotides together. The base does not take in this linking of the nucleotides in a strand. That
is the reason why we say ‗sugar- phosphate‘ backbone. The nucleotides in one strand are
paired with the nucleotides in the other strand according to the base pairing- rule.
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Fig:5.1. Structure of DNA
Activity
1. Recall structures and types of the four bases that make up nucleotide.
2. What types of bonds tie sugar to a phosphate group and the two Nitrogenous bases on each
strands?
3. Why the DNA strands run anti-parallel and exist as a double helix?
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2. Recall the phases of eukaryotic cell division and describe briefly emphasizing on major
events
3. What are the biological purposes of cell division?
The ability of DNA to make copy of itself (DNA-replication) is the basis for reproduction and
inheritance. DNA molecule exists within chromosome (in the nucleus) and is surrounded by a
'soup' of free DNA nucleotides (which is to build new DNA molecules). DNA structure is
double helix and must replicate semi-conservatively. Each formed new DNA molecule
contains one strand from the original (old) DNA and one new strand DNA molecules. Both
new DNA molecules formed are identical to each other and to the original molecule. Several
Enzymes are involved in this process and the main stages are:
1. DNA helicase enzyme - break H-bonds to reveal two single strands and unwind (open)
the helix DNA
2. DNA polymerase follows the helicase enzyme along each single-stranded region,
which acts as a template for the synthesis of a new strand.
3. DNA polymerase assembles free DNA nucleotides into new strands alongside each of
the template strands. The base sequence in each of these new strands is
complementary to its template strand because of base- pairing rule, A-T, C-G.
4. Two-identical DNA molecules to each other and the original one is resulted. Each
contains one strand from the original (old) and one newly synthesized.
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Fig: 5.2.
Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells.
Cell division usually occurs as part of a larger cell cycle. In eukaryotes, there are two distinct
types of cell division: a vegetative division, whereby each daughter cell is genetically
identical to the parent cell (mitosis), and a reproductive cell division, whereby the number of
chromosomes in the daughter cells is reduced by half to produce haploid gametes (meiosis).
Meiosis results in four haploid daughter cells by undergoing one round of DNA replication
followed by two divisions. Homologous chromosomes are separated in the first division, and
sister chromatids are separated in the second division. Both of these cell division cycles are
used in the process of sexual reproduction at some point in their life cycle. Both are believed
to be present in the last eukaryotic common ancestor.
Prokaryotes (bacteria) undergo a vegetative cell division known as binary fission, where their
genetic material is segregated equally into two daughter cells. While binary fission may be the
means of division by most prokaryotes, there are alternative manners of division, such as
budding, that have been observed. All cell divisions, regardless of organism, are preceded by
a single round of DNA replication.
For simple unicellular microorganisms such as amoeba, one cell division is equivalent to
reproduction; an entire new organism is created. On a larger scale, mitotic cell division can
create progeny from multicellular organisms, such as plants that grow from cuttings. Mitotic
cell division enables sexually reproducing organisms to develop from the one-celled zygote,
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which itself was produced by meiotic cell division from gametes. After growth, cell division
by mitosis allows for continual construction and repair of the organism. The human body
experiences about 10 quadrillion cell divisions in a lifetime.
The primary concern of cell division is the maintenance of the original cell's genome. Before
division can occur, the genomic information that is stored in chromosomes must be replicated,
and the duplicated genome must be separated cleanly between cells. A great deal of cellular
infrastructure is involved in keeping genomic information consistent between generations.
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Tips on cell division!!
Multicellular organisms replace worn-out cells through cell division. In some animals,
however, cell division eventually halts. In humans this occurs, on average, after 52
divisions, known as the Hayflick limit. The cell is then referred to as senescent. With
each division the cells telomeres, protective sequences of DNA on the end of a
chromosome that prevent degradation of the chromosomal DNA, shorten. This
shortening has been correlated to negative effects such as age related diseases and
shortened lifespan in humans. Cancer cells, on the other hand, are not thought to
degrade in this way, if at all. An enzyme complex called telomerase, present in large
quantities in cancerous cells, rebuilds the telomeres through synthesis of telomeric
DNA repeats, allowing division to continue indefinitely.
Self-test
1. What is genetic code?
2. How information stored on DNA is utilized?
Code for protein synthesis is specified by DNA and has to be sent to ribosome. DNA is a huge
molecule and remains in nucleus to assemble amino acids in the correct sequence to form
protein.
Events during protein synthesis
i. Transcription – DNA code for protein is rewritten in a molecule of messenger RNA
(MRNA)
ii. MRNA travels from nucleus to ribosome
iii. Free amino acids are transported from cytoplasm to ribosome by transfer RNA (tRNA)
molecules
iv. Ribosome read mRNA code and assembles amino acids presented by tRNA into a
protein by a process = translation
Translation – is process in which mRNA code is converted into a sequence of amino
acids
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DNA transcription mRNA translation tRNA /RNA synthesis protein/polypeptide/
Genetic code
The genetic code is held in the DNA molecule. It is because of the nucleotides sequence in the
DNA molecule made a gene that codes for protein to that each amino acid in the protein is
coded for by a triplet /sequence of three bases/. Hence, a gene is a sequence of base triplets in
the DNA molecule that carries a code for a protein.
1. Since there are 4 bases, there is 43 = 64 possible triplet codes /amino acids/ but only 20
amino acids are used to make all different proteins.
Activity
What is the purpose of the other 44 codes?
None of them is spare or redundant.
2. Only one strands of a DNA molecule carries the code for proteins (It is called sense
strand or coding stand) and the other strand is non-coding or antisense strand.
3. Most amino acids have more than one code, only methionine and tryptophan have one
code.
Arginine has six codes
4. Three triplets (TAA, TAG, and TGA) do not code for amino acids and they are called
stop codons. stop codes signify the end of the coding sequence
5. Degenerate code – the DNA code is non-overlapping codes i.e., each triplet is distinct
from all other triplets.
6. The genetic code is also a universal codei.e. the triplet code TAT in the DNA code for
amino acid tyrosine in human, redwood tree, bacterium or in any organism
E.g. ACC – threonine, GGG-glycine
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Fig:5.6. Genetic code
N.B. It is not just the base that matter but the sequence, e.g.ATT codes of different amino acid
from TTA
The enzyme DNA-dependent RNA polymerase binds with a section of DNA next to the gene
to be transcribed. Transcription factors activate the enzyme. The enzymes ―unwind‖ and
separate the strands of a DNA molecule. The polymerase assembles free RNA nucleotides on
the complementary strand (antisense strand). mRNA (transcribed RNA) leaves the DNA; the
strands of DNA rejoin & re-coil.
N.B. The mRNA molecule now contains the code for the protein that was held in the DNA of
the genes
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Activity
1. How does transcription take place in eukaryotic cells?
2. How does translation take place?
Translation of mRNA code into a protein depends on the interaction within a ribosome
between mRNA and tRNA. All tRNA molecules have same basic structure. The ''cloverleaf''
configuration of the molecules has at one end a triplet of bases called anticodon. The
anticodon is a triplet on tRNA. The other end of tRNA molecule has an attachment site for the
aminoacid that is specified by the mRNA codon. Ribosomes are made from ribosomal RNA
and proteins organized into large & small subunits. Within ribosome, there are three sites
called A, P and E sites.
N.B. The translation of the mRNA code into a protein molecule requires energy that comes
from hydrolysis of GTP /guanoisne triphosphate/ not ATP
Self test
1. How is protein synthesis different in prokaryotic cells?
2. What are the fates of some of proteins-synthesized in our body?
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Though it is similar to eukaryotes, there are some differences like: Prokaryotic cell have no
nucleus. Prokaryotic mRNA does not need post-transcriptional process because it only
contains exons (coding genes) not introns (non-coding genes). Transcription and translation
are coupled - mRNA translated at one end of ribosome while it is start transcribing from DNA
at other end.
Note. Not all amino acids are produced by transamination only those we obtain from our food.
They are called essential amino acid.
Genes are switched on by "transcription factors"- are proteins that bind to a regulatory
sequence of DNA near to the gene they influence. They operate in the following way: The
transcription factors bind to a promoter sequence of DNA near the gene to be activated. RNA
polymerase binds to the DNA/ transcription factor complex. The RNA polymerase activated
and moves away from the DNA along the gene. The RNA polymerase transcribes the
antisense strand of the DNA and the gene is now being expressed.
Like transcription factors that promote gene expression, there are factors to repress (switched
off) gene action. Short interfering RNA (siRNA)
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Is post transcriptional interference
If mRNA is prevented from translating its Codons into amino acid then the protein for which
the gene codes for cannot be built (silenced).
1.10.1.4 Mutations
Self-Test
1. What are mutations?
2. Is there a spontaneous change in the genetic material of an organism?
3. What causes mutation?
4. Are mutation useful, harmful or both? how?
Mutation is the alteration of the nucleotide sequence of the genome of an organism, virus, or
extrachromosomal DNA.
Mutation could occur spontaneously (accidentally) during duplication.
They are rare events.
Each cell contains 6x109/billion/ base parts occurrence
1. Point mutations- changes that involves a single base. There are several types of point
mutations, some of these are:
Substitution- one base is replaced by other base
Addition-a base is missed out during DNA replication.
Deletions – an extra base is added.
2. Chromosomal Mutations- situation where part /segment/ of a chromosome sequence of
DNA is disturbed/ a chromosome is missed/added. Types of chromosomal mutations:
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Euploidy/polyploidy/-is a condition where an organism/ a cell has one complete set
of extra chromosomes/an exact multiple of a complete set.
Variation in number of chromosomes sets (one set of chromosome). E.g –
Triploid ,Tetraploid
Aneuploidy – is a condition where an organism/a cell lost from or added to one or
more chromosomes to/the normal set of chromosome
2 n+1 = trisomy/47 chromosomes, e.g. Down‘s syndrome
2n-1 = monosomics – turner syndrome/45chr.
2n+1+1 = double trisomy
2n-2 – nullisomic, organisms that loss one homologous chromosome.
Gidu syndrome = mental retardation – caused by part of deletion of chromosome
number 5 of man.
Consequence of gene-mutations
Mutations on body cell (non- sex cell) cannot be inherited but may result in one of the
following:
harmless
damage the cell
kill the cell
Make cell cancerous- which might kill the person.
Mutations in different genes will obviously produce different effects but two types of gene are
important in regulating cell division and preventing the formation of a tumor.
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Manipulation of DNA
Genetic engineering
Self test
1. What is genetic engineering?
2. What do you think of human cloning?
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To produce plants and animals that have high growth rate and reduced
susceptibility to disease – reduce use of fertilizers and pesticides.
Animals and plants can be 'tailor made' to show desirable characteristics
Early experiments with human blood transfusion often resulted in the death of the patient for
unknown reasons. In 1901, it was discovered that there were three blood types, A, B, and O,
and that mixing blood from different types caused an immune response that resulted in
clumping. Type AB is rare and was discovered later.
ABO Blood Type: An individual's red blood cells will contain proteins of type A, or B, or
both, or neither. The body produces antibodies that will attack any foreign type. Alleles of
types IA and IB are dominant over type i.
Rh Factor (D antigen): The Rh factor, the second most important blood group system after
the ABO blood group system, was first discovered in Rhesus monkeys. The Rh factor is
inherited independently from the ABO blood type. Genotypes for the Rh factor are +/+, +/-,
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and -/-. People who are +/+ or +/- possess the Rh(D) antigen and test as Rh positive. People
who are -/- do not posess the Rh(D) antigen and test as Rh negative.
Activities
Table 1: The following tables give information on human blood types needed in problems
below. Alleles of types IA and IB are dominant over type i.
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1. A patient is rushed to the emergency room and has suffered severe blood loss. Type AB
blood is in short supply, but the nurse says "Don't worry, he's type AB positive. We can give
him any kind of blood." Explain. (Why is type AB called the universal recipient?)
2. On the battlefield, a medic is treating a soldier who has lost a great deal of blood. They are
out of blood typing supplies so the medic, who is Type O negative, simply donates his own
blood to the patient. Why could this work? (Why is Type O called the universal donor?)
3. There is a practical joker in the maternity ward who removed all the baby id bracelets.
There are three babies that cannot be easily distinguished and the parents want to be sure they
get the right ones back so the doctors do a blood test. A particular mom is homozygous type A
and the dad is type O. The babies have blood types AB, A, and O. Show your work below and
indicate which baby must be theirs.
MOM
IA IA
i IAi IAi
4. The police have rounded up the usual suspects in the latest rash of bookstore robberies. The
thief got a nasty paper cut at the scene of the crime. The suspects are of blood types O, A, B
and AB. The blood at the crime scene contained i alleles. Which suspect therefore cannot
have been involved? Explain.
5. In a paternity case, a single mother claimed that a certain man was the father of her baby.
The man denied it, claiming that her current boyfriend was the father. The court ordered a
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blood test (much cheaper than DNA testing) to see if he could be ruled out as the father. The
mother was Type O and the baby was Type O. The man was Type AB. Is it possible that he
was the father? Why or why not?
6. Why is it that a blood type test can only disprove but never prove paternity? Why are DNA
tests used to "prove" paternity instead?
7. (True Story) In Denmark, a husband and wife who had been unsuccessfully trying to have
a baby went to a fertility clinic. Sperm and eggs were collected from father and mother, and
combined in a petri dish, creating several "test-tube babies". These babies were implanted in
the mother and 9 months later she delivered twins, one with light skin and one with dark skin.
Because this seemed strange, a DNA test was conducted and it was found that both children
were related to the mother, but only the light skinned child was related to the father. How can
this be explained?
8. Rh factors are proteins that were first discovered in the blood of Rhesus Monkeys, but
humans have them too. If you are Rh positive, it means that there are Rh type proteins in your
blood. If you are Rh negative, there are no Rh type proteins in your blood. Positive is
dominant over negative, so heterozygous individuals are Rh positive. Problems can arise
when an Rh negative mother has a child who is Rh positive. Why does the mother's body
attack her own baby in this situation? Why does the situation get worse for the second
pregnancy?
9. The father of two children is type O+, and the mother is type A+. The children are O- and
A+. Given this information, what can you say about the genotypes of father and mother?
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5.4 Introduction to Evolution
Self-test
1. What are the main creationist views on the origin of life on Earth?
2. Explain how Francisco Redi and Louis Pasteur disproved spontaneous generation
theory.
3. How evidences of evolutionist theory support the process of evolution?
Evolution is the gradual change of organisms on the earth over long periods, with new forms
replacing old ones. As evolution has progressed new species are arising, the biodiversity of
the planet increasing, larger and more complex organisms replaced the smaller and some
species has get extinct.
Evolution can also be the change in genetic composition of a population over successive
generations which may be caused by meiosis, hybridization, natural selection or mutation.
This leads to a sequence of events by which the population diverges from other populations of
the same species and may lead to the origin of a new species. Theories about the origin of life
on Earth. The theory of evolution describes how the various forms of life on earth (including
humans) emerged and developed. There are five main theories of the origin of life on Earth:
special creationism
spontaneous generation
eternity of life
cosmozoan theory
biochemical origin
a) Special creationism
Special creation theory states that the different forms of life on earth were created by a
Supreme Being/ God/ at once with six days. Special creation is always linked to religion and
mainly focused on spiritual matters that cannot be seen, touched or measured effectively.
There are two views on the origin of life:
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Progressive creation – accepts the Big Bangs as the origin of the universe. It accepts the fossil
record of a series of creation for all of the organisms but it does not accept these as part of a
continuing process (each is seen as unique creation).
Evolutionary creationism (Theistic evolution) – This view of evolution maintains that God
‗invented‘ evolution and takes some form of an active part in the ongoing process of
evolution.
Intelligent design – a theory states that life developed (formed) due to a combination of
natural forces and the intervention of a supernatural being.
c) Eternity of life
The theory of eternity of life states that the universe has always existed and that there has
always been life in the universe. There is no beginning and no end to life on earth and so life
is neither created nor generated from non-living matters
d) Cosmozoan Theory
States that life on the earth originally came from elsewhere in the universe (possibly from
another planet). E.g. Meteorites brought bacterial spores, germs to the earth. This theory did
not gain any significant support because it lacks evidence and it is strongly linked to the
‗eternity of life‘ theory of the origin life.
e) Biochemical theory
It suggests that life on earth originated as a result of a number of biochemical reactions
producing organic molecules, which combined (associated) to form cells. This theory is also
called abiogenesis; states life originates from chemical inanimate (abiotic substances). The
two scientists (biologists) who developed the theory of abiogenesis (origin of life from
chemicals) were:- Aleksander Oparin (1924) and John Haldane (1929). They both suggested:
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There was an appropriate supply of energy, such as lightening or ultraviolet
light (Uv – rays).
This would provide the energy for reactions that would synthesize a wide range
of organic compounds (amino acids, sugars and fatty acids).
Oparin suggested that the atmosphere of the primitive earth contained NH3, H2, water vapour
(H2O (g)) and CH4. He suggested that at high temperature (above boiling point), these gases
could have undergone a series of chemical reactions and might have formed colloidal
aggregates or coacervates (collections of droplets that composed of molecules of different
types). Oparin considered that these coacervates were able to absorb and assimilate organic
compounds (amino acids, DNA and others) and leading to the first true cells.
J. Haldane – proposed that the chemical reactions of these gases were occurred in the
primitive sea by solar energy and the sea became a ‗hot dilute soup‘ of organic monomers and
small polymers.
In 1953, Stanley Miller tested the biochemical theory. He applied electrical sparks repeatedly
through a mixture of gases (NH3, water, H2 and CH4) that were represent the primitive
atmosphere of the earth (no oxygen) connected a flask of heated water.
Miller leaving the equipment for longer periods of time, a larger variety and more complex
organic molecules were formed including:
Origin of Autotrophy: The first life (cell) appeared on earth – about 4 billion years ago and
they were:- anaerobes, heterotrophs and prokaryotes. They would have fed on organic
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chemicals (soup) which formed spontaneously in the waters of the earth. The three
consecutive lines of evolution of organisms on earth leading to:
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Use and disuse – Lamarck suggested that a structure or process in organism that can be used
continuous will become enlarged or more developed but any structure that is not. Example,
According Lamarck, giraffe had short neck but they stretched their neck to reach high
branches, developed an elongated neck use theory. The wings of penguins would have
become smaller than those of other birds because penguins do not use their wings to fly disuse
theory. Inheritance of Acquired traits – Lamarck believed that traits changed (acquired during
an organism‘s lifetime could be passed on to its offsprings. Example: - Giraffes that had
acquired long necks would have offspring with long necks.
Note: - Nowadays, Lamarck‘s theories are not accepted because the environmental changes
that were believed by Lamarck have brought about the changes in the phenotypes (Physical
appearance) of the organisms have no effect on their gametes and hence their heredity.
In 1858, both Charles Darwin and Alfred Wallace jointly published a scientific paper that
proposed species were modified by natural selection. Darwin visited five of the Galapagos
Islands, made drawings, and collected species. In particular, Darwin studied the finches found
on the different islands and noted there were many similarities between them but have some
obvious differences. Darwin concluded that an ―ancestral finch‖ had colonized the Islands
from mainland and been able to adapt to the different conditions on the islands and evolve
into different species. E.g. He suggested that some finches had evolved into insect eaters
(pointed peak), other in to seedeaters (crushing peak). Darwin summarized his observations in
two main ideas:
• all species tend to produce more offsprings than can possibly survive (Fecundity)
• There is a variation among the offsprings.
• There will be a ―struggle for existence‖ between members of a species because they
are over – reproduced and resources are limited.
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• Some members of a species will be better adapted than others to the environment
because there is a variation in the offspring.
Darwin proposed: - Those members of a species, which are best adapted to their environment,
will survive and reproduce in greater number than other less adapted (died out).
• Those individuals with the advantageous allele of a gene will survive to reproduce in
greater number than other types
• Advantageous alleles pass to their offsprings in greater numbers than other genes
(alleles).
• The frequency of the advantageous allele will be higher in the next generation of a
population.
Mutations are important in introducing variation into population. Any mutation could
produce an allele which:
• Increase in frequency if they are beneficial in their effect, may increase slowly, stable
or decrease if they are neutral and decrease and could disappear if they are harmful
(disadvantages) in their effects.
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Unit 6
Learning Objectives: upon successful completion of this unit, you should be able to:
Self-test
1. What are the important steps to cause infection?
2. What make infectious diseases different from other types of diseases?
Infectious diseases are diseases caused by living organisms called infectious agents like
bacteria, viruses, fungi, protozoa, and helminthes and prions, It occurs as the result of
interactions between pathogenic (disease-producing) microorganisms and the host. All
infectious diseases begin at some surface of the host, whether it is the external surfaces such
as the skin and conjunctiva or internal surfaces such as the mucous membranes of the
respiratory tract, intestine, or urogenital tract.
In order to cause infectious disease a pathogen must accomplish the following steps:-
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1. It must enter the host,
2. It must metabolize and multiply on or in the host tissue.
3. It must resist host defenses
4. It must damage the host.
In order to cause disease, pathogens must be able to enter the host body, adhere to specific
host cells, invade and colonize host tissues, and inflict damage on those tissues. Entrance to
the host typically occurs through different entry route such as the mouth, eyes, or genital
openings, or through wounds that breach the skin barrier to pathogens. Although some
pathogens can grow at the initial entry site, most must invade areas of the body where they are
not typically found. They do this by attaching to specific host cells. Some pathogens then
multiply between host cells or within body fluids, while others such as viruses and some
bacterial species enter the host cells and grow there. Although the growth of pathogens may
be enough to cause tissue damage in some cases, damage is usually due to the production of
toxins or destructive enzymes by the pathogen.
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Contagious disease: A disease that is easily spread from one host to another
Non-communicable disease: A disease that is not transmitted from one host to
another
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• Viremia: viruses in the blood
• Focal infection: systemic infection that began as a local infection
• local tooth infection can moves via blood or lymph to set up a new infection at
another site - rheumatoid arthritis
• Primary: acute infection causing initial illness
• Secondary: occurs after host is weakened from primary infection
• Subclinical (inapparent): no noticeable signs and symptoms
6.1.1 Pathogenicity
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Self-test
What are opportunistic pathogens?
We contact numerous microorganisms daily when we breathe in, ingest with food and drink,
and pick up on skin. Most microbes are harmless and many are beneficial. Vast majority
generate no ill effects and relatively few are pathogens that cause damage. These
microorganisms are classified based on their pathogenicity:-
Primary pathogen is microbe or virus that causes disease in otherwise healthy individual.
Diseases such as plague, malaria, measles, influenza, diphtheria, tetanus, tuberculosis, etc.
These pathogenic organisms are called virulent because of their virulence factor. Virulence
refers to a degree of pathogenicity, which is caused by virulence factors are traits that allow
microorganism to cause disease.
Opportunistic pathogen (opportunist) causes disease only when body‘s innate or adaptive
defenses are compromised or when introduced into unusual location. It can be members of
normal microbiota or common in environment (e.g., Pseudomonas).
Normal microbiota (normal flora) are organisms that routinely reside on body‘s surfaces
and the relationship is delicate balance and some can cause disease if opportunity arise. This
is due to the fact that weaknesses or defects in innate or adaptive defenses can leave
individuals vulnerable to invasion.
• These individuals are said to be immune-compromised
• Factors include malnutrition, cancer, AIDS or other disease, surgery, wounds, genetic
defects, alcohol or drug abuse, and immunosuppressive therapy following procedures
such as organ transplants.
6.1.9. The spread of infection
• Human reservoirs of infection - people who have a disease or are carriers of
pathogenic microorganisms.
• Sick people = actively ill
• Carriers = one who harbors disease organisms in their body without
manifest symptoms (healthy).
• Latent infection carriers = contagious during incubation period or
convalescent period.
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• Zoonoses - are diseases that affect wild and domestic animals and can be
transmitted to humans.
• Direct contact with animal or its waste
• Eating animals
• Blood sucking arthropods
• Nonliving reservoirs - soil, water, and food can be reservoirs of infection.
• Presence of microorganisms is often due to contamination by
feces or urine.
Activity: -
1. Discuss the differences between:-
• Infection and diseases
• Sign and Symptom
• Incidence and prevalence
• Endemic and epidemic
• Acute and Chronic
• Primary and secondary infection
Bacteria, viruses, fungi, protozoa, parasites, and prions are different types of pathogen. They
vary in their size, shape, function, genetic content, and how they act on the body. For
example, viruses are smaller than bacteria, and they can enter a host and take over cells.
However, bacteria can survive without a host.
The common pathogens known as causative agents for different types of infectious diseases
are:-
6.2.1 Bacteria
Self-test
Bacteria are unicellular prokaryotic organisms; they have circular genomes, double-stranded
DNA that is associated with much less protein than eukaryotic genomes. Most bacteria
reproduce by growing and dividing into two cells in a process known as binary fission.
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Despite their commonalities that group them together in the Kingdom Monera, there are a
variety of morphologies among them, but three of the most common are bacillus (rod-shaped),
coccus (spherical), or spirillum (helical rods). The energy sources for bacteria also vary. Some
bacteria are photosynthetic and obtain their energy directly from the sun. Others oxidize
inorganic compounds to supply their energy needs. Still other bacteria generate energy by
breaking down organic compounds such as amino acids and sugars in a respiratory process.
Some bacteria require oxygen (aerobes), while others are unable to tolerate it (anaerobes).
Some bacteria can grow either with or without oxygen (facultative anaerobes).
Bacteria are frequently divided into two broad classes based on their cell wall structures,
which influences their Gram stain reaction. Gram-negative bacteria appear pink after the
staining procedure. Familiar pathogenic gram-negative organisms are Salmonella typhi, which
causes typhoid fever, and Yersinia pestis, which causes plague. Gram-positive bacteria appear
purple after the Gram staining procedure. Examples of pathogenic gram-positive bacteria
are Staphylococcus aureus, which causes skin, respiratory, and wound infections,
and Clostridium tetani, which produces a toxin that can be lethal for humans.
There are trillions of strains of bacteria, and few of these cause diseases in humans. Some of
them live inside the human body without causing harm, for example in the gut or airways.
Some bacteria attack other bacteria and prevent them from causing sickness.
However, some bacterial diseases are deadly which include: cholera, diphtheria, dysentery,
bubonic plague, pneumonia, tuberculosis, typhoid, typhus and etc.
Some examples of bacterial infections are: bacterial meningitis, otitis media, pneumonia,
tuberculosis, upper respiratory tract infection, gastritis, food poisoning, eye infections,
sinusitis, urinary tract infections, skin infections and sexually transmitted diseases. Bacterial
infections can be treated with antibiotics, but some strains become resistant and can survive
the treatment.
6.2.2 Viruses
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Viruses can infect all organisms, from plants and animals to fungi and bacteria. Viruses,
however, are not organisms themselves because, apart from a host cell, they have no
metabolism and cannot reproduce. A virus particle is composed of a viral genome of nucleic
acid that is surrounded by a protein coat called a capsid. In addition, many viruses that infect
animals are surrounded by an outer lipid envelope, which they acquire from the host cell
membrane as they leave the cell. Unlike organisms, in which the genetic material is always
double-stranded DNA, viral genomes may be double- or single-stranded DNA (a DNA virus),
or double- or single-stranded RNA (an RNA virus).
In the general process of infection and replication by a DNA virus, a viral particle first
attaches to a specific host cell via protein receptors on its outer envelope, or capsid. The viral
genome is then inserted into the host cell, where it uses host cell enzymes to replicate its
DNA, transcribe the DNA to make messenger RNA, and translate the messenger RNA into
viral proteins. The replicated DNA and viral proteins are then assembled into complete viral
particles, and the new viruses are released from the host cell. In some cases, virus-derived
enzymes destroy the host cell membranes, killing the cell and releasing the new virus
particles. In other cases, new virus particles exit the cell by a budding process, weakening but
not destroying the cell.
In the case of some RNA viruses, the genetic material can be used directly as messenger RNA
to produce viral proteins, including a special viral RNA polymerase that copies the RNA
template to produce the genetic material for new viral particles. Other RNA viruses, called
retroviruses, use a unique enzyme called reverse transcriptase to copy the RNA genome into
DNA. This DNA then integrates itself into the host cell genome. These viruses frequently
exhibit long latent periods in which their genomes are faithfully copied and distributed to
progeny cells each time the cell divides. The human immunodeficiency virus (HIV), which
causes AIDS, is a familiar example of a retrovirus.
Viruses cause disease by disrupting normal cell function. They do this in a variety of ways.
Some viruses make repressor proteins that stop the synthesis of the host cell's proteins, RNA,
and DNA. Viral activity may weaken cell membranes and lysosomal membranes, leading to
cell autolysis. Some viral proteins are toxic to cells, and the body's immune defenses also may
kill virus-infected cells.
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Viruses are classified using a variety of criteria, including shape, size, and type of genome.
Among the DNA viruses are the herpes viruses that cause chicken pox, cold sores, and painful
genital lesions, and the poxvirus that causes smallpox. Significant RNA viruses that cause
human disease include rhinoviruses that cause most common colds; myxoviruses and
paramyxoviruses that cause influenza, measles, and mumps; rotaviruses that cause
gastroenteritis; and the retroviruses that cause AIDS and several types of cancer.
Viruses invade a host and attach themselves to a cell. As they enter the cell, they release
genetic material. The genetic material forces the cell to replicate, and the virus multiplies.
When the cell dies, it releases new viruses, and these go on to infect new cells. Not all viruses
destroy their host cell. Some of them change the function of the cell. In this way, viruses such
as human papillomavirus (HPV) or Epstein-Barr virus (EBV) can lead to cancer by forcing
cells to replicate in an uncontrolled way.
.A virus may remain dormant for a period before multiplying again. The person with the virus
can appear to have recovered but may get sick again when the virus reactivates. Antiviral
medications help in some cases. They can either prevent the virus from reproducing or boost
the host's immune system.
Antibiotics are not effective against viruses. Using antibiotics against a virus will not stop the
virus, and it increases the risk of antibiotic resistance. Most treatment aims to relieve
symptoms while the immune system combats the virus without assistance from medicine.
6.2.3 Fungi
Self-test
1. What are the important characteristics of fungi which make them different from virus and
bacteria?
2. Why most of fungal treatments are topical?
Fungi are eukaryotic, heterotrophic organisms that have rigid cellulose- or chitin-based cell
walls and reproduce primarily by forming spores. Most fungi are multicellular, although
some, such as yeasts, are unicellular. Together with bacteria, fungi fulfill the indispensable
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role of decomposers in the environment. Many fungal infections will appear in the upper
layers of the skin, and some progress to the deeper layers. Inhaled fungal spores can lead to
systemic fungal infections, such as thrush, or candidiasis. Systemic diseases affect the whole
body.
Those with a higher risk of developing a fungal infection include people who:
use strong antibiotics for a long time
have a weakened immune system, due, for example, to HIV or AIDS, diabetes,
chemotherapy treatment, and those who have undergone a transplant, as they take
medications to prevent their body from rejecting the new organ
Many fungi infect plants and animals. Examples of diseases caused by fungi are ringworm
and histoplasmosis (a mild to severe lung infection transmitted by bat or bird droppings).
Yeasts of the Candida genus are opportunistic pathogens that may cause diseases such as
thrush (a throat infection) among people who are immunocompromised or undergoing
antibiotic therapy.
6.2.3 Protozoa
Self test
Protozoa are unicellular, heterotrophic eukaryotes that include the familiar amoeba and
paramecium. Because protozoa do not have cell walls, they are capable of a variety of rapid
and flexible movements. Protozoa can be acquired through contaminated food or water or by
the bite of an infected arthropod such as a mosquito. Diarrheal disease can be caused by two
common protozoan parasites, Giardia lamblia and Cryptosporidium parvum. Malaria, a
tropical illness that causes 300 million to 500 million cases of disease annually, is caused by
different species of the protozoan Plasmodium.
6.2.4 Helminths
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Helminths are simple, invertebrate animals, some of which are infectious parasites. They are
multicellular and have differentiated tissues. Because they are animals, their physiology is
similar in some ways to ours. This makes parasitic helminth infections difficult to treat
because drugs that kill helminths are frequently very toxic to human cells.
Many helminths have complex reproductive cycles that include multiple stages, many or all of
which require a host. The common helminthes are Ascaries, tape worm, hook worm
Schistosoma etc.
6.2.6. Prions
Self-test
The known prion diseases include Creutzfeldt-Jakob disease (in humans), scrapie (in sheep),
and bovine spongiform encephalopathy ("mad cow disease" in cattle); all known prion
diseases frequently result in brain tissue that is riddled with holes. While some prion diseases
are inherited, others are apparently due to infection by eating infected tissue or inadvertently
through medical procedures such as tissue transplants.
Activities
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4. List two examples of aerobic and anaerobic bacteria.
5. What makes gram positive bacteria different from gram negative bacteria?
Infectious agents may be transmitted through either direct or indirect contact. Direct contact
occurs when an individual is infected by contact with the reservoir, for example, by touching
an infected person, ingesting infected meat, or being bitten by an infected animal or insect.
Transmission by direct contact also includes inhaling the infectious agent in droplets emitted
by sneezing or coughing and contracting the infectious agent through intimate sexual contact.
Some diseases that are transmitted primarily by direct contact with the reservoir include
ringworm, AIDS, trichinosis, influenza, rabies, and malaria.
Indirect contact occurs when a pathogen can withstand the environment outside its host for a
long period of time before infecting another individual. Inanimate objects that are
contaminated by direct contact with the reservoir (for example, a tissue used to wipe the nose
of an individual who has a cold or a toy that has been handled by a sick child) may be the
indirect contact for a susceptible individual. Ingesting food and beverages contaminated by
contact with a disease reservoir is another example of disease transmission by indirect contact.
The fecal-oral route of transmission, in which sewage-contaminated water is used for
drinking, washing, or preparing foods, is a significant form of indirect transmission, especially
for gastrointestinal diseases such as cholera, rotavirus infection, cryptosporidiosis, and
giardiasis.
These modes of transmission are all examples of horizontal transmission because the
infectious agent is passed from person to person in a group. Some diseases also are
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transmitted vertically; that is, they are transmitted from parent to child during the processes of
reproduction (through sperm or egg cells), fetal development, or birth. Diseases in which
vertical transmission occurs include AIDS and herpes encephalitis (which occurs when an
infant contracts the herpes simplex type II virus during birth).
The immune system is the body‘s biological defense mechanism that protects against foreign
invaders. The true roots of the study of the immune system date from 1796 when an English
physician, Edward Jenner, discovered a method of smallpox vaccination. He noted that dairy
workers who contracted cowpox from milking infected cows were thereafter resistant to
smallpox. In 1796, Jenner injected a young boy with material from a milkmaid who had an
active case of cowpox. After the boy recovered from his own resulting cowpox, Jenner
inoculated him with smallpox; the boy was immune. After Jenner published the results of this
and other cases in 1798, the practice of Jennerian vaccination spread rapidly.
In addition Louis Pasteur who established the cause of infectious diseases and the medical
basis for immunization. Pasteur formulated his germ theory of disease, the concept that
disease is caused by communicable microorganisms. In 1880, Pasteur discovered that aged
cultures of fowl cholera bacteria lost their power to induce disease in chickens but still
conferred immunity to the disease when injected. He went on to use attenuated (weakened)
cultures of anthrax and rabies to vaccinate against those diseases.
The immune system is composed of a number of different cell types, tissues and organs. Many
of these cells are organized into separate lymphoid organs or glands. Since attack from
microbes can come at many different sites of the body, the immune system has a mobile force
of cells in the bloodstream that are ready to attack the invading microbe wherever it enters the
body.
Although many of the cells of the immune system are separate from each other, they maintain
communication through cell contact and molecules secreted by them. For this reason the
immune system has been likened to the nervous system.
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The human body has several general mechanisms for preventing infectious diseases. Some of
these mechanisms are referred to as nonspecific or innate defenses because they operate
against a wide range of pathogens. Other mechanisms are referred to as specific or adaptive
defenses because they target particular pathogens and pathogen-infected cells.
Self-test
1. Explain about anatomical and physiological barriers of human body
2. What is inflammation?
Nonspecific mechanisms are the body's primary defense against disease. The Innate immune
system is the first line of defense which is present at birth and changes little throughout the
life of an individual. The cells and molecules of this innate system are mainly responsible for
the first stages of expulsion of the microbe. These mechanisms include anatomical barriers to
invading pathogens, physiological deterrents to pathogens, phagocytosis, inflammation and
the presence of normal flora. An example of an anatomical barrier is the nasal opening to the
respiratory system. This natural opening is a long, convoluted passage covered by mucous
membranes that trap airborne particles and prevent most of them from reaching the lungs.
Other anatomical barriers are the skull and vertebral column, which protect the central
nervous system few pathogens are able to penetrate bone. The skin also is a major anatomical
barrier to microorganisms. The surface layer of dead, hardened cells is relatively dry, and skin
secretions make the surface somewhat acidic. When sweat evaporates, salt is left behind on
the skin. All of these conditions (low moisture, low pH, and high salinity) prevent most
microorganisms from growing and multiplying on the skin. The major medical challenge in
treating burn patients is preventing and treating infections that result because of the absence of
skin that ordinarily would prevent invasion of microorganisms.
Natural openings also are protected by a variety of physiological deterrents. For example,
tears continually flush debris from the eyes. Vaginal secretions are acidic, a hostile
environment that discourages the growth of many pathogens. The eye, mouth, and nasal
openings are protected by tears, saliva, or nasal secretions that contain lysozyme, an enzyme
that breaks down bacterial cell walls. Blood, sweat, and some tissue fluids contain lysozyme
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as well. In addition to lysozyme, the blood has many elements that defend the body from
disease-causing organisms. The white blood cells include several types of phagocytic cells
that detect, track, engulf, and kill invading bacteria and viruses, as well as infected host cells
and other debris. These phagocytic cells are part of the nonspecific immune system. Blood
plasma also includes clotting factors that initiate a clot at the injury site, preventing pathogens
from invading the body further. Finally, the complement proteins in the blood participate in a
cascade of molecular events that result in inflammation, the release of molecules that
stimulate phagocytic cells, and the formation of a complex of proteins that binds to the surface
of bacterial or infected host cells and lyses those cells.
The inflammatory response is another nonspecific defense mechanism that helps to prevent
infectious agents from spreading in the body. Inflammation involves swelling, reddening,
elevated temperature, and pain. Unfortunately, inflammation itself frequently causes tissue
damage and, in severe cases, even death.
Finally, the protective role of the "normal flora" of microorganisms present on and in the body
should not be overlooked. These organisms survive and grow on the skin and in the mouth,
gastrointestinal tract, and other areas of the body, but do not cause disease because their
growth is kept under control by the host's defense mechanisms and by the presence of other
microorganisms. These organisms protect the host by successfully competing with disease-
causing organisms, preventing the latter from invading host tissues. When the growth of the
normal flora is suppressed (for example, due to antibiotic treatment), other "opportunistic"
agents that normally does not grow in or on the body may be able to infect and cause disease.
Summary
The Innate immune system is the first line of defense’ which is present at birth and changes
little throughout the life of the individual. The cells and molecules of this innate system are
mainly responsible for the first stages of expulsion of the microbe.
Some of the most important cells in the innate immune system are phagocytes, since they are
able to ingest and kill microbes. In general the innate immunity includes:-
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Cellular defense (phagocytosis and extracellular killing)
Inflammation
The complement system
Normal flora
Self-test
1. What is the main difference between T and B lymphocytes?
2. Explain about helper and killer T cells
3. What are antibodies?
When these nonspecific mechanisms fail, the body initiates a second, specific line of defense.
Adaptive immune system is brought into action even as the innate immune system is dealing
with the microbe, and especially if it is unable to remove the invading microbe. The key
difference between the two systems is that the adaptive system shows far more specificity and
remembers that a particular microbe has previously invaded the body. This leads to a more
rapid expulsion of the microbe on its second and third time of entry.
This specific immune response enables the body to target particular pathogens and pathogen-
infected cells for destruction. It depends on specialized white blood cells called lymphocytes
and includes T-cells (produced from lymphocytes that matured in the thymus gland) and B-
cells (produced from lymphocytes that matured in the bone marrow).
The two complementary components of the specific immune response are the cell-mediated
response and the antibody-mediated response. The cell-mediated response involves T-cells
and is responsible for directly destroying body cells that are infected with a virus or have
become cancerous, or for activating other immune cells to be more efficient microbe killers.
The antibody-mediated response involves both T-cells and B-cells and is critical for the
destruction of invading pathogens as well as the elimination of toxins.
Both the cell-mediated and antibody-mediated responses are initiated after a particular type of
phagocytic cell, a macrophage, engulfs a pathogen. Macrophages digest the pathogen and then
display antigens from the pathogen on their surface. Antigens are specific molecules, such as
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the proteins on the surface of pathogens, which elicit an immune response. This display helps
the macrophages stimulate specific helper T-cells to release signal molecules called
lymphokines. The lymphokines, in turn, stimulate the cell-mediated and antibody-mediated
responses.
The cell-mediated response occurs when the lymphokines released from the helper T-cells
stimulate other cell types to participate in the immune response. Lymphokine-stimulated killer
T-cells attach to the pathogen-infected cells and destroy them, whereas lymphokine-activated
phagocytic cells produce more toxic molecules that can kill the pathogen directly.
The antibody-mediated response occurs when the lymphokines activate specific B-cells to
produce antibodies (proteins that specifically recognize and bind to antigens). These
antibodies attach to antigens on the surface of the pathogens and signal attack by phagocytic
cells and complement system. Other B-cells go on to become memory B-cells, which respond
quickly by producing more antibodies upon subsequent infection.
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Fig: 6.2 overview of cell-mediated and antibody-mediated immune responses
The innate and adaptive immune systems have different types of cells and molecules, which
are responsible for the two different types of immune systems. In addition they have different
characteristics as it is explained above:-
The cells, molecules and characteristics of innate and adaptive immune systems are
summarized in the table below.
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Table 6.1. The innate and adaptive immunity
Although innate and adaptive immunity are often considered separately for convenience and
to facilitate their understanding, it is important to recognize that they frequently work
together. The various cells of both systems work together through direct contact with each
other, and through interactions with chemical mediators, the cytokines and chemokines.
Here are some examples:-
1. Macrophages are responsible to phagocytsis the infectious microbes and at the same
time produce important cytokines that help to induce the adaptive immune response.
2. Complement components of the innate immune system can be activated directly by
microbes, but can also be activated by antibodies, molecules of the adaptive system.
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Fig. 6.3 Patterns and layers of responses against pathogens
Activity
1. What is the main difference between innate and adaptive immune response?
2. Explain the process of Phagosytosis?
3. What makes normal flora to become opportunistic pathogen?
4. What is the difference between cellular and hum moral arm of immunity?
Hypersensitivity
Autoimmune diseases
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Immunodeficiency
There are four types of hypersensitivity reactions: Type I, Type II, Type III and Type IV. The
Types I, II and III are antibody or immune complex mediated occurring within minutes or
hours after a sensitized individual re-encounters the same antigen. Type IV is cell mediated
(Delayed type hypersensitivity (DTH)). Occurs days after re-encountering the antigen.
Type I Hypersensitivity
Type I reactions (immediate hypersensitivity) are IgE-mediated. Antigen binds to IgE that is
bound to tissue mast cells and blood basophils, triggering release of preformed mediators
(eg, histamine, proteases, chemotactic factors) and synthesis of other mediators (eg,
prostaglandins, leukotrienes, platelet-activating factor, cytokines). These mediators cause
vasodilation, increased capillary permeability, mucus hypersecretion, smooth muscle spasm,
and tissue infiltration with eosinophils, type 2 helper T (TH2) cells, and other inflammatory
cells. Type I reactions develop 1 hour after exposure to antigen.
Type I hypersensitivity reactions underlie all atopic disorders (eg, atopic dermatitis,
allergic asthma, rhinitis, conjunctivitis) and many allergic disorders (eg, anaphylaxis, some
cases of angioedema, urticaria, latex and some food allergies). The terms atopy and allergy
are often used interchangeably but are different:
Atopy is an exaggerated IgE-mediated immune response; all atopic disorders are
type I hypersensitivity disorders.
Allergy is any exaggerated immune response to a foreign antigen regardless of
mechanism.
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Thus, all atopic disorders are considered allergic, but many allergic disorders (eg,
hypersensitivity pneumonitis) are not atopic. Allergic disorders are the most common
disorders among people.
Type II Hypersensitivity
Rhesus Incompatibility
Rhesus D (RhD) antigen is carried by erythrocytes. Children born to RhD− mothers and RhD+
fathers may express RhD on their erythrocytes. Prior to pregnancy, the mother can become
sensitized to RhD antigen through blood transfusion and during pregnancy and especially at
birth by the baby‘s RhD+ erythrocytes coming into contact with the mother‘s immune system.
Some pass across the placenta but most are released into the maternal circulation during
placental shedding. Since RhD is not present in the mother, her immune system responds to it
as a foreign antigen and makes antibodies (Fig.6.4 ). This is usually not a problem during the
first pregnancy but in subsequent pregnancies small amounts of erythrocytes passing across
the placenta stimulate a memory response leading to specific anti-RhD antibody production.
IgG antibodies pass across the placenta and bind to the fetal erythrocytes leading to their
opsonization and lysis. This results in hemolytic anemia of the newborn if not prevented. This
is often call hemolytic disease of the newborn.
Generally, mothers at risk are detected during early stages of pregnancy and monitored
thereafter. At termination of each pregnancy with an RhD+ fetus, RhD(−) mothers are given
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antibodies to RhD which is thought to remove the fetal erythrocytes from the blood stream
and suppress the development of a subsequent immune response.
Blood transfusion
It is common practice to give blood transfusions in cases of severe blood loss. The major
blood group antigens A and B are expressed at the surface of erythrocytes and we have natural
antibodies (mostly IgM) to these antigens. Individuals who are blood group A have antibodies
to B antigens, those who are blood group B will have anti-A antibodies and those who are AB
will have neither. Those who are blood group O will have both antibodies. It is therefore
important to do blood group typing on transfusion donors and recipients. In most cases, this is
done accurately but occasionally accidents occur whereby blood is given to a recipient who
has the reactive isohemagglutinins. This can result in a transfusion reaction which manifests
itself as (a complement mediated) massive intravascular life-threatening hemolysis.
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Type III Hypersensitivity
Type III reactions (immune complex disease) cause inflammation in response to circulating
antigen-antibody immune complexes deposited in vessels or tissue. These complexes can
activate the complement system or bind to and activate certain immune cells, resulting in
release of inflammatory mediators.
Type III reactions develop 4 to 10 days after exposure to antigen and, if exposure to the
antigen continues, can become chronic. Type III disorders include serum sickness, systemic
lupus erythematosus(SLE), rheumatoid arthritis(RA), leukocytoclastic
vasculitis, cryoglobulinemia, acute hypersensitivity pneumonitis, and several types
of glomerulonephritis.
Type IV Hypersensitivity
T cells, sensitized after contact with a specific antigen, are activated by continued exposure
or re exposure to the antigen; they damage tissue by direct toxic effects or through release of
cytokines, which activate T cells, together with dendritic cells eosinophils, monocytes and
macrophages, neutrophils, or natural killer cells. This hypersensitivity starts from 24 h after
contact with an antigen. Disorders involving type IV reactions include contact
dermatitis (eg, poison ivy), subacute and chronic hypersensitivity pneumonitis,
allograft rejection, the immune response to tuberculosis, and many forms of drug
hypersensitivity.
Examples:-Mycobacterium tuberculosis – the bacteria survive within macrophages, which is
the tuberculin reaction
• This is a ‗recall‘ response to purified mycobacterial antigens and is used as the basis of
a skin test for an immune response (not necessarily curative) to TB.
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• The inability to kill all mycobacteria in macrophages by T cells often results in a
chronic stimulation of the mycobacterial specific T cells.
• The cytokines produced are responsible for ‗walling off‘ the macrophages containing
the persistent antigens and thus the production of granulomas.
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6.5.2. Autoimmunity and autoimmune disease
Self-test
Autoimmunity is an acquired immune reactivity to self antigens which lead to tissue damage.
Normally, the immune system can tell the difference between foreign cells and your own
cells. In the case of an autoimmune disease, the immune system mistakes part of your body,
like joints or skin, as foreign. It releases proteins called auto-antibodies that attack healthy
cells. In short autoimmune diseases arise as the result of a breakdown in self-tolerance. Some
autoimmune diseases target only one organ. Type 1 diabetes damages the pancreas. Other
diseases, like systemic lupus erythematosus (SLE), affect the whole body. There are more
than 80 different autoimmune diseases but here are 14 of the most common ones.
Type 1 diabetes:-The pancreas produces the hormone insulin, which helps regulate blood
sugar levels. In type 1 diabetes mellitus, the immune system attacks and destroys insulin-
producing cells in the pancreas. High blood sugar results can lead to damage in the blood
vessels, as well as organs like the heart, kidneys, eyes, and nerves.
Rheumatoid arthritis (RA):-In rheumatoid arthritis (RA), the immune system attacks the
joints. This attack causes redness, warmth, soreness, and stiffness in the joints.
Unlike osteoarthritis, which commonly affects people as they get older, RA can start as early
as your 30s or sooner.
Psoriasis/psoriatic arthritis:- Skin cells normally grow and then shed when they‘re no
longer needed. Psoriasis causes skin cells to multiply too quickly. The extra cells build up and
form inflamed red patches, commonly with silver-white scales of plaque on the skin. Some
people with psoriasis also develop swelling, stiffness, and pain in their joints. This form of the
disease is called psoriatic arthritis.
Multiple sclerosis:-Multiple sclerosis (MS) damages the myelin sheath, the protective coating
that surrounds nerve cells, in your central nervous system. Damage to the myelin sheath slows
the transmission speed of messages between your brain and spinal cord to and from the rest of
your body.
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This damage can lead to symptoms like numbness, weakness, balance issues, and trouble
walking. The disease comes in several forms that progress at different rates. According to
a 2012 study Trusted Source, about 50 percent of people with MS need help for walking
within 15 years after the disease starts.
Systemic lupus erythematosus (SLE):-Although doctors in the 1800s first described lupus as a
skin disease because of the rash it commonly produces, the systemic form, which is most the
common, actually affects many organs, including the joints, kidneys, brain, and heart. Joint
pain, fatigue, and rashes are among the most common symptoms.
Crohn‘s disease can inflame any part of the GI tract, from the mouth to the anus.
Ulcerative colitis affects only the lining of the large intestine (colon) and rectum.
Addison‘s disease:-Addison‘s disease affects the adrenal glands, which produce the hormones
cortisol and aldosterone as well as androgen hormones. Having too little of cortisol can affect
the way the body uses and stores carbohydrates and sugar (glucose). Deficiency of
aldosterone will lead to sodium loss and excess potassium in the bloodstream. Symptoms
include weakness, fatigue, weight loss, and low blood sugar.
Graves‘ disease:-Graves‘ disease attacks the thyroid gland in the neck, causing it to produce
too much of its hormones. Thyroid hormones control the body‘s energy usage, known as
metabolism. Having too much of these hormones revs up your body‘s activities, causing
symptoms like nervousness, a fast heartbeat, heat intolerance, and weight loss.
One potential symptom of this disease is bulging eyes, called exophthalmos. It can occur as a
part of what is called Graves‘ ophthalmopathy, which occurs in around 30 percent of those
who have Graves‘ disease, according to a 1993 study Trusted Source.
Sjogren‘s syndrome:-This condition attacks the glands that provide lubrication to the eyes and
mouth. The hallmark symptoms of Sjogren‘s syndrome are dry eyes and dry mouth, but it may
also affect the joints or skin.
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Hashimoto‘s thyroiditis:-In Hashimoto‘s thyroiditis, thyroid hormone production slows to a
deficiency. Symptoms include weight gain, sensitivity to cold, fatigue, hair loss, and swelling
of the thyroid (goiter).
Myasthenia gravis:-Myasthenia gravis affects nerve impulses that help the brain control the
muscles. When the communication from nerves to muscles is impaired, signals can‘t direct the
muscles to contract. The most common symptom is muscle weakness that gets worse with
activity and improves with rest. Often muscles that control eye movements, eyelid opening,
swallowing, and facial movements are involved.
Pernicious anemia:- This condition causes deficiency of a protein, made by stomach lining
cells, known as intrinsic factor that is needed in order for the small intestine to absorb vitamin
B-12 from food. Without enough of this vitamin, one will develop an anemia, and the body‘s
ability for proper DNA synthesis will be altered.
Pernicious anemia is more common in older adults. According to a 2012 study, it affects 0.1
percent of people in general, but nearly 2 percent of people over age 60.
Celiac disease People with celiac disease can‘t eat foods containing gluten, a protein found in
wheat, rye, and other grain products. When gluten is in the small intestine, the immune system
attacks this part of the gastrointestinal tract and causes inflammation.
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– Have been linked to particular autoimmune diseases and may be important in
their etiology.
• Nature of the auto antigen.
– Target antigens are often highly conserved proteins such as heat shock proteins
(HSPs), stress proteins, enzymes, or their substrates.
The immunological disorders can be caused by the deficiency of immune response of the host
body or the excessive production of the host immune system. Immune deficiencies occur
when one or more components of the immune system are defective. It is classified as primary
or secondary.
Primary immunodeficiency
Defects in lymphoid lineage:- May involve B-cell, T-cell or both. The severity depends on
the number and type of immune components involved.
• T-cell deficiencies: can affect both cell and humoral immunity. Do not response to
various types of pathogens.
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• Complement deficiencies, this one associated with increased susceptibility to bacterial
or fungal infection and/or immune complex disease.
Secondary immunodeficiency
This type is acquired secondary to some agents after birth, more common in malnutrition,
infection, cancer, etc. Patients treated by immunosupressive drugs. The good example is HIV
that causes AIDS.
Activity
A tumor is a mass of tissue that's formed by an accumulation of abnormal cells. Tumor cells
grow, even though the body does not need them, and unlike normal old cells, they don't die.
Cancer is a disease in which cells, almost anywhere in the body, begin to divide
uncontrollably. A tumor is when this uncontrolled growth occurs in solid tissue such as an
organ, muscle, or bone. Tumors may spread to surrounding tissues through the blood and
lymph systems.
Most cancers form a lump called a tumor or a growth. Lumps that are not cancer are called
benign. Lumps that are cancer are called malignant. There are some cancers, like leukemia
(cancer of the blood), that don't form tumors.
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immune system. Surveillance probably acts against viruses not tumors. The evidence for this
is that although there is an increased incidence of tumors in immuno-suppressed individuals,
the most dramatic increase is in tumors associated with oncogenic viruses. Cellular responses
to tumor-associated antigens occur; the antigens may be virus coded, or they may be altered or
over-expressed host genes are produced. Differentiated antigens expressed on tumor can be
detected by monoclonal antibodies or patients' sera. Although the antigens are no restricted to
tumor cells, they are useful for diagnosis and may be targets for antibody-mediated therapy.
Passive immunotherapy with monoclonal antibodies is promising when single cells are
targeted or the problem of poor penetration into tumor masses can be circumvented.
Immunotherapy by active immunization or by passive transfer of cells is still largely
experimental, because of tumor escape mechanisms. Cytokines are active against a few tumor
types.
There is a lot of evidence that tumors can elicit an immune response. Such evidence includes:
Tumors that have severe mononuclear cell infiltration have a better prognosis than
those that lack it.
Certain tumors regress spontaneously (e.g., melanomas, neuroblastomas), suggesting
an immunological response.
Some tumor metastases regress after removal of primary tumor which reduces the
tumor load, thereby inducing the immune system to kill the residual tumor.
Although chemotherapy leads to rejection of a large number of tumor cells, the few
tumor cells that evade the action of the drugs can outgrow and kill the host. However,
the immune system may be able to mount an attack against the few tumor cells that are
spared by the chemotherapeutic agent.
There is an increased incidence of malignancies in immuno-deficient patients such as
AIDS patients who are susceptible to Kaposis sarcoma and transplant patients who are
susceptible to Epstein Barr virus (EBV)-induced lymphoma.
Tumor-specific antibodies and T lymphocytes (detected in cytotoxicity and
proliferative response assays) have been observed in patients with tumors.
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The young and the old population have an increased incidence of tumors. These
members of the population often have an immune system that is compromised.
Hosts can be specifically immunized against various types of tumors demonstrating
tumor antigens can elicit an immune response.
In order for the immune system to react against a tumor, the latter must have antigens that are
recognized as a foreign. A number of alterations in gene expression occur in cells during
tumorigenesis. Tumorigenesis may lead to expression of new antigens (neoantigens) or
alteration in existing antigens that are found on normal cells. These antigens may include
membrane receptors, regulators of cell cycle and apoptosis, or molecules involved in signal
transduction pathways.
Tumor-specific transplantation antigens (TSTA) which are unique to tumor cells and
not expressed on normal cells. They are responsible for rejection of the tumor.
Tumor associated transplantation antigens (TATA) that are expressed by tumor cells
and normal cells.
Although chemical, UV- or virus-induced tumors express neo-antigens, the majority of these
tumors are often weakly immunogenic or non-immunogenic. In most cases, TSTAs cannot be
identified easily. Some of these antigens may be secreted while others may be membrane-
associated molecules.
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Unit 7
Taxonomy of organisms
Dear learners, this unit describes taxonomy and its etymology, an early and modern view of
classification of organisms. It also deals with the major schemes of classification, concepts of
kingdom and species, identification of organisms and nomenclature.
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Brainstorming Questions:
What is Taxonomy?
How diversified organisms the world are managed to be studied?
Explain the differences between classification, nomenclature and
identification.
Etymology of Taxonomy
The term taxonomy was coined by a Swiss naturalist, De Candolle, in the French form as
"taxonomie" in 1813. The word taxonomy was derived from two Greek words: "taxis and
nomos" which means arrangement and law respectively. Thus, taxonomy means the law
governing the classification or arrangement of organisms into taxa. Taxonomy is the basic
science since no start on understanding the wealth of variation can be made until some sort of
classification is adopted. It is also most all-embracing and ultimate of all biological sciences
because taxonomy is not complete until the data from other fields of investigation have been
incorporated.
Although some naturalists use the term taxonomy as synonymous with systematics, but many
naturalists consider taxonomy as one part of systematics, and it is mainly concerned with:
classification, nomenclature and identification of organisms.
Classification: Is ordering/assignment of organisms into hierarchy of ranks or categories
distinguished by certain characters; or based on similarities and/or differences.
Nomenclature: Is the naming of groups of organisms and the rules governing the application
of the names.
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7.1 Early Attempts to Classify Organisms
Brainstorming questions:
The development of modern taxonomy has not a linear path. Taxonomy was started as old as
man himself. Several early Greek and Roman philosophers enumerated organisms. Some of
them are discussed below:
Aristotle (384–322 BC)
Aristotle was a Greek philosopher who contributed most extensively to the development of
the modern biology. Aristotle viewed life was hierarchical and he classified organisms,
mainly history of Animals and other works where he showed naturalist leanings, and later
more empirical works that focused on biological changes and the diversity of life. Later,
Aristotle was replaced by Theophrastus and other naturalists who wrote a series of botany
books that were used for many generations.
He was a keen observer of mainly plants. He was the first taxonomist to write down a
classification in a permanent and logical form. For this reason, he was called the father of
Botany by Linnaeus. In his book "De Historia Plantarum", he classified 480 kinds of plants
based on their habit. However, his work reflects the philosophy, which incorporates the
principle of the rules of dichotomy or the ―Excluded Middle‖. Any given organisms is either
A or not A. According to Theophrastus classification system, there are no any intermediate
organisms. He was typologists, belief that every natural group of organisms has an invariant,
generalized or idealized pattern shared by all members of the group.
He was a Roman scholar and naturalist who wrote encyclopaedic books termed Historia
naturalis, in which he mentioned and categorized plants in terms horticultural practices,
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medicinal uses, and timber use practices. In his classification, he used a similar classification
as his predecessors' errors.
Dioscorides (1st Century AD)
He was a Greek physician who studied and described about 600 medicinal plants in his book
―De Matera Medica‖ with their useful applications.
A. Caesalpinus (1519-1603)
In his book "De Plantis" he illustrated about 1500 plant species. He classified plants based on
definite morphological criteria mainly on the basis of habit, fruits, seeds, and ovaries and their
position.
J. Bauhin (1554-1631) and G. Bauhin (1560-1624)
They were brothers of Swiss botanists who worked separately but along rather similar lines.
G. Bauhin produced to order the state of nomenclature which existed to some extent currently.
He was also notably remembered for his recognition of genera and species as major
taxonomic levels or used a binary nomenclature composed of the genus name followed by a
single specific. J. P. de Tournfort (1656-1708) also carried out further Bauhin's promotion of
the rank of genus with a clear explanation.
Carolus Linnaeus (1707-1778), a Swede Taxonomist and Physician, was the founder of
modern taxonomy both of plants and animals. The system of nomenclature that we employ
today is essentially Linnaeus‘. Linnaeus produced important books that he classified all
known animals, plants and minerals. The two most important works are: Genera Plantarum
(1737) and Species Plantarum (1753), which listed and briefly described the genera and the
species. Though Linnaeus was the father of modern taxonomy, and his classification system
was popular largely because its simplicity, his classification system was artificial-which
depends only on few characteristics like stamens and pistil number and position.
The foundation of modern classification comes mainly after the from the works of other
taxonomists M. Adanson (1727-1806), De Jussieu (1748-1836), and J. de Lamarck (1744-
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1829), A.P. de Candolle and C. Darwin (1859), who never followed artificial system of
Linnaeus classification.
M. Adanson (1727-1806)
Adanson is most remembered for championing the idea that in classification one should use a
great range of characters covering all aspects of the organisms without placing greater
emphasis on some than on others. This is called an empirical approach. Adanson was a severe
critic of Linnaeus' works.
Lamarck is best known for his theory of evolution, Lamarckism, whereby characters
acquired during life become inherited. DeCandolle (1778-1841) wrote a 17 volume books, in
which he first introduced the word taxonomy in the French form Taxonomie. The
evolutionary theory of Darwin (The Origin of Species by Means of Natural Selection, 1859)
had little immediate impact on classifications of organisms. The previous classifications were
based on morphological similarities or dissimilarities. But after Darwin work, evolutionary
thinking was incorporated into classification system and population thinking came into
picture.
However, the early classification systems were broad and vague as indicated by generic terms
like animals, worms, sedges, grasses and trees, etcetera. Thus, the modern classification
system was developed.
Unlike the early classifications the modern classification system of diversified organisms is
depend up on the combined evidence of morphology, ultrastructure and molecular phylogeny.
In classification, though it is organisms that are being classified, their characters /character
states are used to classify or categorize organisms. Different approaches have been developed
to compare these characters. These differences in approach to comparison of character states
are lead to the development of five different classification systems.
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7.2.1. Artificial classification system
In artificial classification system, only one or at most a few characters are selected for use in
making comparison among organisms. Because a few characters are involved, the difficulties
encountered in describing, measuring and comparing the character states usually are minimal.
Ranking is done subjectively. Artificial system is monothetic i.e. possession of unique set of
characters/features is both sufficient and necessary for membership in the group defined.
Artificial system was the first to be used in the classification of organisms, and Theophrastus
and Linnaeus are good example of artificial system of classification.
This classification system is based up on several to many characters selected for their value in
positively correlating with character states of groups in ranks containing high information
content. This system is therefore polythetic i.e. it places together organisms that have the
greatest number of shared features, and no single feature is either essential to group
membership or is sufficient to make an organism a member of the group. Adanson and De
Jussieu are good examples of natural classification system.
It is a classification that aims at reconstructing a sequence starting with the most primitive
character and ending with the most advanced or derived character. It ensures that each taxon
recognized as a monophyletic i.e. has arisen by the diversification of a single ancestor.
According to phyletic classification system, d decision as to which list represents the primitive
and which the advanced state is made primarily by examining the fossil record to discover
which character states are nowadays more common and which are less common than earlier in
the fossil record.
7.2.4. Phenetics classification system
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characteristics of organisms‘. The following methods/approaches are used for determining the
similarity of the studied organisms.
Selection of taxa-called Operational Taxonomic Units (OTUs) for study. Thus may be
species, genera or families.
Selection of character states (minimum of 60 and 80-100 are desirable for
comparision).
Description or measurement of character states.
Ranking of all OTUs into the categories of the taxonomic hierarchy.
7.2.5. Phylogenetic classification system
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Fig: 7.1. The phylogenetic tree of life
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concepts of domains and kingdoms, see the following diagrammatical representation of
mammal and insect and hierarchical classification.
In a hierarchical system, we start at the bottom with individuals (species) and end up at the top
with one all-embracing taxon (Domain). Between the two, there are various taxa of organisms
at different levels of the hierarchy, each of which is subordinate to one and one immediately
higher taxon except the lowest and the highest taxon. The major levels in the hierarchy are the
following:
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Species are a series of recognizably similar individuals distinct from other species; they are
the fundamental bases of the hierarchy of classification. Related species are grouped in to one
genus. Related genera are grouped in to one family. Related families are grouped in one order.
Similarly, related orders put in one class, classes in to division (if plant) and in to phylum (if
animal), and in to kingdom and domain.
The two kingdom concept existed before the 1950s. This concept was classifying organisms
based up on the cell wall present versus absent. Thus, Kingdom Plantae and Kingdom
Animalia were identified. However, after the invention of the Electron Microscope, some
naturalists later questioned this approach. Then the three kingdom systems were developed.
Three-Kingdom Concept
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This kingdom concept/approach classifies all organisms in to three Kingdoms, namely;
kingdom Plantae, Animalia and Protista (for the intermediates, like some algae and protozoa,
which behave like both plants and animals. Still there are other ungrouped organisms, which
lead four kingdom concepts.
The four Kingdoms were Kingdom Plantae, Animal, Protista and Fungi. Fungi are organisms
that do have both plant and animal characteristics.
After the invention of the Transmission Electron Microscope (has a very high-resolution
power- up to 100000x), some biologists were able to investigate the composition of the cell.
The microscope revealed that there are differences in the composition of the cells of few
groups of organisms that were considered members of the Kingdom Plantae, and some
members of the Kingdom Animalia. Thus, they suggested the Five Kingdom approaches;
which are: kingdom Monera, kingdom Fungi, kingdom Protista, kingdom Plantae and
kingdom Animalia.
This concept classifies first kingdom monera in to two groups based on the nucleus and other
organelles have or lacking a membrane. Thus, the six kingdom system was developed, and
these are: kingdom Archaebacteria, Eubacteria, Protista, Fungi, Plantae and Animalia (Figure
7.3).
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Fig: 7.3. The six kingdom systems
Nomenclature is the naming of organisms and the rules governing the application of these
names. The rules of nomenclature begin from Linnaus‘s of classification where he
established the real beginning of a perfect nomenclature of organisms. Especially binomial
nomenclature was practicable after Linnaeus wrote the books "Species Plantarum and
Genera Plantarum". In nomenclatural system, each organism is designated by two names,
the first is the name of the genus; the second is the specific epithet. No two species can have
the same name. The names are always Latin (or Latinized) and the genus is capitalized while
species name is not.
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alphabet. The scientific names of all living organisms are therefore Latin or are treated as
Latin even if they are derived from other languages.
It is the system of naming animals, which applies to both living and extinct animals. The
ICZN is responsible for producing the International Code of Zoological Nomenclature - a set
of rules for the naming of animals and the resolution of nomenclatural problems. The
primary objective of the Code is to promote the stability of the names of taxa (groups of
organisms) by providing rules concerning name usage and the activity of naming new taxa.
International Code of Nomenclature of Bacteria
The International Code of Nomenclature of Bacteria (ICNB) governs the scientific names for
Bacteria, including Archaea bacteria. It denotes the rules for naming taxa of bacteria,
according to their relative rank. As such it is one of the Nomenclature Codes of biology.
Originally the International Code of Botanical Nomenclature dealt with bacteria, and this
kept references to bacteria until these were replaced in 1975. An early Code for the
nomenclature of Bacteria was approved at the 4th International Congress for Microbiology in
1947. These rules are maintained by the International Committee on Systematics of
Prokaryotes.
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International Code of Nomenclature for Cultivated Plants
The need for a comprehensive set of practical, easily understood and internationally
acceptable regulations on the naming of cultivated plants has long been evident. The
International Code of Nomenclature for Cultivated Plants (ICNCP) regulates the names of
cultigens (plants whose origin or selection is primarily due to intentional human activity).
These are, for the most part, plants with names in the classification categories cultivar and
groups. Since cultivated plants are artificial populations maintained and propagated by man,
the botanical hierarchy of infraspecific categories is hardly applicable to cultivated plants. It
is largely replaced by a system based on the taxonomic category cultivar. Cultivar is any
assemblage of cultivated plants which is clearly distinguished by any characters and which
retains its distinguishing characters when reproduced sexually or asexual. It is internationally
recognized term for category of distinct cultivated sorts, which are usually called varieties.
Cultivar names are preceded by the abbreviation Cv. or placed in single quotation marks and
not Latinized names.
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Asteraceae, Lamiaceae. Names of the genera are uninomial and singular nouns. They are
written with capital initial letter. E.g. Hagenia, Datura, Withania and etc. Names of the
species consist of two terms, and called binomial, binominal or binary names. It contains the
genus name in upper case followed by a second term which is peculiar to the species in lower
case. The second term may be adjective or a noun, which is known as specific epithet.
Publication
Publication is the means by which scientific names enter to the biological nomenclature
system. The two basic conditions must be fulfilled before a properly formulated scientific
name can have any legal status in biological nomenclature. Primarily the name must be
published in works that are printed in permanent and made available to the interested public.
Secondly, a name must be accompanied by a written matter or a reference to such description.
Typification
Type is the process of designating a nomenclatural type, or means by which types are
allocated to taxa. A ‗type‘ is an element on which the description associated with the original
publication of a name was based. The ‗type‘ of names of taxa above the Genus and below and
including the Family is a Genus. The ‗type‘ of the names of taxa above Species and below and
including the Genus is a species; and the names of taxa below and including species is a
specimen or sometimes a description or an illustration of a specimen. In nomenclature, there
are different kinds of "Types". Some of these are:
Holotype: It is the sole element used or designated by the author of a name as a type.
Isotype: The duplicates of a holotype.
Syntype: Is any one of two or more elements used by the author of a name who did not
designate a holotype.
Lectotype: Is an element selected subsequently from amongst syntypes to serve as a
‗type‘.
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Neotype: It is an element selected to serve as a nomenclatural type when through loss
or destruction of the above "Types". Dear students please read about other kinds
of "Types".
7.4.5.3. Priority
The principle of priority requires when two or more names apply to the same taxon. In this
case, the name is given generally based up on by the oldest one, which is validly published
name. However, one of the limitations of priority is the starting-point date, which is the date
of publication of a work prior to which no name is considered to have been made available for
zoological code and validly published names for botanical code.
There are certain names that are not considered in the code. For example, homonyms -names
spelt in an identical manner but based on different ‗types‘ of the organism, superfluous
names-names that include the ‗type‘ of another name when published, and tautonyms-name of
a species in which the second term exactly repeats the generic names have no any legal status
in the code. However, tautonyms are allowed in zoological code.
In nomenclature, when two or more names are applied the same taxon, it is known as
synonyms. There are two kinds of synonyms; nomenclatural and taxonomic synonyms. The
first names are based on the same ‗type‘ of the organism and called obligateor homotypic
synonyms. Taxonomic synonyms are based on different ‗type‘ of an organism, and called
heterotypic synonyms.
Authorities and Their Citations
The scientific names of organisms are often written followed by one or more personal names
or the author name, who first published the name in the way that satisfies the criteria of valid
publication or available names. Sometimes it is abbreviated. E.g. Rumex abyssinicus Jacq.,
Plantago lanceolata L. Sometimes, double citations are required. A double citation indicates
there has been a change in taxonomic position or rank. For example, when a taxon below the
rank of genus is transferred to another taxon, but also when a genus or taxon of lower rank is
altered in rank but retains its original epithet. E.g. Carissaedulis Vahl.Later Linnaeus decided
to place the specific epithet "spinarum", and written as Carissa spinarum(Vahl.) L.
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Unit 8
Self-test
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Definition of Ecology
The word ‗Ecology‘ was coined from Greek word 'oikos' meaning 'house' or 'a place to live'
and 'logos' meaning study. Ecology is the study of the households of the planet earth. Living
things depend on each other and on the non-living components of the environment for
survival. Based on this, it is possible to say ecology is the study of the relationship of living
organisms among themselves and with the non-living components of the environment.
Different Authors defined ecology differently. Some of them are:
Ecology is the scientific study of the interactions between organisms and their
environments
The study of the relationships, distribution, and abundance of organisms, or groups of
organisms, in an environment
Ecology deals with relationships between organisms and their physical environments;
between organisms of the same species; between organisms of different species; and between
organisms and the fluxes of matter and energy through biological systems (Environment
includes not only the physical but also the biological conditions under which an organism
lives).
Ecologists study these interactions in order to understand the abundance and diversity of life
within Earth's ecosystems. In other words, why there are so many plants and animals, and why
there are so many different types of plants and animals? To answer these questions, they may
use field measurements, such as counting and observing the behavior of species in their
habitats; laboratory experiments that analyze processes such as predation rates in controlled
settings; or field experiments, such as testing how plants grow in their natural setting but with
different levels of light, water, and other inputs. Applied ecology uses information about these
relationships to address issues such as developing effective vaccination strategies, managing
fisheries without over-harvesting, designing land and marine conservation reserves for
threatened species, and modeling how natural ecosystems may respond to global climate
change.
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Change is a constant process in ecosystems, driven by natural forces that include climate
shifts, species movement, and ecological succession. By learning how ecosystems function,
we can improve our ability to predict how they will respond to changes in the environment.
But since living organisms in ecosystems are connected in complex relationships, it is not
always easy to anticipate how a step such as introducing a new species will affect the rest of
an ecosystem.
1. Abiotic: all non-living components in the biosphere, e.g., air, water, soil,
climate.
2. Autotrophic: when an organism is able to produce its own food using abiotic
components.
3. Biotic: all the living components in the biosphere: animals, plants, micro-
organisms, etc.
4. Biosphere: it is the global sum of all ecosystems, and is the zone where all
living organisms live on earth.
5. Biome: the biosphere is divided into millions of biomes, based on the specific
climate of each region, where the climate determines the unique plant and
animal species that live and are adapted to survive in a region.
6. Carnivores: animals that eat only meat. They are generally predators, like
lions, cheetahs etc., in a specific environment.
7. Ecosystem: the combined physical and biological components of a specific
habitat where animals and plants are interdependent on each other for survival.
8. Herbivores: animals that only eat plants, e.g., buck, cows, goats, sheep, rabbits
etc.
9. Heterotrophic: when an organism is unable to produce its own food, and must
eat other organisms
10. Omnivores: animals that eat both plant and animal matter, e.g., humans, pigs,
baboons.
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11. Saprophytic organisms: organisms that live on dead organic matter because
they are able to decompose (break down) dead plant and animal matter.
12. Scavengers: animals that eat what is left over by predators. Examples are
hyenas, crayfish and vultures.
13. Photosynthesis: a process where plants use sunlight energy, water and CO2
from the air, to produce organic compounds like glucose and inorganic
compounds like O2.
14. Vegetation: the plant life that is found in a biome.
Self-test:
1. What are the branches of ecology?
2. What criteria are employed for this classification?
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Biome: A distinct ecological community of plants and animals living together in a particular
climate.
Biosphere: the aggregation of all ecosystems (the sum of all of the organisms of the earth and
their environment). Biome is the living zone of the planet.
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- Community ecology (or Synecology)
o Community ecology is the scientific study of relationships between organisms of
different species.
- Ecosystems ecology, having to do with the structure and function of the entire suite of
microbes, plants, and animals, and their abiotic environment, and how the parts interact to
generate the whole. This branch of ecology often focuses on the energy and nutrient flows
of ecosystems, and when this approach is combined with computer analysis and
simulation it is often called systems ecology.
- Evolutionary ecology, which may operate at any of these levels but most commonly at
the physiological or population level, is a rich and dynamic area of ecology focusing on
attempting to understand how natural selection developed the structure and function of the
organisms and ecosystems at any of these levels.
- Conservation ecology: -it deals with methods of proper management of natural resources
such as land, water, forests, sea, mines, etc., for the benefit of human beings.
Activity:
1. What are the practical applications of ecology in your daily life?
2.
3.
8.3 Aquatic and terrestrial ecosystems
A natural ecosystem is an assemblage of plants and animals which functions as a unit and is
capable of maintaining its identity such as forest, grassland, an estuary; human intervention is
an example of a natural ecosystem. A natural ecosystem is totally dependent on solar energy.
There are two main categories of ecosystems.
A) Aquatic ecosystem
An aquatic ecosystem is an ecosystem in a body of water. Communities of organisms that are
dependent on each other and on their environment live in aquatic ecosystems. The two main
types of aquatic ecosystems are:
1. Marine ecosystems
2. Freshwater ecosystems
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1. Marine ecosystems cover approximately 71% of the earth's surface and contain
approximately 97% of the planet's water. They are distinguished from freshwater ecosystems
by the presence of dissolved compounds, especially salts, in the water. Approximately 85% of
the dissolved materials in seawater are sodium and chlorine. Organisms found in marine
ecosystems include brown algae, dinoflagellates, corals, cephalopods, echinoderms,
sharks…etc. Fishes caught in marine ecosystems are the biggest source of commercial foods
obtained from wild populations.
2. Freshwater ecosystems
Grass like plants dominate in marshes, while woody trees and/or shrubs dominate in
swamps.
Wetlands are valued wildlife habitats of migratory birds, beaver, otters, muskrats, and
game fishes; they provide natural flood control and serve as groundwater recharging
areas.
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Estuaries: are where fresh and salt water meet.
i. Estuaries are among the most fertile ecosystems in the world
ii. Temperate estuaries usually contain salt marshes which are important in
preventing flood damage during storm surges
iii. Mangrove forests are the tropical equivalent of salt marshes; they cover
nearly 70% of tropical coastlines.
Mangroves are breeding ground and nurseries for several
commercially important fishes, shellfish, and birds.
They also help prevent coastal erosion and provide a barrier against
the ocean during storms/hurricanes.
Activity:
B. Terrestrial ecosystems
Self test
(a) Forests
(b) Grasslands,
(c) Deserts and (d) tundra
(a) Forests: are large areas supporting rich growth of trees. Depending on the climate and type
of trees they are generally grouped into:
i. Tropical rain forests
ii. Temperate deciduous forests
iii. Boreal or north coniferous forests include
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i. Tropical rain forest
Distribution: These are found in the high rain fall areas on either side of the equator.
Such forests are found in the western coast of India, scattered in south East Asia,
some parts of Africa and South America.
Flora and fauna: Tropical rainforests occur in areas by having high temperature and
high humidity and receives above 200 cm of rainfall per year. Soil is rich in humus.
These forests have a very rich biodiversity e.g. Brazilian tropical rain forests have
more than 300 species of trees in an area of 200 square kilometer. Trees are tall
growing up to 50 to 60 m. These forests also support epiphytes, like vines, creepers,
woody creepers and orchid etc. These forests are rich in tree dwelling animals such as
monkeys, flying squirrels, snails, centipedes, millipedes, and many insect species are
common on the forest floor.
ii. Temperate deciduous forests
Distribution: They occur mostly in the Northwest, Central and Eastern
Europe, Eastern North America, North China, Korea, Japan, far Eastern Russia
and Australia. Trees of deciduous forests shed their leaves in autumn and new
foliage grow in spring.
Climate: These forests occur in the areas of moderate climatic conditions such
as temperature ranging but 10 to 200C with a 6 month long winter and an
annual rainfall between 75 to 150 cm. They have its brown soils which are rich
in nutrients.
Flora and fauna: Common trees are oak, beach, heath, chest nut, birch, pine.
These forests also show stratification and have a under story of saplings shrubs
and tall herbs. Prominent grazers include deer, bison and rodents. Rodents play
a very important role in these forests. They feed on seeds, fruits and tree
leaves. Black bear, raccoons, wild cat, wolves, fox and skunks are the
omnivores found in these forests. Hibernation or winter sleep during winter is
a common feature of animals found in these forests. Invertebrate fauna
comprises green flies, aphids, certain moths and butterflies.
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iii. Boreal or north coniferous forests:
• Distribution: Coniferous forests are also known as ‗Taiga‘. They extend as a
continuous belt across North America and north Eurasia below the arctic
tundra. There is no counterpart of these forests in southern hemisphere as there
is no land at this latitude. Climate is cold with long, harsh winter, with mean
annual temperature below 00C. The soils are acidic and poor in nutrients.
• Flora and fauna: Coniferous forests are characterized by evergreen, drought
resistant and woody. Conifers (gymnosprerms) e.g. spruce, fir and pine trees
which bear naked seeds in cones. The animals found in these forests, are red
squirrel, deer, goat, mule, moose etc. The carnivores which feed upon them are
timber wolves, lynxes, and bear. Some common birds are crossbill, thrushes,
warblers, flycatchers, robin and sparrow.
Grasslands
• Distribution: Grasslands are areas dominated by grasses. They occupy about
20% of the land on the earth surface. Grasslands occur in both in tropical and
temperate regions where rainfall is not enough to support the growth of trees.
Grasslands are known by various names in different parts of the world. For
example:
Table 8.1.
Place Name of the grassland
North America Prairies
Eurasia (Europe and Asia) Steppes
Africa Savanna
South America Pampas
India Grassland, Savanna
Grasslands are found in areas having well defined hot and dry, warm and rainy
seasons. Tropical grasslands are commonly called Savannas. They occur in eastern
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Africa, South America, Australia and India. Savannas form a complex ecosystem with
scattered medium size trees in grass lands.
• Flora and fauna: Grasses are the dominating plants with scattered drought resistant
thorny trees in the tropical grasslands. Badgers, fox, ass, zebra, antelope are found
grazing on grasslands which support the dairy and leather industries. Grasslands also
support large population of rodents, reptiles and insects.
Deserts
• Distribution: Deserts are hot and low rain areas suffering from water shortage and
high wind velocity. They show extremes of temperature. Globally deserts occupy
about 1/7th of the earth‘s surface.
• Flora and fauna: Cacti, Acacia, Euphorbia and prickly pears are some of the
common desert plants. Desert animals include shrew, fox, wood rats, rabbits, camels
and goat are common mammals in desert. Other prominent desert animals are,
reptiles, and burrowing rodents insects.
•Adaptations:
Desert plants and animals adapt both hot and dry conditions.
(i) These plants conserve water by the following methods:
They are mostly shrubs.
Leaves absent or reduced in size.
Leaves and stem are succulent and water storing.
In some plants even the stem contains chlorophyll for photosynthesis.
Root system well developed spread over large area.
(ii) The animals are physiologically and behaviorally adapted to desert conditions.
They are fast runners.
They are nocturnal in habit to avoid the sun‘s heat during day time.
They conserve water by excreting concentrated urine.
Animals and birds usually have long legs to keep the body away from the hot
ground.
Lizards are mostly insectivorous and can live without drinking water for several
days.
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Herbivorous animals get sufficient water from the seeds which they eat. Camel
is known as the ship of the desert as it can travel long distances without drinking
water for several days.
Tundra: The word tundra means a "barren land" since they are found in those regions
of the world where environmental conditions are very severe.
There are two types of tundra: arctic and alpine.
• Distribution: Arctic tundra extends as a continuous belt below the polar ice cap and
above the tree line in the northern hemisphere. It occupies the northern fringe of
Canada, Alaska, European Russia, Siberia and island group of Arctic Ocean. On the
South Pole Antarctica tundra in the South Pole is very small since most of it is
covered by ocean. Alpine tundra occurs at high mountains above the tree line. Since
mountains are found at all latitudes therefore alpine tundra shows day and night
temperature variations.
• Flora and fauna: Typical vegetation of arctic tundra is cotton grass, sedges, dwarf
heath, willows, birches and lichens. Animals of tundra are reindeer, musk ox, arctic
hare, caribous, lemmings and squirrel. Most of them have long life e.g. Salix arctica
that is arctic willow has a life span of 150 to 300 years. They are protected from chill
by the presence of thick cuticle and epidermal hair. Mammals of the tundra region
have large body size and small tail and ear to avoid the loss of heat from the surface.
The body is covered with fur for insulation. Insects have short life cycles which are
completed during favorable period of the year.
Activities:
1. What are deciduous trees?
2. Explain two common characteristics of the desert.
3. How do the animals and plants of deserts adapted to heat and drought?
4. Where prairies and steppes are found?
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8.4 Energy flow through ecosystems
The transfer of energy from the source in plants through a series of organisms by eating and
being eaten constitutes food chains. At each transfer, a large proportion of energy is lost in the
form of heat. These food chains are not isolated sequences, but are interconnected with each
other. This interlocking pattern is known as the food web. Each step of the food web is called
a trophic level. Hence green plants occupy the first level, herbivores the second level,
carnivores the third level and secondary carnivores the fourth level. These trophic levels
together form the ecological pyramid.
The organisms of the second trophic level are called primary consumers or herbivores.
Twenty percent (20%) to thirty percent (30%) of net primary production is consumed by the
herbivores. The organisms of the third trophic level are called secondary consumers or
primary carnivores. The organisms of the fourth trophic level are called tertiary consumers or
secondary carnivores. The final carnivore of a food chain is not eaten by other animals, so it is
known as climax carnivore.
In nature, basically two types of food chains are recognized: They are grazing food chain and
detritus food chain.
i) Grazing food chain: starts from the living green plants and goes to grazing herbivores and
on to the carnivores. Ecosystems with such type of food chain are directly dependent on an
influx of solar radiation. Thus, this type of food chain depends on autotrophic energy capture
and the movement of this energy to herbivores. Most of the ecosystems in nature follow this
type of food chain. These chains are very significant from energy standpoint.
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The following are examples of grazing food chain:
1. Aquatic food chain: Phytoplanktons zooplanktonsfish
2. Terrestrial food chain :GrassesRabbitfox
Other feeding groups such as parasites and scavengers form supplementary food chains in the
ecosystem. Parasitic food chains are highly complicated because of the life cycle. Some
parasites are passed from one host to another by predatory in the food chains. External
parasites (ectoparasites) may move from one host to another. Other parasites are transmitted
by insects from one host to another through the blood stream or plant floods. Food chain also
exists among parasites. For instances, fleas that parasitize mammals and birds are in turn
parasitized by protozoan, leptosomes.
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Fig: 8.2: Terrestrial and aquatic food chain
Self test
1. What does food web mean? How it is different from food chain?
In an ecosystem there are a very large number of interlinked chains and forms a food web.
Stability of the ecosystem is maintained by food web. If the linkages in the chains that make
up the web of life are disrupted due to human activities that lead to the extinction of species,
the web will breaks down.
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Fig: 8.3. Food web
Productivity in land ecosystems generally rises with temperature about 30oC, after which it
declines, and is positively correlated with moisture. On land primary productivity is highest in
warm, wet zones in the tropics where tropical forest biomes are located. In contrast, desert
scrub ecosystems have the lowest productivity because their climates are extremely hot and
dry.
A. Primary production
The flow of energy through a terrestrial ecosystem starts with the harnessing of sunlight by
green plants, a process that in itself demands the expenditure of energy. A plant gets its start
by living on the food energy stored in the seed until it produces leaves. Energy accumulated
by plants is called primary production, because it is the first and basic form of energy stored.
Total energy assimilated by the plant is gross primary production. Plants, like all other
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organisms, must expend energy in production, maintenance, and reproduction. This energy is
produced by the process of respiration which librates energy. Energy remaining after
respiration and stored as organic matter is net primary production. Net primary production can
be described by the following equation:
Net primary production (NPP) = gross primary production (GPP) - respiration by the
autotroph (R). Production is expressed in kilocalories per square meter (kcal/m2) and can
also expressed in grams per square meter (g/m2).
B. Secondary production
Net primary production is the energy available to the heterotrophic component of the
ecosystem. The energy left over from maintenance and respiration goes into production,
including both the growth of new tissues and the production of young. This net energy of
production is called secondary production.
Activities:
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II) Pyramid of biomass depicts the amount of biomass at different trophic levels of food
chain or the total weight of living matter per unit area present in the ecosystem.
III) Pyramid of energy depicts the amount of energy at different trophic levels of food chain.
It shows how energy moves throughout an ecosystem. As you move up the pyramid levels,
approximately 90% of the food‘s original energy is lost from level to level because animals
must use their own energy to consume and digest food. The consumers at the top of the
pyramid do not have as much energy available to them because their food, another animal, is
simply not very good at converting the food it eats into energy in its body.
Ecological pyramids are always upright; i. e. the apex is pointed upwards. In some ecosystems
the number and biomass of producers are less and those of consumers are more. So the apex is
directed down wards. This type of pyramid is called inverted pyramid. Inverted pyramid of
numbers is found in parasitic food chain. Inverted pyramid of biomass occur in pond and lake
ecosystems. However, the pyramid of energy is always upright (never inverted).
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8.5 Cycling of Materials (Nutrients)
Every ecosystem has several interrelated mechanisms that affect human life. These are the
water cycle, the carbon cycle, the oxygen cycle, the nitrogen cycle and the energy cycle.
While every ecosystem is controlled by these cycles, in each ecosystem its abiotic and biotic
features are distinct from each other.
All the functions of the ecosystem are in some way related to the growth and regeneration of
its plant and animal species. These linked processes can be depicted as the various cycles.
These processes depend on energy from sunlight. During photosynthesis, carbon dioxide is
taken up by plants and oxygen is released. Animals depend on this oxygen for their
respiration. The water cycle depends on the rainfall, which is necessary for plants and animals
to live. The energy cycle recycles nutrients into the soil on which plant life grows. Our own
lives are closely linked to the proper functioning of these cycles of life. If human activities go
on altering them, humanity cannot survive on our earth.
8.2.1 The Water Cycle
When it rains, the water runs along the ground and flows into rivers or falls directly into the
sea, and part of the rainwater falls on land percolates into the ground. This is stored
underground throughout the rest of the year. Water is drawn up from the ground by plants
along with the nutrients from the soil. Then, water is transpired from the leaves as water
vapour and returned to the atmosphere. As it is lighter than air, the water vapor rises and
forms clouds. Winds blow the clouds for long distances and when the clouds rise higher, the
vapour condenses and changes into droplets, which fall on the land as rain. Though this is an
endless cycle on which life depends, man‘s activities are making drastic changes in the
atmosphere through pollution which is altering rainfall patterns.
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Fig: 8.5. Water cycle
8.2.2 The Carbon cycle
The carbon, which occurs in organic compounds, is included in both the abiotic and biotic
parts of the ecosystem. Carbon is a building block of both plant and animal tissues. In the
atmosphere, carbon occurs as carbon dioxide (CO2). In the presence of sunlight, plants take up
carbon dioxide from the atmosphere through their leaves. The plants combine carbon dioxide
with water, which is absorbed by their roots from the soil. In the presence of sunlight they are
able to form carbohydrates that contain carbon. This process is known as photosynthesis.
Plants use this complex mechanism for their growth and development. In this process, plants
release oxygen into the atmosphere on which animals depend for their respiration. Plants
therefore help in regulating and monitoring the percentage of oxygen and carbon dioxide in
the earth‘s atmosphere. All of mankind thus, depends on the oxygen generated through this
cycle. It also keeps the CO2 at acceptable levels.
Herbivorous animals feed on plant material, which is used by them for energy and for their
growth. Both plants and animals release carbon dioxide during respiration. They also return
fixed carbon to the soil in the waste they excrete. When plants and animals die they return
their carbon to the soil. These processes complete the carbon cycle.
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8.2.3 Nitrogen cycle
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Nitrification – conversion of ammonia in soil to nitrite ions and finally to nitrate ions that are
easily used by plants (aerobic bacteria).
Assimilation
Nitrates are the form of nitrogen most commonly assimilated by plants through root hairs.
Since heterotrophic organisms cannot readily absorb nitrogen as plants do, they rely on
acquiring nitrogen-based compounds through the food they eat. Since plants are the base of
the food chain, the nitrogen-based compounds they have assimilated into their tissue will
continue to pass from one organism to another (through consumption) as matter and energy
transfers through the ecosystem‘s food web.
Ammonification
In ammonification, a host of decomposing microorganisms, such as bacteria and fungi, break
down nitrogenous wastes and organic matter found in animal waste and dead plants and
animals and convert it to inorganic ammonia (NH3) for absorption by plants as ammonium
ions. Therefore, decomposition rates affect the level of nutrients available to primary
producers.
Denitrification
It is the process by which nitrates are reduced to gaseous nitrogen (N2) and lost to the
atmosphere. This process occurs by facultative anaerobes in anaerobic environments. Farmers
with waterlogged fields and soils that have high clay content are especially vulnerable to
nitrogen losses due to denitrification. In short it is conversion of ammonia and ammonium
ions to nitrate and nitrite ions and then back into nitrogen gas and nitrous oxide gas.
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Fig: 8.6 Nitrogen cycle
Activity:
Oxygen is taken up by plants and animals from the air during respiration. The plants return
oxygen to the atmosphere during photosynthesis. This links the oxygen cycle to the carbon
cycle. Deforestation is likely to gradually reduce the oxygen levels in our atmosphere. Thus,
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plant life plays an important role in our lives which we frequently do not appreciate. This is an
important reason to participate in forestation programs.
The phosphorus cycle, is the circulation of phosphorous among the rocks, soils, water, and
plants and animals of the earth. The phosphorous cycle is the simplest of the cycles that we
will examine. For our purposes, phosphorous has only one form, phosphate (PO4-3), which is a
phosphorous atom with four oxygen atoms. This heavy molecule never makes its way into the
atmosphere; it is always part of an organism, dissolved in water, or in the form of rock. When
rock with phosphate is exposed to water (especially water with a little acid in it), the rock is
weathered out and goes into solution. Autotrophs take this phosphorous up and use it in a
variety of ways. It is an important constituent of cell membranes, DNA, RNA, and, of
course ATP. Heterotrophs obtain their phosphorous from the plants they eat, although one
type of heterotroph, the fungi, excel at taking up phosphorous and may form mutualistic
symbiotic relationships with plant roots. These relationships are called Mycorrhizae; the plant
gets phosphate from the fungus and gives the fungus sugars in return. Animals, by the way,
may also use phosphorous as a component of bones, teeth and shells. When animals or plants
die (or when animals defecate), the phosphate may be returned to the soil or water by the
decomposers. There, it can be taken up by another plant and used again. This cycle will occur
over and over until at last the phosphorous is lost at the bottom of the deepest parts of the
ocean, where it becomes part of the sedimentary rocks forming there. Ultimately, phosphorous
will be released if the rock is brought to the surface and weathered. Two types of animals play
a unique role in the phosphorous cycle. Humans often mine rock rich in phosphorous. For
instance, in Florida, which was once sea floor, there are extensive phosphate mines. The
phosphate is then used as fertilizer. This mining of phosphate and use of the phosphate as
fertilizer greatly accelerates the phosphorous cycle and may cause local overabundance of
phosphorous, particularly in coastal regions, at the mouths of rivers, and anyplace where there
is a lot of sewage released into the water (the phosphate placed on crops finds its way into our
stomachs and from there to our toilets). Local abundance of phosphate can cause overgrowth
of algae in the water; the algae can use up all the oxygen in the water and kill other aquatic
life. This is called eutrophication. The other animals that play a unique role in the
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phosphorous cycle are marine birds. These birds take phosphorous containing fish out of the
ocean and return to land, where they defecate. Their guano (droppings of birds) contains high
levels of phosphorous and in this way marine birds return phosphorous from the ocean to the
land. The guano is often mined and may form the basis of the economy in some areas.
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For standard and general criteria for conservation and sustainable use of natural resources, it
should be developed at a local level and be adapted to local ecosystems, cultures, values and
social and economic conditions. Where necessary, networks of protected areas, corridors and
integrated management zones should be established first. Although the principles and
strategies for sustainable resource management is not new concept, is now gaining the world‘s
attention in response to the decline in the quality of the natural resource due to various natural
and anthropogenic factors including modern agricultural expansion and urbanization.
Sustainable use of resources, especially the genetic resources for food and agriculture is vital
for the next generation. Greater resource use-efficiency saves land, water and biodiversity,
and enhances ecological services underpinning food production. In addition, improved
resource-use efficiency can help to reduce pressure on ecosystems, which also subsequently
lead to resource depletion and degradation. That is why direct action is needed to conserve,
protect and enhance natural resources. Intensification practice of agricultural land over natural
landscape often comes together with practices that include high use of inputs, in particular
water, fertilizers, and pesticides is unwise use of resources. These in turn, when not properly
used, deplete soils, pollute water, and destroy biodiversity. World‘s tropical forests remove
from the atmosphere 4.8 billion tones of CO2 a year, or about 18 percent of annual emissions
from burning fossil fuels. Reforestation and reducing the rate of deforestation will not only
mitigate impact of climate change. It should also contribute to sustainability through soil
formation, water purification, biodiversity and pollination mechanisms.
Biodiversity conservation still plays a pivotal role in sustaining and strengthening nutrition. It
enhances the resilience of people, communities and ecosystems, especially to climate change
and market volatility. Natural disasters or extreme weather events, food safety emergencies,
market volatility and civil strife impair the livelihoods of millions of people who depend on
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natural resources for their livelihoods and negatively impact sustainability of food and other
benefits of natural resources.
All of these principles of conservation can be possible through decisions made under various
government and public participations, revenue protection policies, an insurance scheme
incentivizing to diversify and conserve natural resources, adopt alternative resource utilization
strategies, and apply integrated resources management policies among various institutions and
individuals. In addition, promoting responsible and effective governance mechanisms are also
bet methods for resource management principles. Especially, this approach is preferred since
it ensures accountability, equity, transparency and the rule of law. The underpinning processes
must be participatory and involve all key stakeholders, men, women, public and private
sectors and civil society. They need to be provided with an enabling institutional and policy
environment that provides the right incentives that support the adoption of appropriate
practices on the ground. Responsible and effective governance creates trust and encourages
the community to take part in resource conservation.
Self-test
1. Define pollutant and pollution
2. What is the difference between sources and sinks?
Learning Objectives
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After completing this lesson, you will be able to:
• define the terms pollution and pollutants;
• list various kinds of pollution;
• describe types of pollution, sources, harmful effects on human health and control of air
pollution, indoor air pollution, noise pollution;
• describe water pollution, its causes and control;
• describe thermal pollution;
• discuss about soil pollution, its causes and control;
• describe radiation pollution, sources and hazards.
Self-test
1. List types of pollution
2. What are the main sources of pollution?
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• Air pollution
• Noise pollution
• Water pollution
• Soil pollution
• Thermal pollution
• Radiation pollution
Air pollution
Air pollution is recognized as one of the leading contributors to the global environmental
burden of disease, even in countries with relatively low concentrations of air pollution. Air
pollution is a result of industrial and certain domestic activity. An ever increasing use of fossil
fuels in power plants, industries, transportation, mining, construction of buildings, stone
quarries had led to air pollution. Air pollution may be defined as the presence of any solid,
liquid or gaseous substance including noise and radioactive radiation in the atmosphere in
such concentration that may be directly and indirectly injurious to humans or other living
organisms, plants, property or interferes with the normal environmental processes. Air
pollutants are of two types (1) suspended particulate matter, and (2) gaseous pollutants like
carbon dioxide (CO2), NOx etc.
Fly ash Part of smoke released from Settles down on vegetation, houses. Addsto the
suspended participate matter (SPM)in the air.
chimneys of factories and
Leachates contain harmful material
power plants
Particulate pollutants
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Particulate matters suspended in air are dust and soot released from the industrial chimneys.
Their size ranges from 0.001 to 500 µm in diameter. Particles less than 10µm float and move
freely with the air current. Particles which are more than 10µm in diameter settle down.
Particles less than 0.02 µm form persistent aerosols. Major source of SPM (suspended
particulate matter) are vehicles, power plants, construction activities, oil refinery, railway
yard, market place, industries, etc.
Fly ash
Fly ash is ejected mostly by thermal power plants as byproducts of coal burning operations.
Fly ash pollutes air and water and may cause heavy metal pollution in water bodies. Fly ash
affects vegetation as a result of its direct deposition on leaf surfaces or indirectly through its
deposition on soil. Fly ash is now being used for making bricks and as a land fill material.
Lead and other metals particles
The lead particles coming out from the exhaust pipes of vehicles are mixed with air. If inhaled
it produces injurious effects on kidney and liver and interferes with development of red blood
cells. Lead mixed with water and food can create cumulative poisoning. It has long term
effects on children as it lowers intelligence. Oxides of iron, aluminum, manganese,
magnesium, zinc and other metals have adverse effect due to deposition of dust on plants
during mining operations and metallurgical processes. They create physiological, biochemical
and developmental disorders in plants and also contribute towards reproductive failure in
plants.
Gaseous pollutants
Power plants, industries, different types of vehicles – both private and commercial use
petrol, diesel as fuel and release gaseous pollutants such as carbon dioxide, oxides of nitrogen
and sulphur dioxide along with particulate matter in the form of smoke. All of these have
harmful effects on plants and humans. Table 8.3.2 lists some of these pollutants, their sources
and harmful effects.
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CO2 ) of wood and coal, Power •Greenhouse effect
Sulphur compounds(SO2 and plants and refineries, volcanic •Respiratory problems in humans
H2 S)Nitrogen eruptions, Motor vehicle • Loss of chlorophyll in plants
Compound(NO and exhaust atmospheric reaction (chlorosis)
N2O)Hydrocarbons(benzene, Automobiles and petroleum •Acid rain
ethylene) ,SPM industries Thermal power Irritation in eyes and lungs
(Suspended,Particulate plants, Construction • Low productivity in plants
Matter)(Any soild and liquid, activities, metalurgical •Acid rain damages material
particles suspended in the air, processes and automobiles (metals and stone)
(flush, dust lead) Fibres Textiles and carpet weaving •Respiratory problem
(Cotton, wool) industries Cancer causing properties
Poor visibility, breathing problems
•Lead interfers with the
development of red blood diseases
and cancer.
• Smoge (skoke & fog) formation
leads to poor visibility and
aggravates asthma in patients
• Lung disorders
Poor ventilation due to faulty design of buildings leads to pollution of the confined space.
Paints, carpets, furniture, etc. in rooms may give out volatile organic compounds. Use of
disinfectants, fumigants, etc. may release hazardous gases. In hospitals, pathogens present in
waste remain in the air in the form of spores. This can result in hospital acquired infections
and is an occupational health hazard. In congested areas, slums and rural areas burning of
firewood and biomass results in lot of smoke. Children and ladies exposed to smoke may
suffer from acute respiratory problems which include running nose, cough, sore throat, lung
infection, asthma, difficulty in breathing, noisy respiration and wheezing.
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(ii) Prevention and control of indoor air pollution
Use of wood and dung cakes should be replaced by cleaner fuels such as biogas, kerosene or
electricity. But supply of electricity is limited. Similarly kerosene is also limited. Improved
stoves for looking like smokeless chullahs have high thermal efficiency and reduced emission
of pollutants including smoke. The house designs should incorporate a well ventilated kitchen.
Use of biogas and CNG (Compressed Natural Gas) need to be encouraged. Those species of
trees such as baval (Acacia nilotica) which are least smoky should be planted and used.
Charcoal is a comparatively cleaner fuel. Indoor pollution due to decay of exposed kitchen
waste can be reduced by covering the waste properly. Segregation of waste, pretreatment at
source, sterilization of rooms help in checking indoor air pollution.
a. Use of cleaner fuels such as liquefied natural gas (LNG) in power plants,
fertilizer plants etc. which is cheaper in addition to being environmentally
friendly.
b. Employing environment friendly industrial processes so that emission of
pollutants and hazardous waste is minimized.
c. Installing devices which reduce release of pollutants. Devices like filters,
electrostatic precipitators, inertial collectors, scrubbers, gravel bed filters or dry
scrubbers are described below:
i. Filters – Filters remove particulate matter from the gas stream. The
medium of a filter may be made of fibrous materials like cloth,
granular material like sand, a rigid material like screen, or any mat
like felt pad. Bug-house filtration system is the most common one
and is made of cotton or synthetic fibers (for low temperatures) or
glass cloth fabrics (for higher temperature up to 290oC).
ii. Electrostatic precipitators - The emanating dust is charged with
ions and the ionized particulate matter is collected on an oppositely
charged surface. The particles are removed from the collection
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surface by occasional shaking or by rapping the surface. ESPs are
used in boilers, furnaces, and many other units of thermal power
plants, cement factories, steel plants, etc.
iii. Inertial collectors – It works on the principle that inertia of SPM in
a gas is higher than its solvent and as inertia is a function of the
mass of the particulate matter this device collects heavier particles
more efficiently. ‗Cyclone‘ is a common inertial collector used in
gas cleaning plants.
iv. Scrubbers – Scrubbers are wet collectors. They remove aerosols
from a stream of gas either by collecting wet particles on a surface
followed by their removal, or else the particles are wetted by a
scrubbing liquid. The particles get trapped as they travel from
supporting gaseous medium across the interface to the liquid
scrubbing medium. Gaseous pollutants can be removed by
absorption in a liquid using a wet scrubber and depends on the type
of the gas to be removed e.g. for removal of sulphur dioxide
alkaline solution is needed as it dissolves sulphur dioxide. Gaseous
pollutants may be absorbed on an activated solid surface like silica
gel, alumina, carbon, etc. Silica gel can remove water vapour.
Condensation allows the recovery of many by products in coal and
petroleum processing industries from their liquid effluents.
Apart from the use of above mentioned devices, other control measures are:
• Increasing the height of chimneys.
• Closing industries which pollute the environment.
• Shifting of polluting industries away from cities and heavily populated areas.
• Development and maintenance of green belt of adequate width.
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• The emission standards for automobiles have been set, which if followed will reduce
the pollution. Standards have been set for the durability of catalytic converters which
reduce vehicular emission.
• In cities like Delhi, motor vehicles need to obtain Pollution under Control (PUC)
certificate at regular intervals. This ensures that levels of pollutants emitted from
vehicle exhaust are not beyond the prescribed legal limits.
• The price of diesel is much cheaper than petrol, which promotes use of diesel. To
reduce emission of sulphur dioxide, sulphur content in diesel has been reduced to
0.05%.
• Earlier lead in the form of tetraethyl lead was added in the petrol to raise octane level
for smooth running of engines. Addition of lead in petrol has been banned to prevent
emission of lead particles with the vehicular emission.
Activities
1. Which type of pollution is common in your area? Why?
2. Name any three devices that control pollution.
3. State two means of controlling indoor air pollution.
4. What is a PUC certificate?
Atmospheric gases like carbon dioxide, methane, nitrous oxide, water vapour, and
chlorofluorocarbons are capable of trapping the out-going infrared radiation from the earth.
Infra-red radiations trapped by the earth‘s surface cannot pass through these gases and to
increase thermal energy or heat in the atmosphere. Thus, the temperature of the global
atmosphere is increased. As this phenomenon of increase in temperature is observed in green
houses, in the botanical gardens these gases are known as greenhouse gases and the heating
effect is known as greenhouse effect. If greenhouse gases are not checked, by the turn of the
century the temperature may rise by 50C. This will melt the polar ice caps and increase the sea
level leading to coastal flooding, loss of coastal areas and ecosystems like swamps and
marshes, etc.
Noise pollution
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Noise is one of the most pervasive pollutants. A musical clock may be nice to listen during
the day, but may be an irritant during sleep at night. Noise by definition is ―sound without
value‖ or ―any noise that is unwanted by the recipient‖. Noise in industries such as stone
cutting and crushing, steel forgings , loudspeakers, shouting by hawkers selling their wares,
movement of heavy transport vehicles, railways and airports leads to irritation and an
increased blood pressure, loss of temper, decrease in work efficiency, loss of hearing which
may be first temporary but can become permanent in the noise stress continues. It is therefore
of utmost importance that excessive noise is controlled. Noise level is measured in terms of
decibels (dB). W.H.O. (World Health Organization) has prescribed optimum noise level as 45
dB by day and 35 dB by night. Anything above 80 dB is hazardous. The table10.4 gives the
noise intensity in some of the common activities.
Noise pollution is a growing problem. All human activities contribute to noise pollution to
varying extent. Sources of noise pollution are many and may be located indoors or outdoors.
Indoor sources include noise produced by radio, television, generators, electric fans, air
coolers, air conditioners, different home appliances, and family conflict. Noise pollution is
more in cities due to a higher concentration of population and industries and activities such as
transportation. Noise like other pollutants is a byproduct of industrialization, urbanization and
modern civilization.
Effects of noise pollution noise pollution are highly annoying and irritating. Noise disturbs
sleep, causes hypertension (high blood pressure), emotional problems such as aggression,
mental depression and annoyance. Noise pollution adversely affects efficiency and
performance of individuals.
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Prevention and control of noise pollution following steps can be taken to control or minimize
noise pollution-
• Road traffic noise can be reduced by better designing and proper maintenance of
vehicles.
• Noise abatement measures include creating noise mounds, noise attenuation walls and
well maintained roads and smooth surfacing of roads.
• Retrofitting of locomotives, continuously welded rail track, use of electric locomotives
or deployment of quieter rolling stock will reduce noises emanating from trains.
• Air traffic noise can be reduced by appropriate insulation and introduction of noise
regulations for takeoff and landing of aircrafts at the airport.
• Industrial noises can be reduced by sound proofing equipment like generators and
areas producing lot of noise.
• Power tools, very loud music and land movers, public functions using loudspeakers,
etc should not be permitted at night. Use of horns, alarms, refrigeration units, etc. is to
be restricted. Use of fire crackers which are noisy and cause air pollution should be
restricted.
• A green belt of trees is an efficient noise absorber.
Activities
2. Water pollution
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pollution of water are soil erosion, leaching of minerals from rocks and decaying of organic
matter. Rivers, lakes, seas, oceans, estuaries and ground water sources may be polluted by
point or non-point sources. When pollutants are discharged from a specific location such as a
drain pipe carrying industrial effluents discharged directly into water body it represents point
source pollution. In contrast non-point sources include discharge of pollutants from diffused
sources or from a larger area such as runoff from agricultural fields, grazing lands,
construction sites, abandoned mines and pits, roads and streets.
Water pollution is the major source of water born diseases and other health problems.
Sediments brought by runoff water from agricultural fields and discharge of untreated or
partially treated sewage and industrial effluents, disposal of fly ash or solid waste into or close
to a water body cause severe problems of water pollution. Increased turbidity of water because
of sediments reduces penetration of light in water that reduces photosynthesis by aquatic
plants.
(i) Pollution due to pesticides and inorganic chemicals
• Pesticides like DDT and others used in agriculture may contaminate water bodies.
Aquatic organisms take up pesticides from water get into the food chain (aquatic in
this case) and move up the food chain. At higher trophic level they get concentrated
and may reach the upper end of the food chain.
• Metals like lead, zinc, arsenic, copper; mercury and cadmium in industrial waste
waters adversely affect humans and other animals. Arsenic pollution of ground water
has been reported from West Bengal, Orissa, Bihar and Western Utara paradish(U.P).
Consumption of such arsenic polluted water leads to accumulation of arsenic in the
body parts like blood, nails and hairs causing skin lesions, rough skin, dry and
thickening of skin and ultimately skin cancer.
• Pollution of water bodies by mercury causes Minamata disease in humans and
dropsy in fishes. Lead causes displexia, cadmium poisoning causes Itai – Itai disease
etc.
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• Oil pollution of sea occurs from leakage from ships, oil tankers, rigs and pipelines.
Accidents of oil tankers spill large quantity of oil in seas which kills marine birds and
adversely affects other marine life and beaches.
(ii) Thermal pollution
Power plants- thermal and nuclear, chemical and other industries use lot of water
(about 30 % of all abstracted water) for cooling purposes and the used hot water is
discharged into rivers, streams or oceans. The waste heat from the boilers and heating
processes increases the temperature of the cooling water. Discharge of hot water may
increase the temperature of the receiving water by 10 to 15 °C above the ambient
water temperature is called thermal pollution. Increase in water temperature decreases
dissolved oxygen in water which adversely affects aquatic life. Unlike terrestrial
ecosystems, the temperature of water bodies remains steady and does not change very
much. Accordingly, aquatic organisms are adapted to a uniform steady temperature of
environment and any fluctuation in water temperature severely affects aquatic plants
and animals. Hence discharge of hot water from power plants adversely affects
aquatic organisms. Aquatic plants and animals in the warm tropical water live
dangerously close to their upper limit of temperature, particularly during the warm
summer months. It requires only a slight deviation from this limit to cause a thermal
stress to these organisms. Discharge of hot water in water body affects feeding in
fishes, increases their metabolism and affects their growth. Their swimming efficiency
declines. Running away from predators or chasing prey becomes difficult. Their
resistance to diseases and parasites decreases. Due to thermal pollution biological
diversity is reduced. One of the best methods of reducing thermal pollution is to store
the hot water in cooling ponds, allow the water to cool before releasing into any
receiving water body
Ground water pollution Lot of people around the world depend on ground water for
drinking, domestic, industrial and agricultural uses. Generally groundwater is a clean
source of water. However, human activities such as improper sewage disposal,
dumping of farm yard manures and agricultural chemicals, industrial effluents are
causing pollution of ground water.
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Eutrophication - ‗Eu‘ means well or healthy and ‗trophy‘ stands for nutrition. The
enrichment of water bodies with nutrients causes entrophication of the water body.
Discharge of domestic waste, agricultural surface runoff, land drainage and industrial
effluents in a water body leads to rapid nutrients enrichment in a water body. The
excessive nutrient enrichment in a water body encourages the growth of algae
duckweed, water hyacinth, phytoplankton and other aquatic plants. The biological
demand for oxygen (BOD) increases with the increase in aquatic organisms. As more
plants grow and die, the dead and decaying plants and organic matter acted upon by
heterotrophic prtozoans and bacteria, deplete the water of dissolved oxygen (DO).
Decrease in DO result in sudden death of large population of fish and other aquatic
organisms including plants, releasing offensive smell and makes the water unfit for
human use. The sudden and explosive growth of phytoplankton and algae impart
green colour to the water is known as water bloom, or "algal blooms". These
phytoplankton release toxic substances in water that causes sudden death of large
population of fishes. This phenomenon of nutrient enrichment of a water body is
called eutrophication. Human activities are mainly responsible for the eutrophication
of a growing number of lakes and water bodies in the country.
Methods for control of water pollution and water recycling
Control water pollution
Waste water from domestic or industrial sources or from garbage dumps is generally
known as sewage. It may also contain rain water and surface runoff. The sewage
water can be treated to make it safe for disposal into water bodies like rivers, lakes
etc. The treatment involves three stages: primary, secondary and tertiary. This
includes: Sedimentation, coagulation/flocculation, filtration, disinfection, softening
and aeration. The first four steps are primary treatment. The first three steps are
involved in primary treatment remove suspended particulate matter. Secondary
treatment removes organic solids, left out after primary treatment, through their
microbial decomposition. Effluents after secondary treatment may be clean but
contain large amounts of nitrogen, in form of ammonia, nitrates and phosphorous
which can cause problem of eutrophication upon their discharge into a receiving water
body such as river, lake or pond. The tertiary treatment is meant to remove nutrients,
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disinfect for removing pathogenic bacteria, and aeration removes hydrogen sulphide
and reduce the amount of carbon dioxide and make water healthy and fit for aquatic
organisms. This treatment of waste water or sewage is carried out in effluent treatment
plants especially built for this purpose. The residue obtained from primary treatment
one known as sludge.
Water recycling with increasing population the requirement for water is increasing
rapidly. However, the availability of water is limited but an ever increasing water
withdrawal from different sources such as rivers, lakes and ground water is depleting
these sources and deteriorating their water quality. Therefore, it is essential to utilize
the available water with maximum economy. This involves recycling of waste water
for certain uses with or without treatment. Recycling refers to the use of waste-water
by the original user prior to the discharge either to a treatment system or to a receiving
water body. Thus the waste water is recovered and repetitively recycled with or
without treatment by the same user.
Control of water pollution
The following measures can be adopted to control water pollution:
(a) The water requirement should be minimized by altering the techniques involved.
(b) Water should be reused with or without treatment.
(c) Recycling of water after treatment should be practiced to the maximum extent
possible. (d) The quantity of waste water discharge should be minimized.
Activities
1. Name the metals in water that cause Minamata and Itaiitai diseases.
2. When fertilizers and sewage enter a water body, phytoplankton and algae grow rapidly.
What is this phenomenon?
3. What is primary treatment?
4. The water used for cooling purposes in industries may be drained industrial into rivers. To
what extent does this raise the water temperature of the river?
5. What effect does thermal pollution have on the swimming efficiency of fish?
6. What effect does thermal pollution have on metabolism of aquatic animals?
7. State the term for residue left after primary treatment of waste water.
3. Soil pollution
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Addition of substances which adversely affect the quality of soil or its fertility is known as
soil pollution. Generally polluted water also pollutes soil. Solid waste is a mixture of plastics,
cloth, glass, metal and organic matter, sewage, sewage sludge, building debris, generated from
households, commercial and industries establishments add to soil pollution. Fly ash, iron and
steel slag, medical and industrial wastes disposed on land are important sources of soil
pollution. In addition, fertilizers and pesticides from agricultural use which reach soil as run-
off and land filling by municipal waste are growing cause of soil pollution. Acid rain and dry
deposition of pollutants on land surface also contribute to soil pollution.
Plastic bags made from low density polyethylene (LDPE), is virtually indestructible, create
colossal environmental hazard. The discarded bags block drains and sewage systems. Leftover
food, vegetable waste etc. on which cows and dogs feed may die due to the choking by plastic
bags. Plastic is non-biodegradable and burning of plastic in garbage dumps release highly
toxic and poisonous gases like carbon monoxide, carbon dioxide, phosgene, dioxine and other
poisonous chlorinated compounds.
Industrial sources: It includes fly ash, chemical residues, metallic and nuclear wastes. Large
number of industrial chemicals, dyes, acids, etc. find their way into the soil and are known to
create many health hazards including cancer.
Agricultural sources :Agricultural chemicals especially fertilizers and pesticides pollute the
soil. Fertilizers in the runoff water from these fields can cause eutrophication in water bodies.
Pesticides are highly toxic chemicals which affect humans and other animals adversely
causing respiratory problems, cancer and death.
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prior to disposal should be properly treated for removing hazardous materials. Biomedical
waste should be separately collected and incinerated in proper incinerators.
Activities
1. Define soil pollution.
2. Why are plastic bags a big environmental nuisance?
3. How vermicomposting degrades organic waste into a useful substance? What is this
substance used for?
Ionizing radiations cause ionization of atoms and molecules of the medium through which
they pass. Electromagnetic radiations such as short wavelength ultra violet radiations (UV),
X-rays and gamma rays and energetic particles produced in nuclear processes, electrically
charged particles like alpha and beta particles produced in radioactive decay and neutrons
produced in nuclear fission, are highly damaging to living organisms. Electrically charged
particles produced in the nuclear processes can have sufficient energy to knock electrons out
of the atoms or molecules of the medium, thereby producing ions. The ions produced in water
molecules, for example, can induce reactions that can break bonds in proteins and other
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important molecules. An example of this would be when a gamma ray passes through a cell,
the water molecules near the DNA might be ionized and the ions might react with the DNA
causing it to break. They can also cause chemical changes by breaking the chemical bonds,
which can damage living tissues. The ionizing radiations cause damage to biological systems
and are, therefore, pollutants.
Radiation damage the biological damage resulting from ionizing radiations is generally
termed as radiation damage. Large amounts of radiation can kill cells that can dramatically
affect the exposed organism as well as possibly its offspring. Affected cells can mutate and
result in cancer. A large enough dose of radiation can kill the organism. Radiation damage can
be divided into two types:
(b) Genetic damage. Somatic damage refers to damage to cells that are not associated with
reproduction. Effects of somatic radiation damage include reddening of the skin, loss of hair,
ulceration, fibrosis of the lungs, the formation of holes in tissue, a reduction of white blood
cells, and the induction of cataract in the eyes. This damage can also result in cancer and
death. Genetic damage refers to damage to cells associated with reproduction. This damage
can subsequently cause genetic damage from gene mutation resulting in abnormalities.
Genetic damages are passed on to next generation.
Radiation dose-the biological damage caused by the radiation is determined by the intensity
of radiation and duration of the exposure. It depends on the amount of energy deposited by the
radiation in the biological system. In studying the effects of radiation exposure in humans, it is
important to realize that the biological damage caused by a particle depends not only on the
total energy deposited but also on the rate of energy loss per unit distance traversed by the
particle (or ―linear energy transfer‖). For example, alpha particles do much more damage per
unit energy deposited than do electrons.
Radiation effects and radiation doses-A traditional unit of human-equivalent dose is the
rem, which stands for radiation equivalent in man. At low doses, such as what we receive
every day from background radiation (< 1 m rem), the cells repair the damage rapidly. At
higher doses (up to 100 rem), the cells might not be able to repair the damage, and the cells
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may either be changed permanently or die. Cells changed permanently may go on to produce
abnormal cells when they divide and may become cancerous. At even higher doses, the cells
cannot be replaced fast enough and tissues fail to function. An example of this would be
―radiation sickness.‖ This is a condition that results after high doses is given to the whole
body (>100 rem). Nuclear explosions and accidents in nuclear reactors are a serious source of
radiation hazard. The effects of atomic explosions in Nagasaki and Hiroshima are still not
forgotten. The nuclear reactor accident at Chernobyl in 1986 led to deaths of many reactor
personnel and a very large release of radionuclide to the environment causing long term
radiation damage to the people living in the neighboring regions.
Accidents at nuclear power plants nuclear fission in the reactor core produces lot of heat
which if not controlled can lead to a meltdown of fuel rods in the reactor core. If a meltdown
happens by accident, it will release large quantities of highly dangerous radioactive materials
in the environment with disastrous consequences to the humans, animals and plants. To
prevent this type of accidents and reactor blow up, the reactors are designed to have a number
of safety features. Inspite of these safety measures two disasters in the nuclear power plants
are noteworthy- namely at ‗Three Mile Island‘ in Middletown (U.S.A.) in 1979, at Chernobyl
(U.S.S.R.) in 1986. In both these cases a series of mishaps and errors resulted in over heating
of the reactor core and lot of radiation was released into the environment. The leakage from
Three Mile Island reactor was apparently low and no one was injured immediately. However,
in case of Chernobyl the leakage was very heavy causing death of some workers and radiation
spread over large areas scattered all over Europe. People of the city had to be evacuated to
safer places and the plant had to be closed down. These two disasters are a reminder that
nuclear power reactors require a constant up gradation of safety measures. Accidents with
nuclear submarines also points to the same.
Activities
1. Which type of radiations are produced in a microwave oven?
2. State the use of absorbed dose of radiation.
3. How much of radiation can damage internal organs upon its exposure for a few days?
4. What are ionizing and non-ionizing radiations? Give examples.
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Unit 9
1. What is Botany?
2. What are various branches of botany?
3. What organisms are addressed/studied under each sub disciplines of botany
Botany is one of the main branches of Biology concerned with the scientific study of plants.
Botany has several branches. Like algology, bryology, pteridology, plant physiology, plant
ecology, plant anatomy, plant nutrition, plant pathology, dendrology, phytochemistry, cell
biology, histology, phytopathology, phytogeography, geobotany, paleobotany, cell
phytopathology, phytogeography, geobotany and paleobotany are some of the major branches.
9.1.1 Algology
Algology (phycology) is a branch of botany deals with algae. It is derived from two Greek
words: Phycos=algae; Logos=study. This discipline deals with the morphology, phylogeny
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(tree of Life), biology, reproduction and ecology of algae in all ecosystems. Algae can be
defined as:simple, eukaryotic, autotrophic, have a various range of cell morphologies and
diversified life cycle organisms. They differ widely in their distribution, structure,
biochemical traits and eproduction(sexual and asexual). They lack the roots, stems, leaves &
vascular tissues.Algae show the following major morphological variations:
Unicellular:single celled algae.
Colonial: An assemblage of individual cells together.
Filamentous:a morphology in which daughter cells remain attached after cell division.
Siphonaceaous: a morphology in which one large, multi-nucleate cell without cross
walls.
Algae reproduce both asexually and sexually. The common methods of asexual reproductions
are: binary fission, fragmentation, hormogonia and spore production. Isogamy and
heterogamy are the two common sexual reproduction methods.
Ecology and Distribution of Algae
Generally, algae can be found everywhere in nature. They are found from marine to fresh
water, terrestrial land, shaded areas, etc. Various terminologies are applied for microhabitats
of algae. For example, Epipelic: algae live on clay; Epipamic:algae live onsand; Epilithic:
algae live onrocks; Epiphytic:algae live/grow on other plants; Endozoic/epizoic: Live in or
on animals
Currently, there are different divisions of algae. The most common are listed below.
Cyanophyta:a group of blue green algae includes Nostoc, Anabaena, Spirullin,
Oscilatotia, etc.
Chlorophyta: a group of green algae includes Spirogyra, Volvox, Oedogonium, Chlorella,
and others.
Phaeophyta: a group of brown algae includes Fucus, Laminaria, Sargassum, Ectocarpus
Rhodophyta: a group of red algae includes Polysiphonia, Coralline, etc.
Charophyta: Commonly known as stoneworts, usually preferred less oxygenated & hard
water (Ca and Mg carbonates) areas.Example Chara, Vaucheria, etc.
Euglenophyta: Unicellular fresh water algae, plant-animal feature. Example Euglena.
Bacillariophyta: Especial group of algae, abundant in sediments in marine and freshwater
ecosystems. Example Diatoms.
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Economical uses of Algae
Algae have various economical uses like:
Primary Producers
As Fertilizers
Sources of Iodine
In biological research
Pharmaceutical, cosmetic, and industrial applications
Source of different compounds, like: agar, carrageenansand alginates
Applications in Pisciculture
Biofuel production
Carbon sequestration
Bioremediation
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Fig: 9.1.Marchantia (Liverwort)
Hornworts are a group of small, inconspicuous thaloid plants that often grow on moist soils.
They consist of only about 400 named species. They are different from all other
embryophytesin having a single large chloroplast (occasionally two to four) per cell and
chloroplasts have a pyrenoid, both algal feature and absent in all other embryophytes.
Mosses are perennial & remarkably successful plants. Although the mosses are small plants,
they are conspicuous (their wide range of habitats, soft texture and pleasant green
appearance). About 12,000 species of mosses are known. They are the largest and most
familiar group of bryophytes.
The division Pteridophytes also categorized in to four main groups. Namely Psilophyta,
Lycopsida(containing lycopodiales, selaginellales, isoetes), Sphenopsida and
Pteropsida.Psilophyta are characterized by aerial stem, bear small scale like leaves that are
epidermal in origin. This scale like leaves (Prophylls) do not have vascular tissues which
resemble the leaves of bryophyte in having no vascular strand and regarded as appendages
rather than true leaves. Like all other vascular plants, Psilotales possess stomata, but unlike
other vascular plants the stomata are found in the epidermis of the stem.
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Lycophyta are also characterized or distinguished form members of Psilotals by having true
leaves and roots; by association of their sporangia with fertile leaves-sporophylls. They are
known as club mosses because of their small size and their moss like leaves. Dear students,
please read about different divisions of Pteridophytes from various books.
The angiosperms or flowering plants are the most advanced one now a day.Most land plants
familiar to us belong to this groupincludes from grasses to cactuses, tiny herbs to large trees.
This huge and diverse group is divided again into two subgroups; monocotyledons (grasses,
crops, lilies and palms) and dicotyledons(Olea, Ficus, beans, peas, chickpea, etc…).
Seeds contain: embryo, food, endosperm, seed coat or testa and sporophyte. The embryo
within the seed is dormant; it can survive for long periods without additional food or water.
When conditions become favorable, the embryo resumes growth as the seed germinates i. e
upon germination the seeds produce the sporophyte. Seeds have freedom from external water
for transfer of the male gamete or spermatozoids to the female gamete or egg cells. They
produce pollen and pollen tube. Endosperm provides nourishment or food supply for the
growing embryo (young sporophyte).
Seed plants have distinct features. They produce two major features that distinctly distinguish
them from other plants. The first is the seed. The production of seed is a very advanced stage
in plant life. The second is wood. The possession of wood is also another very important
feature. Therefore, the production of seed and wood, which other non-seed plants cannot
produce are unique features.
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Seed plants have also have other many features in common, like:
The gametophytes (male and female) are protected from desiccation and injury
by the protective covering of the ovules called integuments and later embryo is
protected by the seed coat ortesta.
The generalized life cycle of seed plants, which have separate male and female gametophytes
produced by different sized spores is indicated below the Figure.
Seed plants are broadly divided in to two. These are Gymnosperms and angiosperms. The
following are common characteristics of gymnosperms.
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not form true flowers and fruits. They were the first true seed plants. Most are tall evergreen
trees with roots, wood and stems. They are needle shaped leaves. Have vascular tissues for
transport and reproductive structures are found on cones. Seeds are found in female cones.
Angiosperms are the largest group of seed plants with about 90% of all plant species. Their
name Angiosperm derived from Greek words, Angio-container/vessel and sperma- seed= seed
enclosed in vessel or fruits. They are the most abundant and recognized plants. These plants
are a gain divided into two main groups (monocots and dicots) based on cotyledons. They
produce seeds in flowers they do have fruits and advanced vascular tissues.
9.2.1 Invertebrates
There are over a million described species of animals. Of this number about 5% possess a
backbone and are known as vertebrates. All others, constituting the greater part of the animal
kingdom, are invertebrates. The Invertebrates therefore include 95% of all species in the
animal kingdom plus more than half of the animal-like members of the kingdom protista.
Self-test
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→ Invertebrates able to exhibit all types of reproduction.
→ Invertebrates can be categorized as acoelomates, pseudocoelomates or coelomates.
→ Invertebrates show radial symmetry, bilateral symmetry or they may be assymetric.
→ Invertebrates are with different stages of organization.
→ Some invertebrates have common phylogenetic origin; others are only remotely
related. Some are much more closely related to the vertebrates than to other
invertebrate groups.
The word Porifera has been adopted from the Latin porus for pore and Ferre to bear, hence
sponges are called ―pore bearing animals‖ since their body wall is perforated by numerous
tiny pores. The phylum comprises the most primitive and simple multicellular animals that
lack organs. Compared with other metazoans, sponges‘s cells show a high degree of
interdependence that the sponge body resembles a protozoan colony in some respects. Major
classes of Porifera: Class Calcarea (calcispongiae), Class Hexactinellida (Hyalospongiae) or
'Glass sponges', and Class Demospongiae
B. Phylum Radiata
The first groups of true Metazoa (Eumetazoa) are called radiates. The Eumetazoa can be
divided into the Radiata, which are characterized by a primary radial or biradial symmetry,
and the Bilateria, which have a bilateral symmetry. The Radiata are the most primitive of
the Eumetazoa. The radiate animals are made up of two phyla, namely Cnidaria and
Ctenophora, which have got their common name from the type of symmetry they have.
Cnidaria have two basic body plans: polyp and medusa.
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Fig.9.1: a) Polypoid body form. b) Medusoid body form
C. Acoelomate Bilateria
Have no coelom (body cavity). The space between the body wall and the digestive
tract is filled with muscle fibers and loose tissue called parenchyma. They have
bilateral symmetry and defined tissues organized into functional organs. They have a
highly organized nervous system with concentration of nervous tissue and sense
organs in the anterior end (cephalization), excretory system of specialized flame cells
and tubules for elimination of nitrogenous wastes.
Acoelomates include:
-flatworms, phylum Platyhelminthes (Gr. platys, flat, + helmins, worm)
-ribbon worms, phylum Nemertea (Gr. Nemertes, one of the Nereids, mermaids
of Greek mythology) and
-Jaw worms, phylum Gnathostomulida (Gr. gnathos, jaw, + stoma, mouth).
Flatworms (phylum Platyhelminthes) are divided into four classes:
1. Class Turbellaria – Free living Flatworms
2. Class Trematodes - parasitic flukes
3. Class Monogenea – parasitic monogenetic flukes
4. Class Cestoda – tapeworms
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D. Phylum Nematoda (Roundworms)
General characteristics
-Are pseudocoelomate and there are more than 25,000 species.
Nematodes are an extensive group with worldwide distribution.
Bilateral symmetry, Triploblastic structure (endoderm, mesoderm and ectoderm)
Some degree of cephalization = head with sensory organs, they are elongated roundworms
covered with a flexible, nonliving cuticle, lack both cilia and flame cells/bulbs, free living,
aquatic, terrestrial and many parasitic
A handful of good garden soil contains thousands of nematodes.
Some nematodes are plant parasites feeding on plant sap, especially roots.
Caenohabditis elegans, a free-living nematode
o Easy to culture in the laboratory and has become an individual model for
studies of basic developmental biology.
Dioecious; sexes separate with females larger than males; one or two tubular gonads;
Copulatory spicules present in males
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-Dog heartworms (Dirofilaria immitis)
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-Most species prefer aquatic environments, but there are also a number of well known
terrestrial species. They include earthworms, sand worms, bristle worms, clam worms, fan
worms, leeches.
-The fluid that fills the coelom serves a variety of functions.
transports gases and nutritive materials
provides fluid for processing excretory wastes
functions as a hydrostatic skeleton, and
a site for gamete maturation and brooding of embryos.
Classification of phylum Annelida includes:
a) Class – Polychaeta (Tubeworms, Clamworms, and Fanworm
b) Class Oligochaeta (e.g Earthworms)
c) Class Hirudinea( e.g. Leech)
The name Arthropoda means ―jointed foot‖ , are the most successful of all animals and
represents ~ 80% of animal kingdom both in species and ecological distribution. Over a
million species have been identified. Their body is divided into 3 sections: head , thorax
(mid-body region) and abdomen
They have exoskeleton- The rigid outer layer of the arthropod body , composed primarily of
the carbohydrate chitin, provides protection against predators and helps prevent water loss., an
exoskeleton does not grow, arthropods shed their exoskeleton periodically and form a new,
larger one.
Classification includes:
I. Subphylum Trilobita
II. Subphylum Chelicerata
Class Merostomata (horse-shoe crab)
Class Arachnida(spiders, scorpions, mites and ticks)
III. Subphylum Crustacea (shrimp, lobsters, Crayfish, water fleas, copepod & sow bugs)
1. Class Malacostraca
– Order Decapoda
– Order Isopoda
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2. Class Branchiopoda
3. Class Osracoda
4. Class Maxillopoda
– Subclass Copepoda
– Subclass Thecostraca
Infraclass Cirripoda
IV. Subphylum Myriapoda
– Class Diplopoda (eg millipedes)
– Class Chilopoda (eg centipedes)
V. Subphylum Hexapoda
–Class Insecta (insects)
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Activities
1. Compare and contrast the polyp and medusa forms of cnidarians
2. Describe the structure and function of the stinging cells for which cnidarians are
named.
• Pollination- many cross pollinated plants depend on insects for pollination and fruit
set. Eg Honey bees, aid in pollination of crops.
• Seed dispersal, natural enemies of other pests, decomposition
• Soil formation: Soil invertebrates include ecosystem engineers that are powerful
drivers of soil physical functions (water dynamics, aeration and protection from
erosion hazards). They play an important role in carbon cycling, as they control the
carbon sequestration process and influence greenhouse gas emission. Example, soil
insects such as ants, beetles, larval of cutworms, crickets, collumbola, make tunnels in
soil and facilitate aeration in soil. They become good manure after death and enrich
soil.
Invertebrates as a Resource
Example
• Source of food for humans, bait for fishing(Sponges for bathing ), Corals, Conchs,
Oysters and others for jewelry,
• Bees as pollinators of crops: Honey bees are mass produced and transported to farms
during flowering periods to insure adequate pollination of crop plants, without
pollination fruits and vegetables from insect pollinated crops will not be produced.
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• Wasps, beetles, mantids, spiders, for biocontrol
• Medicinal use of leeches: Medicinal leeches are still used to reduce bruising and
scarring after surgery
Silk production
• Ecteinascidin – from tunicates – tested for treatment of breast and ovarian cancers
• Omega Conotoxin MVIIA – extracted from cone snails (Conus magnus) – potent pain
killer
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Invertebrates as Food
Examples
• Mollusca (squid, mussels, clams, oysters, scallops, snails, abalone), Crustacea (shrimp,
lobsters, crabs, spider crabs), Insecta (beetles, ants, termites, grasshoppers, bees),
Echinodermata (sea cucumbers, sea urchins), Cnidaria (jellyfish) and Annelida (palolo
worms)
• Bait for Fishing. For example: Earthworms (Oligochaeta), Insect larvae (Neuroptera –
night crawlers) , Shrimp, etc.
• Invertebrate used in Jewelry includes: Morpho butterflies, Scarab beetles, Rare corals
and Oysters and Conchs for pearl and mother of pear
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Sub phylum vertebrata are diverse, there are about 53, 000 living vertebrates. They are
divided into two super classes and 9 classes as following:
Superclass Agnatha (jawless fish)
Class Myxini – hagfish
Class Pteraspidomorphi – lampreys
Superclass Gnathostomata (jawed vertebrates)
Class Chondrichthyes: cartilaginous fishes
Class Sarcopterygii:sarcopterygians or fleshy-finned fishes
Class Actinopterygii: ray-finned fishes
Class Amphibia – frogs, salamanders, caecilians
Class Reptilia – turtles, tuatara, lizard. Snake, crocodiles
Class Aves – birds
Class- Mammalia
Activities
3. Why are you not likely to see members of the super class Agnathans around
your area?
4. Collect a fish from the aquarium or lake and attempt to classify as either
cartilaginous or bony fish.
Class Amphibia
Amphibians are cold blooded animal with moist, hairless skin through which water can pass
in and out. Nearly all amphibians live the first part of their lives in water and the second part
on
Land-a double life reflected in the name amphibian, which comes from the Greek words
amphi, meaning ―both,‖ and bios, meaning ―life.‖ Amphibians were the first animals with
backbone to adapt to life on land. They are the ancestors of reptiles, which in turn gave
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rise to mammals and birds.
Scientists recognize more than 5,000 species of amphibians, all of which are members of
one of three main groups: frogs and toads, salamanders, or caecilians. Frogs and toads are
the most abundant of all amphibians, numbering more than 4,000 species. Frogs have
smooth skin and long limbs. Toads, in contrast, have warty skin and short limbs.
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- Urodelas are usually found in or near water and often reside in moist soil under rocks or
logs. ---The adults usually spend most of their time on land and have a diet consisting of
insects and worms and burrow in mud at the bottom of marshes
Frogs and toads (Order Anura)- Members of this order have the following characteristics:
-―Anura‖ comes from the Greek words meaning no tail, making these the ―tail-less
amphibians‖. Since their skin absorbs oxygen most efficiently when damp and tends to lose
water rapidly, remaining near water is necessary for most frogs (and salamanders). As a
defense mechanism some frogs (e.g., poison arrow frogs) secrete potent toxins into the mucus
layer of their skin.
-Hind legs are longer than front limbs; and by this they are well adapted for hopping, jumping
and swimming.
- Live in aquatic environment, although some are well adapted to drier habitats.
- Larval forms are called tadpoles lacking true teeth, are usually herbivorous, and develop
hind limbs before front limbs (which is the opposite of Urodela larvae).
- Larvae also lack external gills, having opercular chambers that allow water to flow over
internal gills, before exiting through a spiracle.
c) Order Gymnophiona (Caecilians). They have the following features:
-Lack legs (dig by ramming its bony head through the soft dirt)
-Members of this order are blind and legless amphibians that are shaped like worms. They
burrow in moist soil in tropical habitats of Africa and South America, feeding on soil
invertebrates such as worms and insects. Some caecilians live in moist soil that is rich in
decayed plant matter.
Class Reptilia
There are about 6,550 living species of reptiles worldwide. Reptiles live in a wide range of
habitats, including forests, swamps, grasslands, deserts, oceans, and mountains. The name
"reptile" is generally applied to any of a group of ectodermic (cold-blooded i.e. need an
"outside" source of heat to generate adequate body heat) vertebrates in the Class Reptilian.
Reptiles must regulate their body temperature by behavior, either by basking in the sun to
keep warm or by hiding under cover to keep cool. Reptiles have dry and not slimy skin. They
are covered in scales or a shell. If they have legs, they have claws on their toes. Reptiles can
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be far from water sources because their skins retain water better than that of amphibians.
Reptiles lay amniotic eggs that have a leathery shell preventing rapid water loss. Reptiles were
the first animals to fully escape a dependence upon the availability of an open body of water.
What adaptations were required for this transition?
Thick, dry skin with scales, which was less prone to desiccation (water loss).
Amniotic eggs were one of the most important evolutionary innovations.
Structures of amniotic egg:
• Air cell: located in the large end of the egg.
• Yolk: the principal nutritional source for the embryo.
• Albumen: clear, cushioning protein surrounding the yolk.
• Chalazae: whitish cord-like proteins that support the yolk in the center of the albumen.
• Shell membranes: there are two of these surrounding the albumin.
• Shell: is composed mainly of protein embedded with calcium carbonate. If the hen lays
brown
eggs, the brown pigments are added to the shell in the last hours of shell formation. The shell
contains several thousand pores that permit the egg to "breathe
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eggs in the moist interior of the female‘s body, and for fertilization to occur before the
hard shell is added around the egg.
Breathing. Muscles of the rib cage expand and contract to pump larger quantities of
air into larger, more advanced lungs.
Classification of reptiles is still being resolved, and zoologists have been revising
the various classifications of reptiles. There are three important groups that we will
consider here:
Turtles and Tortoises (Order Chelonia): among which the body is surrounded by a
protective shell.
Lizards and Snakes (Order Squamata): Snakes evolved from a legged lizard, and
some still possess vestigial leg bones.
Crocodiles and Alligators (Order Crocodylia): In several ways crocodiles more
closely resemble birds than other reptiles, such as in building nests and caring for their
young. Possibly there was a close relationship among the dinosaur ancestors from
which crocodiles and birds descended.
Activity: Explain how the adaptations of early reptiles enabled these animals to live
on land?
Birds are the direct descendents of theropod type dinosaurs, and certain key traits of birds can
be linked to anatomical features of these dinosaurs:
• Feathers are composed of the same material (keratin protein) as the scales of reptiles. They
provide efficient insulation to both hot and cold environments and form an aerodynamic
surface necessary for flight.
• Bones and skeleton adapted for flight. If you have ever carved a turkey, you have
encountered the fused collarbone called the furcula (or the ‗wish bone‘) and a large sternum
bone called the ‘keel’ to which the large flight muscles are attached. The bones are said to be
pneumatic (filled with air spaces) to reduce weight, and these air spaces participate in
respiratory
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oxygen storage.
• Endothermy or being ‗warm-blooded‘. Unlike modern reptiles, birds can generate enough
heat internally to regulate and maintain a constant body temperature, thus allowing birds to
inhabit habitats (think of penguins) unacceptably cold for reptiles. There is some evidence that
this trait evolved among the theropod ancestors of birds.
For terrestrial vertebrates the greatest numbers of species are found among the birds. Some
familiar birds are representatives of the major Orders, such as: Eagles and hawks,
Hummingbirds, Owls, Penguins, Pigeons, Parrots, Songbirds (robins, warblers, orioles, etc),
Woodpecker.
Activity: Why do you think that some birds are not able to fly even if they
have wings? Describe it.
Although mammals appear to have evolved early during the Mesozoic (even before birds),
they did not rise to predominance until the ecological niches become vacant with the demise
of the dinosaurs.
Activities
1.Describe the characteristic features of mammals
2.Distinguish mammals from other vertebrates
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• Internal fetal development. Among placental mammals (the most common type) the
circulatory system of the fetus and mother become intimately intertwined within a placenta,
where exchange of nutrients and waste products can occur. This allows long-term internal
development of the fetus.
A single jaw bone on either side. In all other vertebrates, there is more than one bone on
each side of the jaw.
Four chambered heart with the main artery leaving the heart curves to the left becoming
the aortic arch. (In birds it curves to the right and in all other vertebrates there is more
than one main artery leaving the heart)
Muscular diaphragm separates the thoracic cavity from the abdominal cavity.
This group of mammals, also known as the placental is characterized by having:- A placenta -
a reproductive structure, which is housed in the uterus of the female by which the developing
embryo connects to the mother to get nutritive support. The offspring of eutherians receives
all its nutritional needs through the placenta that links it to the mother to develop into a fully
developed organism before birth. The period of development (gestation period) varies with the
species of mammal but undoubtedly longer than that in the metatherians that we have just
described above. For example the gestation period in the whales is 2 years, in mouse 21 days,
and in humans the period is 9 months. These mammals are the most abundant and diverse of
the class representing 94% of the species of mammals.
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Activity:
Why a young marsupial mammal such as kangaroo enters to abdominal pouch after birth?
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Unit 10
Learning Objectives: This is chapter highlights the major areas of application of biology to
human and the environment. Thus, at the end of this chapter students are expected to
List the different areas where biological knowledge can be applied
Describe and understand the application of biological sciences in the different
areas/sectors
Understand the application of biology in forensic science and warfare
Self-test
1. Describe the application of biology in different areas such as medicine, Environmental
engineering, Biosystem engineering, Chemical engineering, Biosensor technology,
industries (like Food, brewery, pharmaceutical, tannery and textile) and agriculture etc.
2. Discuss the role of biological knowledge in forensic science and warfare
10.1 Application of Biology in medicine and other health sciences (Fast diagnosis tools,
drug and vaccine production, gene therapy, immuno-diagnosis, immunotherapy,
transplantation, medicinal plants, etc)
Biotechnology contributes much towards the growing public and global health needs. It has
revolutionized mankind since its existence. It provides effective diagnostics, prevention and
treatment measures including production of novel drugs and recombinant vaccines. It gives
effective drug delivery approaches, new methods for therapeutics, nutritionally enriched
genetically modified crops and efficient methods for environmental cleanup. Accordingly, life
quality and expectancy have been increased worldwide through the services provided by
biotechnology.
Parasitic and infectious diseases like Acquired Immunodeficiency Syndrome (AIDS) and
tuberculosis (TB) have been diagnosed rapidly at relatively low cost. Molecular diagnostic
tools including polymerase chain reaction (PCR), recombinant antigens and monoclonal
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antibodies have been used for this purpose. Biotechnology has also offered modern diagnostic
test kits, rickettsial, bacterial and viral vaccines along with radiolabelled biological
therapeutics for imaging and analysis. Vaccination by making recombinant vaccines has the
potential to eradicate non-communicable diseases like cancer. Naked DNA vaccines, viral
vector vaccines and plant-derived vaccines are found to be most effective against a number of
bacterial and viral diseases.
For example, extremely thin pieces of skin could be cut free and would obtain enough
nourishment from the serum in the graft bed to stay alive while new blood vessels are being
formed. This free grafting of skin, together with the flap techniques constituted the main
therapeutic devices of the plastic surgeon in the correction of various types of defects. Skilled
manipulations of such grafts produced surprising improvements in the appearance of those
born with malformed faces and in the disfigurements resulting from severe burns. Cornea,
which structurally is a modified form of transparent skin, can also be free grafted, and corneal
grafts have restored sight to countless blind eyes.
It is extremely important that the malfunction of an organ system can be corrected with
transplantation of an organ (eg, kidney, liver, heart, lung, or pancreas) from a donor.
However, the immune system remains the most formidable barrier to transplantation as a
routine medical treatment. The immune system has developed elaborate and effective
mechanisms to combat foreign agents. These mechanisms are also involved in the rejection of
transplanted organs, which are recognized as foreign by the recipient's immune system.
Understanding these mechanisms is important, as it aids in understanding the clinical features
of rejection and, hence, in making an early diagnosis and delivering appropriate treatment.
Knowledge of these mechanisms is also critical in developing strategies to minimize rejection
and in developing new drugs and treatments that blunt the effects of the immune system on
transplanted organs, thereby ensuring longer survival of these organs
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Plants have been used as medicine since time immemorial. The FAO estimated in 2002 that
over 50,000 medicinal plants are used across the world. The WHO estimates that some 80%
of the world's population depends mainly on traditional medicine primarily of plants origin.
For standard production and utilization, WHO formulated a policy on traditional medicine in
1991, and since then has published guidelines for them, with a series of monographs on
widely used herbal medicines.
Medicinal plants may provide three main kinds of benefit: health benefits to the people who
consume them as medicines; financial benefits to people who harvest, process, and distribute
them for sale; and society-wide benefits, such as job opportunities, taxation income, and a
healthier labour force. However, development of plants or extracts having potential medicinal
uses is blunted by weak scientific evidence, poor practices in the process of drug
development, and insufficient financing. Traditional healers, Biologist, chemical engineers
and health professionals are highly responsible to advance such huge opportunity.
Bioengineers can apply their expertise to other applications of engineering and biotechnology,
including genetic modification of plants and microorganisms, bioprocess engineering, and
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biocatalysis. Working with doctors, clinicians and researchers, bioengineers use traditional
engineering principles and techniques and apply them to real-world biological and medical
problems.
10.3 Application of Biology in agriculture (soil fertility, tissue culture, animal breeding
and transgenic animals, plant disease and pest management)
Food supply for the fast growing population is mainly constrained by the loss of soil fertility
and diseases of crops and animals. In addition, lack of advanced tool remains a problem. The
multiple applications of biology in agriculture have substantially improved the production and
supply of food for human as well as feed for animals. The following are some few examples
on the advancements of agricultural production involving knowledge of biology and
technology.
Soil fertility management practices using biological knowledge include the use of organic
fertilizer, bio-fertilizers, crop rotation with legumes and the use of improved germplasm,
combined with the knowledge on how to adapt these practices to local conditions.
Plants can be propagated quickly and in large quantity by tissue culture technique. The
example is palm trees, orchids, bananas, and carrots. Using this technology large quantity of
food with desired quality can be produced in reasonably little area. Genetic Engineering has
produced seedless fruits such as watermelon, papaya, orange and grape. This will significantly
reduce the crop cycle. Moreover, farmers used to plant crops traditionally using conventional
tools. With the advancement of biology and technology, they now can plant crops in many
different cultivation ground along with more efficient cultivation methods.
Animal breeding addresses the genetic value of livestock. Selecting for breeding animals with
superior traits in growth rate, egg, meat, milk, or wool production, or with other desirable
traits has revolutionized livestock production throughout the entire world. Animals can also be
genetically modified (transgenic animals) for valuable traits. There are many potential
applications of transgenic methodology to develop new and improved strains of livestock.
Practical applications of transgenics in livestock production include enhanced prolificacy and
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reproductive performance, increased feed utilization and growth rate, improved carcass
composition, improved milk production and/or composition, modification of hair or fiber, and
increased disease resistance. Development of transgenic farm animals will allow more
flexibility in direct genetic manipulation of livestock. Gene transfer is a relatively rapid way
of altering the genome of domestic livestock. The use of these tools will have a great impact
toward improving the efficiency of livestock production and animal agriculture in a timely
and more cost-effective manner. With ever-increasing world population and changing climate
conditions, such effective means of increasing food production are promising.
Applications of animals in research are also another area of animal biotechnology. Biomedical
research involving the use of animals has been the cornerstone of medical progress for the
past several centuries, but ethical concerns about the use of vertebrates, which are more
commonly understood to be sentient animals, have led researchers, veterinarians, and others in
laboratory animal science to search for alternatives. Hence invertebrates can serve as
replacements for their vertebrate counterparts in many areas of research, testing, and
education as shown in Table below.
Table 10.1. Selected invertebrate used in developmental biology, diseases and genetic models
Model Species used
Bone morphogenic proteins Drosophila
Calcium signaling Asterina pectinifera
Cilia regulation of development pathways Caenorhabditis elegans
Chromatin insulators Drosophila
Developmental glycobiology Drosophila
Formation of the nervous system Drosophila
Gene regulatory network Echinoidea
MicroRNA function in embryogenesis C. elegans
Pattern signaling and retinal development Drosophila
Pituitary patterning Drosophila
Regulatory switches Drosophila
Semophorin in developing nervous system Caelifera (grasshopper)
Tubulogenesis Drosophila
Nitrous oxide signaling during neural Locusta, Schistocerca, Acheta,
development Manduca, Drosophila
Aging Bivalves, Drosophila, Caenorhabditis
elegans, Macrostomum lignano
(flatworm)
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Hypoxia Drosophila, Daphnia magna, C. elegans
Freeze tolerance Various species of insects
Wound healing Hirudo medicinalis,
Drosophila, C. elegans
Sleep regulation Drosophila
Stem cell roles in cancer Drosophila, C. elegans
Epilepsy Drosophila, C. elegans
Mitochondria-associated diseases C. elegans
Gene regulation C. elegans, Drosophila
Pests and diseases are severe challenges for crop production. Disease in crops is adversely
reducing quantity or quality of yield. Organisms that cause infectious disease in crops include
fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms, phytoplasmas, protozoa,
nematodes and parasitic plants. Different biocontrol methods are developed to combat these
diseases. Pests can also be controlled using integrated biological knowledge as described
below.
Pest control:
Pest control is one of the primary applications of biology in agriculture. Biological knowledge
has developed a method to suppress or control the population of undesirable insects, other
animals or plants. This is done by introducing, stimulating or artificially raising their natural
enemies to economically unimportant levels. Among the mechanisms used are natural ones,
such as predation, parasitism or herbivory.
Creation of plants resistant to pests:
Another application of biology in agriculture is the development of plant varieties resistant to
pests. Around the world, unwanted animals are a threat to agricultural crops. These
significantly reduce yield and affect almost every aspect of the plants. Through conventional
breeding, some insect resistant crops have been created. Recently there have been great
advances in biotechnology. For example, resistance to pests and diseases of crops has
increased through genetically modified plants, which implies the reduction of chemical
control of pests.
Selective breeding to improve agricultural plants and animals:
Since the 18th century, knowledge about biology has been used to carry out crossings of
related species. Selective breeding seeks to improve traits such as taste, color, disease
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resistance and productivity. At the beginning of the 20th century, genetics began to be used to
develop new varieties of plants and animals. This has brought important changes in
agriculture, especially in the productivity of some crops.
Understanding the effects of climate on crops:
Biology help understand how climate change affect crops. For example, temperature plays an
important role in the different biological processes that are critical for the development of the
plant. The optimum temperature varies for germination, growth and reproduction. These
optimum temperatures must occur at certain times in the life cycle of the plant; otherwise, the
growth and development of the plant may be affected.
In addition, through the development of biotechnology and molecular biology, plant has been
genetically engineered to produce their own pesticide. So they no longer need to be spayed
manually. Among those plants are apples, pear, cabbage, broccoli, and potatoes.
Industrial biotechnology, also known as white biotechnology, is the modern use and
application of biotechnology for the sustainable production and processing of bioproducts
such as food substances, chemicals, bio-materials and fuels from renewable sources, using
living cells and/or their enzymes. Primarily, the enormous capability of microorganisms and
their enzymes are utilized for the production of food supplements such as vitamin B2, many
other pharmaceuticals such as drugs and vaccines, bioplastics such as polylactic acid, energy
carriers such as biogas and bioethanol, detergents, pulp and paper, quality textiles fibers, and
many agricultural products. Most importantly, single cell proteins (SCP) can be produced
from wide range of microorganisms. Best examples are mushroom, spirulina, yeast, green
algae. SCP technology is a promising area in alleviating food security in ever growing
population.
Food preservation is another area of industrial biotechnology which if the processes to stop
food spoilage due to microbial action. The biological methods of food preservation have
become increasingly important. These consist of adding cultures of innocuous
microorganisms of high purity to the food. The cultures have an inhibitory effect on the
undesirable decomposition microorganisms
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10.5 Application of Biology in waste treatments and recycling (Bioenergy,
bioremediation, water treatment, biomining)
Biotechnological processes are used for wastewater treatment and reuse. This area coordinates
engineers, biologists, chemists. Appropriately designed waste management system can be
utilized to remove hazardous wastes from the environment and for the production of
renewable energy such as bio-fuels and hydrogen. Particularly, for preventing environmental
pollution through environmental engineering, activated sludge process, trickling filters,
biotrickling filters, oxidation ponds, anaerobic treatment, composting units and biogas
reactors are used extensively among the waste treatment technologies. Bio-mining is also one
area of interest where chemical mining is substituted by microorganisms that can efficiently
extract minerals from natural ores. Note that chemical mining generates many pollutants in
the environment.
Forensic biologists inspect crime scenes for potential sources of evidence such as blood,
saliva, and hair, and then they analyze the specimens in a laboratory, focusing on DNA
analysis. Additionally, fingerprints are also important to investigate crime and the paternity
case of a child; this is because each individual has unique fingerprints that do not change
throughout life. Based on their investigations, forensic biologists write up their findings in
technical reports and are called upon to testify in court. Finally, this data is used to investigate
the related transgression, and then these facts are put forward in the court that‘s quite helpful
in order to castigate the criminal. These days 'bioinformatics is widely acceptable in the field
of forensic science because, with the help of computational tools, it became quite
uncomplicated and reliable to gather evidence regarding a particular crime scene.
Self-Test
1. What is biological warfare?
2. Do you know the reason why the use of biological warfare is not allowed?
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Biological warfare (BW) also known as germ warfare is the use of biological toxins or
infectious agents such as bacteria, viruses, and fungi with the intent to kill or incapacitate
humans, animals or plants as an act of war.
Biological weapons include any microorganism (such as bacteria, viruses, or fungi) or toxin
(poisonous compounds produced by microorganisms) found in nature that can be used to kill
or injure people. The act of bioterrorism can range from a simple hoax to the actual use of
these biological weapons, also referred to as agents. A number of nations have or are seeking
to acquire biological warfare agents, and there are concerns that terrorist groups or individuals
may acquire the technologies and expertise to use these destructive agents. Biological agents
may be used for an isolated assassination, as well as to cause incapacitation or death to
thousands. If the environment is contaminated, a long-term threat to the population could be
created.
Activities
1. Describe the principles behind gene therapy, immuno-diagnosis and immunotherapy
2. Discuss the principles behind transplantation incompatibility
3. What is the difference between antibiotics and vaccines in combating diseases?
4. Outline how insulin is produces at large scale
5. How do you advice the Ethiopian government to include single cell protein technology
in food security program
6. Study a typical solid waste or waste water treatment system and describe the major
phases and their purposes
7. Have you ever heard the term “Bacterial Cement” what is it and how and where it is
applied?
8. How can fingerprints, hair and fibers, and blood evidence be used to solve a crime?
9. Can you mention other practical application of forensic science?
10. Why biological warfare is more dangerous than other warfare?
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