General Biology Lecture Note (2

General Biology (Biol.
1012)
Objectives
 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
05/17/2024 Lecture note for General Biology (Biol. 1012)

Chapter One: Introduction
Biology is the scientific study of life and living organisms, encompassing
their structure, function, growth, evolution, distribution, and taxonomy.
The term biology is derived from the Greek words "bios" (life) and "logos"
(study)
 term Biology was coined by Pierre-Antoine de Monet and
Jean-Baptiste de Lamarck in the late 1700s.
 Initially, Biology focused mainly on Botany and Zoology, but as time went
on, the field grew to include many new branches and technologies.
But 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.

Zoology: The
scientific study
of the behavior,
structure,
physiology,
Cell Biology: classification, Molecular Biology:
Focuses on and distribution Studies the
the structure of animals. molecular basis of
biological activity
and function between
of cells, the biomolecules in
basic units of various systems of a
life. cell.
Genetics:
Biology
Concerned
with the study Ecology: The study of
of genes, interactions among
genetic organisms and their
variation, and environment.
heredity in
organisms. Botany: The
science of
plant life.
05/17/2024 Lecture note for General Biology (Biol. 1012) 3
1.2. The origin and nature of life
 The origin of life refers to the process by which lifeforms
first arose on Earth.
 Life is typically characterized by the ability to grow,
reproduce, maintain homeostasis, respond to stimuli, and
evolve over time.
 The first living things to appear were the simplest creatures,
single-celled organisms, these came more complex, multi-
cellular organisms.

• Characteristics of life
•Cellular organization: All living organisms consist of one or more
cells.
•Metabolism: Conversion of energy by converting chemicals and
energy into cellular components (anabolism) and decomposing
organic matter (catabolism).
•Growth and Reproduction: Ability to reproduce and pass genetic
information to offspring.
•Response to Stimuli: Ability to respond to environmental changes.
•Adaptation through Evolution: Changes over time to adjust and
survive in their environment.
Theories on Origin of life
1. Theory of Special Creation

• This theory posits that life was created by a supernatural entity or
divine force at some point in the past.
•this theory aligns with religious and cultural beliefs, providing a
spiritual explanation for the origin of life rather than empirical
scientific evidence.
•Offers a straightforward explanation for the complexity and
diversity of life without the need for understanding complex
scientific concepts.
•Does not offer testable or falsifiable hypotheses and is not
supported by genetic evidence indicating the evolution of species
over time.
2. Theory of Spontaneous Generation:
 Also known as abiogenesis
 this theory suggests that life arose from non-living matter, such
as mud or rotting material, spontaneously.
 Historically observed phenomena, such as maggots appearing on
decaying meat, were misinterpreted to support this theory.
 Experiments by Louis Pasteur and others conclusively disproved
spontaneous generation for macroscopic life, showing that life
comes from pre-existing life.
 It does not stand up to the modern understanding of biology and
is no longer considered scientifically valid.
3. Theory of Catastrophism:
 This theory modifies the Theory of Special Creation by suggesting that life
has been created multiple times by God following major catastrophes like
geological disturbances.
 Each catastrophic event supposedly wiped out existing life forms, leading
to the creation of entirely new species.
 Supported by observations of sudden changes in the fossil record and
geological strata.
 Aligns with the evidence of sudden changes in the fossil record coinciding
with catastrophic geological events.
 Does not explain the gradualism observed in the fossil record or the
mechanism of species change and adaptation.
 Implies that life's diversity arises in fits and starts, rather than as a
continuous process.
 4. Cosmozoic Theory (Theory of Panspermia):
 Suggests that life exists throughout the Universe and was spread
to Earth through space, perhaps by meteorites, comets, or cosmic
dust.
 Finds some support in the discovery of organic molecules in
space and microorganisms that can survive extreme conditions.
 Does not explain the origin of life itself but rather the distribution
of life in the Universe.
 The survivability of microorganisms during space travel is also
still under investigation.
 Proposed by Richter in 1865 and later supported by Arrhenius in
1908
 Some microorganisms can survive harsh space-like conditions,
suggesting life could travel through space.
 While organic molecules have been found in space, there is no
direct evidence of living organisms being transported to Earth.

Theory of Chemical Evolution:
 Also known as the Materialistic or Physico-chemical Theory
 this suggests that life on Earth began through a slow and gradual process of
chemical evolution around 3.8 billion years ago.
 proposed by A.I. Oparin and J.B.S. Haldane in the early 20th century.
 life evolved from simple organic molecules through chemical reactions
driven by Earth's early environmental conditions.
 While it explains the formation of life's building blocks, it does not fully
elucidate the complexity of the transition from non-living chemistry to living
cells.
 Fits well with the principles of natural selection and biological evolution,
providing a continuous process from chemistry to biology.

The Nature and Characteristics of Life
 Life is a unique condition that sets living organisms, including animals and
plants, apart from inorganic matter and deceased entities.
 It encompasses a series of processes that sustain a state of existence.
 Amongst the plethora of life forms, humans are considered the most complex,
prompting an exploration into the multifaceted nature of human life and death.
 Humans exhibit three dimensions of existence:
1.Physical Life: This is the fundamental state of being, grounded in our bodily
existence.
2.Mental Life: The mind enhances our capabilities and extends the reach of our
activities.
3.Spiritual Life: The spirit elevates our existence to its highest potential, enabling
what we might term 'maximized living'.
Physiology: The physical manifestation of life is evidenced through a myriad of
biological functions that maintain our corporeal presence

1.3. Scientific methods
 are systematic approaches to inquiry used to investigate
phenomena, acquire new knowledge, or correct and integrate
previous knowledge.
 To ensure research is based on empirical and measurable
evidence subject to specific principles of reasoning.
 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.
Observation - Quantitative and qualitative measurements of the world.
Inference - Deriving new knowledge based upon old knowledge.
Hypotheses –A suggested explanation.
Rejected Hypothesis - An explanation that has been ruled out through
experimentation.
Accepted Hypothesis - An explanation that has not been ruled out through
excessive experimentation and makes verifiable predictions that are true.
Experiment - A test that is used to rule out a hypothesis or validate something
already known.
Scientific Method - The process of scientific investigation.
Theory - A widely accepted hypothesis that stands the test of time. Often tested,
and usually never rejected.
The scientific method is based primarily on the testing of hypotheses by
experimentation. This involves a control, or subject that does not undergo the
process in question

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

Chapter Two : Biological Molecules
 Are Referred to as the molecules of life (bio-molecules) that are basically
found in a living cell and categorized as organic and inorganic molecules
 The organic biomolecules are proteins, carbohydrates, lipids and nucleic
acids.
 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.

2.1. Carbohydrates: 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).
 Based on the number sugar units they contain, they are
categorized into three
 Monosaccharides
 Disaccharides
 Polysaccharides
Monosaccharides
 are the simplest forms of sugar and the most basic units (monomers) from which
all carbohydrates are built.
 They are usually colorless, water-soluble, and crystalline organic solids.
•Most monosaccharides have the formula
(CH2O)x, where x ≥ 3.
• are the building blocks of disaccharides
(such as sucrose, lactose and maltose)
 aldehydes or ketones, or
and polysaccharides (such as cellulose substances that yield these
compounds on hydrolysis.
and starch). Example: Glucose is
aldehyde and fructose is
Ketone.

Glucose
 Is a simple sugar with the molecular formula C₆H₁₂O₆
 primary source of energy for the body's cells.
 It is transported through the bloodstream and taken up by 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.
 concentration of glucose in the blood is regulated by
hormones such as insulin and glucagon.
 Insulin lowers blood glucose levels by facilitating the uptake of glucose into
cells,
 while glucagon increases blood glucose levels by signaling the liver to release
stored glucose.
Fructose
 a hexose sugar & has the same chemical
formula as glucose but a different structure.
 It is found in fruits, honey, and root vegetables
and is the sweetest of all natural sugars.
 In the human body, fructose is converted to
glucose in the liver.
 Fructose is a ketose (a non-reducing sugar).
Galactose:
 Similar to glucose in structure and another hexose sugar.
 It is not as sweet as glucose or fructose and is found in milk sugar (lactose) along
with glucose.
 It is metabolized in the liver and is a component of several important biomolecules

Ribose:
 A five-carbon (pentose) sugar,
 a crucial part of ribonucleic acid (RNA) and several other
biological molecules, including ATP and coenzymes.
 It is known for its role in forming the backbone of genetic
material and energy molecules
Mannose:
 Is a hexose sugar structurally similar to glucose but with a
different arrangement of hydroxyl groups.
 It plays a role in human metabolism, particularly in the
glycosylation of certain proteins.

 Monosaccharides are used very quickly by cells.
 Monosaccharides are characterized by the number of carbon
atoms they contain:
•Trioses have three carbon atoms.
•Tetroses have four carbon atoms.
•Pentoses have five carbon atoms.
•Hexoses have six carbon atoms.
•Heptoses have seven carbon atoms.
The monosaccharides can also be distinguished by their functional
groups:
•Aldoses: with an aldehyde group (-CHO) at the end of the
molecule, such as glucose and galactose.
•Ketoses: with a ketone group (C=O) in the middle of the
molecule, such as fructose.

• Disaccharides:
• are carbohydrates that consist of two monosaccharide residues linked by a glycosidic bond.
• When digested, disaccharides are hydrolyzed into monosaccharides before they can be absorbed by the
body.
• Sucrose: This is the most well-known disaccharide, composed of glucose and fructose. It is commonly
known as table sugar and is used extensively as a sweetener in the food industry. Sucrose is obtained
from sugar cane or sugar beets.
•Sucrose is a non-reducing sugar.

•Lactose: Found in milk and dairy products, lactose is made up of glucose and
galactose.
•It is broken down by the enzyme lactase, which is found in the intestines of
mammals.
•Some adults have lactose intolerance, which means they do not produce
enough lactase, leading to digestive problems when consuming dairy
products.
Maltose: or malt sugar,
 is composed of two glucose units.
 It is less sweet than sucrose and is produced when starch is
broken down, as happens during the germination of seeds (such
as barley) and in the digestive systems of humans.
 Maltose is important in brewing and in the production of
certain foods and beverages.
Trehalose:
 Is a natural sugar made of two glucose molecules.
 It is found in mushrooms, yeast, and certain invertebrates.
 Trehalose has the unique ability to protect organisms and cells
from extreme environmental conditions like desiccation and
freezing.

Polysaccharides:
 are long chains of monosaccharide units bound together by
glycosidic linkages.
 They are complex carbohydrates and serve various functions in
both plants and animals, including structural support, energy
storage, and cell recognition.
 May be branched or unbranched
 Polysaccharides are classified based on their structure and
function into three main types:

1.Storage Polysaccharides:
a.Starch: plant-based polysaccharide composed of two types of
molecules, amylose and amylopectin.
 Amylose is linear & unbranched chain of glucose monomers
linked by α-1,4 glycosidic linkages,
 Amylopectin is a branched polysaccharide with α-1,6 linkages at
the branch points.
 It is completely insoluble in water.
 Starch is the main form of stored carbohydrate in plants and is
an important energy source for humans.
b. Glycogen: referred to as animal starch
 Is a highly branched polysaccharide of glucose.
 It serves as a form of energy storage in animals, fungi, and
bacteria.
 In humans, it is stored in the liver and muscles and is mobilized
during times of energy need.

2. Structural Polysaccharides:
Cellulose: A major component of plant cell walls,
 It provides structural support to plants and is the most abundant
organic polymer on Earth.
 It is indigestible by humans but is an important dietary fiber which
aids in digestion.
 While the β-1,4 linkage cannot be broken down by human
digestive enzymes, herbivores such as cows, koalas, buffalos, and
horses are able to digest plant material that is rich in cellulose with
the help of specialized flora in their stomach.
Chitin:
 Similar in structure to cellulose but with nitrogen-containing side
groups,
 chitin is found in the exoskeletons of arthropods and the cell walls
of fungi.
 It is a tough, protective biopolymer that also serves as a structural
component.
 The properties of a polysaccharide molecule depend on
 Its length (though they are usually very long)
 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'

2.2. Lipids
Lipids diverse range of organic compounds crucial to human health, serving
as
 cell membrane building blocks,
 energy sources, hormone producers, and
 key players in food digestion, nutrient absorption,
 Cellular signaling.
 Lipids are composed of carbon and hydrogen chains that may bond with
other atoms to form various lipids.
 Due to their nonpolar molecular structure Lipid are insoluble in water
and soluble organic solvent
 Triglycerides, a type of lipid, are fats when solid at room temperature and
oils when liquid.
 There are two main types of fat cells: white and brown.
 In humans, lipids appear mainly as triacylglycerol, cholesterol, and polar
lipids, with the latter category comprising phospholipids, glycolipids, and
sphingolipids.

•Lipids exist in either liquid or non-crystalline solids at room temperatures and are colorless,
odorless, and tasteless.
Structure of Lipids
• Have a much lower proportion of water than other molecules such
as carbohydrates.
•They are made from two molecules: Glycerol and Fatty Acids.
•A glycerol molecule is made up of three carbon atoms with a hydroxyl group
attached to it and hydrogen atoms occupying the remaining positions.
•Fatty acids consist of an acid group at one end of the molecule and a
hydrocarbon chain, which is usually denoted by the letter ‘R’.
•They may be saturated or unsaturated.
•A fatty acid is saturated if every possible bond is made with a Hydrogen atom,
such that there exist no C=C bonds.
•Unsaturated fatty acids, on the other hand, do contain C=C bonds.
Classification of Lipids
Classified according to their hydrolysis products and according to similarities in
their molecular structures.
Three major subclasses are recognized:
1. Simple lipids
(a) Fats and oils which yield fatty acids and glycerol upon hydrolysis.
(b)Waxes, which yield fatty acids and long-chain alcohols upon hydrolysis.
Fats and Oils
•Both are called triacylglycerols because they are esters composed of three fatty
acids joined to glycerol, trihydroxy alcohol.
• Fatty acids are the simplest form of lipids and serve as building blocks for more
complex lipids.
• They consist of a carboxyl group attached to a long hydrocarbon chain.
•Waxes are esters of long-chain fatty acids with long-chain alcohols. They are
highly hydrophobic and serve as protective coatings.

2. Compound lipids
(a)Phospholipids
 are a major component of cell membranes.
 They contain two fatty acids, a phosphate group, and a glycerol
molecule.
 The phosphate group is hydrophilic,
 While the fatty acid chains are hydrophobic, making these
molecules amphipathic.
(b)Glycolipids, which yield fatty acids, sphingosine or glycerol, and
a carbohydrate upon hydrolysis.
3. Derived lipids:
 Hydrolysis product of simple and compound lipids is called
derived lipids.
 They include fatty acid, glycerol, sphingosine and steroid
derivatives.
 Steroid derivatives are phenanthrene structures that are quite
different from lipids made up of fatty acids.
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
Saturated and Unsaturated Fatty acids
Unsaturated fatty acids
Saturated fatty acids •
are more complex fatty acids with bent hydrocarbon chains
linked together by one or more carbon-carbon double bonds
• are the simplest form of fats that are unbranched linear with a terminal carboxylic acids group.
chains of CH2 groups linked together by carbon-carbon • The term ‘unsaturated’ indicates that the carbons atoms do
single bonds with a terminal carboxylic acid. not have the maximum possible hydrogen atoms bound to
• The term ‘saturated’ is used to indicate that the maximum carbon atoms.
number of hydrogen atoms are bonded to each carbon atom • Due to the presence of double bonds, the cis and trans
in a molecule of fat.
•
conformation of these molecules are important. The
The general formula for these acids is CnH2n+1COOH.
• Fatty acids obtained from an animal source are mostly even-
unsaturated fatty acids found in the human body exist in the
numbered linear chains of saturated fatty acids. cis conformation
• Saturated fatty acids usually have a higher melting point • Unsaturated fatty acids have a lower melting point as
than their counterparts which is why saturated fatty acids compared to saturated fatty acids, and thus they exist in the
remain in the solid-state at room temperatures. liquid state at room temperatures
• These are mostly solid and are found in animal fat like • Most vegetable oils and fish oils are some of the important
butter, meat, and whole milk. But some saturated fatty acids sources of unsaturated fatty acids
are also found in vegetable sources like vegetable oil,
coconut oil, and peanut oil.

Functions of Lipids :
1. Energy Storage: release large amounts of energy, making them an efficient
form of energy storage.
2. Structural Components: basic structure of cell membranes
3. Insulation and Protection: In animals, fats serve as insulation to maintain
body temperature and as a protective cushion around vital organs.
4. Signaling Molecules: steroid hormones and eicosanoids, act as signaling
molecules, mediating communication between cells.
5. Vitamins and Pigments: Some lipids, such as vitamin A, D, E, and K, are
vital for human health and serve various functions including vision, blood
clotting, and antioxidant activity.
6. Digestion and Absorption: Bile acids, which are derived from cholesterol,
emulsify dietary fats to enable their digestion and absorption.

 A protein is a compound made of small carbon compounds called amino
acids.
 Make up about 15% 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.
 are the building blocks of life, essential for the structure, function, and
regulation of the body's tissues and organs.
 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
 A peptide forms between the amino group of one amino acid and the
Proteins can be classified
1.Based on Structure:
1. Fibrous Proteins: These proteins have long, filamentous shapes and are generally
insoluble in water. E.g collagen in connective tissues and keratin in hair and nails.
2. Globular Proteins: soluble in water, and include many enzymes, antibodies, and
hormones.
3. Membrane Proteins: proteins can act as receptors or channels for the transport of
substances across cell membranes.
2.Based on Function:
1. Enzymatic Proteins
2. Structural Proteins
3. Transport Proteins: (e.g., hemoglobin).
4. Storage Proteins: (e.g., ferritin for iron storage).
5. Signal Proteins: (e.g., hormones and growth factors).
6. Defensive Proteins: Provide defense mechanisms, such as antibodies in the immune
system.
7. Regulatory Proteins: Control and coordinate cellular functions, like transcription
factors.

3. Based on Solubility and Precipitation (historical method):
 Albumins: Soluble in water and coagulable by heat (e.g., serum
albumin).
 Globulins: Water-soluble but precipitable by salts (e.g.,
immunoglobulins).
 Fibrinogen: Involved in clotting and precipitable by half-
saturation with ammonium sulfate.
4. Based on Chemical Composition:
Simple Proteins: Yield only amino acids upon hydrolysis.
Conjugated Proteins: Contain a non-proteinaceous group called a
prosthetic group, such as lipoproteins, glycoproteins, and
metalloproteins.
Structure of Proteins:
•Primary Structure: The sequence of amino acids in a polypeptide chain, which is
determined by the DNA sequence of the gene encoding the protein.
•Secondary Structure: Localized folding of the polypeptide chain into structures
such as alpha-helices and beta-sheets, held together by hydrogen bonds.
•Tertiary Structure: The overall three-dimensional shape of a protein molecule,
formed by the full range of interactions among amino acid residues.
•Quaternary Structure: The assembly of multiple protein subunits, which can be
the same or different, into a larger functional complex.

Functions of Proteins:
1) Enzymes: making them proceed at a much faster rate.
2) Structural Components: Providing support and shape to cells and forming
important structures in the body like collagen in connective tissues and
keratin in hair and nails.
3) Transport: Proteins like hemoglobin transport oxygen in the blood; others
transport nutrients across cell membranes.
4) Signaling: Proteins are involved in transmitting signals within and between
cells.
5) Regulatory: Proteins regulate cellular processes by turning genes on and off
or signaling other cells to do so.
6) Immunological: Antibodies are proteins that bind to foreign substances in
the body, marking them for destruction by the immune system.
7) Movement: Muscle contractions are driven by the proteins actin and
myosin.

Nucleic acids:
 are biopolymers essential for all known forms of life.
 They are the molecules that store, transmit, and express genetic information in
cells.
There are two main types of nucleic acids:
1. Deoxyribonucleic Acid (DNA): is the carrier of genetic information.
 It is a double-helical molecule consisting of two long biopolymer strands
coiled around each other to form a double helix.
 made of simpler molecules called nucleotides, each containing one of four
bases (adenine [A], cytosine [C], guanine [G], and thymine [T]), a sugar
molecule (deoxyribose), and a phosphate group.
2. Ribonucleic Acid (RNA):
 RNA is involved in various roles in coding, decoding, regulation, and
expression of genes.
 Like DNA, RNA is assembled as a chain of nucleotides,
 but unlike DNA, it is usually single-stranded.
 It also differs slightly in its chemical structure (the sugar in RNA is ribose)
and uses uracil (U) in place of thymine.
Functions of Nucleic Acids:
1) Storage of Genetic Information: DNA holds the instructions for an organism's
or each cell's development and reproduction.
2) Transmission of Genetic Information: DNA replicates and passes on genetic
information to the offspring during reproduction.
3) Protein Synthesis: RNA is essential in various steps of synthesizing proteins,
which are crucial for the cell's structure and function.
4) Catalytic Roles: Some RNA molecules, known as ribozymes, have catalytic
properties and can carry out biochemical reactions.
Structure of Nucleic Acids:

5) Nucleotides: The basic building blocks of nucleic acids. Each nucleotide
consists of a five-carbon sugar, a phosphate group, and a nitrogenous base.
6) Backbone: The sugar and phosphate form the backbone of the nucleic acid
structure, with the bases attached to the sugars.
7) Base Pairing: In DNA, bases pair through hydrogen bonding: A pairs with T (or
U in RNA), and C pairs with G.

2.6 Water
 Water is a vital chemical substance that is essential for the survival of all
known forms of life.
 It is a simple molecule consisting of two hydrogen atoms bonded covalently
to one oxygen atom, giving it the chemical formula H2O.
Physical Properties:
 Is a tasteless, odorless, and nearly colorless liquid, which may appear blue in
large quantities.
 It is a polar molecule, which means that there is an uneven distribution of
electron density.
 This gives water its ability to dissolve many other substances, earning it the
nickname “the universal solvent.”
 It also has a high heat of vaporization, requiring a substantial amount of
energy to change from liquid to vapor.
Chemical Properties:
 Water is a solvent for a myriad of chemical substances, and it is involved in
many chemical reactions.
 It is a medium for transporting nutrients and waste products in organisms.
 In liquid form, it undergoes self-ionization where one water molecule donates
a proton to another water molecule to form H3O+ (hydronium) and OH−
(hydroxide) ions.
 Water participates in the hydrolysis reactions, which is the breaking of bonds
in molecules with the addition of water, such as the digestion of food.
Biological Significance:
 Water is crucial for all cellular processes. It is involved in the metabolic reactions within
cells, including respiration and photosynthesis.
 It acts as a temperature buffer, stabilizing the internal environment of organisms
(homeostasis).
 primary component of the interstitial fluid and is used for transportation of substances
in biological systems.
 It serves as a lubricant and cushion for joints, the spinal cord, and in the amniotic sac
surrounding fetuses in the womb.

 Water cycles through the environment via the hydrologic cycle, which includes
evaporation, condensation, precipitation, and runoff
 It is an essential component of all ecosystems and is necessary for all forms of life,
from the simplest microbial life forms to complex organisms.
Distribution on Earth:
 About 71% of the Earth’s surface is covered by water, mostly in oceans and large
bodies of water.
 However, less than 3% of the world’s water is freshwater, the majority of which is
trapped in glaciers and polar ice caps.
 The availability of clean, fresh water is essential for human health and civilization.
Challenges:
 Despite its abundance, access to clean and safe drinking water is a problem in many
parts of the world due to pollution, overuse, and distribution challenges.
 Water scarcity is becoming a more pressing issue with climate change, as patterns of
water circulation change, affecting agriculture and food security.

2.5. 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.
There are 13 essential vitamins, each of which has a specific role in the body, and
they are divided into two categories: water-soluble and fat-soluble.
Water-soluble vitamins:
 Vitamin C (Ascorbic Acid): Important for the synthesis of collagen, the
absorption of iron, and the maintenance of immune system health.
 B Vitamins: are vital for turning glucose into energy and ensuring the health
of nerves, muscles, and the heart.
 These vitamins aid in food metabolism, support the nervous and digestive
systems, and promote skin health.
 They are involved in creating essential molecules in the body, including
coenzyme A, hormones, and neurotransmitters, and play a role in fat
metabolism.
 B Vitamins are key for synthesizing amino acids and red blood cells, and they
are important for maintaining the structure and appearance of hair, skin, and
nails.
 They are also essential for brain health and emotional well-being, as well as
for the formation of red blood cells and the upkeep of the central nervous
system.

Fat-soluble vitamins:
Vitamin A (Retinol): Vital for healthy vision, skin health, and
immune function.
Vitamin D: Essential for the regulation of calcium and
phosphorus, and in maintaining proper bone structure.
Vitamin E (Tocopherol): Acts as an antioxidant, helping to protect
cells from the damage caused by free radicals.
Vitamin K: Important for blood coagulation and regulating blood
calcium levels.
Functions of Vitamins:
 They act as catalysts in enzymes reactions, with small amounts
of vitamins necessary to turn proteins, carbohydrates, and fats
into energy.
 Some vitamins (e.g., A, D, E, K) are also important for vision,
bone growth, cell function, and cell protection.
 They support the immune system, brain function, and the
nervous system.
 Vitamins help in the production of DNA, hormones, and other
2.7. 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.

Chapter Three: The cellular basis of life
 In the late 1600s, an English scientist named Robert Hook was the first to
observe plant cells using a simple microscope.
 Later, in the 1830‘s two German scientists named Mathias Schleiden and
Theodore Schwann were proposed that all living things are composed of
cells.
 A German pathologist, Rudolph Virchow extended this idea by
contending that cells arise only from other cells.
05/17/2024 Lecture note for General Biology (Biol. 101 50

2)
3.1 The cell theory
 The cell theory states that all organisms are composed of cells
 A cell is the basic structural and functional unit of living
organisms.
 All cells arise from pre-existing cells (continuity of life from one
generation to another has a cellular basis).
A typical eukaryotic cell has 3 major parts:
o The plasma membrane: the outer boundary of the cell.
o The cytoplasm: the intracellular fluid packed with organelles,
small structures that perform specific cell functions.
o The nucleus: an organelle that controls cellular activities.

2)
3.1.1 Cell organelles
 An organelle is a specialized subunit within a cell that has a

specific function.
 In eukaryotes it is a double membrane bound structure
 In Prokaryotes it is not membrane bound structure.
 On the basis of membrane covering, there are two kinds of cell
organelles these are:
 membranous organelles that include Endoplasmic reticulum
(Rough and Smooth), Golgi bodies, mitochondria,
chloroplasts, nucleus, lysosomes, peroxisomes and vacuoles

2)
 Non-membranous organelles that include ribosomes (70s and
80s), centrosomes, cilia and flagella, microtubules, basal bodies
and microfilaments
 3.1.2 Structure and function of organelles
 The nucleus:
 have oval or spherically shape
 it is largest central structure
 surrounded by a double-layered membrane
 In the nucleus, DNA directs protein synthesis and
 serves as a genetic blueprint during cell replication.

2)
Cont.
 It governs most cellular activities and serves as the cell‘s master.
 It is surrounded by a nuclear envelope and
 contains chromatin and one or more nucleoli.
 The nucleus serves as the cell’s command center, directing gene expression
and mediating the replication of DNA during the cell cycle.
The Nuclear envelope
o surrounds nuclear material
o Most ions and water soluble molecules transfer b/n nucleus and cytoplasm
through this pores
Chromatin: The term chromatin means "colored material"
 it is composed DNA coils bound to histone protein.
Nucleoli: The nuclei of most cells contain one or more lightly stained structures
called nucleoli that actively engage in synthesizing of ribosomes.

2)
Cont.
Cytoplasm: Cytosol is a complex jelly like material
o Contain a number of distinct, highly organized membrane-
enclosed structures.
o They are similar in all cells, but with some variations depending
on the cell specialization.
o These organelles occupy about half of the total cell volume.
o All cells contain six main types of organelles- the
endoplasmic reticulum, Golgi complex, lysosomes,
peroxisomes, mitochondria, and vacuoles.
Endoplasmic reticulum (ER)
 It is a fluid-filled membrane system
 There are two different
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General Biology (Biol. ER
101 and rough ER. 55
2)
The rough Endoplasmic Reticulum
o It contains dark particles called ribosomes.

o The rough ER in association with ribosomes produces and releases a variety
of proteins, into the fluid-filled space enclosed by the membrane
Smooth Endoplasmic Reticulum:
 Is a meshwork of interconnected tubules and does not have ribosomes, then
it looks smooth
 Does not produce proteins.
 Serves in packaging and discharging site for protein molecules that are to
be transported from the ER.
o The membrane wall of the smooth ER contains enzymes for synthesis of
lipids. In liver cells,
05/17/2024 the
Lecture note smooth ER(Biol.contains
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2)
The Golgi complex:
o Is associated with the ER and contains sets of flattened,
curved, membrane- enclosed sacs, stacked in layers.
o Number of stacks vary in cells; cells specialized for
protein secretion have hundreds of stacks, whereas some
have only one.
o It performs the following important functions.
1. Processing/modifying proteins that comes from ER
2. Sorting and directing finished product to their final
destination.
3. The smooth ER of the liver and kidney cells are
responsible for the detoxification and inactivation of
drugs.

2)
Lysosomes:
 serve as the intracellular -digestive system.
 are membrane-enclosed sacs
 contain powerful hydrolytic enzymes
 digest and remove unwanted cellular debris and foreign
materials
 Lysosomes vary in size and shape, and about 300μm in a
cell.
Peroxisome:
 are membrane bounded vesicles that contain specific enzymes.
 Peroxisome action results in production of hydrogen peroxide.
 Hydrogen peroxide (H2O2) is broken down to water and oxygen by catalase.
 Peroxisomes in the liver produce bile salts from cholesterol and also break
down fats.
2)
Mitochondria:
Mitochondria are the ‘power houses‘‘ of a cell.
 Each is enclosed by a double membrane –
 a smooth outer membrane, and
 enfolded inner membrane called cristae, which project into an inner
cavity filled with a jelly-like matrix.
 Cristae contains 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 different dissolved enzymes (Citric acid cycle enzymes)
that are important in preparing nutrient molecules.

2)
Cont.
o Mitochondria are unusual organelles in two ways:

• They have their own unique DNA ( mitochondrial DNA) in matrix.
• Mitochondria have the ability to replicate themselves even when
the cell to which they belong is not undergoing cell division.
Chloroplasts:
o Are part of plastids and participate in the process of photosynthesis
 They are located in outer surface of the cell to receive enough light.
 are green colored due to the chlorophyll pigments.
 Contain a double membrane and internal stacks of membrane-bound discs
called thylakoids, which contain chlorophyll.
 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 lightLecture
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(Biol. 101 60
Vesicles:
• are membrane bound sacs
• used to store or transport substances around the cell.
• Lysosomes are actually Vesicles.
Vacuoles:
• are essentially larger Vesicles
o They are membrane bound organelles
o have no specific shape and contain water with a number of different
compounds within it.
o depending on the type of cell, vacuoles have different functions.
o In plant cells they are important in maintaining Turgor Pressure.

2)
Cytoskeleton :
 It is a complex protein network that act as the
“bone and muscle” of the cell.
o Four distinct elements for cytoskeleton are,
Microtubules, Microfilaments, Intermediate
filaments and micro tubular lattice.
o Generally, cytoskeletons determine/ provide the:
 shape of a cell
 structural support
 organizing its contents
 substances movement through cell (cilia,
flagella and intra cytoplasmic vesicles), and
 Contribute to movements of the cell as a whole
2)
Plasma/cell membrane
 It is a fluid lipid bilayer embedded with proteins.
 It serves as a mechanical barrier; it is selective permeable
membrane.
 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 (negative charged) head of
phosphate group and two non-polar ( neutral) fatty acid tails.
 The polar end is hydrophilic (water loving) and the non-polar
end is hydrophobic (water
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63
2)
Cont.
The fluidity of the membrane gives flexibility to the cell .
 The Functions of the plasma Proteins
1.Channel proteins allow a particular molecule to cross membrane freely (e.g.,
Cl- channels).
2. Carrier proteins= selectively interact with a specific molecule so it can cross
the plasma membrane (e.g., Na+‑K+ pump).
3. Cell recognition proteins: are glycoproteins that allow the body’s immune
system to distinguish between foreign invaders and body cells.
4. Receptor proteins: are shaped so a specific molecule (e.g., hormone) can bind
to it or antibody.
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2)
Cont.
5. Enzymatic proteins :carry out specific metabolic reactions.
6. Junction proteins :join animal cells, so tissues can function.

3.1.3 Cellular diversity
 Cells exhibit a vast range of sizes, shapes, and structures across and
within different organisms,
 3.1.3.1 Cell Shape
• Cells have different shapes. For example;
• Nerve cells have long extensions.
• Skin cells have a shape which is flat.
• Egg cells have shape which is like sphere, and some bacteria are
rod in shape.
2)
3.1.3.2 Cell Size
• Cells range in size from one millimeter down to one micrometer
• Some cell can be seen without using magnification instruments as

they are enough to be seen by the naked eye.
Example, egg of birds/reptiles and a neuron cell of giraffe, which is 2
meters in length.
3.1.4 Transport across the cell membranes
• The plasma membrane is selectively permeable.
• Lipid-soluble substances and small ions can passively diffuse
• Uncharged/non-polar molecules oxygen, carbon dioxide and
fatty acids are highly lipid-soluble and readily permeate the
membrane.
2)
Cont.
o Charged particle sodium/potassium ions and polar molecules

such as glucose and proteins have low lipid solubility, but are
very soluble in water.
o The phospholipid bilayer is a good barrier around cells, especially
to water soluble molecules.
o There are four basic mechanisms:
1. Diffusion and facilitated diffusion
2. Osmosis
3. Active transport
4. Bulk transport

2)
Cont.
Diffusion
 Is the passive movement of particles from an area of high
concentration to an area of low concentration until equilibrium is
reached.
 It doesn't require energy and is driven by the kinetic energy of the
particles themselves.
 This process occurs with small, nonpolar molecules that can easily
cross the phospholipid bilayer of the cell membrane, such as oxygen
and carbon dioxide.

2)
Cont.
factors that influence the rate of net diffusion across a membrane
are:
1. permeability of the membrane
2. surface area of the membrane
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 and molecular weight , that if
increased, decreases the rate of diffusion.

2)
Cont.
Facilitated Diffusion
 Is also a passive process, but it's necessary for substances that
cannot readily diffuse through the lipid bilayer due to their size,
charge, or polarity.
 It involves carrier proteins or channel proteins that span the
membrane.
 Examples include the transport of glucose into cells through the
GLUT transporter and ions through ion channels.
 a carrier protein to facilitate the transfer of a particular
substance across the membrane ''downhill'' from higher to lower
concentration.
 does not require energy2)
Osmosis:
 Is the diffusion of water across a semipermeable membrane from an area of
low solute concentration (high water potential) to an area of high solute
concentration (low water potential).
 It's a vital process in biological systems, crucial for maintaining cell turgor
pressure and for the transport of water in and out of cells and across tissues.
 Osmosis can cause cells to swell or shrink, leading to changes in cell function
and, in extreme cases, cell death.
3. Active Transport
 involves the movement of molecules against their concentration gradient, from
an area of low concentration to high concentration.
 requires energy, usually in the form of ATP, because it is working against the
natural entropy of the molecules.
 is carried out by specific proteins embedded in the cell membrane, known as
pumps.
 example is the sodium-potassium pump (Na+/K+-ATPase) which maintains the
electrochemical gradient in nerve and muscle cells by moving sodium out of
the cell and potassium into the cell against their concentration gradients.
2)
Cont.
Active transport
o Is energy consuming transport of molecules
or ions across a membrane against its natural
tendency to diffuse in the opposite direction.
o 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

2)
4. Bulk Transport
Bulk Transport includes processes that move large particles, or large
quantities of smaller molecules, into or out of cells, requiring energy.
There are two main types:

1. Endocytosis: This is the process by which cells ingest external fluid,
macromolecules, and large particles, including other cells.
 It can occur through phagocytosis (cell eating),
 pinocytosis (cell drinking), and receptor-mediated endocytosis (specific
molecules are taken in after they bind to a receptor).
2. Exocytosis: is the process by which the contents of a cell vacuole are released to
the exterior through fusion of the vacuole membrane with the cell membrane.
This process is important for the secretion of substances such as neurotransmitters
and hormones.
2)
Chapter Four : Cellular Metabolism and Metabolic Disorders
4.1 Cellular metabolism
 Metabolism is the sum of chemical reactions that takes place
within each cell of a living organism

It provides energy for vital processes and synthesizing of new
organic materials.
Metabolism can be catabolic that convert nutrients/food to energy
and anabolic involving in synthesis of larger biomolecules.
4.1.1 Enzymes and their role in metabolism:
Enzymes are biological catalysts that speed biochemical reactions
Enzymes speed up reactions by lowering activation energy without
being affected by the reaction.
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• Enzymes often adapt their structure to fit their substrates, a
process known as "induced fit,".

•Enzymes are highly selective, typically catalyzing a single
chemical reaction.
• Metabolic pathways consist of a series of enzymatically driven
reactions occurring in a sequential manner, with each step
facilitated by a distinct enzyme specific to that reaction.
•4.1.2 Chemical nature and classification of enzymes
•All known enzymes are proteins with the exception of recently
discovered RNA enzymes

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•On the basis of differences in chemical nature, the enzymes may be
described as:
 Simple enzymes: are made up of only protein (polypeptide).
They contain no chemical groups other than amino acid residues.
E.g. Digestive enzymes.
 Conjugate Enzymes: formed from two parts-a protein part called
apoenzyme (e.g., flavoprotein) and a non-protein part named
cofactor.
 The complete conjugate enzyme, consisting of an apoenzyme and
a cofactor, is called holoenzyme.

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•If a cofactor is bound to the apoenzyme, it is called prosthetic group.
•For example, cytochromes that have porphyrins as their prosthetic groups.
•If, a cofactor attaches to the apoenzyme only at the time of reaction, it is called a
coenzyme.
•Metallo-enzymes: Metal cofactors like K+,Mg++,Mn++and Cu++are involved
in the enzymic reactions.
•If the metal is being part of the molecule, as iron of haemoglobin or cytochrome,
the enzymes are called metallo-enzymes.
•Isoenzymes (Isozymes): At one time it was believed that an organism has only a
single enzyme for a given step of a metabolic reaction.
•However, substrate may be acted upon by a number of variants of an enzyme
producing the same product

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Classification of Enzymes
Many enzymes have been named by adding “ase” to the name
of their substrate, source, discovery and for a broad function
E.g Urase , DNA polymerase
Based on the convention enzymes are classified into six
groups based on the reaction they catalyze
1. Oxidoreductase- oxidation reduction reaction
2. Transferase- transfer chemical groups from one molecule to
another
3. Hydrolase – transfer chemical groups into water(cleaves bond
with the help of water)
4. Lyase- removal of double bond by addition of groups to double
bond or form double bond by removal of groups
5. Isomerase- transfer of groups within the same molecule
6. Ligase- formation of bonds by condensation reaction (join two
79 molecules by formation
Lecture note for General of new chemical bond)
Biology (Biol. 1012) 05/17/2024
Factors affect the Rate of Enzyme Reactions
 The factors that mainly influence any enzyme catalyzed reactions are;
1. Substrate concentration
 As the substrate concentration increases, the rate increases because
more substrate molecules can collide with active sites = more ES
complexes
 At higher concentrations the enzyme molecules become saturated
with substrate, and there are few free active sites, so adding more
substrate doesn't make much difference
2. Enzyme concentration
 When compared to substrate concentration, the concentration of
enzyme is always very low. Hence, increasing the enzyme
concentration will always increase the reaction rate
3. Temperature:
 Enzymes, being proteins, are denatured by heat and become inactive as
the temperature increases beyond a certain point. The temperature at
which the reaction rate is maximum is known as optimum
80 temperature.
Lecture note for General Biology (Biol. 1012) 05/17/2024
4. pH
 Enzyme has an optimal pH
5. Inhibitors
 Some compounds have the ability to combine with certain
enzymes but do not serve as substrates and therefore block
catalysis. These compounds are called inhibitors.
6. Cofactors (coenzymes)
A non-protein helpers for catalytic activity of enzymes
7. Other factors such as state of enzyme, time and activators also

affect enzyme catalyzed reaction to certain extent.
81 Lecture note for General Biology (Biol. 1012) 05/17/2024

How enzymes work (important!)
1) Enzymes lower a reaction’s

activation energy
 activation energy: is amount of
energy needed to disrupt stable
molecule so that reaction can
take place.

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Enzymes
Lower a
Reaction’s
Activation
Energy

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Enzymatic reaction steps
1. Substrate approaches active site

2. Enzyme-substrate complex forms
3. Substrate transformed into products
4. Products released
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84
4.2 Bioenergetics and biosynthesis
4.2.1 Cellular respiration
Most living organisms obtain energy by breaking down organic
molecules (catabolism) during cellular respiration.
 Cellular Respiration is broken into three main parts.
1.) Glycolysis: sugar splitting phase (glucose is the sugar)
2.) Krebs Cycle (Citric Acid Cycle): Extracts the energy from
glucose
3.) Electron Transport Chain/ATP Synthase: Turns the energy
into ATP for the body to use

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Glycolysis: anaerobic respiration
• The first step in the degradation of glucose, which breaks down

glucose to pyruvate.
•The main purpose of glycolysis is the generation of energy (ATP).
• 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.
•Invest 2 ATP to start the reaction
•Produces two molecules of NADH from NAD+
•Produces 4 new ATP molecules
•NET GAIN: 2 ATP (4 Produced - 2 Invested
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Stage 1: Glycolysis
Location: Occurs in the cytoplasm just outside of mitochondria in

two phases.
A. Energy investment phase(step 1-5): Put 2 ATP in to start the
reaction
B. Energy yielding phase(6-10) : NET gain 2 ATP. (4 – 2 = 2)
MAIN GOAL: To split glucose

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What happened for 2 pyruvates?
Basically three options depending on the environmental conditions

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The citric acid cycle
consists of eight successive reactions
 Location: Mitochondrial Matrix
 Main Goal: Break down pyruvate to carbon dioxide and release
more energy

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Step 2: Citrate isomerized to isocitrate
Dehydration Hydration
Enzyme: aconitase
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Step 3: Isocitrate to -ketoglutarate
1st NADH produced 1st CO2 removed
Enzyme: isocitrate dehydrogenase

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Step 4: Succinyl-CoA formation
2nd NADH produced, 2nd CO2 removed
Enzyme: -ketoglutarate dehydrogenase

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Step 5: Succinate formation
Enzyme: succinyl-CoA synthetase

A GTP (ATP) produced

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Steps 6: Fumarate formation
Enzyme: Succinate dehydrogenase
A FADH2 produced

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Steps 7: Malate formation
Enzyme: fumarase

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Step 8: Malate to Oxaloacetate
3rd NADH produced
Enzyme: malate dehydrogenase

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Citric Acid Cycle:
Overview
Input: 2-carbon units

Output: 2 CO2
1 GTP
3 NADH: 2.5X3=7.5 ATP
1 FADH2: 1.5X1=1.5 ATP
Total: 10 ATP
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Electron Transport Chain
 Location: Inner Membranes of Mitochondria
 Main Goal: Use hydrogen ions and electrons to make up to 34 ATP
 In aerobic respiration, electron transport is the final step in the break-down of
glucose.
 It also is the point at which most of the ATP is produced.
 High-energy electrons and hydrogen ions from NADH and FADH2 produced
in the Krebs cycle are used to convert ADP to ATP.

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4.2.2 Biosynthesis
 Photosynthesis : is the process by which green plants, algae, and some bacteria
convert light energy, usually from the sun, into chemical energy in the form
of glucose.
 6CO2+6H2O+lightenergy→C6H12O6+6O2
 takes place in the chloroplasts of plant cells.
 The main inputs are carbon dioxide (CO₂) from the atmosphere and water
(H₂O) from the soil.
 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.

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 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.

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Photoautotrophs (―self-feeders using light)
 are organisms that can synthesize their own food from inorganic substances
using light as an energy source.
 Examples: Green plants, algae, cyanobacteria
Characteristics:
 Possess chlorophyll or similar pigments to capture light energy.
 Transform light energy into chemical energy in the form of ATP.
 Use ATP to fix carbon from carbon dioxide into organic compounds like glucose.
Importance:
 Base of the food chain in most ecosystems.
 Primary producers, contributing to the global oxygen supply through
photosynthesis.
 Crucial in carbon sequestration and reducing greenhouse gases.
Heterotrophs: are organisms that cannot synthesize their own food and rely on other
organisms — both plants and animals — for nutrition.
Characteristics:
•Do not have the ability to use sunlight directly.
•Obtain energy by consuming organic substances, which were originally produced by
photoautotrophs or other heterotrophs.
•Include all animals, most fungi, and many bacteria.
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 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.


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The photosynthetic apparatus
 Have organelles called plastids which

contain pigments or can store nutrients.
 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.
 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.


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 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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 Carotenoids: These red, orange or yellow-colored pigments
absorb bluish-green light. Examples of carotenoids are
xanthophyll (yellow) and carotene (orange) from which carrots
get their color.
 Phycobilins: These red or blue pigments absorb wavelengths of

light that are not as well absorbed by chlorophylls and
carotenoids. They are seen in cyanobacteria and red algae.
 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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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.
The photosynthetic process
a. Light-Dependent Reactions:
 occur in the thylakoid membranes of chloroplasts where chlorophyll and
other pigments absorb sunlight.
 The main steps in light-dependent reactions are:
1) Photon Absorption
2) Water Splitting (Photolysis)
3) Electron Transport Chain (ETC)
4) ATP Synthesis
5) NADPH Formation
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Light-Independent Reactions (Calvin Cycle):
 Also known as the Calvin-Benson cycle
 Do not require light directly but use the ATP and NADPH produced in the light-
dependent reactions.
 Takes place in the stroma of chloroplasts and involves the following steps:
1) Carbon Fixation: Carbon dioxide from the atmosphere is attached to a five-
carbon molecule called ribulose bisphosphate (RuBP) by the enzyme
RuBisCO, resulting in a six-carbon compound that immediately splits into two
three-carbon molecules called 3-phosphoglycerate (3-PGA).
2) Reduction Phase: ATP and NADPH are used to convert 3-PGA into
glyceraldehyde-3-phosphate (G3P). Some of the G3P molecules are used to
produce glucose and other sugars, while the rest are recycled to regenerate
RuBP.
3) Regeneration of RuBP: ATP isnote
Lecture used to convert
for General some of the G3P back into
Biology (Biol.
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Chapter -6: Infectious diseases and Immunity
 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
be 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.

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In order to cause infectious disease a pathogen must accomplish the
following steps:-
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.
Infection and Disease
 Infection is when harmful microorganisms like bacteria, viruses,
fungi, or parasites enter and multiply in the body.
 Disease is any condition that disrupts the normal function of the
body.
 It can be due to infections, but can also arise from genetic factors,
environmental factors, or lifestyle choices.
All infections can lead to disease, not all diseases are caused by infections.
Diseases can be chronic or acute, and they can affect different parts of the body,
not just where an infection might be present.
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Sign, symptom and Syndrome
Sign: A change in a body that can be measured or observed as a result of
disease.
 can be detected by someone other than the person affected.
 E.g. A fever can be measured with a thermometer, and high blood
pressure can be detected with a blood pressure monitor.
 Symptom: A change in body function that is felt by a patient as a result
of disease reported by the person affected but
 not easily measured or observed by others.
 This could include feelings of nausea, pain, or fatigue
 Syndrome: A specific group of signs and symptoms that accompany a
disease

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Classifying infectious diseases
Communicable disease: A disease that is spread from one host to another
Non-communicable disease: A disease that is not transmitted from one
host to another
B. Classifying infectious diseases by occurrence of diseases
1) Incidence: fraction of a population that contracts a disease during a
specific time
2) Prevalence: fraction of a population having a specific disease at a
given time
3) Sporadic disease: disease that occurs occasionally in a population
4) Endemic disease: disease constantly present in a population
5) Epidemic disease: disease acquired by many hosts in a given area in a
short time
6) Pandemic disease: worldwide epidemic

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An Infection can be classified based on Extent of host
involvement
Local infection: Pathogens are limited to a small area of the body
abscesses
Systemic infection: an infection throughout the body by blood
and/or lymph
 Toxemia: toxins in the blood
 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

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c. Severity or duration of infectious disease
Scope of infectious disease can be defined as :-
•Acute: disease develops rapidly
•Chronic: disease develops slowly
•Subacute: symptoms appear between acute and chronic
•Latent: disease with a period of no symptoms when the causative
agent is inactive

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Disease development and stages
•Incubation period: This is the initial stage after the
microbe enters the body, but before symptoms
appear. may not feel sick during this phase.
•Prodromal period: characterized by appearance of
first mild signs and symptoms.
The microbial population begins to increase, and
the body starts to recognize the infection, which
might result in general symptoms like mild fever,
fatigue, or headache.
•Period of illness: the number of microbes peaks, and symptoms become most
severe.
•Period of decline: The body's immune response and, if applicable, medical
treatments start to reduce the number of infecting microbes. Symptoms begin to
lessen in severity.
 Period of convalescence: In this final stage, the body gradually returns to normal
as it recovers. There may still be mild symptoms or a general feeling of tiredness,
but the overall health improves until full recovery.
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Pathogenicity
 Primary pathogen is microbe or virus that causes disease in
otherwise healthy individual due to their virulence factor.
 Virulence refers to a degree of pathogenicity
 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).

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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.

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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.
• 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
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Types of infectious disease and their causative agent
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

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Bacteria
Are unicellular prokaryotic organisms
 reproduce asexually through binary fission, where a single cell divides into
two identical daughter cells.
Belong to Kingdom Monera
have a rigid cell wall made of peptidoglycan, which protects the cell and
gives it shape.
Motile and can move using appendages such as flagella or through gliding
mechanisms.
Found in different shapes (bacillus (rod-shaped), coccus (spherical), or
spirillum (helical rods)).
The energy sources for bacteria also vary.
Some bacteria are photosynthetic
Others oxidize inorganic compounds
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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 can also divided into two broad classes based on their cell wall
structures, and 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 exotoxin that can be lethal for
humans.
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Viruses
Viruses lack the basic cellular structure and metabolic processes needed for life.
They cannot grow, reproduce, or carry out metabolic functions without a host.
Viruses consists of genetic material enclosed in a protein coat called a capsid.
 Some viruses also have an additional lipid envelope derived from the host cell's
membrane.
 Viruses can contain either DNA or RNA as their genetic material, which can be
single-stranded or double-stranded.
Viruses must infect host cells to replicate. They capture the host's cellular
machinery to synthesize new viral particles.

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 Viruses are much smaller than bacteria, typically ranging from
about 20 to 300 nanometers in diameter.
 Many viruses are pathogenic and can cause a variety of
diseases, from mild illnesses like the common cold to severe
conditions like HIV/AIDS or COVID-19.
 Viruses can spread in numerous ways, including direct contact,
airborne droplets, bodily fluids, and vector transmission
through insects.
 Some viruses can remain dormant within their hosts for
extended periods before reactivating and causing symptoms.

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The process of viral infection and replication generally follows these steps:
Attachment: The virus attaches to the host cell membrane using specific binding
molecules that match receptors on the cell's surface.
Entry: This can occur through direct penetration, endocytosis, or fusion with the
cell membrane.
Uncoating: The viral capsid (protein shell) disassembles, releasing the viral genetic
material into the host cell's cytoplasm.
Replication: The virus uses the host cell's machinery to replicate its genetic
material.
Assembly: Newly synthesized viral components and genetic material are
assembled into new virus particles.
Release: The new viruses exit the host cell and go on to infect new cells. This
release can happen through lysis, where the cell is destroyed, or through budding,
which may not immediately killLecture
the note
cell.for General Biology (Biol.
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Viruses are classified based on the kind of genetic material they have:
1) DNA viruses include ones like the herpes virus, which can lead to chickenpox,
cold sores, and genital sores, and the poxvirus, which is known for causing
smallpox.
2) RNA viruses include the rhinoviruses that are behind most common colds;
myxoviruses and paramyxoviruses that cause flu, measles, and mumps;
rotaviruses that bring on stomach flu; and retroviruses, which are responsible
for AIDS and certain cancers."
Why Antibiotics Are Not Effective Against Viruses?
•Antibiotics target specific structures or metabolic pathways in bacteria, such as
cell wall synthesis, protein synthesis, or DNA replication.
•Since viruses do not possess these structures or carry out these metabolic
processes independently, antibiotics have no effect on viruses. Viruses replicate
using the host cell's machinery, thus avoiding the mechanisms antibiotics use to
kill bacteria.
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Why Viral Drug Discovery challenging
 Viruses have high mutation rates, especially RNA viruses, which makes them rapidly
evolve and develop resistance to antiviral drugs.
 Viral life cycles are closely integrated with host cell processes, making it difficult to find
drug targets that disrupt the virus without also harming the host cells.
 Limited knowledge of viral structures and functions compared to bacteria also hampers
the development of effective antiviral drugs.

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Fungi
 Are a diverse group of organisms that differ significantly from plants and animals,
possessing several unique features
Cell Structure:
 Fungi are eukaryotic, meaning their cells contain a nucleus and other
organelles enclosed within membranes.
 Unlike plant cells, fungal cells have cell walls made of chitin, a strong, flexible
compound also found in the exoskeletons of insects.
Modes of Nutrition:
 Fungi are heterotrophs (cannot make their own food through photosynthesis
like plants).
 they absorb nutrients from their environment.
 They do this by secreting enzymes that break down complex substances into
smaller, absorbable components.
Reproduction:
 Fungi can reproduce both sexually and asexually.
 Asexual reproduction is common and occurs through spores, budding, or
fragmentation.
 Sexual reproduction involves the fusion of two compatible fungal hyphae,
leading to genetic recombination
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Generalthe
Biologyformation
(Biol. of spores that can
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endure harsh conditions.
Fungi……………………
• Mycelium: an extensive, branching network of hyphae (thread-like structures)

that grow through and digest the substrate.
• Spore Formation: Spores are the primary means of dispersal, and they can be
incredibly resilient, surviving extreme environments and lying dormant until
conditions are favorable for growth.
• Symbiotic Relationships: Many fungi form symbiotic relationships with other
organisms.
• For example, mycorrhizal fungi enhance plant nutrient uptake in exchange for
carbohydrates from photosynthesis.
• Lichens are another example, where fungi form symbiotic associations with
algae or cyanobacteria.

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Fungi…………………
Ecological Roles:
 Fungi play critical roles in ecosystems, particularly in nutrient cycling and
decomposition.
 They are among the few organisms capable of breaking down wood and other
complex organic materials, recycling nutrients back into the ecosystem.
Biochemical Pathways:
 Fungi can produce a wide range of secondary metabolites, some of which are
useful in medicine and industry.
 Examples include antibiotics like penicillin, immunosuppressants, and various
enzymes used in manufacturing.

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Fungi
 3 forms of fungi are

 multicellular ( filamentous mold)
 Unicellular yeasts
 Dimorphic fungi
 Types of Fungal Infections
Superficial and Cutaneous Infections: These affect the skin, nails, and hair.
Common examples include:
 Athlete’s foot (Tinea pedis): Infection of the foot, particularly between the
toes.
 Ringworm (Tinea corporis): Forms ring-shaped, red patches on the skin.
 Jock itch (Tinea cruris): Affects the groin area.
 Scalp ringworm (Tinea capitis): Occurs on the head and scalp.
 Nail fungus (Onychomycosis): Affects fingernails or toenails, causing
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discoloration and thickening.
Systemic Infections: These affect internal organs and are typically more severe,
such as:
 Candidiasis: Can affect the mouth, throat, and genitals; systemic candidiasis can
affect the bloodstream and internal organs.
 Aspergillosis: Usually affects the lungs, but can also spread to other organs.
 Cryptococcosis: Often begins as a lung infection but can spread to the brain.
Risk Factors for Fungal Disease

 Weakened Immune System: Individuals with compromised immunity, such as HIV/AIDS
patients, organ transplant recipients, or cancer patients undergoing chemotherapy, are
at higher risk.
 Use of Antibiotics: Broad-spectrum antibiotics can disrupt the normal balance of flora
in the body, increasing the risk of fungal infections.
 Environmental Exposure: Exposure to contaminated bird droppings can increase risk,
especially for infections like histoplasmosis or cryptococcosis.
 Chronic Health Conditions: People with
Lecture note for diabetes, obesity,
General Biology (Biol. or respiratory diseases are
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Protozoa
• are unicellular,
• Heterotrophs, consuming bacteria, algae, or organic debris, while others are
autotrophs, performing photosynthesis.
•Parasitic forms absorb nutrients directly from their hosts.
• Do not have cell walls,
• Many protozoa are motile, using cilia, flagella, or pseudopodia (temporary
projections of the cytoplasm) to move.
•Mobility helps them find food, escape predators, and disperse to new
environments.
•They are predominantly aquatic, existing in both freshwater and marine
environments.
•Some species are also terrestrial, inhabiting moist soils, and others are parasitic,
living inside the bodies of other organisms.
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Protozoa………
 Protozoa play critical roles in ecological systems as decomposers and as a part

of the food web, providing nutrients for higher organisms and controlling
bacterial populations.
 Some protozoa are pathogens and can cause diseases in humans, animals, and
plants.
 Examples include Plasmodium (malaria), Giardia (giardiasis), and Trypanosoma
(sleeping sickness).
 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.

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Helminths
• Are multicellular parasitic worms, can be seen with the naked eye when
mature.
• Unlike protozoa, helminths have complex body structures with organs and
systems including digestive, excretory, nervous, and reproductive systems.
• They are broadly categorized into three groups: nematodes (roundworms),
cestodes (tapeworms), and trematodes (flukes).
• Involve multiple stages of development, often requiring one or more
intermediate hosts before reaching maturity in the definitive host.
• Transmission can occur through contaminated food, water, soil, or through
vector transmission (e.g., mosquito for filarial worms).
• cause various diseases, such as schistosomiasis (caused by schistosome
flukes), ascariasis (caused by Ascaris lumbricoides), and tapeworm infections
(various species of Taenia).
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Prions
 are composed of an abnormal form of a normal cellular protein known as the prion
protein (PrP).
 Unlike other infectious agents, prions contain no nucleic acids, meaning they lack DNA
or RNA.
The normal prion protein is found on the surface of cells, particularly in the brain.
Prions propagate by inducing the misfolding of normal prion proteins into the pathogenic
form. This misfolded protein can then convert other normal proteins into the misfolded
prion form, creating a chain reaction that spreads throughout the brain.
Prion diseases are invariably fatal and include conditions such as Creutzfeldt-
Jakob Disease (CJD) in humans,
Bovine Spongiform Encephalopathy (BSE, also known as "mad cow disease") in
cattle, and Chronic Wasting Disease (CWD) in deer and elk.
These diseases affect the brain structure, leading to symptoms such as rapid
mental deterioration, memory loss, personality changes, and physical
impairments.
Prions are extraordinarily resistant to methods that typically destroy pathogens, including
heat, radiation, and standard sterilization procedures. This makes them particularly
challenging to eliminate from medical and surgical instruments.
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Modes of transmission
 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.
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Host defenses against infectious diseases
The human body has a complex and multi-layered defense system against
infectious diseases.
This system can be divided into two main categories: the innate immune
system and the adaptive immune system.
1. Innate Immune System(Nonspecific mechanisms)
are the body's primary and the first line of defense against disease.
 present at birth and changes little throughout the life of an individual.
Physical Barriers: The skin and mucous membranes act as physical barriers to block
pathogen entry.
Chemical Barriers: Enzymes in saliva, stomach acid, and antimicrobial peptides in sweat
and sebum help destroy pathogens.
Cellular Defenses: Specialized cells such as macrophages and neutrophils ingest and
destroy invading microorganisms.
Inflammatory Response: This response is triggered by infection or injury, resulting in
increased blood flow and immune cell activation to the affected area.
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Innate Immune System…………..
 Tears cleanse the eyes

 Acidic vaginal secretions prevent potential infections.
 Enzymes like lysozyme in tears, saliva, and mucus break down
bacterial walls to protect openings like the eyes, mouth, and
nose.
 Lysozyme is also found in blood and sweat.
 White blood cells in the blood consume and destroy invaders
through a process known as phagocytosis.
 Blood also contains clotting agents to prevent further invasion
at injury sites and proteins that cause inflammation, stimulate
phagocytes, and destroy
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2. Adaptive Immune System
 Is a specific defense that develops throughout our lives as we are exposed to
various pathogens or immunized through vaccinations:
Lymphocytes: This system involves B cells and T cells, two types of lymphocytes
that recognize specific antigens on pathogens.
 B cells: Produce antibodies that bind to antigens, neutralizing them or
marking them for destruction.
 T cells: Activate other immune cells.
 Cytotoxic T cells: Destroy infected cells directly.
 Regulatory T cells: Moderate immune responses.
 Memory Cells: After an infection, memory B and T cells form and provide
immunity against future infections by the same pathogen.

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2. Adaptive Immune System……….
 A specific response that targets particular pathogens and infected cells,
adapting and improving during the individual's lifetime.
 When a person receives a flu vaccine, the vaccine contains parts of the
influenza virus, which are recognized as foreign by the immune system.
Acquired immunity has two branches:

1) Humoral or antibody-mediated immunity, which has antibodies
floating around in body fluids, focusing on microbes outside of
cells, made by B-cells.
2) Cellular or cell-mediated immunity, carried out by T-cells
themselves, directly attacking infected or abnormal cells.

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Physical and Chemical Signals
 Cytokines: These are chemical messengers that guide cells
towards sites of inflammation, infection, and trauma.
 Interferons: Proteins that are produced in response to viral
infections; they prevent virus replication and activate immune
cells.
 Behavioral and Physiological Defenses
 Cough Reflex: Expels pathogens from the respiratory tract.
 Sneezing: Rapidly expels nasal fluid to flush out pathogens.
 Vomiting and Diarrhea: Expel pathogens ingested via
contaminated food or drink.
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Adverse immune reactions (responses)
 The aim of the immune responses is to protect the body from
damage from any environmental agents including pathogens
and also from cancer,
 but adverse immunological reactions can occur and cause
adverse effects to the host due to:
 Exaggerated immune response and/or
 producing inappropriate immune response against self
components.
 Due to failure of appropriate recognition mechanism.
 Production of more damage than it prevents, immune
responses (especially to some antigens) can lead to more severe
tissue damaging reactions (immunopathology).

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There are three types of immunological disorders.
1) Hypersensitivity
2) Autoimmune diseases
3) Immunodeficiency
Hypersensitivity:
 when the immune system overreacts to foreign substances that
are typically harmless.
 An example is when someone has an allergic reaction to peanuts.
 There are four main types of hypersensitivity:
 Type I: This immediate reaction is caused by IgE antibodies.
 When an antigen binds to IgE on certain cells, it releases
substances like histamine, leading to symptoms such as swelling,
mucus production, and spasms.
 These reactions typically occur within an hour of exposure.
 Type II: Involves antibodies that attack the body's own cells or
tissues.
 Type III: Involves immune complexes that cause inflammation.
 Type IV: This delayed reaction is not caused by antibodies but by
immune
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2. Autoimmune Diseases:
 are a class of disorders where the body's immune system mistakenly attacks its
own healthy cells and tissues.
 There are over 80 recognized autoimmune diseases, and they can affect almost
any part of the body.
 Some of the most common autoimmune diseases include:
 Type 1 diabetes - the immune system attacks insulin-producing cells in the
pancreas
 Rheumatoid arthritis - the immune system attacks the joints, causing
inflammation and damage
 Psoriasis and psoriatic arthritis - the immune system causes skin cells to
multiply too quickly, leading to inflamed patches
 Multiple sclerosis - the immune system attacks the protective coating around
nerve cells, disrupting communication
 Systemic lupus erythematosus (lupus) - the immune system can attack various
organs and tissues throughout the body
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 The exact causes of autoimmune diseases are not fully understood, but
they are believed to involve
 a combination of genetic, environmental, and hormonal factors.
 Women are more commonly affected, making up about 80% of
autoimmune disease cases.
 Symptoms can vary widely depending on the specific disease and affected
body parts, but
 commonly include fatigue, fever, joint pain, skin rashes, and digestive
issues.
 While there is no cure for autoimmune diseases, treatments typically aim to
reduce immune system activity and manage symptoms.
 This may involve medications, dietary changes, and other therapies

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3. Immunodeficiency:
 This occurs when the immune system is not working properly
and cannot mount an effective defense against infections.
 It can be inherited, like in Severe Combined Immunodeficiency
(SCID), or acquired, such as with HIV/AIDS, which damages
immune cells and leads to a progressive failure of the immune
system.
 There are two main types:
Primary Immunodeficiency
 present from birth due to genetic problems that cause
mutations.
 It can impact both the acquired (specific) and innate (general)
immune system and can affect either the lymphoid or myeloid
groups of immune cells.

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Lymphoid defects: These can impact B-cells, T-cells, or both, and how severe it is
can depend on how many and which types of immune parts are involved. B-cell
issues often lead to bacterial infections, while T-cell problems can weaken the
body's defense against a variety of infections.
Myeloid defects:
These affect the innate immunity, particularly cells that eat and kill invaders.
 An example is Chronic Granulomatous Disease (CGD), which causes problems
in killing ingested microbes, leading to chronic infections and granulomas, and
is also associated with inflammatory conditions like colitis.
Secondary Immunodeficiency
 This type develops later in life due to external factors like malnutrition,
infections, cancer, or the use of drugs that suppress the immune system.
 A well-known example is HIV/AIDS, where the virus damages the immune
system, making the person vulnerable to a wide range of infections.

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Tumor immunology
 A tumor is a cluster of unnecessary and abnormal cells that keep growing
instead of dying.
 Tumors can form solid masses in organs, muscles, or bones and potentially
spread to other parts of the body.
 The immune system is thought to prevent many cancers by destroying
abnormal cells early on, especially those associated with viruses.
 The body can recognize antigens (markers) on tumor cells; these antigens
might come from viruses or from the body's own cells that have changed.
 These tumor-associated antigens can help diagnose cancer and may be
targeted by treatments like monoclonal antibodies.
 Although such treatments show promise, especially when targeting individual
cancer cells, it's still challenging because tumors can find ways to evade the
immune system.
 Treatments using cytokines, which are immune signaling molecules, have
been effective against a few types of tumors.
 Most immunotherapies are still being tested because of these challenges.

Evidence for immune reactivity to tumor
 Tumors with lots of immune cells often have a better chance of recovery.
 Some cancers, like skin cancer and nerve cell cancer, can shrink on their own,
hinting at an immune attack.
 When the main tumor is removed, sometimes smaller, spread-out cancers
shrink too, as if the immune system is better able to attack them.
 Even after chemotherapy kills most cancer cells, the immune system might
still target the few that are left.
 People with weak immune systems, like those with AIDS or organ transplants,
are more likely to get certain cancers, showing the immune system’s role in
fighting cancer.
 Doctors have found specific antibodies and killer immune cells in people with
cancer, which attack only cancer cells.
 Infants and older adults get cancer more often, possibly because their
immune systems aren't as strong.
 Vaccines against certain cancers can work, proving that immune cells can
respond to cancer cells.


 For the immune system to fight against tumors, the tumors need to have
markers, called antigens, that the immune system sees as foreign.
 When cells turn cancerous, they may either create new antigens or change
existing ones that normal cells have.
 These changes could be in cell cycle controllers, growth signal receivers, or
other cell-communicating parts.
There are two main kinds of tumor antigens:
 Tumor-specific transplantation antigens (TSTA): These are only found on
tumor cells and not on normal cells.
 Tumor-associated transplantation antigens (TATA): These are found on both
tumor and normal cells.
 Even though tumors caused by chemicals, sunlight, or viruses can have new
antigens, they usually don't trigger a strong immune response. It's often hard
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identify TSTAs because they might be hidden or not very noticeable.
Lecture note for General Biology (Biol. 1012)
Chapter 7-Taxonomy of organisms
 Taxonomy is the science of classification, identification, and naming of

organisms, including the systematic arrangement of organisms into a coherent
scheme.
 The goal of taxonomy is to organize the vast diversity of life on Earth into
categories that can be used for identification and study.
 The word taxonomy was derived from two Greek words "taxis"
meaning arrangement and "nomos" meaning law, first introduced
by the Swiss naturalist De Candolle in 1813.
 The law governing the classification or arrangement of
organisms into taxa

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Practices of Taxonomy
• 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.
• Identification: Is the naming of an organism or a specimen by reference to an
already existent classification.
• It involves referring an individual specimen to a previously classified and
named system.
• N.B: Classification precedes nomenclature.

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Taxonomy during the Greek and Roman Philosophers-
Essentialists
a. Aristotle (384–322 BC)
 A Greek philosopher who made significant contributions to
biology.
 He viewed life as hierarchical and classified organisms based on
their natural traits, focusing on their biological changes and
diversity.
 His works were foundational, later succeeded by other naturalists
like Theophrastus.
 the first to classify living things into plants & animals
• Animals: into “animals with blood” & “animals without blood”
• animals with blood: live-bearing & egg-bearing,
• Without blood: insects, crustacea and testacea (molluscs)

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b. Theophrastus (370–285 BC)
 Student of Aristotle and Plato

 Known as the father of Botany, he was the first to document a
systematic classification of plants in his book "De Historia
Plantarum."
 He classified 480 types of plants and believed in clear-cut categories,
with no intermediate organisms, a concept known as the “Excluded
Middle.”
 The most significant contribution of Theophrastus includes:
1) Classification of plants into trees, shrubs, sub-shrubs, herbs,
annuals, biennuals and perennials.
2) Distinction between flowering (such as superior and inferior
ovaries, free and sympetalous corollas) vs. non-flowering plants.
3) Differences between external (organs) vs. internal structures.
4) Recognition of different kinds of sexual (ovary position, hypo-,
peri- and epigynous, fruit type, etc) and asexual reproduction.
5) Understood basic anatomy of 1012)
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sepals and petals, modified leaves.
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Pliny the Elder (23-79 A.D.)
 A Roman scholar who wrote encyclopaedic books termed "Historia
Naturalis,"
 categorizing plants by their uses in horticulture, medicine, and timber
Dioscorides (1st Century AD) - A Greek physician who described around 600
medicinal plants and their uses in "De Materia Medica.“
A. Caesalpinus (1519-1603) - Authored "De Plantis," classifying about 1500
plant species based on clear morphological features like plant habits and
reproductive structures.
J. Bauhin (1554-1631) and G. Bauhin (1560-1624) - Swiss botanist brothers who

advanced the classification of plants, promoting the use of genus and species as
major taxonomic levels.
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Carolus Linnaeus (1707-1778)
• A Swedish taxonomist who is considered the father of modern taxonomy.
• He introduced a simpler classification system, using characteristics such as
the number and position of stamens and pistils.
• His seminal works, "Genera Plantarum" and "Species Plantarum," laid the
groundwork for contemporary taxonomic nomenclature.
 Post-Linnaean taxonomists like M. Adanson, De Jussieu, J. de Lamarck, A.P.
de Candolle, and Charles Darwin further refined classification systems,
moving away from Linnaeus’s artificial system to incorporate evolutionary
perspectives and broader morphological characteristics.
 who never followed artificial system of Linnaeus classification.

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M. Adanson (1727-1806)
 was a scientist who believed that when classifying living things, you should
look at a wide range of their characteristics equally,
 This way of classifying is known as the empirical approach.
 Lamarck is best known for his theory of evolution, Lamarckism, whereby
characters acquired during life become inherited.
 He thought that if an organism changes during its life to adapt to its
environment, like a giraffe stretching its neck to reach leaves, those changes
could be passed on to its children.

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De Candolle (1778-1841)
• wrote 17 volumes about plants and was the first person to use
the term 'taxonomy' (the science of classification) in French.
• He helped to organize the knowledge of plant species.
Charles Darwin
 known for his book 'The Origin of Species' in 1859, proposed the
theory of natural selection.
 Although his ideas didn't immediately change how organisms
were classified, they eventually led scientists to consider
evolution and relationships between species when classifying
them, rather than just looking at their physical features.
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Modern Views of Classification (Schemes of Classification)
 Modern classification schemes have evolved significantly from earlier systems

and incorporate a variety of scientific disciplines, including genetics,
biochemistry, and molecular biology.
Phenetic Classification
 This is based on the overall similarity between organisms, usually in
morphology or other observable traits, without regard to phylogenetic
relationships.
 uses a quantitative framework to assess overall similarity, often employing
statistical analysis to evaluate the degree of similarity among organisms.

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1. Artificial classification system
 Classifies organisms based on one or a few selected characteristics that are
easily observable, such as color, size, or shape.
These characteristics may not necessarily reflect the true evolutionary
relationships between the organisms.
 The main goal is to simplify identification and organization of species based
on superficial traits. It is not concerned with phylogenetic relationships.
 Since it does not consider the evolutionary history and often only a few traits,
it can group together organisms that are not closely related while separating
those that are closely related genetically.
 Theophrastus and Linnaeus are good example of artificial system of
classification

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2. Natural classification system
 Groups organisms based on their overall similarities, including a wide range of
genetic, anatomical, and physiological characteristics.
More importantly, it reflects the evolutionary and genetic relationships
among organisms.
 The aim is to map out the evolutionary pathways and relationships among
different organisms, offering a more comprehensive understanding of biodiversity.
Examples: Modern classification schemes that use genetic data to determine
relationships are examples of natural classification systems.
Phylogenetic trees based on DNA or protein sequences are typical outputs of
this system.
 It consider both visible and molecular features, which helps in understanding
evolutionary processes and biological diversity.

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 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.
 Based on similarity but uses different characters and lacks pre-
selected features.
 It compares organisms using features like anatomy, physiology,
pathology, biochemistry, reproduction, and cytology.
 Adanson and De Jussieu are good examples of natural
classification system.

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Phyletic or Evolutionary classification system
 Classifies organisms based on their evolutionary history and sequence of
evolution.
 It considers both ancestral traits and derived traits that have evolved due to
adaptation and speciation.
Organisms are grouped together if they share a common lineage, taking into
account the entire range of characteristics, from physical form to genetic
information, across all evolutionary time.
The aim is to place organisms into groups that reflect the lines of evolutionary
descent rather than just structural similarities.
Examined of fossil record is made to identify the primitive and the advanced
state

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Phenetics Classification System (Numerical Taxonomy)
 Focuses on classifying organisms based on the overall similarity between
individuals, using a large number of characteristics without considering
whether traits are evolutionarily derived or ancestral.
 It often uses quantitative methods to assess similarity, employing statistical
techniques to evaluate and organize data.
 Characteristics are given equal weight, and the output is usually a dendrogram
that shows clustering based on overall similarity.
 The primary aim is to provide a depiction of the phenotypic similarity between
species, regardless of their phylogenetic relationships.

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Phylogenetic classification system
 Classifies organisms based on their evolutionary relationships.
 It specifically considers shared derived characteristics (synapomorphies) that
are indicators of common ancestry.
 Phylogenetic trees are constructed using data from morphology,
biochemistry, and molecular features such as DNA sequences. These trees
illustrate how species are related through evolutionary history.
 The goal is to depict the branching evolutionary pathways that connect all life
forms, highlighting how groups of organisms diverged from common
ancestors.
The method works as follows:
 Select monophyletic taxa
 Select characters of evolutionary interest.
 Describe and/or measure character states.
 Determine homologies of characters and character states.
  Generate trees or cladograms.
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Key Differences
 Evolutionary Classification integrates the chronological sequence of
evolution into the classification and aims to reflect phylogenetic
relationships but with a broader consideration of evolutionary history.
 Phenetics focuses solely on measurable similarities and differences in traits,
using a non-hierarchical approach that does not necessarily reflect
evolutionary relationships.
 Phylogenetic Classification is strictly about evolutionary relationships and
lineage branching, which makes it the most focused on depicting accurate
evolutionary paths based on shared derived characteristics.

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Domains of Life and the Hierarchical System of Classification
• Domains was introduced by Carl Woese and colleagues in the late 20th century,
fundamentally reshaping our understanding of the tree of life
•The three domains are identified and organized based on the difference between
eukaryotes and prokaryotes (Domain Archae bacteria, Eubacteria and Eukarya).
•Eubacteria: consists of prokaryotic organisms that are characterized by a lack
of a nucleus and other membrane-bound organelles.
•Archaea: Like bacteria, archaea are prokaryotic and lack a nucleus.
 They are genetically and biochemically distinct from bacteria and often
thrive in extreme environments such as hot springs and salt lakes. They
possess unique membrane lipids and gene transcription machinery more
similar to eukaryotes.
•Eukarya: includes all plants, animals, fungi, and protists. The complexity of
cellular structure and function is markedly higher in eukaryotes than in
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prokaryotes.
Hierarchical System of Classification
 organizes biological diversity into a nested structure where each level
represents a greater degree of specificity.
 Developed by Carl Linnaeus in the 18th century
Domain: The highest, most inclusive level.
1) Kingdom: Animalia, Plantae, Fungi, Protista, and Monera
2) Phylum: based on basic structural similarities and developmental
characteristics.
3) Class: organisms that share common attributes.
4) Order: A more specific category within a class, defining creatures that are
even more closely related.
5) Family: Have more significant anatomical and DNA similarities than those in
previous levels.
6) Genus: A group of closely related species. The genus name is capitalized in
the binomial nomenclature.
7) Species: The most specific level of classification, which describes individuals
that can interbreed and produce viable offspring under natural conditions.
The species name is always in lowercase and paired with the genus in
binomial nomenclature.

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Concepts of the Kingdom
 Kingdom is a taxonomic rank, which is the highest rank or in the more recent
three-domain system, it is the second rank below the Domain.
 kingdom systems were developed based on the diversity of organisms and to
produce inclusive all-inclusive classification system.
The Two- Kingdom Concept/Approach
 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.

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Three-Kingdom Concept
 This approach classifies all organisms in to three Kingdoms, namely; kingdom
Plantae, Animalia and Protista
The Four-Kingdom Concept: Kingdom Plantae, Animal, Protista and Fungi.
The Five-Kingdom Concept
•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.
• Thus, they suggested the Five Kingdom approaches; which are: kingdom
Monera, kingdom Fungi, kingdom Protista, kingdom Plantae and kingdom
Animalia.

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The Six-Kingdom Concept
 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

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Binomial Nomenclature
 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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The Purpose of giving names to organisms
 Serves as a means of reference and avoids the need for continuous use of an
inconvenient descriptive phrase.
 used for act as vehicle of communication, to universalize the organism and to
avoid any names.
 In the world, there are many languages, and many of them use different
alphabets.
 Even within a single language the same name is often used in different senses to
denote different kinds of organisms, or same organism is known by more than one
name.
 Thus, the Code of nomenclature tries to avoid the defects of vernacular names
and for this reason sets of rules have been drawn up.
 Scientific names are written in Latin form as well as in Latin alphabet.
 The scientific names of all living organisms are therefore Latin or are treated as
Latin even if they are derived from other languages.

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International Code nomenclature
o The code is a rulebook that contains principles, rules and recommendations
which form the basis of the system of nomenclature.
o It provides stability in the naming and classification of organisms.
o Varies international codes are established for different groups of organisms
(plants, animals, fungi, bacteria, cultivated plants).
 For ICBN: International Botanical Congress;
 For ICZN: International Congress for Zoological Nomenclature
 International Code of Nomenclature of Bacteria
 For Cultivated plants: The International Commission for the Nomenclature
of Cultivated Plants.
 For Fungi: The International Commission for the Taxonomy of Fungi (ICTF).

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International Code of Zoological Nomenclature (ICZN)
 It is the system of naming animals, which applies to both living and extinct
animals
International Code of Nomenclature of Bacteria
 governs the scientific names for Bacteria, including Archaea bacteria.
 It denotes the rules for naming taxa of bacteria, according to their relative rank.

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International Code of Nomenclature for Cultivated Plants
 regulates the names of cultigens (plants whose origin or selection is primarily
due to intentional human activity).
 plants with names in the classification categories cultivar and groups.
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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Operative Principles of Nomenclature
The nomenclature code has set certain provisions, called Operative Principles
of Nomenclature. These provisions are publication, typification and priority.
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.
1) The name must be published in works that are printed in permanent and
made available to the interested public.
2) A name must be accompanied by a written matter or a reference to such
description.

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Typification
o Type is the process of designating a nomenclatural type, or means by which
types are allocated to taxa.
o A ‘type‘ is an element on which the description associated with the original
publication of a name was based.
o The ‘type‘ of names of taxa above the Genus and below and including the
Family is a Genus.
o 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".

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o Some of these are:
 Holotype: It is the only 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‘.
 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".

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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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Chapter 8: Ecology and Conservation of Natural Resources
The word Ecology‟ was coined from Greek word 'oikos' meaning
'house' or 'a place to live' and 'logos' meaning study.
 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

Ecological terminologies and their definitions
Abiotic: all non-living components in the biosphere, e.g., air, water, soil,
climate.
Autotrophic: when an organism is able to produce its own food using abiotic
components.
Biotic: all the living components in the biosphere: animals, plants, micro-
organisms, etc.
Biosphere: it is the global sum of all ecosystems, and is the zone where all living
organisms live on earth.
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.
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.
Vegetation: the plant life that is found in a biome.

Branches of ecology
Ecology can be divided depending on the following concepts:-
1) Hierarchic: organism, population, community, ecosystem, biosphere
2) Taxonomic: plant ecology, animal ecology, microbial ecology, avian ecology,
etc.
3) Time/Place: marine ecology, tropical ecology, freshwater ecology

Hierarchical structure of ecological systems
Organism: fundamental unit of ecology. No smaller unit in biology has an
independent life in the environment.
Population: A group of organisms consisting of a number of different
populations that live in defined area and interact with each other.
Community: A group of organisms consisting of a number of different species
that live in an area and interact with each other
Ecosystem: a biological community plus all of the abiotic factors influencing
that community.
Biome: A distinct ecological community of plants and animals living together in
a particular climate.

Fig: 8.1. Hierarchical structure of ecological systems
Some examples of ecological branches
Population ecology (or Autecology)
 It is concerned with population growth including birth rates and death rates,
 fluctuation, spread and interactions (scientific study of relationships between
organisms of the same species).
Community ecology (or Synecology)
 is the scientific study of relationships between organisms of different species.
Ecosystems ecology
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.
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
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.

8.3 Aquatic and terrestrial ecosystems
There are two main categories of ecosystems.
A. Aquatic ecosystem
B. Terrestrial ecosystems
A) Aquatic ecosystem
 An aquatic ecosystem is an ecosystem in a body of water.
 There are two main types of aquatic ecosystems:
 Marine ecosystems
 Freshwater ecosystems

1. Marine ecosystems
 Approximately 71% of the earth's surface is covered by marine
ecosystems and
 It 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
 Freshwater ecosystems (occupy only about 2% of earth‘s surface).
Example
oRivers and streams: flowing-water ecosystems
oLakes and ponds: standing-water ecosystems
A large lake has three zones:
a. The littoral zone is a shallow-water area along the shore of a lake or
pond where light reaches the bottom; it is the most productive section of
the lake.
b. The limnetic zone is the open water beyond the littoral zone; it extends
down as far as sunlight penetrates to permit photosynthesis.
c. The profundal zone is beneath the limnetic zone; light does not
penetrate effectively to this depth (no plants or algae found here).
i. Tropical rain forest
 are found in the high rain fall areas on either side of the equator (found in
the western coast of India, scattered in south East Asia, some parts of Africa
and South America).
 have high temperature and high humidity
 receives above 200 cm of rainfall per year.
 Soil is rich in humus.
 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.
 support epiphytes, like vines, creepers, woody creepers and orchid etc.
 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
a. 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.
b. Climate:
• occur in moderate climatic conditions
• have temperature ranging from10 to 200C with a 6 month long winter and
• have annual rainfall between 75 to 150 cm.
• have brown soils which are rich in nutrients.
c. 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.
iii. Boreal or north coniferous forests:
 Coniferous forests are extend as continuous belt across North America
and north Eurasia below the arctic tundra.
 Climate is cold with long, harsh winter,
 have mean annual temperature below 00C.
 The soils are acidic and poor in nutrients.
 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
b. Grasslands
• 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 Africa, South America, Australia and India.
 Savannas form a complex ecosystem with scattered medium size trees in
grass lands.
•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.
c. Deserts
• 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.
• 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.
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.
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.
d. Tundra:
o The word tundra means a "barren land“ and
o They are found in very severe environmental conditions.
o There are two types of tundra: arctic and alpine.
o Arctic tundra extends as a continuous belt below the polar ice cap and above
the tree line in the northern hemisphere.
o 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.
oAlpine 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.
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.
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.
Organisms get energy when they eat plants and transfer it when they are being
eaten by other organisms and this 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.
The food chains
The transfer of food - energy from plants to animals and then to other animals by
successive stage of feeding is called a food chain.
A food chain is also defined as "the sequence of organisms that are related to
each other for their source of food."
Each stage of the food chain is known as trophic level.
The first trophic level is occupied by the autotrophic organisms, so they are
called producers.
The organisms of the second trophic level are called primary consumers or
herbivores.
Of the total net primary production, twenty percent (20%) to thirty percent
(30%) 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, two types of food chains are recognized: They are
i. grazing food chain
ii. detritus food chain.
i) Grazing food chain:
o starts from the living green plants and goes to grazing herbivores and on to
the carnivores.
o in grazing food chain energy is captured by autotrophic organisms and move
this energy to herbivores.
oMost of the ecosystems in nature follow this type of food chain.
The following are examples of grazing food chain:

Aquatic food chain: Phytoplanktons zooplanktons fish
Terrestrial food chain :Grasses Rabbit fox
ii. Detritus food chain
The organic wastes, exudates and dead matter derived from the grazing food
chain are generally termed as detritus.
The energy contained in this detritus is not lost to the ecosystem as a whole;
rather it serves as the source of energy for a group of organisms (detritivores)
that are separated from the grazing food chain.
In some ecosystems, considerably more energy flows through the detritus
food chain than through the grazing food chain.
In the detritus food chain the energy flow remains as a continuous passage
rather than as a stepwise flow between discrete entities.
The organisms of the detritus food chain are many and include algae,
bacteria, slime molds, actinomycetes, fungi, protozoa, insects, mites,
crustacea, centipedes, molluscs, rotifers, annelid worms, and nematodes.
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.
Food chain also exists among parasites. For instances, fleas that parasitize
mammals and birds are in turn parasitized by protozoan, leptosomes.
Fig: 8.2: Terrestrial and aquatic food chain

The food web
•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.
Fig: 8.3. Food web

Ecosystem productivity
Productivity in land ecosystems generally rises with temperature about 30 oC,
after which it declines, and is positively correlated with moisture.
On land primary productivity is highest in warm, wet zones of the tropical
rain forest biomes.
In contrast, desert scrub ecosystems have the lowest productivity because
their climates are extremely hot and dry.
A. Primary production
•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.
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/m 2) 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.
Ecological pyramid
•Ecological pyramid is the graphic representation of the number, biomass and
energy of the successive trophic levels of an ecosystem.
• The concept of ecological pyramid was first described by Charles Elton.
•Ecological pyramids represent the trophic structure (feeding relationships) and
trophic function (efficiency of energy transfer through biotic components) of an
ecosystem.
Types of ecological pyramid
I) Pyramid of number depicts the number of individual organisms at different
trophic levels of food chain.
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).
Fig: 8.4. Pyramid of Energy
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.
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.
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 atmosphere
through pollution which is altering rainfall patterns.
Fig: 8.5. Water cycle
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 (CO 2).

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.
Plants therefore help in regulating and monitoring the percentage of oxygen
and carbon dioxide in the earth‘s atmosphere, depends.
on the All oxygen of generated man kind through this thus 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.
Nitrogen cycle
•78% of the air is nitrogen
•Plants use nitrogen in their cellular processes
•Nitrogen is present in our DNA and RNA and in amino acids (proteins).
•The food chain largely moves nitrogen around.
Nitrogen Fixation: is the conversion of atmospheric nitrogen (N2) into reactive
compounds such as ammonia (NH3) and nitrate (NO3-).

oThe breaking of the bonds between the nitrogen atoms requires a great deal of
energy and occurs naturally in two primary ways:
i. Abiotic Fixation:
o Nitrate is the result of high energy fixation in the atmosphere from lightning
and cosmic radiation.
o In this process, N2 is combined with oxygen to form nitrogen oxides such as
oThis high energy fixation accounts for approximately10% of the nitrate
entering the nitrogen cycle.
ii. Biological fixation:
It is accomplished by a series of soil micro-organisms such as aerobic and
anaerobic bacteria.
Often, symbiotic bacteria such as Rhizobium are found in the roots of legumes
and provide a direct source of ammonia to the plants.
In root nodules of these legumes, the bacteria split molecular nitrogen into two
free nitrogen atoms, which combine with hydrogen to form ammonia (NH 3).
The following plants are common examples of legumes: clover, alfalfa, soy
beans, and chick peas.
The breakdown of these legumes by bacteria during ammonification actually
returns excess nitrogen not utilized by the plant to the surrounding soil.
Therefore, to promote sustainable soil fertility, it is beneficial to use these
agricultural crops in rotation with other plants, such as corn, that are more
profitable but deplete the available nitrogen in the soil some free-living aerobic
bacteria, such as Azotobacter, and anaerobic bacteria, like Clostridium, freely
fix nitrogen in the soil and in aquatic environments.
Some members of the photosynthetic cyanobacteria phylum fix nitrogen in
aquatic environments as well.
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 (NH 3)
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 (N 2) 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.
Fig: 8.6 Nitrogen cycle
The Oxygen Cycle
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, 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.
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 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.
Fig: 8.7 Phosphorus cycle
8.6 Conservation of natural resources
8.6.1 Principles of conservation of natural resources
 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.
 Ecosystem productivity tends to increase with temperature up to around
30°C, beyond which it decreases, and is also positively correlated with
moisture levels.
 The highest primary productivity on land is found in warm, moist tropical
regions where tropical forests thrive.
 In contrast, desert scrub ecosystems exhibit the lowest productivity due
to their extremely hot and dry climates.
 Primary production begins with plants converting sunlight into energy, a
process that uses energy stored in seeds until leaves are produced.
 The energy that plants accumulate is known as primary production, with
the total energy assimilated referred to as gross primary production.

Ecological pyramid
 Is the graphic representation of the number, biomass and energy
of the successive trophic levels of an ecosystem.
 The concept of ecological pyramid was first described by
Charles Elton.
 Ecological pyramids represent the trophic structure (feeding
relationships) and trophic function (efficiency of energy transfer
through biotic components) of an ecosystem.

2. Cycling of Materials in Ecosystems
 Ecosystems consist of various interdependent cycles that significantly impact

human life, including the water, carbon, oxygen, nitrogen, and energy cycles.
 During photosynthesis, plants absorb carbon dioxide and release oxygen,

which animals use for respiration.
 The water cycle is driven by rainfall essential for the survival of plants and
animals.
 The energy cycle replenishes the soil's nutrients that support plant growth
 Human survival is deeply connected to these cycles' stability, as alterations by

human activities could jeopardize our existence on Earth.

The Water Cycle
 The water cycle begins with rainfall, part of which flows over
land into rivers and seas, while some percolates into the ground,
staying there for the rest of the year.
 Plants absorb this groundwater, drawing nutrients from the soil.
 Water is then transpired as vapor from the leaves back into the
atmosphere.
 Being lighter than air, the vapor rises, forming clouds that are
carried away by winds.
 As these clouds ascend, the vapor condenses into droplets that
fall as rain.
 This perpetual cycle, crucial for life, is increasingly disrupted by
8.2.2 The Carbon cycle
 The carbon cycle integrates both organic and inorganic components of

ecosystems, encompassing abiotic and biotic elements.
 Carbon, essential for the structure of plant and animal tissues, exists in the
atmosphere primarily as carbon dioxide (CO2).
 Plants absorb this CO2 through their leaves and, using sunlight, combine it
with water drawn from the soil to synthesize carbon-rich carbohydrates
through photosynthesis.
 Herbivorous animals contribute by consuming plants, using the carbon for

energy and growth, and exhaling CO2 during respiration.
 Both plants and animals eventually return carbon to the soil through waste
and decomposition. This continuous flow of carbon among the atmosphere,
plants, animals, and soil is what completes the carbon cycle, balancing CO2
levels and sustaining life
Nitrogen cycle
 Nitrogen, comprising 78% of Earth's atmosphere, is a vital component for
living organisms, forming part of DNA, RNA, and proteins.
 The nitrogen cycle describes the transformation and movement of nitrogen
through the environment and within living organisms.
 Nitrogen Fixation: This process converts atmospheric nitrogen (N2) into
reactive compounds like ammonia (NH3) and nitrate (NO3-).
 Carried out by soil microorganisms such as Rhizobium in legume root
nodules, transforming N2 into ammonia, which plants can use.
 This is also a process in some free-living bacteria in soils and water bodies.
 Nitrification: This is the conversion of ammonia in soil to nitrite and then to
nitrate, which plants can easily use, facilitated by aerobic bacteria.

Assimilation: Plants absorb nitrates through their roots, incorporating them into
biological molecules. Animals then obtain nitrogen by consuming plants or plant-eating
organisms, transferring nitrogen throughout the food chain.
Ammonification: Decomposers like bacteria and fungi convert organic nitrogen from
waste and dead organisms back into inorganic ammonia, making it available again for
plant absorption.
Denitrification: Finally, nitrates in the soil are converted back to nitrogen gas (N2) by
bacteria, returning it to the atmosphere. This step can result in nitrogen loss from soils,
particularly in waterlogged or clay-rich fields.

Phosphorus cycle
 Phosphorus cycles through rocks, soil, water, and living organisms.

 It primarily takes the form of phosphate, which does not enter the atmosphere
but remains in organisms, water, or rock.
 Phosphate from weathered rock dissolves in water and is absorbed by plants,
then moves through the food chain as it is consumed by animals. Decomposers
return phosphorus to the soil or water from waste and dead organisms,
completing the cycle.
Sustainable Resource Management:
Over-mining of phosphorus for fertilizers can accelerate the cycle, causing
eutrophication and harming aquatic life. The conservation and efficient use of
natural resources, including phosphorus, are crucial to maintain land, water, and
biodiversity and ensure food security for future generations. Strategies include
reducing deforestation, promoting reforestation, and conserving biodiversity to
mitigate
05/17/2024
climate change and maintain ecosystem services.
Lecture note for General Biology (Biol. 1012)
8.6 Conservation of natural resources
8.6.1 Principles of conservation of natural resources
• 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.
• Intensification practice of intense 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
• The major strategies of natural resource management techniques

are in-situ and ex-situ.
8.7 Environmental pollution and public health
• Developmental activities such as construction, transportation and

manufacturing
• Deplete the natural resources
• Produce large amount of wastes that leads to pollution
• Untreated or improperly treated waste is a major cause of

pollution of rivers and environmental degradation causing ill
health and loss of crop productivity.
Pollution and pollutants
• Pollution - addition of undesirable material as a result of human

activities.
• The agents which cause pollution are called pollutants.

• Pollutants may be defined as
• Physical,
• Chemical or
• Biological substance unintentionally released into the
environment
• Which is directly or indirectly harmful to humans and other

living organisms.
Types of pollution
• Air pollution
• Noise pollution
• Water pollution
• Soil pollution
• Radiation pollution
Air pollution
• Air pollution may be defined as the presence of any solid,

liquid or gaseous substance in the atmosphere which 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.
1. Particulate pollutants
• Particulate matters suspended in air are dust and soot
• 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.
2. 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.
Prevention and control of air pollution
(i)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.
• The house designs should incorporate a well ventilated kitchen.
• Those species of trees such as baval (Acacia nilotica) which are

least smoky should be planted and used.
• Charcoal is a comparatively cleaner fuel.
• Segregation of waste, pre-treatment at source, sterilization of

rooms help in checking indoor air pollution
(ii) Prevention and control of industrial pollution
• Use of cleaner fuels such as liquefied natural gas (LNG) in power plants, fertilizer
plants etc.
• Employing environment friendly industrial processes so that emission of pollutants
and hazardous waste is minimized.
• Installing devices which reduce release of pollutants. Devices like filters,
electrostatic precipitators, inertial collectors, scrubbers, gravel bed filters or dry
scrubbers
iii. Control of vehicular pollution
• Setting emission standards for automobiles will reduce the

pollution.
• In cities like Delhi, motor vehicles need to obtain Pollution

under Control (PUC) certificate at regular intervals.
• Using diesel than petrol. To reduce emission of sulphur

dioxide, sulphur content in diesel has been reduced to 0.05%.
• To prevent emission of lead particles with the vehicular

emission do not use petrol that has been added lead to it.
Global Warming and Greenhouse Effect
• The long-term rise in the average temperature of the Earth's
climate system
• Carbon dioxide in the atmosphere is important because of the

greenhouse effect
• It traps some of the heat from the sun and keeps the surface of the Earth
warm enough for life.
• But the build-up of carbon dioxide gas and other green house
gasses (carbon dioxide, methane, nitrous oxide, and
chlorofluorocarbons) in the atmosphere acts like a blanket and
traps heat close to the surface of our Earth causing global
Noise pollution
• Noise by definition is -sound without value or -any noise that is

unwanted by the recipient
• Noise pollutants can be indoor or outdoor such as stone cutting

and crushing, loudspeakers, shouting by hawkers selling their
wares, movement of heavy transport vehicles, 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.
2. Water pollution
• Addition or presence of undesirable substances in water is
called water pollution.
• Can be caused by
• Industrial- Industrial effluents with toxic substances
• Agricultural-Agricultural runoff laden with excess fertilizers and
pesticides, or
• Domestic human activities - sewage water with human and animal
wastes.
• Rivers, lakes, seas, oceans, estuaries and ground water
sources may be polluted by
• Point-discharged from a specific location such as a drain pipe carrying
industrial effluents discharged directly into water body or
• Non-point sources- 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.
Ground water pollution
• Generally groundwater is a clean source of water for a lot of

people around the world for drinking, domestic, industrial and
agricultural uses.
• Ground water pollution is caused as a result of improper sewage

disposal, dumping of farm yard manures and agricultural
chemicals, industrial effluents
• Eutrophication - Eu‘ means well or healthy and trophy‘ stands
for nutrition.
• 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.
• Which 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 protozoans 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.
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
Primary treatment remove suspended particulate matter.
Secondary treatment removes organic solids, left out after primary treatment,
through their microbial decomposition.
• The tertiary treatment is meant to remove nutrients, 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
• 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.
3. Soil pollution
• 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 runoff 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.
Control of soil pollution
• Indiscriminate disposal of solid waste should be avoided.
• Stop the use of plastic bags and instead use bags of degradable materials like
paper and cloth.
• The organic matter from domestic, agricultural and other waste should be
segregated and subjected to vermicomposting which generates useful manure
as a by product.
• The industrial wastes prior to disposal should be properly treated for

removing hazardous materials (Sewage treatment).
• Biomedical waste should be separately collected and incinerated in proper

incinerators.
Radiation pollution: sources and hazards
• The increase in over the natural background radiation.
• There are many sources of radiation pollution such as nuclear wastes

from nuclear power plants, mining and processing of nuclear material etc.
• Radiation is a form of energy travelling through space.
• The radiations emanating from the decay of radioactive nuclides are a

major sources of radiation pollution.
• Radiations can be categorized into two groups namely

• the non-ionizing radiations and
• the ionizing radiations.
• 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:

• (a) Somatic damage (also called radiation sickness) damage to cells that
are not associated with reproduction - and
• (b) Genetic damage (damage to cells associated with reproduction).
Chapter Nine : Introduction to Botany and Zoology
9.1. Introduction to Botany
 Botany, a primary branch of biology, focuses on the scientific study of plant
life.
 It includes various subfields such as algology, bryology, pteridology, and many
others, each specializing in different aspects of plant research and study.
9.1.1 Algology or phycology: is the study of algae.

 Algae are simple, eukaryotic organisms that can perform photosynthesis.
 They vary greatly in size and form, ranging from single-celled organisms to
complex multicellular forms.
 are crucial for their ecological roles and have significant economic uses
ranging from biofuel production to use in pharmaceuticals.
 There are many types of algae, like blue-green algae, green algae, brown
algae,
05/17/2024 and red algae. Algae Lecture
have note lots ofBiology
for General practical
(Biol. 1012) uses, like being used in food,
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

9.1.2. Bryology and Pteridology
 Bryology studies mosses and liverworts
 Bryophyta is divided into three classes: Liverworts, Hornworts, and Mosses.
 Liverworts are named for their resemblance to the human liver and come in
various sizes and forms, with about 8500 species.
 Hornworts are small plants found in moist soils, with around 400 species and
unique chloroplast characteristics.
 Mosses, the largest group with about 12,000 species, are well-known for their
adaptability and green appearance.
 Pteridophytes: are categorized into four main groups: Psilophyta, Lycopsida,
Sphenopsida, and Pteropsida. Psilophyta have stem-like leaves lacking
vascular tissues, while Lycopsida, also known as club mosses, have true leaves
and roots.
 These plants play important roles in ecosystems and are studied for their
diversity and ecological functions.

9.1.3. Seed plants
 Seed plants, including gymnosperms and angiosperms, are the dominant plants
on Earth.
 They produce seeds, which are crucial for their reproduction and survival.
 Angiosperms, or flowering plants, are the most advanced group, ranging from
grasses to large trees, and are further divided into monocots and dicots.
 Seeds contain an embryo, food, and a protective coat, allowing them to survive
harsh conditions until they germinate.
 Seed plants also produce wood, a unique feature distinguishing them from non-
seed plants.
 They have a dominant sporophyte phase and megaphyllous leaves.
 Gymnosperms, like conifers, have naked seeds borne on cones, while
angiosperms have seeds enclosed within fruits.
 Angiosperms are the most abundant and diverse group, with advanced vascular
tissues and reproductive structures in flowers

9.2. Introduction to Zoology
9.2.1. Invertebrates
General Characteristics of Invertebrates
 Animals lacking backbones.
 They are the most abundant creatures on Earth
 They are multicellular, heterotrophic, and often mobile, though some lower species are
stationary filter feeders.
 Vary greatly in size, structure, and adaptations for survival.
 They reproduce in various ways and can be classified as acoelomates,
pseudocoelomates, or coelomates.
 They exhibit radial symmetry, bilateral symmetry, or asymmetry.
 Invertebrates range in organizational complexity, some sharing common ancestry while
others are distantly related. Certain invertebrates are more closely related to
vertebrates than to other invertebrate groups.

A. Phylum Porifera (Sponges):
 Pore-bearing animals due to their perforated body walls.
 They are the most primitive multicellular animals lacking organs.
 are mostly marine and aquatic, varying in size and exhibiting radial symmetry or
asymmetry.
 Their bodies are supported by spicules made of calcium, silica, or sponge fibers.
 They are filter-feeders, with pores and a central cavity for gas exchange.
 Reproduction occurs sexually or asexually through budding or gemmules.
 Examples include classes Calcarea, Hexactinellida, and Demospongiae.
B. Phylum Radiata:
 have primary radial or biradial symmetry.
 They include phyla Cnidaria and Ctenophora, both lacking advanced tissue
organization.
 These animals have gastrovascular cavities for extracellular digestion and tentacles
for food capture.
 Radiates possess simple nerve cells and sense organs like statocysts and ocelli.
 They exhibit various forms like polyps and medusas, allowing for diverse ecological
roles.
05/17/2024
Examples include classes Hydrozoa,
Lecture note forScyphozoa,
General Biology (Biol. Cubozoa,
1012) and Anthozoa. 279
C. Acoelomate Bilateria:
 Acoelomates lack a coelom and have bilateral symmetry.
 They have defined tissues and organs with a nervous system concentrated
in the anterior end.
 Examples include flatworms (Platyhelminthes), ribbon worms (Nemertea),
and jaw worms (Gnathostomulida).
D. Coelomate Animals: Protostomes vs. Deuterostomes:
 Protostomes have determinate development, while deuterostomes have
indeterminate development.
 In protostomes, the blastopore becomes the mouth, whereas in
deuterostomes, it becomes the anus.
 Both groups develop a coelom, but in deuterostomes, it originates from an
evagination of the archenteron.

E. Phylum Nematoda (Roundworms):
 Are a large group of animals found worldwide.
 They have a simple body structure with bilateral symmetry and a complete digestive
tract.
 They lack circular muscles(cilia and flame cells) in their body wall and have longitudinal
muscles only.
 Nematodes can be free-living or parasitic, living in various environments like water, soil,
and inside other organisms.
 Some parasitic nematodes infect humans and animals, causing diseases like hookworm
and filariasis.
 Examples include hookworms, filarial worms, and giant intestinal roundworms.

F. Phylum Arthropoda (Jointed-Legged Animals):
 are the most successful animals, representing about 80% of the animal kingdom.
 Have an external skeleton made of chitin, providing protection and support.
 Their bodies are divided into distinct segments, with each segment often bearing a pair
of jointed appendages.
 have specialized limbs or appendages that are jointed, allowing for diverse movements
and functions.
 also exhibit bilateral symmetry, meaning their bodies can be divided into two mirror-
image halves.
 They have a circulatory system where blood or hemolymph circulates freely within the
body cavity, rather than within vessels.
 Arthropods possess a well-developed nervous system, including a brain and paired
nerve cords.
 They respire through various structures such as gills, tracheae, or book lungs,
depending on the specific group of arthropods.
 Arthropods are incredibly diverse and inhabit a wide range of environments, including
terrestrial, freshwater, and marine habitats.
 They play crucial roles in ecosystems as pollinators, decomposers, predators, and prey,
contributing to the balance of various ecosystems.

Services Provided by Invertebrates:
 Invertebrates offer ecosystem services like pollination, seed dispersal, natural
pest control, decomposition, and soil formation.
 They are used as food sources, fishing bait, jewelry materials, and medicinal
resources.
 Invertebrates yield pharmacologically active compounds for various medical
treatments, showcasing their importance in different industries and
ecosystems.

9.2.1 Characteristics of vertebrates
Vertebrates share several key characteristics:

i) Head with brain and skull
ii) Vertebral column, which replaces the notochord during development,
encasing the brain in protective bone or cartilage.
iii) Neural crest ectoderm, a unique group of stem cells involved in forming
various structures.
iv) Highly developed internal organs, including specialized kidney and excretory
systems, endocrine glands producing multiple hormones, and a specialized
heart with a closed circulatory system.
v) Endoskeleton made of cartilage and/or bone, providing strength and
flexibility.
Vertebrates are classified into two superclasses and nine classes, totaling
approximately 53,000 living species.
 Superclass Agnatha (jawless fish): Classes Myxini (hagfish) and
Pteraspidomorphi (lampreys).
 Superclass Gnathostomata (jawed vertebrates):
 Classes Chondrichthyes (cartilaginous fish),
 Sarcopterygii (fleshy-finned fish), Actinopterygii (ray-finned fish), Amphibia
(frogs, salamanders, caecilians),
 Reptilia (turtles, tuatara, lizards, snakes, crocodiles),
 Aves (birds), and Mammalia (mammals).
 Agnatha, or jawless fish, include
 the hagfish (Myxini) and lampreys (Pteraspidomorphi).
 Hagfishes lack vertebrae and regulate body salts poorly, while lampreys
exhibit both parasitic and non-feeding adult stages.
 Gnathostomata, or jawed vertebrates, include Chondrichthyes (cartilaginous
fish) and Osteichthyes (bonyLecture
05/17/2024
fish). Cartilaginous fish evolved jaws and paired
note for General Biology (Biol. 1012) 285
 Amphibians:
 meaning "both life" (Start their lives in water and later live on land)
 They were the first vertebrates to adapt to land, paving the way for reptiles,
mammals, and birds.
 There are over 5,000 amphibian species, mainly grouped as
 frogs and toads,
 salamanders, or caecilians.
 Frogs have smooth skin and long legs, while toads have warty
skin and short legs.
 They have moist, hairless skin and typically spend part of their lives in water
and part on land.
 amphibians evolved features like legs for mobility, skin and lungs for
breathing, and a better blood system for oxygen delivery.
There are three orders of amphibians:
1) Salamanders and Newts: They have long bodies and tails, and they live near
water, eating insects and worms.
2) Frogs and Toads : These tail-less amphibians have long hind legs for jumping
and swimming. They live near water and their young, called tadpoles,
develop into adults.
3) Caecilians : These legless creatures resemble worms and live underground in
moist soil, feeding on insects
05/17/2024 and
Lecture note forworms.
General Biology (Biol. 1012) 286
Reptiles: belonging to Class Reptilia,
 Encompass around 6,550 species globally and
 Inhabit diverse environments like forests, deserts, and oceans.
 Unlike mammals, they're ectothermic, meaning they rely on external heat
sources to regulate their body temperature.
 Their dry, scaly skin helps in preventing water loss, and they lay amniotic eggs
with a leathery shell, allowing them to reproduce away from water bodies.
Reptiles are classified into three main groups:
Turtles and Tortoises: have protective shells enclosing their bodies.
Lizards and Snakes: Snakes evolved from legged lizards, some still retaining
remnants of leg bones.
Crocodiles and Alligators: These reptiles exhibit bird-like traits, including nest-
building and parental care, suggesting a close evolutionary relationship with birds
and ancient
05/17/2024
dinosaurs. Lecture note for General Biology (Biol. 1012) 287
Birds: belonging to Class Aves
 Feathers: Made of keratin, the same material as reptile scales, feathers provide
insulation and form aerodynamic surfaces essential for flight.
 Bird bones, including the fused collarbone (furcula or "wishbone") and the large
sternum (keel), are adapted for flight. Their bones are pneumatic, filled with air
spaces to reduce weight and aid in oxygen storage for respiration.
 Birds are warm-blooded, capable of internally generating heat to maintain a
constant body temperature, unlike reptiles.
 Birds are the most diverse group of terrestrial vertebrates, with various species
belonging to different Orders, such as
 Eagles,
 Hummingbirds,
 Owls, penguins, pigeons, parrots, songbirds, and
05/17/2024
woodpeckers.
Lecture note for General Biology (Biol. 1012) 288
Mammals
 belonging to Class Mammalia,
 emerged during the Mesozoic era but became dominant only after the
dinosaurs disappeared.
 They have distinct features:
1) Hair: provides insulation and helps mammals stay warm, allowing them to be
active in various environments, even in cold climates.
2) Mammary Glands: These glands produce milk
3) Placental mammals have a placenta that connects the fetus to the mother,
allowing for nutrient exchange and long-term development inside the mother's
womb.
4) single jaw bone on each side, distinguishing them from other vertebrates.
5) Their heart has four chambers, with the main artery curving to the left, unlike
birds and other vertebrates.
6) Muscular Diaphragm: This separates the chest cavity from the abdominal
cavity, aiding in breathing

Mammals are classified into three subclasses:
Eutheria (Placentals): have a placenta for nourishing their developing offspring
inside the mother's womb before birth.
They represent the majority of mammal species, with varied gestation periods,
like two years in whales, 21 days in mice, and nine months in humans.
Metatheria (Marsupials): Marsupials, like kangaroos and koalas, carry their
developing young in an external pouch. They are less common and are
predominantly found in Australia.
Monotremes: This group, exemplified by the platypus, lays eggs, retaining a
primitive characteristic of their ancestors.

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General Biology (Biol.

05/17/2024 Lecture note for General Biology (Biol. 1012)

05/17/2024 Lecture note for General Biology (Biol. 1012)

05/17/2024 Lecture note for General Biology (Biol. 1012)

1. Theory of Special Creation

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•Sucrose is a non-reducing sugar.

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Structure of Nucleic Acids:

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are inorganic compounds used by the body as building material,

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 An organelle is a specialized subunit within a cell that has a

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o It contains dark particles called ribosomes.

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o Mitochondria are unusual organelles in two ways:

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05/17/2024 Lecture noteMembrane

5. Enzymatic proteins :carry out specific metabolic reactions.

6. Junction proteins :join animal cells, so tissues can function.

• Some cell can be seen without using magnification instruments as

o Charged particle sodium/potassium ions and polar molecules

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There are two main types:

 Metabolism is the sum of chemical reactions that takes place

within each cell of a living organism

process known as "induced fit,".

Lecture note for General Biology (Biol.