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Topic 3: Cell Structure, Reproduction and Development

3A: Cell Structure

2. Eukaryotic Cells 1: Common Cellular Structures
Eukaryotic cells can be found in organisms such as animals, plants and fungi.
The cytoplasm and the nucleus are known together as protoplasm.
They cytoplasm contains components that perform cell functions while the nucleus contains
the info needed to produce the chemical substances upon which the cell is made of.
The ultrastructure of a cell are the structures that that can only be observed in detail using the
electron microscope.

Membranes are important as an outer boundary to the cell and the intercellular (internal)
membranes, they also control substance movement into and out of the cell, membranes inside
the cell also localize enzymes in reaction pathways and keep biological molecules separate.
The Nucleus:
The nucleus is the largest organelle inside the cell, it is spherical in shape and is surrounded by
a double nuclear membrane with holes or pores.
Chemical substances can pass in and out of the nucleus through the pores so the nucleus can
control events in the cytoplasm that allow substances to go into and outside of the cell.
The nuclear envelope includes nucleic acids and proteins. The nucleic acids are DNA and
When the cells are not dividing, the DNA is bonded to the protein to form chromatin.
Also, in the nucleus contains nucleolus which are extra-dense areas of almost pure DNA and
protein. The nucleolus is involved in the production of ribosomes.

They are located inside the cytoplasm and are the powerhouses of the cell, they oxidize
simple molecules to form ATP in a series of complicated biochemical reactions which is then
used to provide energy to the organism.
Mitochondria have an inner and an outer membrane and they have their own genetic material,
so that when a cell divides, the mitochondria replicate themselves controlled by the nucleus.
Mitochondrial DNA is part of the whole genome of the organism.
The inner membrane is folded to form cristae, which give a very large surface area,
surrounded by a fluid matrix which helps in respiration.
The fact that mitochondria (and chloroplasts) have their own DNA leads scientists to think
that these organelles originated as symbiotic eubacteria living inside early eukaryotic cells.
During millions of years, they have become an integral part of the eukaryotic cell.
The Centrioles:
They are located near the nucleus and consist of a bundle of nine sets of tubules, they are
involved in cell division, when the cell divides, the centrioles pull apart to produce a spindle
of microtubules that are involved in the movement of the chromosomes.

80S and 70S Ribosomes:

Ribosomes are made of rRNA and protein, the contain a larger subunit and a smaller subunit.
The main type of ribosomes in eukaryotic cells are 80S ribosomes.
The S stands for Svedberg, the unit used to measure how quickly particles fall to the bottom
of the tube (settle) in a centrifuge.
The rate of settling depends on the size and shape of the particle, when 80S ribosomes are
broken into their two units, they are made up of a 40S small subunit and a 60S large subunit.
The ratio of RNA:Protein in 80S ribosomes is 1:1.
70S ribosomes are also contained in eukaryotic cells in the mitochondria and in the
chloroplasts of plant cells, though they are mainly found in prokaryotic cells.
They consist of a small 30S subunit and a larger 50S subunit and the ratio of RNA:protein in
70S ribosomes is 2:1.
The 70S ribosomes are reproduced in the mitochondria and chloroplasts independently when
a cell divides. This provides good evidence for the endosymbiotic theory.
Lysosomes destroy and break down torn out organelles in the body, they are spherical and dark
and are inside the cytoplasm, they contain a powerful mix of digestive enzymes.
They fuse with each other and with a membrane-bound vacuole which contains either food or
an obsolete organelle and their enzymes break down the contents into molecules that can be
reused again.
Lysosomes might fuse with the outer cell membrane to release enzymes outside the cell as
extracellular enzymes, perhaps to destroy bacteria or in digestion.
Lysosomes will self-destruct if an entire cell is too old, needs to be removed during
development, has a mutation or is under stress, its lysosomes will rupture releasing their
enzymes which then destroy the entire contents of the cell in what is known as programmed
cell death (apoptosis).


a jelly-like liquid that makes up the bulk of

the cell and contains the organelles

an organelle containing the nucleic acids

DNA (the genetic material) and RNA, as
well as protein, surrounded by a double
nuclear membrane with pores

Protoplasm the cytoplasm and nucleus combined

the detailed organization of the cell, only

visible using the electron microscope

Intracellular inside the cell

the granular combination of DNA bonded to

Chromatin protein found in the nucleus when the cell is
not actively dividing

an extra-dense region of almost pure DNA

and protein found in the nucleus; it is
involved in the production of ribosomes and
control of growth and division
rod- like structures with inner and outer
Mitochondria membranes that are the site of aerobic

the infoldings of the inner membrane of the

Cristae mitochondria which provide a large surface
area for the reactions of aerobic respiration

Eubacteria true bacteria (prokaryotic organisms)

bundles of tubules found near the nucleus

and involved in cell division by the
Centrioles production of a spindle of microtubules that
move the chromosomes to the ends of the

a set of overlapping protein microtubules

Spindle running the length of the cell, formed as the
centrioles pull apart in mitosis and meiosis

the main type of ribosome found in

eukaryotic cells, consisting of ribosomal
80S ribosomes RNA and protein, made up of a 60S and
40S subunit; they are the site of protein

the ribosomes found in the mitochondria

70S ribosomes and chloroplasts of eukaryotic cells and in
prokaryotic organisms

a theory that suggests mitochondria and

chloroplasts originated as independent
Endosymbiotic theory prokaryotic organisms that began living
symbiotically inside other cells as

organelles full of digestive enzymes used to

Lysosomes break down worn-out cells or organelles or
digest food in simple organisms

the breakdown of worn-out, damaged or

Apoptosis (Programmed Cell Death)
diseased cells by the lysosomes
3. Eukaryotic Cells 2: Protein Transport

Rough Endoplasmic Reticulum (RER) and Smooth Endoplasmic Reticulum

A system of membranes trapping a fluid-filled space and the surfaces are covered with
ribosomes, it folds and processes proteins coming from the ribosome.
The RER has a large surface area for the synthesis of all these proteins. It then stores and
transports the proteins within the cell after they have been made.
Smooth Endoplasmic Reticulum is the same as the RER but with no ribosomes, they synthesize
and process lipids and steroids, they are found a lot in the testes and the liver.

The Golgi Apparatus:

A group of fluid-filled, membrane-bound, flattened sacs. Vesicles are often seen at the edges
of the sacs. It processes and packages new lipids and proteins. It also makes lysosomes.
It is made up of stacks of parallel, flattened membrane pockets formed by vesicles from the
endoplasmic reticulum fusing together.
Protein Production:
1. Proteins are made at the ribosomes.
2. The ribosomes on the rough endoplasmic reticulum (ER) make proteins that are excreted
or attached to the cell membrane. The free ribosomes in the cytoplasm make proteins
that stay in the cytoplasm.
3. New proteins produced at the rough ER are folded and processed (e.g. sugar chains are
added) in the rough ER.
4. Then they’re transported from the ER to the Golgi apparatus in vesicles.
5. At the Golgi apparatus, the proteins may undergo further processing (e.g. sugar chains
are trimmed or more are added).
6. The proteins enter more vesicles to be transported around the cell. e.g. extracellular
enzymes (like digestive enzymes) move to the cell surface and are secreted.
4. Prokaryotic Cells

Prokaryotic cells can be found in bacteria, cyanobacteria and archaebacteria.

Bacterial Cell Walls:
All bacteria cells have walls, the content of the cell is usually hypertonic to the medium so
water moves inside the cell by osmosis and cells prevent the cell from bursting. It also
maintains the shape of bacteria, and gives support and protection to the contents of the cell.
The walls have a layer of peptidoglycan that consists of many parallel polysaccharide chains
with short peptide cross-linkages producing an enormous molecule with a net-like structure.
In some bacteria, a capsule can be found (slime layer is some cases) around the cell walls,
they are produced from starch, gelatin, protein or glycolipid, and protects the bacterium from
phagocytosis by white blood cells, they also cover the cell markers on the cell membrane that
identify the cell so the capsule can make the bacteria be pathogenic yet not be detected
easily by the autoimmune system, e.g. the bacteria that cause pneumonia, meningitis,
tuberculosis (TB) and septicemia. However; many capsulated bacteria do not cause disease.
Which suggest that capsules evolved to help the bacteria survive very dry conditions.
Pili and Flagella:
Pili (singular pilus) are hundreds of thread-like protein projections on the surface of some
bacteria, they are used for attachment to a host cell and for sexual reproduction, however,
they make the bacteria more vulnerable to virus infections, as a bacteriophage can use pili as
an entry point to the cell.
Some bacteria have flagella (singular flagellum) which they use to move themselves, they are
made of a many-stranded helix of the protein flagellin, they move the bacterium by rapid
Cell Surface Membrane:
The cell surface membrane in prokaryotes is similar in both structure and function to the
membranes of eukaryotic cells, however, bacteria have no mitochondria, the cell membrane
is the site of some of the respiratory enzymes.
Prokaryotic cells have single circular strands of genetic material, which is not contained in a
membrane bound nucleus, a key difference between eukaryotic and prokaryotic cells, also the
DNA is folded and coiled in an area called a nucleoid.
Plasmids are much smaller circles of DNA, found is come bacteria, that code for a particular
aspect of the bacterial phenotype in addition to the genetic information in the nucleoid.
70S Ribosomes:
Prokaryotic cells have 70S ribosomes that code for protein, they consist of a small 30S
subunit and a larger 50S subunit and the ratio of RNA:Protein in 70S ribosomes is 2:1.

Major Differences Between Eukaryotic and Prokaryotic Cells:

Eukaryotic Cells Prokaryotic Cells

found in bacteria, cyanobacteria and

found in animals, plants and fungi.

Membrane-bound organelles. No Membrane-bound organelles.

70S and 80S ribosomes. 70S ribosomes.

DNA enclosed in an envelope. DNA not enclosed in an envelope.

Circular DNA.
Gram Staining & Bacterial Cell Walls:
Gram-positive Bacteria:
The cell walls of Gram-positive bacteria have a thick layer of
peptidoglycan containing chemical substances such as
teichoic acid within the net-like structure.
The crystal violet/iodine complex in the Gram stain is
trapped in the thick peptidoglycan layer and resists
decoloring when the bacteria are dehydrated using alcohol.
As a result, the bacteria do not pick up the red safranin
counterstain and appear purple/blue when viewed in a light

Gram-negative Bacteria:
The cell walls of Gram-negative bacteria have a thin layer of
peptidoglycan with no teichoic acid between the two layers
of membranes. The outer membrane is made up of
This layer dissolves when the bacteria are dehydrated in
ethanol. This exposes the thin peptidoglycan layer and the
crystal violet/iodine complex is washed out. The
peptidoglycan then takes up the red safranin counterstain.
The cells appear red when viewed in a light microscope

A large, net- like molecule found in all bacterial cell walls

Peptidoglycan made up of many parallel polysaccharide chains with short
peptide cross- linkages.

A layer formed from starch, gelatin, protein or glycolipid,

found around the outside of some bacteria.

Thread-like protein projections found on the surface of

some bacteria.

Bacteriophage Virus that attacks bacteria.

Many-stranded helixes of the contractile protein flagellin

Flagella found on some bacteria; they move the bacteria by rapid

Mesosomes Infoldings of the cell membrane of bacteria.

The area in a bacterium containing the single circular loop

of coiled DNA.

Small, circular pieces of DNA that code for specific

aspects of the bacterial phenotype.

A staining technique used to distinguish types of bacteria

Gram Staining
by their cell wall.

Bacteria that contain teichoic acid in their cell walls and

Gram-positive Bacteria
stain purple/blue with Gram staining.

A chemical substance found in the cell walls of Gram-

Teichoic Acid
positive bacteria.

Bacteria that have no teichoic acid in their cell walls; they

Gram-negative Bacteria
stain red with Gram staining.

Cocci Spherical bacteria. Bacilli Rod-shaped bacteria.

Bacteria with a
Spirilla twisted or spiral Vibrio’s

Obligate Aerobes Organisms that need oxygen for respiration.

Organisms that use oxygen if it is available, but can respire
Facultative Anaerobes
and survive without it.

Organisms that can only respire in the absence of oxygen

Obligate Anaerobes
and are killed by oxygen.
5. The organization of cells
The human body starts with cells and ends with organ systems, starting from the smallest
thing that you can’t see by the naked eye to large organ systems that carry out main body
functions such as respiration. Below is the organization of cells in the human body:-

Cells: are the building blocks of life, they make up every single organ
and part of the body we have, are present everywhere, and cannot be
seen by the human eye

Tissues: are groups of specialized cells, which carry out particular

functions in the body

Organ: are structures made up of several different types of tissues to

carry out particular functions in the body

Organ system: are groups of organs working together to carry out

particular functions in the body
IAS Biology Unit 2 – Topic 1

3B – Mitosis, Meiosis, and Reproduction:

1. The cell cycle:
The process of production is split into two, asexual reproduction, which produces genetically
identical offspring from a single parent by the process of mitosis, and sexual production, which
produces offspring that are genetically different from their parents through the fusion of two
sex cells called gametes, which are formed by the process of meiosis. This lesson will be
focusing on mitosis.
Before splitting into two cells, a cell has to go through the cell cycle, which includes 2 different
large phases, interphase and mitotic phase, which are split up into smaller phases. Interphase
comes first, and is responsible for preparing the cell before it goes into the phase of mitosis,
including no cell division whatsoever, while mitosis is the phase which includes the cell division
process. First, we’ll talk about interphase, and it includes 3 different phases, which are:-
1. G1 phase: This phase comes between the end of the previous cell cycle and the
beginning of the new one. During this phase, the cell will take up material to make
proteins and other types of needed materials, to allow it to grow and increase in size
2. S phase: The stage of DNA Replication, where the chromatids become double-stranded
or sister chromatids, to become ready for the next mitosis process.
3. G2 phase: The last phase of interphase is similar to the G1 phase. During this phase,
the cell will make more organelles and will synthesize the enzymes needed for the
process of mitosis

Between each one phase and the other are checkpoints

containing a cyclin-CDK (cyclin dependent kinase) complex,
which make sure that everything is running smoothly and that
the cell can move on to the next phase. If it cannot, the whole
process may be terminated or that part of the process before
the checkpoint may be repeated.

At the end of interphase and around the beginning of the

mitotic phase, the chromosomes will start to condense and
appear colored. This happens because the DNA starts to coil
around a protein called histone, where each coil is called a
nucleosome. These identical chromosomes will be divided
during the mitotic phase which is looked at in the next lesson.
After the DNA has coiled around the histone, the
chromosomes will be condensed and you’ll be able to easily see them by an electron

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

2. Mitosis:
The main phase of cell division, and actually the shortest, is the phase of Mitosis. It is a
continuous process which is split up into 4 different phases, prophase, metaphase, anaphase,
and telophase (PMAT):-
1. Prophase: during this phase, the chromosomes can are condensed and can be clearly
seen. The nucleolus completely breaks down and the centrioles will start to form the
2. Metaphase: now, the centrioles would’ve migrated to the opposite poles of the cells and
the nuclear membrane has broken down and the sister chromatids have lined up on the
metaphase plate or the equator of the cells. The spindles will bind to the centromere of
the sister chromatids which holds them together
3. Anaphase: the spindles will now contract, separating the sister chromatids from each
other and the two sets of chromosomes will now be on the opposite poles of the cell
4. Telophase and Cytokinesis: During telophase, the nuclear envelopes reform, the
chromosomes de-condense and the centrioles are reformed. During cytokinesis
however, a cleavage furrow forms in the middle of the cell due fibers tightening on the
center of the cell. These fibers keep tightening until the cell splits into two. In plant
cells however, a cell wall forms in the middle of the cell and then the cell splits up into

Remember that the spindle is what moves the chromosomes. It must form before the
chromosomes start to move.

It should be noted that mitosis doesn’t produce any variation at all, because the cells are
genetically identical. This is good because the organism can reproduce on its own and at a very
rapid pace. However, because it doesn’t produce variation, one change in the environment may
lead to the whole species dying as they have not grown to adapt to it.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Observing mitosis under the microscope

Observing different stages of mitosis under the microscope

1. Using a bottle fill a bottle with 1 mol dm-3 of HCL and place this bottle in a 40°C
water bath for 15 minutes
2. Place a garlic clove into the bottle and make sure that the roots are submerged in
acid, then wait for 5 minutes. Remove the roots, and rinse them with water.
3. Using scissors, carefully cut off the roots (3-5mm long) making sure they fall onto a
watch glass
4. Add one drop of 1% acetic orcein to the watch glass, making sure that the root tips
are covered, then wait for 2 minutes
5. Remove the excess stain and transfer the root tips to a microscopic slide and spread
them with a mounted needle
6. Add one more drop of acetic orcein then cover the slides with cover slips, and wrap
them with a paper towel several times, then press gently with your thumb onto the
cover slip to squash and spread the root tips out.
7. Transfer the slide on the stage of the microscope, then observe and count the number
of cells undergoing each mitotic phase, and compare them.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

3. Sexual Reproduction and Meiosis:

Asexual reproduction is not used solely in a lot of organisms, it produces genetically identical
offspring, so very limited genetic variation but spontaneous mutations occur, most organisms
have a system of sexual reproduction to achieve genetic variation in order to survive as a
Sexual reproduction produces a genetically different offspring resulting form the fusion of two
gametes, and it involves sexual organs, it also produces a significant amount of genetic
variation which aids in survival in a changing environment.

Chromosomes are located in the cytoplasm, the occur in pairs.
A cell containing two full sets of chromosomes is called diploid, and if the cell contains only
one full set of chromosomes, it’s called haploid.
If two diploid cells combined to form a new individual in sexual reproduction, the offspring
would have four sets of chromosomes to avoid this, haploid nuclei are formed with one set of
chromosomes within the specialized cells called gametes.
Sexual reproduction occurs when two haploid nuclei fuse to form a new diploid cell called a
zygote in a process called fertilization.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Formation of Gametes:
Gametes are formed in the special sex organs, often called gonads.
In plants the female gametes called ovules are produced in the ovaries, and the male gametes
are produced in the anthers, the gametes are contained in a spore in what is known as pollen.
In animals, the male gonads are the testes, they produce gametes known as spermatozoa,
known commonly as sperm, the female gonads are the ova, male gametes are much smaller
than female ones, but they are produced in higher quantities than female gametes.

In order for cells to divide and be halved to form gametes, a type of nuclear division known as
meiosis occurs, it occurs only in sex organs, in animals, the gametes are directly formed from
meiosis, however, in plants, meiosis forms special male cells called microspores and female
cells called megaspores, which then develop into gametes. Meiosis provides the variation
needed for the evolution of species.
Like mitosis, DNA is replicated in interphase, then once the cell has all the material it needs, it
can enter meiosis.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Before meiosis starts, the chromosomes replicate to form chromatids joined by a centromere
as in mitosis.
During prophase 1 of meiosis the two chromosomes (homologous pairs) stay together,
crossing over (recombination) will introduce genetic variation as the chromatids are broken
and then combine again randomly. Much like mitosis, the nuclear membrane and nucleolus
break down and the centrioles migrate to the poles to form the spindle. The centromeres do
not split in the first division of meiosis, so pairs of chromatids move to the opposite ends of
the cell.
Then after that the cells go into a second division without further replication of any
chromosomes, and much like mitosis, the centromeres will divide and chromatids will move
to the opposite poles of the cell. And finally, the nuclear membranes re-form as the
chromosomes decondense and become invisible.
Cytokinesis will produce 4 haploid daughter cells, each with half the chromosome number of
the original parent cell. These daughter cells later develop into gametes.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

The Importance of Meiosis:

Meiosis produces haploid gametes, which prevents the
following generations from having progressively more
genetic material, it’s also the main driving force behind
genetic variation via the following ways:
1. Crossing Over: occurs in prophase one, where
large multi-enzyme complexes mix and match
bits of paternal and maternal chromatids
together at the chiasmata. This is important in
that the exchange of genetic material leads to
added genetic variation and errors in the process
will lead to mutation which further introduces
combinations of variation.
2. Independent Assortment (Random Assortment):
occurs at metaphase one in the process of
meiosis, when the chromatids line up on the
metaphase plate, where the maternal and
paternal chromosomes are distributed into the
gametes completely at random. There are more
than eight million possible genetic combinations
within the sperm or the egg.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1


Diploid (2n) A cell with a nucleus containing two full sets of chromosomes.

Haploid (n) A cell with a nucleus containing one complete set of chromosomes.

Zygote The cell formed when two haploid gametes fuse at fertilization.

The fusing of the haploid nuclei from two gametes to form a diploid
zygote in sexual reproduction.

Polyploidy A cell or an organism with more than two sets of chromosomes.

Gonads The sex organs in animals.

The female sex organs in both animals and plants; they produce the
female gametes called ovules in plants and ova in animals.

Male sex organs in plants that produce the male gametes contained in
the pollen.

Ovules The haploid female gametes in plants.

Pollen The spore which contains the haploid male gametes of plants.

The male sex organs in animals that produce the male gametes –

Spermatozoa The haploid male gametes in animals.


Ova The haploid female gametes in animals (singular= ovum).

The result of meiosis in plants that develop into the spore (pollen)
containing the male gametes.

The result of meiosis in plants that develop into the female gametes,

Homologous Matching pairs of chromosomes in an individual which both carry the

pairs same genes, although they may have different alleles.

The process by which large multienzyme complexes cut and re-join

Crossing over
parts of the maternal and paternal chromatids at the end of prophase I,
introducing genetic variation.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Chiasmata The points where the chromatids break during recombination.

Mutation A permanent change in the DNA of an organism.

Independent The process by which the chromosomes derived from the male and
assortment female parent are distributed into the gametes at random.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

4. Gametes: Structure & Function

The process of gametogenesis is responsible for making gametes and meiosis is part of the
process, as well as mitosis. Now, we will look more in-depth into the shape of gametes and
how they are adapted to their functions.
From puberty onwards, the male and female gametes are produced by the process of
gametogenesis. However, in females, the mitotic divisions occur since birth to form diploid
oocytes which remain inactive until priority.

The male animal gamete: Spermatozoa

Made in the testes, the male gametes are responsible for carrying the genetic information in
their nucleus and delivering it to the female gamete by penetrating its jelly structure (zona
pellucida) using the enzymes in the acrosome. To do this, the spermatozoa must stay suspended
in the semen so that they can be transported towards the female gamete.
1. Acrosome: is a membrane bound storage site, which contains digestive enzymes used
to penetrate through the zone pellucida to allow the sperm to fuse with the female
2. Nucleus: contains the genetic material in the form of condensed haploid chromosomes
3. Mitochondria: these are packed into the middle piece to supply the sperm’s tail with
ATP so that it can keep lashing to move the sperm.
4. Microtubules: in the tail, these microtubules produce whip-like movements to keep the
sperm in the semen suspension and help it swim towards the ovum
5. Tail: a flagellum that propels the sperm to allow it to move in the liquid environment.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

The female animal gamete: Ova

Made in the ovary, the ova do not move on their own and only move slowly by peristalsis, so
they wait for the sperm to approach them in the fallopian tube. They have a zona pellucida,
which is a protective jelly that surrounds them. The ova usually contain food, in order to help
the embryo develop (after the process of fertilization).
1. Zona Pellucida: is a protective “jelly-like” layer that surrounds the oocyte
2. Cytoplasm: contains a food reserve in order to feed the developing embryo
3. Cell surface membrane: the cell membrane surrounds the genetic material and food
4. Follicle cells: these cells are important in fertilization (next lesson)

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

The male plant gamete: Pollen

Made in the anthers, which are the equivalent of the testes in the plants, pollen or microgametes
has two nuclei, the pollen tube nucleus and the generative nucleus.
1. Pollen tube nucleus: is responsible for making a pollen tube which penetrates through
the stigma, style, and ovary.
2. Generative nucleus: splits into two and goes down the pollen tube to fuse with the
female gametes.
3. Thick resistant wall: a protective layer surrounding the cell surface membrane

The female plant gamete: Ovule

Produced by the ovary in the plant (same as in animals), ovules or mega gametes are the female
plant gametes, and are attached to the wall of the ovary by a special tissue called the placenta

1. Female gamete: the male gamete (pollen) will fuse with it to produce an embryo
2. Two polar nuclei: the other generative nucleus fuses with the synergids to produce an

Make sure you use correct biological terminology particularly when there are words that have
similar sounds but very different meanings such as ovule and ovary

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Gametogenesis The formation of the gametes by meiosis in the sex organs.

A cell in an ovary which may form an ovum if it undergoes meiotic


The region at the head of the sperm that contains enzymes to break
down the protective layers around the ovum.

Zona Pellucida A layer of protective jelly around the unfertilized ovum.

The diploid generation in plants that produces spores by meiosis.

Gametophyte The haploid generation in plants that gives rise to the gametes by
Generation mitosis.

Sporophyte The diploid main body of the plant.

Microgametes The male gametes produced in plants, the pollen grains.

The male nucleus that will control the production of the pollen tube in
Tube Nucleus

The male nucleus that will fuse with the female nucleus.

A tube that grows out of a pollen grain down the style, into the ovary
Pollen Tube and through the micropyle of the ovule to carry the generative nucleus
(which divides to form two male nuclei) to the ovule.

The pad of special tissue that attaches the plant ovule to the ovary
Placenta (Plant)

Mega-gamete The female gamete, the egg cell, in plants.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

5. Fertilization in mammals and plants

With asexual reproduction, you’re making sure that the same genetic material is inherited along
the generations. However, animals have two ways of sexually reproducing offspring with
different genetic material through fertilization:
1. External fertilization: this type of fertilization occurs outside the body, and is usually a
matter of chance. The male and female release their gametes and then it is a matter of
chance whether they fuse to form an embryo. This usually happens in aquatic
environments as the spermatozoa is prone to dying, however, it is not an efficient way
of fertilization on land
2. Internal fertilization: the more common type of fertilization which usually happens inside
the female’s body. In some species, the male releases his spermatozoa and then the
female transfers it to her body. However, in more advanced species such as humans,
the spermatozoa is transferred to the female in the process of mating, which greatly
increases the chances of fertilization as the gametes are kept in a moist environment
and are as close as they can be.

Fertilization in humans
As in any other species, female and male gametes need to meet and fuse together to produce
an embryo, and this happens through the following steps:-
1. Ovulation and beginning: the sperm will only survive a day or two in the female
reproductive system while the ova survive only 8 hours after ovulation. When ovulation
occurs, the ova are still in Meiosis I, and are about to finish, which means they have
not fully matured. A sperm’s head touches the outside of the ovum and the acrosome
reaction begins and the acrosomes in the sperms burst to release digestive enzymes
which digest the follicle cells and the zona pellucida, and many sperms are needed to
penetrate through the zona pellucida.
2. Spermatozoa entering the ovum: eventually, one sperm will make its way through the
zona pellucida which forces the ovum to start Meiosis II to fully mature for the process
of fertilization. Other sperms will be stopped from entering because ion channels turn
the charge of the inside of the cell from negative to positive, so sperm are stopped from
3. Cortical reaction and fertilization membrane: the sperm absorbs water and swells,
releasing the nucleus containing the genetic material into the ovum, as the
spermatozoa’s head is inside the ovum while the tail is outside it. Cortical granules in
the cytoplasm of the ovum will release enzymes which destroy sperm-binding sites and
harden the jelly of the zona pellucida, creating a fertilization membrane and stopping
any other sperms from entering.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Remember that many areas of biology are linked. A question could test these links; for example,
the acrosome is a specialized lysosome.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

Fertilization in plants
Fertilization in plants occurs differently in comparison to that in humans, and goes through the
following steps:-
1. Pollination and pollen tube creation: during pollination, the pollen will land onto the
stigma of the plant. If it recognizes it (them being the same species) then a pollen tube
will start growing, otherwise, it will not. The pollen tube penetrates through the stigma,
style, and eventually reaches the micro pile of the ovary, this is done because the tip of
the pollen tube produces digestive enzymes.
2. Reaching the micro pile: the pollen tube nucleus and the generative nucleus (after it
splits into two nuclei) will travel down the pollen tube and once they reach the micro
pile, the pollen tube nucleus degenerates and the generative nuclei go into the micro
pile to perform double fertilization
3. Double fertilization: here, one of the generative nuclei will fuse with the polar nuclei in
the ovule and form an endosperm, which is responsible for feeding the newly formed
embryo. The other generative nucleus will fuse with the female egg cell to form a
diploid zygote. Fertilization is complete and the embryo starts to grow and develop

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 1

The transfer of pollen from the anther to the stigma, often from one flower
to another.

External The process of fertilization in which the female and male gametes are
Fertilization released outside of the parental bodies to meet and fuse in the environment.

Internal The fertilization of the female gamete by the male gamete, which takes
Fertilization place inside the body of the female.

The process by which a male animal transfers sperm from his body directly
into the body of the female.

The reaction seen when the sperm reach the oocyte and enzymes are
released from the acrosome and digest the follicle cells and the zona

Polyspermy The fertilization of an egg by more than one sperm.

The reaction seen when cortical granules in the cytoplasm of the ovum
release enzymes into the zona pellucida; these enzymes destroy the sperm-
binding sites and also thicken and harden the jelly of the zona pellucida.

Fertilization The tough layer that forms around the fertilized ovum to prevent the entry
Membrane of other sperm.

Conception The term used for fertilization of the ovum in humans.

(Of pollen) the process by which a pollen tube starts to grow out of the
pollen grain to transfer the male nuclei to the ovule.

The process that occurs in plants in which one male nucleus fuses with the
two polar nuclei to form the triploid endosperm nucleus and the other fuses
with the egg cell to form the diploid zygote.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
3C – Development of organisms
1 Cell Differentiation

Cells contain the same genetic information but different cells perform different functions, they
differentiate in a process known as cell differentiation and develop into different tissues and
Cells contain specific proteins that relate to the function of the cell, which means that certain
genes need to be expressed in different types of cells.
Chromosomes have several genes, each coding for something different, genes are found in
specific places of the chromosome knowns as the locus of the gene, genes usually have two
different versions known as alleles.
Some features are controlled by multiple alleles, more than two alleles, no matter how many
possible genes control it, and any diploid individual will only inherit two alleles. In some cases,
the patterns of inheritance are complex such as the case in the blood group ABO where three
alleles are present, A, B, O, A and B are dominant to O which is recessive, but A and B are
codominant, which means both alleles are expressed and produce proteins.
Many features are polygenic which means that they are determined by many interacting genes,
such as eye color and intelligence, they are determined by several different genes at different
loci and by interactions with the environment in some cases.
Digenic (dihybrid) inheritance is an experiment in which the inheritance of two pairs of
contrasting characteristics at the same times, if the results is not what was expected, it can be
attributed to many factors such as:
- Small sample size.
- Experimental error.
- The process is random and so sometimes, unexpected results occur.
- Unexpected ratios can mean the genes being examined are both on the same
chromosome (they are linked).
Gene Linking:


Cell the process by which a less specialized cell becomes more specialized
Differentiation for a particular function

Locus place on a chromosome where any particular gene is found

Multiple Alleles more than two possible variants at a particular locus

Codominant both alleles are expressed in the phenotype

when genes for two different characteristics are found on the same
Gene Linkage chromosome and are close together so they are linked and inherited as a
single unit

Polygenic phenotypic characters determined by several interacting genes

the inheritance of two pairs of contrasting characteristics at the same
2 Interactions between Genes and the Environment
Discontinuous Variation: phenotypic features which are either present or not, usually inherited
on one or at most a small number of genes.
Continuous Variation: phenotypic features which show a huge range of values; they are usually
polygenic and are also affected by environmental factors.
Operon: a unit consisting of linked genes which is thought to regulate other genes responsible
for protein synthesis.
Twin Studies:
Identical twins have the same genetic material.
Non-identical twins have non-identical DNA but, because they are the same age, they are more
likely to have a similar environment than ordinary siblings.
Ordinary siblings are useful as a control group. If they show a greater difference, it suggests
that the environment has a stronger influence on that characteristic.
A team at University College, London studied 5000 pairs of twins aged between 8 and 11 years
that were brought up together. Their results, published in 2008, showed that 77% of the variation
in BMI and waist circumference of the children was caused by their genes and 23% by their home

Remember that discontinuous variation has simple genetics, only one gene makes a difference:
one difference, one gene.
Continuous variation is often caused by a wide range of factors and genes.
3 Controlling gene expression
As there are many genes in the human body, and there are many combinations of genes which
produce different proteins that determine what the cell’s function and role in the body is, there
are ways of altering the two processes of protein synthesis, transcription and translation. Here,
we will learn the different ways of altering gene expression.
Transcription factors:
Transcription factors are proteins which control which genes are turned on (transcribed) and
which are turned off (not transcribed), by binding to regions on the DNA called promotor
sequences, which come right before the beginning of the gene, upstream of it, to show RNA
polymerase that the gene starts at that point. Moreover, they also bind to enhancer sequences,
which the transcription factor bonds to in order to activate the genes needed to be transcribed,
by changing the structure of the chromatin, either by opening it or tightening it. Different
transcription factors can switch on or switch off one gene, and so, this leads to great amounts
of control, where if one transcription factor doesn’t do the job, the other will.
RNA splicing:
After the transcription factors have determined which genes need to be transcribed and which
don’t, and the mRNA is fully transcribed, it still cannot exit the nucleus to begin the process
of translation. The mRNA after transcription is called pre-mRNA, as it contains introns and
exons, where the introns and some of the exons need to be removed. Enzymes called
spliceosomes will join the exons together in order to form the mRNA. Here, the exons can be
joined in many different ways, and this is why we say one mRNA can produce many different
proteins, because if the order of exons differs, so will the order of amino acids and different
polypeptide chains will be coded for.
Epigenetics study how the DNA can be further modified without changes to the DNA base
sequence, but how the cells read the gene itself. The ways of modification are:-
1. DNA methylation: a process that is responsible for silencing the gene so that it is not
transcribed, by adding a methyl group at the site where a cytosine meets a guanine with
a phosphate bond between them. This is done by an enzyme called DNA methyl
transferase and can be reversed by DNA demethylation, where the methyl group is
2. Histone modification: there are two types of histone modification, histone acetylation,
where an acetyl group (COCH3) is added to a lysine on the histone, opening up the
structure of the histone and activating the chromatin, allowing the genes to be
transcribed. While histone methylation adds a methyl group to a lysine on the histone
to deactivate the region of genes on it, or sometimes, activate it.
3. Non-coding RNA (ncRNA): in males, there is only one X chromosomes, while in
females, there are 2. In order to maintain genetic balance, one of the X chromosomes
will be inactivated at random, due to the presence of the X-inactive specific script
(Xist) gene on one of the X chromosomes forming a Xist ncRNA. This ncRNA will
randomly coat one of the X chromosomes and will start supercoiling it until it forms
an inactive Barr body that will stay in the nucleus, and does nothing. The ncRNA can
also act on histones to activate or deactivate regions of genes.
Cell differentiation:
With cell differentiation, unspecialized cells will become specialized through genetic
modification by the production of a protein which determines its function, the following is a
summary of the process which causes a cell to specialize:-
1. Chemical stimulus (e.g. transcription factor)
2. Some genes switched on, others switched off
3. Pre-mRNA produced from these genes
4. mRNA splicing occurs to modify the mRNA even more,
producing the post or final mRNA
5. Translation of the mRNA produces a protein
6. The cell is permanently modified and its function is
4. Stem cells
At the very beginning after fertilization, the zygote starts as a cleavage, but as it moves towards
the lining of the uterus it starts dividing to form a ball of cells called the morula (containing
10-30 cells). At this stage, the cells of the embryo, called the embryotic stem cells, are described
as totipotent, where they can form any type of cell in the body. The cells will keep dividing
until, 5-6 days later, they form a blastocyst, and one day later, the cells on the outer side of
the blastocyst specialize into the placenta, and the cells on the inner side become pluripotent,
able to form all types of cells but placenta cells.
Types of stem cells
Stem cells at each stage of development differ, and there are 3 different types:-
1. Embryonic stem cells: these stem cells can be found in the morula, and will be totipotent,
able to form any type of cells, however, by the stage of the blastocyst, they are
pluripotent, but still useful as they can form many types of cells, except the placenta.
2. Umbilical cord stem cells: this is a rich source of pluripotent stem cells, and it can be
frozen and used later throughout the child’s life to treat them or restore some cells,
however, some diseases are already present before birth even in pluripotent stem cells,
and so, diseases cannot be treated using stem cells
3. Adult stem cells: even though the stem cells have developed, some of them are still
unspecialized and are described as multipotent, as they can form a limited range of
Development of an organism
The biggest example of this can be seen when globin genes are switched on and off to create
fetal hemoglobin during the pregnancy, which has a higher affinity for oxygen than normal
hemoglobin. However, when the pregnancy is near its end, the production of globin moves
towards the liver and to the spleen from the yolk sac in the embryo, and near birth, the bone
marrow has taken over the production of globin and the genes coding for fetal hemoglobin are
5. Using stem cells
In theory, stem cells contained in the bone marrow can be extracted from the patient and
treated to form any type of cells.
Scientist have not been successful in producing new tissue as it is very difficult to control the
differentiation of the cells, in the cases that they succeeded in curing one condition, they have
developed cancer by then.
Stems cells are extracted from embryonic cells which is an unacceptable process in some
countries and has raised ethical and practical difficulties.
The problems arising from embryonic cells have led scientists to research stem cells from adult
stem cells, which are then seeded into a collagen-based framework to grow and form the
required cells, and to be returned into the patient’s body with no risk of rejection.
Therapeutic Cloning:
Somatic cell cloning or therapeutic cloning is an experimental technique used to produce large
quantities of healthy tissue hoping it can cure diabetes type 1, Alzheimer’s disease... etc.
Scientist are still trying to determine the exact triggers that control cell differentiation.
There’s a shortage in donor eggs to use and some ethical objections have arised.
In case of the treatment of genetic diseases, the cell nucleus needs to be genetically modified
before being added to the empty ovum otherwise the genetic mutation will be carried.

Risks and Benefits:

- No one knowns exactly how the genes in the cells are turned on or off but
understanding transcription factors and epigenetic mechanisms so we’re coming close.
- There are some concerns that stem cells could cause the development of cancer,
which is aided by some evidence.
- There are no cures for the conditions stem cell therapy will solve.1
- Organ transplants would no longer be a problem if cells made from the patient’s body
could be produced.

Induced Pluripotent Stem Cells:

A team of researchers took adult mouse cells and, using genetic engineering techniques,
reprogrammed them to become pluripotent again thus producing stem cells without using an
The induced pluripotent stem cells (iPS cells) renew themselves.
The team replicated the process in humans, they used harmless, genetically modified viruses
to carry a group of four genes for specific transcription factors into skin cells.
The induced pluripotent human stem cells appear to be very similar, although not identical, to
human embryonic stem cells in their behavior.
The team even managed to make their iPS cells develop into brain cells and heart muscle cells.
The technology overcomes the ethical objections to using embryonic tissue as a source of stem
There is also no risk of rejection if cells from an individual are used to provide their own stem
Who can use stem cells?
Stem cell therapy is used around the world and has potential to cure many different and strong
diseases, such as:-
1. Parkinson’s disease: Parkinson’s disease happens when the neuron that is responsible
for producing dopamine in the body stops working, and this causes the hands to start
shaking uncontrollably and eventually causes the whole body to stop moving. Scientists
are hopeful that stem cells could replace these missing neurons and enable the body to
produce dopamine once more
2. Type 1 diabetes: Type 1 diabetes develops when the islets of Langerhans are lost or stop
producing insulin, leading to uncontrollable glucose concentrations which could be
fatal. Even though insulin shots do exist, they are only a temporary solution for a huge
problem. Scientists are trying to get stem cells to form islets of Langerhans, and then
they would want to inject them into a type 1 diabetes patient, so that insulin can be
produced once more. However, this is not currently possible.
3. Damaged nerves: when this happens, a part of the nerve may be cut off or stops
working, causing the body to experience permanent partial or full paralysis. Scientists
are trying to see if stem cells can help regrow these damaged nerves so that people with
this type of disability are able to gain some form of control again.
4. Organs for transplant: many people die due to missing organs or malfunctioning ones,
and currently, scientists are trying to use stem cells in order to produce organs by
manipulating their pluripotency or their multipotency in specialization to produce these
Ethical issues concerned with using stem cells
There are a number of ethical issues concerned with using each type of stem cell, listed below:-
1. Using embryotic stem cells by IVF raises issues because once you’ve extracted the stem
cells, the embryo is destroyed, and that same embryo could’ve developed into a fetus
and eventually a human being
2. Embryos have the right to life as they are genetically unique individuals
3. If adult stem cells are extracted, the process could bring a lot of discomfort to the
However, there are benefits to using stem cells too:-
1. They could save many lives
2. They could improve the quality and excellence of life for many people
To help societies make decisions, regulatory authorities will interfere, in the following ways:-
1. Looking at research proposals to decide if they are allowed – for example if a research
includes embryos, it won’t be allowed
2. Licensing and monitoring centers – makes sure that only trained staff are able to
perform researches related to stem cells
3. Producing guidelines and codes of practice – to make sure all scientists are following
the same procedure during these researches
4. Monitoring developments in scientific research – so that guidelines can be updated
and any advancements made are benefited from
5. Providing information to governments and professionals – this allows the society to
understand why studying embryos is important and why they are involved.
Therapeutic cloning and iPS cells:
iPS cells are adult stem cells which are taken and genetically modified to get them back to
being pluripotent, and this removes all the ethical issues listed above, however, these cells are
hard to grow into pluripotent stem cells, so it might be more expensive and time consuming
to do so. As for therapeutic cloning, we’ve already established that stem cells are useful in
treating diseases and helping to improve the excellence of life, however, some people are afraid
that scientists may use stem cells to produce cloned cells, and so, a cloned baby. Many religions
forbid this and this could give rise to many ethical and social issues, as individuals may no
longer be genetically different.

protein that binds to the DNA in the nucleus and affects the
Transcription Factor
process of transcribing DNA into RNA

specific region on the DNA to which transcription factors

Promoter Sequence
bind to stimulate transcription

specific region of DNA to which transcription factors bind

Enhancer Sequence and regulate the activity of the DNA by changing the
structure of the chromatin

segments of a DNA or RNA molecule containing information

coding for a protein or pept ide sequence

segments of a DNA or RNA molecule containing information

which does not code for a protein or peptide sequence

mRNA that is transcribed directly from the DNA before it has

been modified

enzyme complexes that act on pre-mRNA, joining exons

together after the removal of the introns

methylation of DNA (addit ion of a methyl - CH3 group) to a

DNA Methylation cytosine in the DNA molecule next to a guanine in the DNA
chain and prevents the transcription of a gene

removal of the methyl group from methylated DNA enabling

DNA Demethylation
genes to become active so they can be transcribed

densely supercoiled and condensed chromatin where the

genes are not available to be copied to make proteins

addition of an acetyl group (-COCH3) to one of the lysines in

the histone structure, which opens up the structure and
Histone Acetylation
activates the chromatin, allowing genes in that area to be

addition of a methyl group (- CH3) to a lysine in the histone;

Histone Methylation methylation may cause inactivation or activation of the
region of DNA, depending on the position of the lysine

98% of the RNA, which does not code for proteins but
Non-coding RNA (ncRNA) affects the transcription of the DNA code, modifies the
chromatin structure or modifies the products of transcription
IAS Biology Unit 2 – Topic 4

4A – Plant structure and function

1 The Cell Wall
Both animal cells and plant cells contain cytoplasm, nucleus, rough and smooth endoplasmic
reticulum, Golgi apparatus and mitochondria. But plant cells contain cell walls, which animal
cells do not have.
Observing the Cells under a Microscope:

Having cell walls means that the shape of plant cells is less random than animal cells.
Plant cells are made of insoluble cellulose and provide strength and support to the plant, they
are freely permeable to anything that is dissolved in water, however compounds like lignin and
suberin when added to the cells, reduce the permeability of the cell wall.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Plant Cell Walls Are Made of Many Layers:

The Middle Lamella is made when cells divide into two, mainly consists of pectin
(polysaccharide) which acts as a glue, it has many negatively charged carboxyl groups which
combine with positive calcium ions to form calcium pectate, which then binds to the sides of
the cellulose, the cellulose microfibrils build up on both sides of the middle lamella, these walls
are very flexible, with all the microfibrils being arranged in the same direction, these are called
primary cell walls.
Secondary thickening occurs as the planet ages, a secondary cell walls builds up with the
microfibrils densely laid at different angles to each other which makes the composition much
more rigid. Hemicellulose helps harden it even further. In some plants, lignin is added to cells
walls to produce wood which makes it even more rigid, in many plants there are many long
cells are that are completely lignified, these are called plant fibers, they’re used in clothing,
building material, ropes and paper.

The Chemistry of Cellulose:

Cellulose is a complex carbohydrate made of long chains of glucose joined together by
glycosidic bonds.
There are too types of glucose, α-glucose and β-glucose, the difference is small but the effect
is large on the properties of the polymer.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Different isomers make different bonds on adjacent glucose molecules, the monomers in starch
are α-glucose, but in cellulose they’re β-glucose joined by 1,4 glycosidic bonds, but one of the
monomers has to be inverted so the bonding can take place.
This linking means that the hydroxyl groups would stick out on both sides, because of this
hydrogen bonds can be made between the partially positively charged hydrogen atoms of the
hydroxyl groups and the partially negatively charged oxygen atoms, this is called cross-linking,
it holds the chains firmly together.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

The presence of many hydrogen bonds make cellulose very strong.

Cellulose molecules don’t coil or spiral, they stay in long straight chains.
Most animals don’t have the enzymes needed to break 1,4 glycosidic bonds between β-glucose
so they can’t digest it, so it acts as fiber in diets, which is very important in diets.
Cellulose microfibrils are deposited in layers held together by hemicellulose matrixes and other
carbohydrates, they act as glue.
The combination of cellulose microfibrils in the matrix makes composite material.
Cells are turgid (firm) most of the time, giving strength and support to the plant in vertical
positions, yet the plant can wilt when there’s a shortage in water and become flaccid (floppy).

In primary cell walls that don’t have lignin in them, materials pass through special cytoplasmic
bridges called plasmodesmata which are produced as the cell divides as the cells do not separate
completely and threads of cytoplasm remain between them, these threads pass through new
cells and substances can pass from one cell to another through the cytoplasm, the
interconnected cytoplasm of the cells is called symplast.
Cells walls are thinner in the region of the plasmodesmata.
In the secondary thickening, areas around the plasmodesmata do not have secondary thickening
in them, which leaves thin areas of the cell wall called pits.
There is no cytoplasm in xylem cells, but pits allow water to move between the vessels which
is essential in maintaining a flow of water at even pressure.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Cell Wall a freely permeable wall around plant cells, made mainly of cellulose

a waterproof chemical that impregnates cellulose cell walls in cork

tissues and makes them impermeable

a chemical that impregnates cellulose cell walls in wood and makes

them impermeable

the first layer of the plant cell wall to be formed when a plant cell
Middle Lamella divides, made mainly of calcium pectate (pectin) that binds the
layers of cellulose together

a polysaccharide that holds cell walls of neighbouring plant cells

together and is part of the structure of the primary cell wall

Primary Cell the first very flexible plant cell walls to form, with all the cellulose
Walls microfibrils orientated in a similar direction

Secondary Cell the older plant cell wall in which the cellulose microfibrils have built
Wall up at different angles to each other making the cell wall more rigid

Hemicelluloses polysaccharides containing many different sugar monomers

long cells with cellulose cell walls that have been heavily lignified so
Plant Fibres
they are rigid and very strong

a material made of two or more materials which combined together

make a composite with different properties from either of the
constituent materials

Turgid swollen

Flaccid floppy, soft

cytoplasmic bridges between plant cells that allow communication

between the cells

all of the material (cytoplasm, vacuole, etc.) contained within the

surface membrane of a plant cell

thin areas of cell wall in plant cells with secondary thickening, where
plasmodesmata maintain contact with adjacent cells; in xylem
vessels, where the cells are dead, they become simple holes through
which water moves out into the surrounding cells

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

2 Plant Organelles
Fluid filled spaces surrounded by membranes inside the cytoplasm.
They are temporary in animal cells, but they are permeant in non-woody plant cells and have
an important role.
They make up to 80% of the cells and are surrounded by a special membrane called tonoplast
which many different protein channels and carrier systems and controls controls the movements
of substances into and out of the cell thus the water potential of the cell.
The vacuoles contain cell sap, a solution containing various solution which cause water to
move inside the cell by osmosis, which keeps the cell turgid.
Vacuoles mainly maintain the shape of the cell, as well as store pigments which will prevent
them from leaking to the cytoplasm unless it’s heated, they also store protein, they contain
lytic enzyme and act similarly to lysosomes and they also store waste products.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Plants have chloroplasts which is an important distinguishing factor between plant and animal
cells, as plant cells make their own food by photosynthesis.
Chloroplasts are included only in the green part of the plants, but the genetic material needed
to code for chloroplasts is contained in all cells.
Cells in flowers, seeds and roots contain no chloroplasts and neither do the internal cells of
stems or the transport tissues, the majority of plant cells do not have chloroplasts.

Chloroplasts are similar to mitochondria as in they both:

- Are large organelles with a biconvex shape.
- Contain their DNA.
- They are surrounded by an outer membrane.
- Both have highly folded inner membranes to provide a greater surface area for
enzyme-controlled reaction.
- Are thought to have been free-living prokaryotic organisms that were engulfed by and
became part of other cells.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

However, they have two key differences, Chloroplasts:

- Are the site of photosynthesis.
- Contain chlorophyll, a green pigment responsible for trapping energy from light.

Specialized organelles that are colorless and store starch, they get their name from what
makes up starch, amylose and amylopectin.
The starch can be converted to glucose and used to provide energy.


The specialized membrane that surrounds the permanent vacuole in

Tonoplast plant cells and controls movements of substances into and out of the
cell sap.

Cell sap The aqueous solution that fills the permanent vacuole.

A specialized form of diffusion that involves the movement of solvent

molecules down their water potential gradient.

Organelles adapted to carry out photosynthesis, containing the green

pigment chlorophyll.

The green pigment that is largely responsible for trapping the energy
from light, making it available for the plant to use in photosynthesis.

Amyloplasts Plant organelles that store starch.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

3 Plant Stems
Stems provide plants with support as well as movement of materials such as water and mineral
Some stems contain chlorophyll and carry out photosynthesis.
Not all plants have stems but most of them do.
The main types of stems are the xylem, the phloem and the sclerenchyma.
Cambium is a layer of unspecialized cells which divide, giving rise to more specialized cells
that form both the xylem and the phloem.

The stems contain many types of tissues:

The outer layer is called the epidermis and provides no support, only protection to the layers
underneath it.
The main type of tissue is parenchyma which are unspecialized cells, they can be modified in
several ways so they become suitable for storage and photosynthesis.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Collenchyma cells are located outside the stem, they have thick primary cellulose walls so
they provide strength, but they are also living so they stretch with growth.

They provide support to the plant, much like xylem vessels, they are made of bundles of dead
cells that run vertically up the stem, they are longer but not as wide, they have a hallow lumen
and end walls, which xylem doesn’t have (the end walls).
Their cells are lignified which means they’re thickened and they have more cellulose than any
other plan cells.
Sclerenchyma are associated with the vascular bundles.
When they are done growing, they produce a secondary cell wall between the normal cell and
the cell membrane, which is thicker than the normal cell membrane and has more lignin, the
growth of the secondary cell wall is called the second thickening which make plant fibers even
more strong.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Xylem Vessels:
Xylem vessels transport water and mineral ions up the plant as well as provide support.
The vessels are long, tube-like structures that are formed from dead cells, joined end to end
but they have no end walls, making for an uninterrupted tube that allows water and mineral
ions to pass up through it easily.
The walls are thickened by lignin, which helps support the plant.
Water and mineral ions are transported from the roots to the leaves and shoots in the
transpiration stream.
Water moves out of the xylem into the surrounding cells through the specialized pits in the
walls of the xylem vessels.
Xylem vessels are located around stem and are part of the vascular bundles.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Phloem is made of living tissue, and it transports food molecules around the plant, both up
and down, in active process known as translocation.
The phloem is made up of many cells that are joined together to form very long tubes.
The cells do not get lignified and thus the contents remain living.
As a result of the cell walls being pierced, specialized sieve plates will form and the phloem
sap flows through the holes in these plates.
Mature phloem cells have no nucleus, tonoplast and some other organelles as they break down
while the gaps in the sieve plate are being made, filling the phloem sieve tube with phloem
The phloem’s survival relies on the companion cells which are very active cells with organelles,
they are connected to the phloem sieve tubes through the plasmodesmata.
The cell membranes of the companion cells have many inner foldings that increase the surface
area over which they transfer sucrose into the cell cytoplasm, as well as many mitochondria to
provide the needed ATP.

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Relatively unspecialized plant cells that act as packing in stems and roots
to give support.

Plant cells with areas of cellulose thickening that give mechanical strength
and support to the tissues.

Plant cells that have very thick lignified cell walls and an empty lumen
with no living contents.

Sclereids Sclerenchyma cells that are completely impregnated with lignin.

Xylem The main tissue transporting water and minerals around a plant.

Phloem The main tissue transporting dissolved food around the plant.

Vascular Part of the transport system of a plant, with phloem on the outside and
Bundle xylem on the inside - often with strengthening sclerenchyma.

The layer of unspecialized plant cells that divide to form both the xylem
and the phloem.

The first xylem the plant makes; it can stretch and grow because the walls
are not fully lignified.

Metaxylem Consists of mature xylem vessels made of lignified tissue.

The movement of water up from the soil through the root hair cells,
Transpiration across the root to the xylem, then up the xylem, across the leaf until it is
Stream lost by evaporation from the leaf cells and diffuses out of the stomata
down a concentration gradient.

Translocation The active movement of substances around a plant in the phloem.

The perforated walls between phloem cells that allow the phloem sap to
Sieve Plates

Very active cells closely associated with the sieve tube elements that
supply the phloem vessels with everything they need and actively load
sucrose into the phloem.

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IAS Biology Unit 2 – Topic 4

4 The importance of water and minerals in plants

Same as humans, plants make use of certain resources in order to survive and produce energy
through the process of respiration, the following are some minerals that plants need in order
to survive.
Why do plants need water?
Water is a medium for many metabolic reactions, and plants are made of 90% water while we
are made of 70% water, plants need water because
1. For photosynthesis: plants combine water and carbon dioxide to produce glucose and
energy through the process of photosynthesis
2. For support: non-woody plants rely on water to keep them upright, as it makes the
cytoplasm press against the cell wall which causes the plant cell to be turgid, keeping
it upright
3. For transport: water is transported in the xylem tissues, and it has minerals dissolved in
it, the water goes through the transpiration stream, and is transpired at the leaves
4. To keep them cool: evaporation of water at the leaves cools the plants
Why do plants need minerals?
Plants also need other minerals to survive, such as:
1. Nitrates: Nitrate ions are used to make amino acids, and thus proteins. They are also
used to make DNA and hormones. If the plant does not have nitrates, it becomes yellow
and wilts out.
2. Calcium: Calcium ions combine with pectin in the middle lamella to make calcium
pectate which strengthens the cell wall. They are also important in the permeability of
the cell membranes, and if the plant lacks them, growing points die young and the plant
becomes yellow
3. Magnesium: Magnesium is used to make the green pigment chlorophyll, which trap
sunlight for the process of photosynthesis. Magnesium is also used to activate some
enzymes and nucleic acids. Without it, the plant becomes yellow on older leaves and
growth stops.

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IAS Biology Unit 2 – Topic 4

5 Using plant starch and fibers

We already know that plants aren’t only a source of food, however, in that aspect, they are
very beneficial. Plants can store a lot of energy in the form of starch, for example, potato stores
starch in its tubers during winter in order to survive tough condition, which means that the
energy consumption is lowered as much as possible to preserve heat.
Plant fibers
Plant fibers are usually long sclerenchyma and xylem vessels joined in a bundle which makes
them very strong and tough, meaning they have great tensile strength, which means that they
cannot be easily broken under high tension. Along with their flexibility, this makes them useful
for many things, even in buildings!
How fibers are processed to make products
Usually, fibers are produced through decomposers breaking down the materials around the
fibers after the plant dies. However, there is a much quicker industrial way of making fibers,
by using enzymes and chemicals which do the job quicker. If we use cotton as an example,
once it is picked from its plant, it is ready fiber however it is not enough to be useful, so the
fibers will be spun in order to make long and continuous fibers that will then be woven to
make fabric. When synthetic fibers were developed, people were amazed by them as they were
cheap, and simple as an alternative to natural fibers. However, it was then discovered that
synthetic fibers do not ‘breathe’, meaning they don’t absorb liquids such as sweat. Moreover,
synthetic fibers are not sustainable, meaning they cannot be replaced, whereas natural fibers
that come from plants can be replaced.
Wood, made of lignified cellulose fibers embedded in hemicelluloses and lignin, is a composite
and very strong material, as it is resistant to compression and can be used in buildings. It also
does not crack, and is flexible. Moreover, wood is an insulator by nature, so during winter, it
keeps heat and during summer, it doesn’t absorb the heat, as opposite to bricks which have
their temperature according to their environment. Wood is also carbon neutral, which means it
intakes a certain amount of CO2 and releases the same amount when burnt, and is also a great
renewable source of energy, as trees can be replanted to get more wood. Lastly, wood can be
used in things other than buildings, such as baskets, cricket bats, boats, and furniture.

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The problem with plastics is that they are made from oil-based products that means that they
are non-sustainable which is why people are thinking of bioplastics as a suitable and sustainable
alternative for plastics. Moreover, there are many issues arising from plastics, the fact that they
are non-biodegradable is one of the biggest issues that are being thought of, because this
means that they will not be broken down by decomposers and may harm the habitat.
Bioplastics solves these, as it is a biodegradable type of plastic (breaks down after 80 years
only!) and they are also sustainable, as they are made from crops such as maze and wheat.
There are many uses of bioplastics, some are used in our daily life even, such as:
1. Thermoplastic used to make capsules which contain drugs, as it is shiny, easy to swallow
and absorbs water which allows for easy digestion
2. PLA (polylactic acid) has the same properties as polyethene, but is biodegradable
3. Poly-3-hydroxybutyrate is like polypropene
Bioplastics can also be burnt once their life is over, because if they are broken down by
decomposers, they’ll produce the gas methane which is bad for the environment. Instead, you
can burn them down to release energy.
However, bioplastics do have their disadvantages, as they do not contain all the properties that
oil-based plastics have, some of which are very useful. Moreover, bioplastics are very expensive
as they are still new technology, and are still being developed. Moreover, if we use crops such
as maze and wheat to make bioplastics, then we are taking food away from those who have
nothing to eat, and who can decide whether these crops should be used for food or for

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Determining tensile strength

Determining tensile strength from a celery stalk

1. Carefully remove 9 fibrous strings from the celery stalk using a knife and a white tile
as your cutting surface
2. Inspect the strings, making sure they have no breaks cuts, and the diameter is
constant across the strings and that they are all of the same length and width
3. Cut the strings to 3 groups of lengths, 3 at 10 cm, 3 at 15cm, and 3 at 20cm
4. Clamp one of the 10cm strings between two retort stands making sure they are held
securely, and place a cushioning under the strength
5. Start adding masses, 10g at a time, making sure the cushioning is under the masses,
so that they do not fall onto your hand or strike the bench once the string breaks
6. Once the string breaks, record the mass needed to break the strings.
7. Repeat the procedure for the other lengths and find the mean mass needed to break
each length of string

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IAS Biology Unit 2 – Topic 4

6 Plant-based medicines
Plants contain a vast amount of chemical substances that have many functions and have been
used as medicine in the past, and still are.
Discovering new medicines in undiscovered plants is one of the main reasons for conservation
of species and habitat.
Bacteria causes disease in animals and plants alike, millions of crops are destroyed due to
bacteria, some plants have antimicrobial properties as a result, the chemical defenses can
include both antiseptic compounds and antibiotics.
Bacteria reproduce under ideal conditions by binary fission, to investigate bacteria, we need to
culture them which involves growing large amounts of bacteria to measure them somehow.
They will need to be in the ideal temperature, pH level and all nutrients and water provided
for them, they are usually grown in agar jelly which provides them with nutrients in a petri
dish which is then kept in an incubator to control temperature.
Extra care is taken when dealing with bacteria even if it’s harmless because there will always
be a chance to develop a mutant pathogenic strand, the risk of contamination of the harmless
culture by pathogenic bacteria from the environment and growing a pure strands means that
any other microorganism from the air or your skin will contaminate it.
Health and safety precautions must be followed carefully, aseptic techniques to ensure the
sterility of everything at all times.
- All equipment must be sterile already before the culture is started.
- Once the culture has grown is does not leave the lab.
- The instrument used to add bacteria to the petri dish must be sterilized by dipping it in
ethanol and passing it over a Bunsen burner.
- Leave a yellow flame Bunsen burner nearby to create conviction currents that will
destroy airborne bacteria.
- All cultures should be disposed of safely by sealing them in plastic bags and sterilizing
them at 121 °C for 15 minutes under high pressure.
Always consider the danger of infecting people, animals or plants accidentally when conducting
such experiments.

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One of the major advantages of extracting and purifying the beneficial drugs found in plants
is that it is possible to give known, repeatable doses of the active ingredient.

Core Practical 9
Investigating the Antimicrobial Properties of Plants
1. Prepare an extraction of the plant that you want to test by crushing the plant with a
pestle and a mortar and adding distilled water as needed.
2. Soak a small paper disk in the extract.
3. Prepare a petri dish with agar jelly.
4. Prepare Bunsen burner and keep it on, and close at all time, keep it on a blue flame
when sterilizing equipment but on a yellow flame when not.
5. Dip the inoculating loop in ethanol and pass on a blue flame then add the bacteria to
the petri dish.
6. Spread the bacteria on the agar jelly with a sterilized instrument like before.
7. Seal the petri dish like so to avoid contamination but to also allow aerobic respiration
since bacteria needs air to reproduce.

8. Test for clear areas, any clear areas of jelly around these samples indicate that the
bacteria are not growing and this suggests an antimicrobial chemical is present.

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7 Developing new drugs

Currently, drugs go through many stages of research and development before they are sold to
the people, however, this wasn’t the case in the older days.
William Withering and digitalis soup
William Withering, originally a British doctor had a patient
come to him with heart problems, however, Withering
couldn’t really help the patient, so the patient went off to see
the local “wise woman”, which treated the patient using a
soup, which Withering bought the recipe of. The soup
contained about 20 different herbs, one of them was
foxgloves, and Withering guessed that digitalis, which is the
chemical found inside foxgloves, was the reason why that
patient became healthy. Over the next amount of years,
Withering tested a variety of potions made of foxglove on
several sick patients, and when he got the dose right, many patients with kidney problems
became healthy and their kidneys started producing a lot of urine, however, when he got the
dose wrong, side-effects such as nausea and vomiting appeared. Some patients even came
close to dying because foxgloves can be poisonous. Withering discovered that the foxglove
would need to be boiled and dried so that its effects can be reduced, and the patient can be
easily treated.
Testing new medicine
Nowadays, medicine goes through a lot of research and development, and in order for it to be
sold, it has to be:
1. Effective – cures, relieves, or prevents symptoms of the disease it is designed against
2. Safe – non-toxic without unacceptable side-effects
3. Stable – can be stored from time to time and used under normal conditions
4. Easily taken into the body and removed from it – able to get to its target in your body
and then get excreted
5. Can be made on a large scale – can be manufactured in a pure form, cheaply, and in
large quantities
Researches look for chemicals which bind to our active sites of enzymes in our bodies in order
to cure certain diseases, they do this using computer models. Once a medicine needs to be
tested, it follows a certain international procedure, beginning with testing on tissues and organs
in labs, to see if the compound does what it is supposed to, a stage at which many types of
medicine fail.

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Drug development and animal testing

Before drugs are tested on humans, scientists need to make sure that the drug does not break
down to form a toxic or inactive substance instead of doing its job. Although it brings up many
ethical issues, testing on animals is needed as to make sure there are no harmful side-effects
that come from the drugs. However, animals are replaced with computer models wherever
possible, and mice or rodents are used as they have similar a genetic make-up to us and can
be placed in humane conditions very easily. If the drug passes
this tests without any failures or misshapes happening, then
the drug can transition into clinical trials
Clinical trials
Throughout the clinical trials regulatory authorities will
monitor the whole process and take decisions about
licensing the medicine. In these drug trials, some patients
will be given a placebo, an inactive substance that looks like
the drug but has no actual effect. The trials are split into 3
phases, which are:
1. Phase 1 – The new medicine is given to a group of people which are completely
healthy, this is done to see if the drug has any unexpected side effects
2. Phase 2 – The new medicine is given to 500 people carrying the disease, and a
placebo or the current treatment is given to 500 other people carrying the disease as
well, and here the effect of the drug can be monitored by the scientists and any
notable side-effects can be seen.
3. Phase 3 – The drug will now be tested on 1000 people carrying the disease to further
observe the disease, this is done because with larger sample sizes because patterns
emerge from a larger group of people and lifestyles would not matter
Double-blind trials
Phase 2 and 3 are carried out as double-blind trials, in a sense that neither scientist nor the
patient knows if the patient took a placebo or the actual medicine. This is done because of
the placebo effect, where the patients appear to respond to the drug simply because they
believe that it’ll do them well, a psychological effect more than a biological effect. During
certain trials, the trial will be so successful to a point where it is halted early, because if it is
seen that the medicine is successful in phase 3, then it becomes unethical not to release the
medicine to treat sick people. Once the drug is seen to be safe, during phase 3, the company
will then apply to license the medicine so that they can sell it on a world-wide level.
However, the trials keep on going even after the medicine has been sold in the market in
order to make sure that there are no risks and if there are, that they are not greater than the
benefit of the medicine.

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IAS Biology Unit 2 – Topic 4

4B – Classification:
1. The principles of classification
Due to so much biodiversity (which is the measure of the variety of living organisms and their
genetic differences), scientists need to classify organisms into different groups because:
1. It helps them monitor changes in populations of different types of organisms
2. Helps them understand how different types of organisms are related
The science of describing, classifying, and naming living organisms is called taxonomy.
The history of taxonomy
The whole reason behind the classification system is to group organisms, clearly identify them,
and represent their ancestral relationships. In the beginning of the classification system, people
used to classify animals based on their physical features, otherwise called their morphology.
Usually, they looked at analogous features, which are features between two organisms that
look similar or perform the same function, and that’s how they placed two organisms into the
same group.
However, in order for this sort of classification to be valid, homologous structures should also
be looked at, which are features that show genuine ancestry. When we look at a cat’s leg, a
bird’s wing, and a human’s arm, even though they all look different, their structure contains
similar bones and they’ve been made for similar functions, but look differently due to
adaptations to the environment and the genotype these organisms inherited throughout the
The main taxonomy groups
There are 8 taxonomic groupings, and the following order shows them from largest to smallest:
domain, kingdom, phylum, class, order, family, genus, and species. We’ll be looking more in
depth into the 3 domains, and each of their kingdoms, as follows.
1. Archaebacteria – these are ancient bacteria which reproduce asexually, and are thought
to be early relatives of the eukaryotes, were usually found in extreme conditions, but
are now being found everywhere.
1. Eubacteria – the true bacteria we know which reproduces asexually, the one that infects
us with diseases and is used in the gut for digestion

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Before we get into the eukaryota domain we need to know some terms, autotrophic organisms
are ones which make their own food, and heterotrophic organisms are ones which feed on
other organisms. Saprophytic organisms get their energy from dead matter, and parasitic
organisms get their energy off of leeching from other organisms.
1. Protista – a group of diverse microorganisms which reproduce asexually and can be
autotrophic or heterotrophic, (e.g. amoeba)
2. Fungi – a group of heterotrophic (micro)organisms which can be saprophytic or
parasitic, and can reproduce sexually or asexually
3. Plantae – are autotrophs which make their own food using chlorophyll which captures
energy from sunlight to use it in photosynthesis (e.g. flowering plants). The plantae can
reproduce asexually or sexually.
4. Animalia – Heterotrophs which will use their body to move at some stage of their life
(e.g. tigers). The Animalia can reproduce sexually or asexually
The binomial naming system
Lastly, in order for scientists to classify organisms clearly and accurately, they decided to come
up with a naming system called the binomial system, which names animals in two parts, the
first part is the genus and the second part is the species. The genus always has to be a capital
latter, and can be shortened, and the name has to be italic (e.g. Bellis perennis or B.perennis)

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2. What is a species?
To any ordinary person, the definition of “species” could be much simpler than that of a
scientist. The reason behind this is that species are used to measure biodiversity, so different
definitions will be used in different circumstances.
The morphological species concept
This definition was used for a while, it placed two organisms into a species based on how
similar their outer and sometimes inner morphology is. It is completely based on physical
appearance and nothing else, and in many cases this works, as we wouldn’t mistake an eagle
for an owl, however, it has some limitations:
1. The appearance of organisms can be affected by many factors (e.g. environment)
2. Sexual dimorphism – in some species, the males and females will look completely
different even though they are from the same species (e.g. Mallards)
The reproductive species concept
This definition states that “a group of organisms which interbreed to produce fertile offspring”
are a species, however, this isn’t completely correct. It has the following limitations:
1. Populations of organisms of different species may be unable to interbreed because they
are not in the same area, not because they are of different species
2. Some plants can interbreed with similar species and produce fertile offspring
A more accurate definition of this concept would be “a group of organism in which genes can
flow between individuals” or “a group of organisms with similar characteristics that are all
potentially capable of breeding to produce fertile offspring”
Other definitions of species
1. Ecological species model – organisms are grouped based on the ecological niche they
occupy in the environment
Limitation: some organisms can have many niches, or different organisms can have the
same niche
2. Mate recognition species model – this concept is based on fertilization techniques
including mating behaviors
Limitation: many species can cross pollinate or mate with other species and produce
fertile offspring
3. Genetic species model – this compares the DNA between two organisms and checks
similarities in order to identify them as species
Limitation: no way of knowing how similar organisms’ DNA need to be to identify them
as one species, and DNA analysis is costly and time-consuming

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Limitations of all species models

1. Many species, especially new ones, have never been seen breeding
2. Plants of related species can interbreed and produce fertile offspring
3. Many organisms do not produce sexually, so any definition regarding reproduction or
reproductive behavior is irrelevant
4. Fossil organisms cannot reproduce and most of the time, have no accessible DNA
Identifying species and the importance of DNA in classification
Molecular phylogeny is one of the most important tools in classification, it is the analysis of
the genetic material of organisms to establish their evolutionary relationships. Back in the old
days, analyzing DNA and keeping track of records was difficult, however, with technology and
IT taking over the world, DNA records can be easily tracked using computers. The process of
DNA sequencing in molecular phylogeny reveals the base sequences, which leads to DNA
profiling that looks at non-coding parts of the DNA to try and find a pattern. Similarities in
patterns will identify relationships between individual organisms.
Analyzing DNA shows us that some organisms that we thought to be different turned out to
be of the same species, it was only the environment that made them look similar, and shows
us that organisms that we thought to be the same were from completely different species.

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3. Domains, Kingdoms, or both?

Ways of establishing relationships between individuals
In the beginning, scientists used morphology to group organisms, however, biochemical
relationships and DNA analysis is increasingly being used to prove relationships that were
suggested by analysis of morphology. A known method of establishing relationships is using
gel electrophoresis which separates the DNA and RNA fragments and looks for similar patterns
in the DNA and RNA of different individuals in order to establish a relationship between them.
Other patterns and structures have also been analyzed to establish relationships between groups
of individuals:
1- Blood pigment: The analysis of blood pigment has shown that vertebrates have the same
blood pigment, hemoglobin, and thus the relationship was established
2- Similar sequences of amino acids are looked at when establishing relationships between
individuals at higher taxonomy groups (i.e. Phylum)
The last way of establishing a relationship is a phylogenic tree.
This tree orders individuals from the same ancestor, which may
not even exist anymore, and shows how closely related they
are. Even though the individuals come from the same ancestor
they are different due to environmental conditions, mutations,
and genetic variation.

Two domains or three?

We’ve already spoken about domains in 4B.1, however, scientists started out with 2 domains,
Eukaryotes and Prokaryotes. There is a theory which states that the chloroplast and the
mitochondria were prokaryotic organisms which were engulfed by the earliest eukaryotic
ancestor to become part of the eukaryotic cell. Scientists searched more into the structure of
these two domains and due to technological advances which allowed them to look more into
the microscopic structures, 3 domains were established, Bacteria, Archaea, and Eukaryota. The
Archaea are very different from the Bacteria, and are thought to be close relatives of the
Eukaryota. At first, scientists thought they live in extreme conditions only, however, they are
increasingly finding Archaebacteria everywhere. The Archaea is different from the Bacteria and
the Eukaryota in the following ways:
1. They divide by binary fission, a process that is completely different from how bacteria
divides, but similar to the cell cycle
2. They have a unique cell membrane structure and unique membrane proteins, different
from those of the Eukaryota and the Bacteria
There are other ways in which Archaea differ but these are the two main reasons.

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Critical evaluation
In order to validate any hypothesis made by any researcher due to conducting an investigation,
critical evaluation must be performed. During critical evaluation, peer review occurs where two
scientists will repeat the same investigation and compare their results. If their results are
identical to each other and to the results of the original investigation, then the hypothesis is
valid, otherwise, it isn’t.
How many kingdoms?
The first classification system grouped animals into two taxonomy groups, the plant kingdom
and the animal kingdom. Even fungi were considered plants because they did not move.
However, due to technological advances and scientists learning more about taxonomy groups,
the two domains, Prokaryotes and Eukaryotes were established and 5 kingdoms were named:
Plantae, Animalia, Fungi, Protista, and Monera (prokaryotes). However, as we said above, the
two domains were later found to be 3 domains instead, as Archaea and Bacteria were
completely different, it caused the Monera kingdom to split into Archaebacteria and Eubacteria,
forming 6 kingdoms: Plantae, Animalia, Fungi, Protista, Archaebacteria, and Eubacteria. To
remind yourself of the properties of each of these kingdoms and their relationships, visit section
4B.1: The principles of classification.

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4C – Biodiversity and Conservation:

1. Biodiversity and endemism
Biodiversity is defined in two ways, the species diversity which depends on the species
richness and the species abundance, and the genetic diversity which is based on the number of
alleles in the gene pool. It can also be said that biodiversity is a term to describe the variety of
life on earth.
Why is biodiversity important?
Biodiversity is one of the reasons why life is balanced, it has so many areas of importance,
such as:
1. Interdependent – rich biodiversity allows large-scale ecosystems to function and self-
regulate, but it also means that large-scale ecosystems are interlinked, so if biodiversity
decreases in one ecosystem, the natural balance may be destroyed in another ecosystem.
2. Purification – biodiversity means the ecosystem will have many types of plants and
decomposers. Plants clean the air and water by in-taking CO2 for photosynthesis, and
decomposers break down dead matter and make it non-toxic in order to clean the
3. Rainwater and Natural disasters – plants absorb a lot of water from the soil and then
release it into the environment through the transpiration stream by evaporation, which
produces clouds which produce rain elsewhere. Plants roots also hold the soil together,
which affects how water runs off or is absorbed by the soil, which reduces the risk of
4. Genetic diversity – this allows us to cross-breed and cross-pollinate plants as well as
genetically engineer them to produce improved versions of species. Plant biodiversity
also provides the potential of plants to produce chemicals which are important in
improving the excellence of life.

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Assessing biodiversity at the species level

We can measure the biodiversity at species level using species richness, which is the number
of different species in an area, and relative species abundance, which is the evenness of
distributions of the different species of different types of organisms that make-up species
richness. We could also measure biodiversity using:
1. Species richness – using species richness, scientists were able to identify biodiversity
hotspots, which are areas of unusual biodiversity, such as the wet tropics (e.g. The
Amazon rainforest). These areas will include a variety of land and marine animals as
well as many species of plants. However, these areas have a lot of natural resources
such as gas, wood, and oil, which are wanted by people, which is why biodiversity is
decreasing because humans are destroying these ecosystems to gain these natural
2. Endemism – when a species is described as endemic, it means that the species belongs
to one area and cannot be found anywhere else. However, areas with high biodiversity
will not necessarily have a lot of endemic species.
There are many ideas about why there are some areas with high biodiversity, however, the
current model suggests that:
1. A stable ecosystem will allow many stable relationships between organisms to develop
2. High levels of productivity (high level of photosynthesis) allows many niches to be
3. If organisms grow and reproduce rapidly, more mutations can develop which lead to
more adaptations and thus, more filled niches
Measuring species abundance
When we’re measuring biodiversity, we’re seeing the number of different species in a specific
area. Remember, if we have 5 species and each have 20% abundance in area A, and have 5
species but one has 60% abundance and the others have 10% abundance in area B, then area
A will be more diverse as the abundance of species is even. However, when we talk about
areas with high species abundance area areas which will be more vulnerable to damage and
loss as they have a lot of natural resources which humans will want.

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2. Measuring biodiversity
We’ve talked about biodiversity and its definition, now we’ll talk about how to
measure biodiversity and how to measure the heterozygosity in a population to
check if it has healthy genetic variation or not.
The diversity index
In order to measure biodiversity we have a formula which includes the species richness and the
species abundance of an area:
D = N (N – 1)
Σ n (n - 1)
D = Diversity index
N = the total number of organisms of all species
n = total number of organisms of each individual species – abundance of different species
Σ = sum of all values that follow (calculate n (n - 1) for each species, then add them together)

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How biodiversity varies

We’ve already talked about what reasons the current model suggests behind an environment
with high biodiversity, but in general, whenever the environment has extreme living conditions,
biodiversity will usually be low. In this case, any change in conditions, any selection pressure
will cause a big impact on population numbers. Moreover, these types of ecosystems (e.g. high
pressured deep oceans or deserts) have many unfilled niches, so if a new organism comes into
the environment, it can become adapted and established rapidly and overpower any existing
species which is competes with it for food.
However, if the environmental conditions are good and the environment itself is not hostile,
then we’ll see high biodiversity, such as in the wet tropics. Here, almost all niches are filled
and so species moving in our out almost have no effect, and the reason behind why biodiversity
here might decrease is due natural disasters or human produced disasters (e.g. floods,
volcanoes, storms). Since these areas are usually biodiversity hotspots, these types of disasters
may cause the complete loss of a certain species which was endemic for that area.
Lastly, measuring biodiversity is not always accurate, because some species will migrate
seasonally to other environments as they cannot survive in their current environment during
that season, and others may not be present at the time of day in which you measure
Biodiversity within a species
We’ll also look at gene pools when measuring biodiversity in species, and the variants of each
gene. We must remember that mutations change the gene pool as they may result in new
alleles, which changes the allele frequency (relative frequency of a particular allele in a
population). Moreover, the gene pool might be changed by selection pressure, as sometimes,
disadvantageous features can become advantageous due to a change in the environment. This
causes the individuals with the advantageous alleles to survive, grow, reproduce and pass on
the advantageous allele to the next generation, thus increasing the allele frequency. The
opposite happens with a disadvantageous allele, where natural selection will cause the
individuals holding that allele to rapidly decrease in number or eventually die out.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Measuring genetic biodiversity

Without variation, a population is vulnerable and can be easily wiped out by a disaster. To
know whether a population is (genetically) healthy, we’ll need to use the heterozygosity index.
This can be done by analyzing the DNA and checking which genotype has two bands not one
for each allele, as these individuals will be heterozygotes, while individuals with one band for
each allele will be homozygotes. To calculate the heterozygosity index for a particular DNA
sequence, the following formula can be used:

Number of heterozygotes
Heterozygosity index
Number of individuals in the population

This way the genetic health of a population can be calculated. For example, if a population has
a heterozygosity index of 0.2, then it is not healthy, but if it has an index of 0.75, it is a healthy
population with a lot of genetic biodiversity. Scientists use this measure to identify the areas
with the highest biodiversity in order to conserve them and direct funds towards them. Once
these measures are known and regularly updated, scientists can also monitor changes in
biodiversity anywhere.
Lastly, we need to know that isolated areas will usually have a high amount of endemic species,
which originated from common ancestors but underwent speciation due to them adapting to
different ecological conditions and advantages which were available to them. Usually, areas
with many endemic species usually have high biodiversity, but do not have a lot of genetic
variation, as DNA analysis shows that isolated endemic species are usually closely related,
which means natural selection can greatly affect the biodiversity in these kinds of environments.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

3. Adaptation to a Niche
Ecology is the study of the relationships of organisms to one another and to their physical
Niche the role of an organism within the habitat in which it lives.
The key feature in any species survival is how well it’s adapted for its niche, since the
characteristics that lead to its survival will be passed down to newer generations when the
species reproduce.

Successful Adaptation:
1. Anatomical Adaptations: an adaptation apparent in the
structure and form of an organism.
For example, the thick blubber layer in whales and seals and
the sticky hairs in sundew flowers.

2. Physiological Adaptations: an adaptation that concerns the way the body works and
differences in biochemical pathways and enzymes.
For example, diving mammals can stay underwater
for much longer because when they go underwater
their heart rate drops significantly so less blood is
pumped and less oxygen is used, also their main
muscles work more effectively via anaerobic
respiration, which means oxygen carrying blood is
directed to the brain and the heart (this is called mammalian diving response).

3. Behavioral Adaptations: an adaptation

that changes the programmed or instinct
based behavior of an organism causing
for a better adaptation and survival.
For example, insects and reptiles move
their bodies to face the sun and get
maximum sunlight when the
temperature is low, which allows them
to warm up and move fast enough to
feed and escape predators and vice
versa when the temperature is high.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Adaptations for Survival:

Fungal Carnivores:
Some fungi types are carnivorous and have developed
special types of adaptation:
Some types of fungi live in soil and have developed these
adaptations to capture worm, they produce sticky nets or
adhesive pads to trap worms (nematodes), and some live
inside the living worm.
Some types of fungi actively lasso the worms, by trapping them in loops of its hyphae called
constriction loops (both anatomical and physiological adaptations are involved here), when the
worm moves into the ring it inflates up and grips it while additional hyphae is produced and
penetrate the body of the worm, digesting and absorbing the nutrients from it.

Anatomical Adaptations:
1. Large eyes for wide range and long eye
lashes to protect against sand.
2. Long slit like nostrils that can close to
protect against sand and wind.
3. The upper lip is split, hairy and sensitive
to help identify leaves and to protect
against thorns.
4. The hump helps insulate heat, the heat
inside it allows for easy evaporation of
sweat over the rest of the skin, which helps in cooling down.
5. The feet are large and flat to spread the weight of the body and protect from heat
6. Tough pads on knees prevent heat damage.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Physiological Adaptations:
1. Fine hairs on skin can get erect to form
insulation layer.
2. They can withstand varying core body
temperatures, from 2○C range to 6○C under
extreme conditions.
3. Can lose drastic amounts of amounts of
water and make it up in 10 minutes of
drinking without any change to the osmotic
potential of blood, and blood does not
become thick when camel is dehydrated.
4. Hump acts as food store, and fat is broken down to release energy and water.
Water Balance:
1. Can withstand loss of 30% of body weight without any damage and can go up to 10
days without water.
2. Can drink up to 180 liters of water without affecting osmotic potential of blood.
3. Water is produced when fat in hump is broken down.
4. They can withstand huge temperature variations which means it can minimize water
loss by sweating, and kidney produce very concentrated urine, which allows it to drink
salty water, and when camel is dehydrated, urine production is reduced, reducing water
5. Camels can always produce dilute milk even when dehydrated for successful breeding.

Behavioral Adaptations:
1. When the camels are dehydrated and its hot, they sit down early before the sand gets
hot with their legs bent to absorb less heat as possible.
2. They position themselves away from the heat as necessary.
3. Groups of camels lay down together to minimize amount of body exposed to heat.
4. Camels eat many types of vegetation which their height enables them to access, but
other animals can’t.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

4. Gene Pool and Genetic Diversity

Population: Is a breeding group of individuals of the same species occupying a particular
habitat and a particular niche.
Gene Pool: Is the sum total of all the genes in a population at a given time.
The frequency of alleles changed based on environmental changes by natural selection and
Selection pressure is seen when an environmental change occurs and could cause certain
mutations that are advantageous to the survival of the species to increase rapidly. The
organisms with the resistant allele like in the case of warfarin and rats, would reproduce
successfully giving passing on the resistant allele to the next generation and eventually the
entire population will have the allele.
Speciation involves a change in allele frequency and is driven by selection pressures over time.
The number of individuals carrying a certain allele in a population determines the allele
The general formula the allele frequencies for the dominant and recessive phenotypes in the
gene pool of a population:
p represents the frequency of the dominant allele and q represents the frequency of the
recessive allele.
This formula is unusable because it’s impossible to distinguish between heterozygotes and
dominant homozygotes based on their phenotype.

The Hardy-Weinberg Equilibrium:

This equation is used to describe the frequencies of alleles and genotypes within a stable
theoretical population that is not evolving:

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

The following is assumed when using this equation, which of course is not realistic:
• There are no mutations.
• There is random mating.
• The population is large.
• The population is isolated (no immigration or emigration - no organisms move in or
move out).
• There is no selection pressure (all genotypes are equally fertile/ successful).

Mutations occur spontaneously in species; however, they do not affect the population rapidly,
but occasionally, mutations will rise and advantageous alleles will become established in the
gene pool.
Random mating means that the likelihood of two individuals mating is independent of their
genetic make-up, if mating occurs randomly, the frequency of alleles will stay the same, non-
random mating occurs when a phenotype feature affects the mating probability.
The equation is only valid if applied to a large population, the chance of losing an allele by
random events is reduced in large populations.


The effect of one or more environmental factors that determine

Selection Pressure whether an organism will be more or less successful at surviving
and reproducing; selection pressure drives speciation.

The mathematical relationship between the frequencies of alleles

Hardy-Weinberg and genotypes in a population; the equation used to describe this
Equilibrium relationship can be used to work out the stable allele frequencies
within a population.

The migration of either whole organisms or genetic material into

or out of a population and into another population, tending to
Gene Flow
make different populations more alike, but changing the allele
frequencies within each individual population all the time.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

5. Reproductive Isolation and Speciation

Is the formation of a new species, it happens as a result of isolation of parts of a population,
the important factors are reproductive isolation and the reduced gene flow between the
As a result of the isolation, the selection pressures on each species would be different and
natural selection would occur differently, changing the phenotype and genotype as a result of
isolation and when the two species reunite, they cannot interbreed.
Hybridization also causes two closely related species to breed forming fertile offspring but, in
some cases, when crossed with the parent species, they don’t produce fertile offspring so a
new species has been formed.

Isolating Mechanisms:
1. Geographical isolation: by a physical barrier such as a river.
2. Ecological isolation: two populations inhabit the same region, but develop
preferences for different parts of the habitat.
3. Seasonal isolation: (also known as temporal isolation), the timing for flowering or
sexual receptiveness differs for two species.
4. Behavioral isolation: when they don’t recognize potential mating partners anymore
due to a mutation in skin color or patterns.
5. Mechanical isolation: a mutation occurs that changes the genitalia of animals.

Allopatric Speciation:
Is a type of speciation that occurs when populations are physically or geographically separated
and there can be no interbreeding or gene flow between the populations and it is the main
evolutionary process.
Physical isolation occurs as part of natural changes.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Adaptive Radiation:
Occurs when one species develops rapidly from more than one type of species, which all fill
different ecological niches. Some examples of Adaptive Radiation are:
1. Marsupials are animals that protect their babies in pouches, and monotremes which lay
eggs where the only mammals in Australia before it separated from the rest of the world
and many marsupials evolved to fill different ecological niches, such as koalas and
2. Darwin’s finches were discovered on the Galapagos Islands, with genetic variation in
alleles leading to lots of variation that is a great example on adaptive radiation, over
several million years, at least 14 species of finch developed from the original ancestor
species. Food was an important selection pressure, so finches with similar beaks must
mate together, otherwise the offspring would be less likely to survive. Although the
finches specialize and feed on particular types of food. and vary considerably in size
and appearance, DNA analysis has shown that genetically they are remarkably similar.

Sympatric Speciation:
Is a type of speciation that occurs between populations of a species in the same place; they
become reproductively separate by mechanical, behavioral or seasonal mechanisms; gene flow
continues between the populations to some extent as speciation occurs.
Sympatric species are closely related and are in overlapping regions.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Population Bottlenecks:
The effect of an event or series of events that dramatically reduces the size of a population and
causes a severe decrease in the gene pool of the population, resulting in large changes in allele
frequencies and a reduction in genetic diversity.
For example, an environmental disaster could lead a drastic decrease in population size which
reduced the gene pool dramatically, the survivor group are vulnerable to complete loss of
important alleles and the effect of a single mutation or a new individual is amplified.

Founder Effect:
The loss of genetic variation that occurs when a small number of individuals become isolated,
forming a new population with allele frequencies not representative of the original population.
Any unusual genes in the founder members of the new population may become more frequent
as the population grows.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

6. Conservation: Why and How?

The variety of life has been becoming more and more extensive, but it’s also threatened by
human activity, human population is growing at rapid rates, demand on supplies is increasing,
we are taking more supplies than we need and they are being depleted.

Climate change has been highly suggested to be linked to our activities, temperatures are rising
and extreme weather events have been occurring more and more.
The extinction of species and losing genetic biodiversity causes a reduction in global
biodiversity, some species have already become extinct and lots of species are endangered,
they have low populations and their habitat is threatened.

Conservation involves the protection and management of endangered species in hope them not
going extinct.

Zoos provide captive breeding programs that involve allowing animals to breed under
controlled environments, animals that are endangered or that are already extinct in the wild,
through breeding, we can increase the population number.
Although some problem arose, such as animals having problems breeding outside of their
natural habitat which is often hard to recreated in zoos and lots of people think it’s a cruel act
to keep the animals captive even if its for the animals’ own good.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Seedbanks store a huge number of different species of plant seeds in hopes of helping in their
preservation and to conserve endangered plant species, the seeds can be used to regrow species
that have become extinct in the wild.
The seedbanks also help conserve genetic diversity by storing many seeds with different alleles
of the same species.
Seedbanks provide the cool and dry conditions which are necessary for storage for long periods
of time and they also test the seeds for genetic diseases and if they can be regrown back, and
new seeds are harvested and restored as well.
Advantages to Having Seedbanks:
1. Cheaper than storing fully grown plants.
2. Lots of seeds can be stored in a small space.
3. Less manual labor is needed.
4. Seeds can be stored anywhere cool and dry, conditions of growth from the natural
habitat are hard to recreate.
5. Seeds are less likely to be damaged by disease or natural disaster.
Disadvantages to Having Seedbanks:
1. Testing for viability is expensive and time consuming.
2. It’s too expensive to store and test all types of seeds regularly.
3. It’s difficult to collect seeds from some plants that grow in remote locations.

Reintroducing Organisms to The Wild:

Organisms from zoos and seedbanks can be reintroduced to the wile which can increase the
population numbers in the wild, which helps conserve their numbers and stops them from
being endangered, it also helps organisms that rely on these plants or animals for food or as a
It also contributes to the restoration of habitats that has been lost.
It does give rise to some problems though:
• Reintroduced organisms could bring back new diseases to habitats.
• They might also behave differently than organisms raised in the wild.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
IAS Biology Unit 2 – Topic 4

Scientific Benefits to Seedbanks and Zoos:

Scientists can benefit from seedbanks, as they can study how plant species are successfully
grown back from seeds, seeds can also be used to grow endangered species for use in medical
research, which means we don’t have to remove endangered species from the wild, but
studying data from seedbank would also means it’s a small and interbred population, so data
may not represent wild plants.
Scientists can benefit from zoos as they increase their knowledge in animal behavior,
physiology and nutritional needs, which could help in conservation efforts in the wild, also
zoos can carry out research not possible on species in the wild such as nutritional or
reproductive studies, but again animals in captivity may act differently to animals in the wild.

Educating and raising awareness about conservation is greatly benefited by zoos as they let
people get close to animals and increases their enthusiasm for conservation work, and
seedbanks allow trainings to be held and seedbanks to be set up all around the globe.

© 2018 – Arranged and Edited by: Abdulrahman Tabaza and Omar Minawi
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