Unit 2: Simplified Lecture Notes

iA2
Biology
iAS Biology
Unit 2
Cells, Development, Biodiversity and
Conservation
Simplified Lecture Notes
Dr. Mohab Megahed

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CONTENTS
Topic 3: Cell structure, Reproduction and Development

• The Ultrastructure of cells 1
• Cell cycle 12
• Gametogenesis and Embryonic development 19
• Stem cells 25
• Studying variation 28
Topic 4: Plant Structure and Function, Biodiversity and Conservation
• Plant physiology 31
• Contemporary drug testing 37
• New Taxonomic grouping 39
• Understanding epigenetics 40
• Ecology & evolution 44
• Core practical 54
Dr. Mohab Megahed

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Ultrastructure of cells
Types of cells
Eukaryotic cells Prokaryotic cells
Nucleus and membrane bound organelles No nucleus or membrane bound organelles
Examples: Animal cells, plant cells, fungal Example: Bacterial cells only
cells
N.B: For a structure to be called a cell it must have:-

› Cell membrane.
› Cytoplasm.
› Genetic material.
© Dr. Mohab Megahed

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Animal cell
1. Nucleus:
› Largest organelle in the cell.
› Has a double membrane (nuclear envelope).
› The outer membrane is covered by ribosomes while the inner
layer is smooth.
› This double membrane has nuclear pores.
The nucleus contains:
1. Nucleolus: Tiny rounded deeply stained structure
2. Genetic material:
› Consists of DNA coiled around histone protein.
› If the cell is not dividing, genetic material appears as dispersed
islands.
› If the cell is dividing, genetic material appears as thread-like
structures.

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Functions of the nucleus:
› Nuclear pores: to facilitate exchange of substances between the nucleus and the
cytoplasm (for example exit of mRNA).
› Nucleolus: formation of ribosomes.
› Genetic material:
1. Stores genetic information.
2. Controls metabolic reactions.
3. Controls cell division.
2. Endoplasmic reticulum
› Flattened interconnected single membrane bound sacs.
› There are two types of endoplasmic reticulum:
Rough endoplasmic reticulum (rER) Smooth endoplasmic reticulum (sER)
Covered by ribosomes. Not covered by ribosomes.
Functions: Function:
› Synthesis & transport of proteins. › Synthesis & transport of lipids.
› Formation of Golgi body.

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3. Golgi body
› Formed by fusion of vesicles released from RER.
› Stack-like collection of flattened single membrane bound sacs known as cisternae.
› It is surrounded by vesicles.
› It has two surfaces:
- A forming surface facing the nucleus.
- A maturing surface facing the cell membrane.
Function of Golgi:
Responsible for modification, packaging and export of proteins
Sample Question:
Describe how insulin is formed and secreted from the cells of pancreas.
› Ribosomes on RER are responsible for formation of the primary protein structure.
› Inside RER, folding into tertiary structure takes place.
› Transport vesicles arise from RER to fuse with the forming surface of Golgi body.
› Inside Golgi, modification of proteins takes place. For example, by addition of
carbohydrates forming a glycoprotein.
› The modified protein (insulin) is packaged in secretary vesicles that pinch off the
maturing surface and move towards the cell membrane to be exocytosed.
N.B:
1) Other possible fates of proteins:
› May stay in the cytoplasm.
› May be part of the cell membrane.
2) Factors that a cell is a secretory cell:
› Prominent RER and Golgi body.
› Large number of ribosomes and
mitochondria.
› Presence of microvilli in the cell
membrane.

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Comparison between Endoplasmic Reticulum and Golgi body:
Similarity Both are single membrane bound.
Differences -Endoplasmic reticulum has interconnected sacs
while Golgi body is a stack-like collection of sacs.
-Only endoplasmic reticulum may be covered by
ribosomes.
-Only Golgi body has a forming surface & a
maturing surface.
4. Ribosomes:
› Non-membrane bound.
› Smallest organelles in the animal cell (20
nm).
› Each ribosome has 2 subunits: a large
subunit and a small subunit.
› Chemical structure: rRNA and proteins.
› There are two types of ribosomes:

80S (Larger) 70S (Smaller)
-Outer Nuclear membrane. - Bacterial cells.
- RER. - Inside mitochondrion.
- Free in cytoplasm. - Inside chloroplasts.
Function of ribosomes:
Formation of primary protein structure (polypeptide chain).

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5. Mitochondria:
› Double membrane bound.
› The outer membrane is smooth while the inner layer is folded into cristae (to increase
surface area for the enzymes of aerobic respiration).
› Mitochondria contain mitochondrion matrix with the following inclusions:
• DNA loops.
• 70S ribosomes.
• Enzymes.
• Phosphate granules.
Function of mitochondria:
Site of aerobic respiration.
6. Lysosomes
› Single membrane bound.
› Stores hydrolytic enzymes.
Functions of lysosomes:
› Breakdown of old organelles.
› Breakdown of cells after death (Autolysis).
› Breakdown of bacteria inside phagocytes.
N.B: Microtubules:
Minute structures consisting of tubulin protein.
Functions of microtubules:
› They form the cytoskeleton; so they guide organelles moving inside the cell.
› Formation of:
• Flagella.
• Cilia.
• Centrosomes.

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7. Centrosome:
› Non-membrane bound.
› Consists of 2 centrioles.
› Each centriole consists of 27 microtubules arranged in 9 triplets.
Function of centrosomes:
They duplicate during cell division and move to the opposite poles of the cell
to be able to hold spindle fibers.
N.B: Centrosomes are only found in animal cells.

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Plant cells
Same organelles as the animal cell plus:
1. Chloroplasts: Double membrane bound

› Both membranes are smooth.
› They contain Thylakoid membranes which:
› Store chlorophyll pigment.
› Are grouped in grana connected by intergranal thylakoids.
› They contain stroma
with the following
inclusions:
• DNA loops.
• Enzymes.
• 70S ribosomes.
• Starch grains.
Function of chloroplasts:
Site of photosynthesis.

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2. Amyloplasts:
› Double membrane bound.
› Store concentric layers of amylopectin.
Function of amyloplasts:
Convert amylopectin to glucose according to the needs of the
cell.
N.B: Amyloplasts are only found in plant cells.
3. Sap vacuole:
› Single membrane bound.
› This membrane is known as Tonoplast.
› Contains sap solution (water, salts, mineral ions).
Function of sap vacuole:
Maintains turgidity
Double membrane Single membrane bound Non-membrane

bound
bound
Nucleus Endoplasmic reticulum Ribosomes
Mitochondria Golgi body Centrosomes
Chloroplasts Lysosomes (Nucleolus)
Amyloplasts Sap vacuole

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Bacterial cell (Prokaryotic cell)
Structures that must be present in the bacterial cell:

› Cell wall: made of murein (Peptidoglycan)
› Cell membrane
› Cytoplasm
› Nucleoid:
• Circular DNA.
• No histone protein.
• They don’t form chromatin.
› 70S ribosomes
› Food stores (Oil droplets)

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Structures that may be present in the bacterial cell
› Slime Capsule: Thick layer of polysaccharides that protects the cell from antibodies,
antibiotics and dehydration. It also acts as a food store.
› Flagellum: Allows for movement by propulsion.
› Pili: Allow bacteria to attach to each other and to nearby surfaces.
› Plasmids:
• They have non-essential genes.
• Used by humans in genetic replication.
› Mesosomes: Enfoldings of the cell membrane that may store chlorophyll pigment or
respiratory enzymes.
N.B:
1- According to the shape of the colony, bacteria may be described as:
› Coca
› Bacilli
› Spirilla
2- According to staining, bacteria could be either gram positive (Purple) or gram negative (Pink).
Comparison between Eukaryotic & Prokaryotic cells

Eukaryotic Prokaryotic
Size Larger Smaller
May be unicellular or
Cellular nature Always unicellular
multicellular
Cell division Mitosis or Meiosis Mitosis
Reproduction Sexual or Asexual Asexual
Nucleus Present Absent
Linear DNA Circular DNA
Genetic material Histone present No histone
Forms chromatin No Chromatin
Membrane bound
Present Absent
organelles
Cell wall Maybe present or absent Always present
Ribosomes(free
80S 70S
ribosomes)
Plasmids, Pili & Slime
Never present May be present
capsule

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Cell Cycle
1) Interphase (80% of cell cycle duration)
1. G1 phase: 1st phase of growth
• ATP formation.
• Protein synthesis.
• Duplication of oragnelles.
2. S phase: Synthesis of DNA

In this phase, DNA replication takes place leading
to doubling of the DNA content of the cell so that
when the cell divides, each daughter cell can restore
the original DNA content.
3. G2 phase: 2nd phase of growth

• Enlargement of cytoplasm.
• Duplication of centrioles.
N.B Interphase summary:

Interphase is the preparation for cell division
in which duplication of organelles, replication
of DNA and enlargement of cytoplasm all take
place.
2) Cell division
i. Nuclear division: Mitosis and Meiosis.
ii. Cytoplasmic division: Cytokinesis.
Mitosis
It occurs in 4 steps
› Prophase
› Metaphase
› Anaphase
› Telophase

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1) Prophase
› Nuclear envelope and nucleolus disappear.
› Chromosomes condense and become visible as thread-like structures.
› Centrioles start their journey to the opposite poles of the cell.
› Spindle fibers formation starts.
2) Metaphase
› Centrioles arrive to the opposite poles of the cell.
› Spindle fibers are fully formed.
› Chromosomes are aligned at the equator of the cell held by spindle fibers attached to their
centromeres.

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3) Anaphase
› Spindle fibers shorten.
› Sister chromatids are separated due to the breakage of the centromere.
› They are now called single chromosomes and each of them is moving towards one pole
of the cell.
4) Telophase (Reverse of prophase)

› Spindle fibers are broken down.
› Nuclear envelope and nucleolus reform.
› Chromosomes decondense and the genetic material appears as dispersed islands of
chromatin again.

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3) Cytokinesis
Intucking of the cell membrane separating the cell
into two daughter cells.
N.B Significance of Mitosis:

It produces two genetically identical diploid cells which is important for:
1. Growth: by increasing the number of cells.
2. Tissue repair: by replacing damaged cells.
3. Asexual reproduction.
N.B Significance of the cell cycle:

Interphase summary + Significance of mitosis.
DNA content graph
N.B Homologous chromosomes

Def: Chromosomes having alleles for the same characteristics over the same loci, one belongs to
the father and the other belongs to the mother.

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Overview on meiosis
2n
Meiosis I
n n
Meiosis II
n n n n
Meiosis I
1) Prophase I
Same as mitosis +
› Pairing up of homologous chromosomes forming bivalents.
› Crossing over between non-sister chromatids of the homologous pair with reshuffling of
alleles. This produces a new combination of alleles on each chromosome. (1st cause of
variation)

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2) Metaphase I
Random assortment of homologous chromosomes above and below the equatorial plate producing
a new combination of chromosomes in each daughter cell. (2nd cause of variation)
3) Anaphase I
Shortening of spindle fibers with no breakage of the centromere.
4) Telophase I
Same as mitosis.
Cytokinesis
Same as mitosis.
Meiosis II
Same as mitosis.

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N.B Causes of Variation in meiosis:
Prophase I:
Crossing over between non sister chromatids of the homologous pair with reshuffling of alleles.
This produces a new combination of alleles on each chromosome. (1st cause of variation)
Metaphase I:
Random assortment of homologous chromosomes above and below the equator producing a new
combination of chromosomes in each daughter cell. (2nd cause of variation)
N.B Significance of meiosis:
› It gives rise to variation which increases adaptation the environment.
› It’s a reduction division producing haploid gametes so the diploid full set of
chromosomes is restored after fertilization with no doubling of the chromosomal number.

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Gametogenesis and Embryonic Development

Gametogenesis in plants
Gametogenesis in males Gametogenesis in females
• The anther contains Microspore cells which • The ovule contains Megaspore cells which are
are diploid. diploid.
• They undergo meiosis to give 4 different
• They undergo meiosis to give 4 different haploid nuclei.
haploid nuclei. • 3 of the formed cells die and only 1 continues
• Each of the 4 cells formed undergoes 2 to undergo 3 mitotic divisions forming an
mitotic divisions to form a pollen grain. embryo sac with 8 haploid nuclei.
• The first mitotic division forms a pollen
tube nucleus & a generative nucleus.
• Only the generative nucleus undergoes the
second mitotic division forming 2 male
nuclei.
Each Pollen grain contains 3 haploid nuclei: Each Embryo Sac contains 8 haploid nuclei :
• 2 male nuclei:: • 1 egg nucleus: fertilized by one of the

1 haploid nucleus fertilizes the male nuclei forming a zygote.
haploid female egg cell forming a • 2 synergid nuclei: attract the male nucleus
diploid zygote. to the egg nucleus.
The other haploid nucleus fuses • 2 polar nuclei that fuse forming a diploid
with the diploid polar nuclei nucleus.
forming the triploid Endosperm. • 3 antipodal nuclei.
• 1 pollen nucleus that forms the pollen
tube.

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Fertilisation in plants
› When the pollen grain lands on the stigma of the same species, it absorbs nutritive fluid
and germinates. Now the pollen tube nucleus can guide the secretion of enzymes,
digesting the style and forming the pollen tube.
› The pollen tube forms a pathway from the stigma above to the micropyle below through
the style. This allows for the descent of the male generative nuclei for double fertilisation
to occur. (Role of pollen tube)
› Double fertilisation occurs as follows: a haploid generative nucleus fuses with the haploid
egg nucleus in the ovule forming a diploid zygote, and the other haploid male generative
nucleus fuses with the diploid polar nuclei forming a triploid endosperm that forms a
food store.

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Gametogenesis in mammals
Males (Testes) Females (Ovary)
Spermatogenesis in Males Oogenesis in Females
Spermatogenesis
› It occurs through mitosis followed by meiosis.
› Spermatogenesis is a continuous non-cyclic process that starts at puberty and ends by
death.
Oogenesis
› It occurs through mitosis followed by meiosis.
› Oogenesis is a discontinuous cyclic process that starts at puberty and ends at menopause.
It occurs on a monthly basis.
› Meiosis I occurs at the time of ovulation every month producing a secondary oocyte that
is released in the outer third of the oviduct.
› Only in case of sperm head arrival to the secondary oocyte membrane, the secondary
oocyte undergoes meiosis II producing a mature ovum ready for fertilisation and a polar
body that dies.

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Gametes in animals
Sperms
› Sperms are: Many to increase chances of fertilization.

Mini to swim easily consuming less energy.
Motile to swim reaching the secondary oocyte in the oviduct.
› Shape: stream-lined shape to break resistance while swimming.
› Structure:
1) Head:-
• Cell membrane.
• Little cytoplasm to be small enough for easy movement consuming less energy.
• Haploid nucleus to restore the diploid full set of chromosomes after fertilisation
and to avoid doubling of chromosomal number.
• Acrosome: Acrosomal reaction.
2) Midpiece: contains mitochondria which are responsible for:
• aerobic respiration (1)
• which produces ATP (2)
• as a source of energy for moving the tail for swimming (3)
3) Tail: consists of microtubules needed for swimming to reach the 2ry oocyte in the
oviduct.

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Egg cells
› Egg cells are large in size to increase surface area which increases chances of fertilization
and to be able to store enough energy.
› Structure:
1) Follicular cells of the corona radiate: They secrete chemicals to attract the male sperm
and trigger their capacitation. (Full maturation)
2) Zona pellucida & Cortical granules: Cortical reaction.
3) Food stores (oil droplets): To provide energy for future mitotic division of the potential
zygote.
4) Huge number of mitochondria: They are responsible for aerobic respiration which
produces ATP as a source of energy for future mitotic division of the potential zygote.
5) Haploid nucleus: To restore the diploid full set of chromosomes after fertilisation and to
avoid doubling of chromosomal number.
Comparison between sperms and egg cells
Similarity:
› Both are produce by meiosis.
› Both have haploid nuclei.
Differences:
› The sperm is smaller & stream-lined while the egg cell is large and rounded.
› The sperm has an acrosomal cap while the egg cell has cortical granules.
› The egg cell has much more mitochondria & larger food stores than the sperm.
› Only the sperm has a tail.
› Only the egg cell has follicular cells & zona pellucida.

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Fertilisation in mammals
› The follicular cells of the corona radiata secrete chemicals to attract male sperms and
trigger their capacitation.
› The sperm passes in between follicular cells to reach the zona pellucida.
› When the sperm reaches zona pellucida, its acrosomal cap swells and fuses with the
sperm head membrane. This allows for exocytosis of hydrolytic enzymes that digest the
zona pellucida forming a tunnel for sperm penetration to reach the 2ry oocyte membrane.
(Acrosome reaction)
› Once the sperm head gets in contact with the secondary oocyte membrane the following
occurs:
1) Meiosis II occurs which converts the secondary oocyte into a mature ovum ready for
fertilisation.
2) Endocytosis of the sperm haploid nucleus to fuse with the ovum haploid nucleus
forming a diploid zygote.
3) Exocytosis of the enzymes in cortical granules that fuse with zona pellucida. These
enzymes convert the zona pellucida into a tough fertilisation membrane to prevent
polyspermy (entry of other sperms). (Cortical reaction)

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Stem cells
Fate of the zygote
› The zygote divides by mitosis producing an embryo.
› The 16 cell stage embryo is known as morula.
› Each cell in the embryo now is totipotent.
N.B Totipotent:
Def. It’s an undifferentiated cell that can give rise to any type of tissue. All the genes are switched
on. It can divide an unlimited number of times. (No Hayflick’s limit)
› A fluid filled cavity appears in the centre of the embryo forming a blastocyst. The
blastocyst has two regions:
1) Outer cell layer: It gives rise to the placenta & fetal membranes. (Extraembryonic
tissues)
2) Inner cell layer: It is pluripotent.
N.B Pluripotent:
Def. Undifferentiated cells that can give rise to any type of tissue except extraembryonic tissues.
All the genes are switched on except genes of placenta & fetal membranes. It can divide an
unlimited number of times. (No Hayflick’s limit)

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Stem cells
Def: They are undifferentiated cells that can give rise to any type of tissue.
Properties: All their genes are switched on. They can divide an unlimited number of times (No
Hayflick’s limit).
Sources of stem cells:

1) Embryonic stem cells produced by embryo splitting during IVF. (Totipotent)
2) Umbilical cord blood sampling. (Pluripotent)
3) Bone marrow sampling. (Multipotent)
How cells specialize

› A certain stimulus arrives to the cell which maybe chemical such as a hormone. This
stimulus leaves some genes switched on & active while it switches off other genes.
› Only switched on genes are transcribed and translated producing certain proteins.
› These proteins cause permanent alteration to the structure & function. The cell is now
said to be specialized.
Evaluation of stem cells:

Advantages:
They are (properties) so they are used to treat patients by:
1) Tissue repair through replacement of damaged cells.
2) Producing organs for transplantation.
Disadvantages:
1) Risk of Cancer due to uncontrollable cell divison.
Tissue rejection if taken from another person.
Infection due to transmission of pathogens.
2) Difficulty to find the exact triggers of differentiation.
3) There is an ethical controversy.

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Ethical controversy:
Against:
› An embryo is a potential life that may be terminated during stem cell research.
› It encourages IVF in which females are given high doses of hormones that may be
carcinogenic.
› It’s a highly costing process which may lead to discrimination according to the financial
status.
› It opens doors for gene manipulation (designer babies).
For:
› Embryo splitting doesn’t involve killing embryos.
› The ultimate fate of most embryos is death.
› Benefits outweigh risks and the welfare of mankind is a priority.
› Alternatives to embryonic stem cells are not successful yet.
Regulatory authorities
They are needed to set codes of practice regulating stem cell research.
For example: Deciding the maximum age of used embryos
Deciding on the maximum number of embryos to be used in the stem cell
research
These authorities should include:
1) Stem cell researchers: to provide informed opinions based on their knowledge &
expertise.
2) Others (religious figures or human rights activists): to provide a balanced counter
argument.
N.B: Advantages of taking stem cells from the same person:
› Same genetic makeup so same antigens & no risk of tissue rejection.
› Low risk of infection.

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Variation
Types of Variation
Continuous variation Discontinuous variation
(Weight, height, IQ, etc…) (Gender, Blood group)
Affected by the environment & genes Affected by the genes only
Controlled by many genes on different loci
Controlled by one gene only
(Polygenic inheritance)
Usually represented by a histogram or a curve Usually represented by a bar graph
N.B Important definitions:

• Phenotype: Observable features of a certain individual that usually arise from interaction
between genes and the environment.
• Polygenic inheritance: A characteristic is controlled by many genes on different loci. This
gives rise to continuous variation.
• Gene locus: Position of a certain gene on a certain chromosome.
Examples of variation
1) Height
› The achievement of the genetic potential for height is controlled by many environmental
factors. (It is affected by both genes and the environment)
› Environmental factors affecting height includes:
• Diet containing calcium, vitamin D & proteins.
• Presence of chronic diseases or infections.
• Stretch sports.
2) Siamese cats
› They have a gene coding for tyrosinase enzyme which converts tyrosine
into melanin, so according to genes, these cats are expected to be black in
colour.
› However, their core body temperature is high enough to denature
tyrosinase, so the cats turn to be white in colour all over their bodies
except for the extremities which are affected by the external environment.
› Cold environment may lead to black extremities while a hot environment
may lead to white extremities.

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3) MAO A levels
› High Levels of MAO A Tendency for aggression & antisocial behavior.
› Low levels of MAO A Depression & Parkinson’s disease.
› The levels of MAO A show an example of interaction between genes & the environment.
› Environmental factors affecting MAO A levels might include:
• Maltreatment & stress during childhood increase MAO A levels.
• Repeated physical traumas to the head decrease MAO A levels.
4) Tumours
› There are two types of genes controlling the speed of the cell cycle:
• Protooncogenes that that increase the speed.
• Tumour suppressor genes that decrease the speed.
› The normal activity of both types of gens leads to an average speed of the cell cycle. (No
tumours)
› However, a mutation might occur changing protooncogenes into ooncogenes leading to a
marked increase in the speed of the cell cycle ending up by tumour formation.
› This mutation might be due to genetic or environmental factors such as:
• Chemical: Tar / Asbestos gas.
• Radiators: X-ray & UV rays of the sun.
• Viruses: HIV & HPV.
Assessment of variation
Twin studies
› Identical twins have the same genes, so any difference is due to environment only.
› Non-identical twins have different genes, so any difference is due to the genes (mainly)
and the environment.
› This …… is affected by both genes and the environment.
› Evidence for environmental contribution: similarity between identicals is not 100%.
› Evidence for genes contribution: similarity between identicals is higher than non-
identicals.
› The effect of …… is higher than ……
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Plant Physiology
Cellulose
› It’s a polymer of β-glucose monomers joined together by β-1,4 glycosidic bonds formed
through condensation reactions. Every other monomer is inverted so that bonding can
take place.
› A cellulose molecule is straight & unbranched.
› Cellulose molecules are joined together by intermolecular hydrogen bonds. (Cross
linkages)
› A microfibril consists of many cellulose molecules cross linked by hydrogen bonds.
› The cell wall consists of cellulose microfibrils embedded in a matrix of hemicellulose and
protein.
Comparison between starch & cellulose

Similarity:
Both polymers of glucose monomers joined together by glycosidic bonds formed through
condensation reaction.
Differences:
› Starch consists of α-glucose while cellulose consists of β-glucose.
› In cellulose, every other monomer is inverted while in starch, all monomers have the
same orientation.
› Only starch may have 1,6 glycosidic bonds.
› Cellulose is straight & unbranched unlike starch which may be helical (amylase) or
branched (amylopectin).
› Only cellulose has intermolecular hydrogen bonds.

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Cell wall arrangement
Cell wall
Middle lamella
› It’s a glue-like material consisting of calcium & magnesium pectate.
› It holds the microfibrils of adjacent cell walls together. This increases tensile strength.
Primary cell wall
› Consists of one layer only.
› It has a net-like arrangement of microfibrils. (Criss-cross pattern)
› These microfibrils are embedded in a matrix of hemicellulose & pectin.
Secondary cell wall
› Consists of multiple layers.
› Within each layer, microfibrils are parallel to each other but they form angles with other
layers. (Overall net-like)
› These microfibrils are embedded in a matrix of hemicellulose & pectin.

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Plasmodismata Pits
Cytoplasm filled tunnels Cytoplasm filled grooves

Differences No secondary or primary No secondary cell wall but
cell walls the primary wall is present
Lined by cell membrane Lined by cell membrane

Similarities Facilitate intercellular Facilitate intercellular
transport transport
Properties of the cell wall/plant fibres
› Tensile strength due to the net-like arrangement of microfibrils within the cell wall.
› Flexibility due to the presence of the matrix and the glue-like middle lamella.

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Plant Stem
Xylem
› Hollow dead vessels with no end plates.
› It has thick lignified walls, as lignin is deposited in the secondary cell wall.
› Xylem has pits.
› Function: Transport of water & mineral ions from roots to leaves. It also provides
structural support.
Adaptations of xylem
1) High tensile strength due to the net-like arrangement of microfibrils in the cell wall, and
presence of lignin in the 2ry cell wall. This helps to withstand high water pressure.
2) Lignin is water proof. This prevents leakage of water outside xylem vessels.
3) Xylem has pits. This allows to bypass any blockage.
4) Xylem has no end plates so that water can be transported from the roots to the leaves.
5) Xylem is narrow. This maintains high pressure. (Capillarity)
Properties of lingocellulose fibres
1) High tensile strength.
2) Flexibility matrix (lignin reduces flexibility)
3) Water-proof presence of lignin.
4) Light in weight xylem vessels are hollow & dead.
Cambium
A layer of undifferentiated cells that can give rise to other types of tissue.

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Phloem
› Sieve tubes with perforated end plates.
› Responsible for translocation of sucrose & amino acids from source to sink.
› Translocation is a bidirectional process.
Sclerenchyma
› Closed structures with tapering ends.
› Hollow & dead with thick lignified walls.
› Function: provides structural support.
Comparison between xylem & sclerenchyma

Similarities:
› Both have thick & lignified walls.
› Both are hollow & dead.
› Both provide structural support.
Differences:
› Xylem has no end plates while sclerenchyma has closed tapering ends.
› Only xylem has pits.
› Only xylem has transports water & mineral ions.

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Plant Root
N.B
Importance of water
› Perfect transport medium as it moves in one unbroken column so it delivers
mineral ions from the root to the leaves
› Water is a reactant in photosynthesis
› Cooling of the leaves
Importance of mineral ions

› Nitrate ions Amino acids Proteins Enzymes Photosynthesis
Growth
› Magnesium ions Chlorophyll pigment Traps sunlight Photosynthesis
Growth
› Calcium ions Calcium pectate in the middle lamella Holds microfibrils
of adjacent cell walls together Higher tensile strength Better growth

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Contemporary Drug Testing

Drug testing
Historical drug testing Contemporary drug testing
Historical drug testing

William Withering tried digitalis soup on a number of patients
and he had the following results:-
› Some improved
› Some didn’t improve
› Some died
He was the first to extract the active ingredient
adjust the dose
Contemporary drug testing
Preclinical phase Clinical phases

(Animal testing phase)
Phase I Phase II Phase II
Preclinical phase (Animal testing)
The drug is tested on animals to monitor & exclude toxicity.
N.B: Laboratory bred rats may be used in this phase, why?
› Animal testing allows scientists to check how the drug is
metabolized in a whole organism to exclude toxicity.
› Rats have a similar genetic makeup to that of humans.
› Laboratory bred organisms have the advantage of being
genetically similar to each other.

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Clinical phase I
› The drug is tested on healthy paid volunteers
› This aims at monitoring & excluding any major unexpected side effects.
Clinical phase II
› The drug is tested on a small number of patients. (100-500)
› This aims at:
• Monitoring effectiveness.
• Confirming safety.
• Adjusting the dose.
Clinical phase III
› The drug is tested on a large number of patients. (1000-5000)
› This allows to have a representative sample o we can undergo statistical analysis
comparing the tested drug to other drugs already available in the market.
N.B: Both clinical phases II & III include the use of placebo & double blind trials:
• Placebo: A control drug with no active ingredient. It’s used for comparison
with the real drug & to assess the magnitude of psychological effect.
• Double blind trials: Neither the doctor nor the patient know who is taking the
real drug & who is taking placebo. This eliminates bias.
Comparison between historical & contemporary drug testing

Similarities:
› Both include testing patients.
› Both include extraction of the active ingredient.
› Both include adjusting the dose.
Differences:
› Only contemporary drug testing:
• includes animal testing.
• involves healthy volunteers.
• pays volunteers.
• involves placebo & double blind trials.
• involves statistical analysis.

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Taxonomic grouping
Taxonomy:
› Def. The science of classifying living organisms into groups. This could be according to
morphology, behavior or molecular features. Living organisms with similar features are
placed in the same group.
› Old taxonomic grouping: classified living organisms into 5 kingdoms.
› New taxonomic grouping (by Carl Woose-1977):
• It divided living organisms into 3 domains: Eukarya, Archaea, and Bacteria.
• This classification is based on molecular phylogeny.
› Molecular phylogeny: Molecular refers to comparing molecules in the 3 domains such
as proteins, DNA, RNA, ribosome structure, cell membrane & cell wall structure as well
as ability to resist extreme conditions. Phylogeny is a term that refers to ancestral
relationships. (order of evolution)
N.B: Both archaea & bacteria are prokaryotic cells while eukarya domain includes
eukaryotic cell.
N.B: Eukrya & archaea are closely related.
Phylogenetic tree of life
How to validate a new evidence?

1) The new evidence should be written in a scientific paper.
2) The scientific paper is peer reviewed looking for: validity of methods, reliability of results
& plagiarism exclusion. Peer review is done before publishing.
3) Critical evaluation is done which includes: repeating all experiments to check if the results
would be replicated or not & comparing the results to other studies. This allows to collect
more evidences through cross-checking.
N.B: Where to publish a scientific paper?
Scientific journal/magazine/book
Scientific conference
Internet
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Understanding Epigenetics
› Gene expression can be regulated by chemical modifications to chromosomes. These are
known as epigenetic changes.
› Epigenetics are not similar to mutations; they don’t change the base sequence of DNA.
They only affect gene expression, in other words, they determine if the gene would be
switched on or switched off.
› This is achieved through chemical tags added to DNA or or to the associated to DNA
known as histones.
› All Chemical tags attached to the DNA or histone are known as the epigenome of the
cell.
› Epigenetic modifications may normally occur during
development of an organism and may also be induced later in
life by environmental factors such as diet, smoking or
exercise.
› When a cell divides to make daughter cells, many of these
chemical tags are also passed on to the next cell. So epigenetic
modifications are heritable.
N.B Epigenetics refers to changes in DNA that alter the expression of genes
without changing base sequence of DNA itself. These changes can be caused by
environmental factors and are heritable.
› This Regulation/modification of gene expression is achieved through chromatin

remodeling:
Chromatin remodeling:
Chromatin is a term referring to the complex formed by DNA & Histones.

The addition of certain chemical tags to histones or the DNA changes how tightly packed the
chromatin is.
› When chromatin is tightly packed, the DNA wrapped around histone is not accessible to
RNA polymerase and transcription factors. If RNA polymerase and transcription factors
can’t bind, then transcription cannot occur and thus the gene is not expressed (silencing
of the gene). Tightly packed chromatin is known as Heterochromatin.
› When chromatin is loosely packed, the DNA
is exposed and is accessible to RNA
polymerase and transcription factors. RNA
polymerase can bind and transcription takes
place thus the gene is expressed. Loosely
packed chromatin is known as Euchromatin.
Now we need to understand examples of the chemical tags added to DNA & Histones and how
this leads to chromatin remodeling.

41
These chemical tags include: DNA methylation, Histone methylation & Histone acetylation.
DNA Methylation
› Methyl groups are added to the DNA at specific locations called CpG sites – this is where
cytosine in found next to guanine in the DNA chain.
› Methyl groups are added to the cytosine base by an enzyme called DNA
methyltransferase.
› DNA methylation inhibits transcription through attracting other proteins that condense
chromatin so it becomes tightly packed (heterochromatin) & DNA is inaccessible to
transcription factors and RNA polymerase enzyme. (Methylation may also physically
block the binding of RNA polymerase & transcription factors)
› The addition of methyl groups to DNA is known as methylation and their removal in
known as demethylation.
Histone Methylation
› Histones can be modified by the addition of Methyl group to the amino acid Lysine.
› This addition of positively charged Methyl group adds positive charges to Lysine so it is
strongly bonded to the negative charges of DNA. This stimulates to the formation of
more tightly packed chromatin which is also known as Heterochromatin leading to
silencing of the gene.
› Removal of Methyl group from Histone is known as Histone demethylation.

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Histone Acetylation
› Histone can also be modified by the addition of acetyl group to the amino acid Lysine.
› This addition of negatively charged Acetyl group neutralizes the positive charge of
Lysine so it is no more bonded to the negatively charged DNA. This stimulates the
formation of loosely packed chromatin which is also known as Euchromatin leading to
gene expression.
› Removal of Acetyl group from Histone is known as Histone deacetylation.

In a Nutshell:
Genes are silenced by: DNA Methylation, Histone Methylation & Histone Deacetylation.
Genes are expressed by: DNA Demethylation, Histone Demethylation & Histone
Acetylation.

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Practice Question
Histone acetyltransferase is an enzyme involved in the acetylation of histone proteins.

a) Explain the role that histone acetyltransferase plays in the expression of genes. (3)
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b) Explain what is meant by the term epigenetics. (2)
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c) Explain how the action of DNA methyltransferase can alter gene expression. (6)
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Ecology
Basic definitions
› Habitat: The place where a living organism seeks food, shelter & reproduction
› Population: Number of living organisms in a certain area or habitat from a certain
species
› Community: All living organisms in a certain area or habitat
› Ecosystem: Interaction between living organisms & the non-living environment
› Niche: Role of a living organism in its habitat (How a living organism exploits resources
in its habitat). For example: feeding niche, nutrient cycle niche & habitat niche.
Adaptations to niche
› Anatomical adaptations: structural features
› Physiological adaptations: biochemical features for
metabolic reactions
› Behavioural adaptations
Natural selection
› A mutation occurs introducing favourable allele coding for a desirable characteristic
which is……
› Individuals with the desirable characteristic survive more as……
› Surviving individuals reproduce passing the alleles of…… to their offspring. This
increases allele frequency
How natural selection leads to evolution?
Due to natural selection, some of the members of a certain species may become markedly different
up to the extent of being unable to reproduce with the original members of the species. This is
known as reproductive isolation which leads to speciation.
N.B: Causes of reproductive isolation:

1) Mechanical isolation: incompatible sex organs
2) Behavioural isolation: different mating behaviour
3) Gametic isolation: the female gamete fails to attract a male gamete
N.B: Speciation: evolution of different species from a common ancestor

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Biodiversity
Biodiversity= Species Richness + Genetic diversity.
Species richness
Def: The number of different species in a certain area or habitat. It
doesn’t take abundance into consideration. It’s measured by random
sampling.
Importance of high species richness biodiversity:
› Animals & plants are interdependent.
› Animals depend on plants as sources of food & maybe habitats.
› Plants depend on animals as seed dispersal is done by birds,
pollination is done by bees & animal wastes act as manure.
› So in high biodiversity, the ecosystem can function & self-regulate while in low bio
diversity, the natural equilibrium is lost.
Genetic diversity
Def: Variety of alleles in the gene pool of a certain population. It’s measured by DNA analysis.
Importance of high genetic diversity:
› High variety of alleles in the gene pool which measures the chances of having favourable
alleles coding for desirable characteristics such as disease resistance (/better hunting
skills/water deficiency tolerance in plants)
› This increases adaptation to the environment leading to more survival.
Inbreeding effect
Def: Mating of closely related individuals.
1) Low genetic diversity: as there is no introduction of new alleles by outbreeding
2) Promotes homozygosity: it increases the chances of the appearance of recessive inherited
disorders in the offspring.
Endemic species
Def: Species that are only found in one geographical location. Endemic species are commonly
seen in islands as they might have evolved in the island & failed to migrate out. (Endemic
species=Obligatory outbreeding)
Small population effect

1) Low genetic diversity: As they already have a small gene pool & they undergo obligatory
inbreeding
2) Genetic drift: Permanent loss of a favourable allele when an organism accidentally dies
out.

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Founder effect
Def: When a small number of members of a certain population moves
to another area establishing a new population. This new population is a
small population
Conservation
Def: Protection of endangered species from extinction.
N.B: Extinction maybe due to:

1) Biotic factors Diseases
Lack of food
2) Abiotic factors Temperature
Water availability
3) Habitat loss Floodings
Deforestation
Conservation of animals
Animal conservation could be either insitu (natural reserve) or exsitu (zoo). Insitu conservation
has the advantages of natural intraspecific and interspecific relationships. As well as less stress &
discomfort. This encourages animals to grow & reproduce which increases genetic diversity.
However, the challenging biotic & abiotic factors usually make insitu conservation impossible.
Captive breeding programs in zoos
Zoos aim at encouraging reproduction & protection from predation. This increases population size
leading to larger gene pool with higher genetic diversity. This is followed by reintroduction into a
natural habitat.
How to encourage breeding
› Selection of suitable mates & records of breeding are kept in stud books.
› Encouraging interzoo animal movement, this is a form of outbreeding which increases
genetic diversity by introducing new alleles.
› Using modern technology such as AI or IVF to increase reproduction.
Preparation for reintroduction
› Encouraging wild behaviour through reducing the mass of food offered and hacking out.
› Selection of a suitable natural habitat.
› Raising awareness of the residents of the selected habitat about the risk of extinction and
human practices increasing this risk.

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Conservation of plants
› Select large number of seeds from different plants in different countries to increase
genetic diversity.
› Seeds are X-rayed to check for embryo viability & food stores.
› Surface sterilization of seeds by a cotton soaked in ethanol to remove any bacteria that
may cause diseases or decomposition.
› Seeds are stored in dry cold conditions. Drying prevents activation of bacterial enzymes
so it prevents diseases and decomposition as well as seed enzymes so it prevents
germination. Drying reduces freezing effect. Very low temperature inhibits the enzymes
of bacteria so less diseases and decomposition as well as seed enzymes so no
germination.
› Storage conditions should be checked on regular basis by removing a random sample of
seeds & planting them in the soil ( If germination success is lower than 75% you will
O
need to readjust storage conditions) then replace removed seeds by others from the plants
you have grown.
Why we use seed banks not whole plants?

› Large number of seeds can be stored so larger gene pool with higher genetic diversity.
› This large number can be stored in a small space so it is cost effective.
› We can freeze seeds but we can’t freeze a whole plant.
› Removing seeds doesn’t affect parent plant.

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Calculating Biodiversity
Species richness: number of different species present in a certain area.

Species evenness: is a measure of the relative abundances of different species in a certain area.
Practice: Use this table to select the wood with the highest species evenness and explain your
answer.
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Simpson’s biodiversity Index
It is a quantitative measure of diversity in a habitat that gives a comparable score.
Formula:
or
N= Total number of organisms of all species.
n= number of organisms in a certain species
∑= Sum of.
Practice:
Scientists surveyed two fields to assess their biodiversity. For both fields, Calculate the index
of Simpson’s diversity and decide which has the greatest biodiversity.
wont I
5311
660 X
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90
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Calculating Genetic diversity
Genetic diversity: the variety of alleles in the gene pool of a certain population. Measured by
DNA analysis for the genome of individuals.
Genetic diversity can be estimated by observing the physical differences between individuals in a
certain population.
If a population has a wide variety of different alleles, it is more likely for this population to have a
large percentage of heterozygous individuals. So to take a quantitative estimate of genetic
diversity we can use a formula know as heterozygosity index which is calculated as follows:
h= Number of heterozygous individuals in a certain population
Total population size
Practice: Calculate the heterozygosity index for a population of 8000 in which there are 3000
heterozygous individuals.
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However, as mentioned in the definition, the most accurate method of measuring genetic diversity
is to undergo individual DNA analysis.

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The Hardy-Weinberg principle
It is a mathematical formula allowing scientists to use simple equations to calculate allele

frequency in a certain population.
The frequency of a dominant allele (F) is represented by the letter p.
The frequency of a recessive allele (f) is represented by the letter q.
This allows us to derive the first simple formula:
p+q=1
Then from crossing two heterozygous parents they derived the second formula:
P2 + 2pq + q2 = 1
However, this Hardy- Weinberg principle makes several unrealistic assumptions including:
› No mutations.
› No natural selection.
› Random mating is occurring.

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Practice Question 1
What is the value of p if q=0.3?
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Calculate the frequency of all possible genotypes in this population.
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Practice Question 2
If there are 700 individuals suffering from cystic fibrosis in a population of 25000, then,
using the Hardy-Weinberg principle, calculate how many individuals are symptomless
carriers of the recessive allele.
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Introduction to Investigation Questions

Important Terms
› Accuracy:
• This means how correct your measurements are.
• To ↑ accuracy: change the measuring method and use more sensitive measuring
apparatus (sensitive measurements).
› Validity:
• This means how correct is your experimental procedure.
• To ↑ validity: keep all other factors constant to have a fair test (controlled variables).
› Reliability:
• This means how similar your results are.
• To ↑ reliability: replicate your experiment and get average.
Data Organization
Tabulation
› Independent Variable:
It is the variable controlled by the experimenter, it comes in the first column (left and upper / X-
axis).
› Dependent Variable:
It refers to the measured results which depends on the independent variable, it comes in the second
column (right and down).
› Label all columns and rows.
› Include SI units in the heading of your columns and rows.
Remember:
𝑆𝑆𝑆𝑆𝑆𝑆 𝑜𝑜𝑜𝑜 𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟𝑟
› you will be asked to calculate the mean =
𝑇𝑇ℎ𝑟𝑟𝑟𝑟𝑟𝑟 𝑟𝑟𝑆𝑆𝑆𝑆𝑛𝑛𝑟𝑟𝑟𝑟
Graph
› Independent variable on X-axis.
› Dependent variable on Y-axis.
› Use more than 50% of the graph.
› Plot all points accurately. Use circles, crosses or dots.
› Join points with neat straight lines, don’t extrapolate.
› Don’t forget the units in your axes labels.

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Unit 2 Core Practicals

1) Investigating Mitosis by Root Tip Squash
Root structure
› Protective root cap: Zone of dead cells (1mm)
› Zone of cell division: cells are large in number but small in
size (Mitosis)
› Zone of cell elongation: cells are large in size but small in
number
Practical steps
1) Cut the terminal 1 cm of onion root using a scalpel.
2) Transfer to a watch glass containing 2 cm³ of HCl. This softens the tissue by dissolving the
middle lamellae which is a glue-like material holding cells together.
3) Transfer using forceps to a microscopic slide with a drop of stain (Examples:
Acetocarmine, Acetic orcein, Feulgen stain, Schiff’s reagent, Toliudine blue). This
highlights chromosomes to be visible.
4) Use a scalpel to cut the tissue again into smaller pieces. This increases surface area for
better uptake of stain by diffusion.
5) Cover the tissue sample with a cover slip.
6) Insert the slide into a slide warmer. Heat provides kinetic energy to intensify the stain by
increasing the rate of diffusion.
7) Insert the microscopic slide over filter paper. Using your hands, apply gentle pressure
vertically downwards. This is known as squashing which is needed to flatten the sample
and separate cells to be easily viewed under the light microscope (Avoid lateral movement
of the cover slip to prevent overlapping of cells which damages the sample)
8) Place the slide on the stage of a light microscope. Use the low power lens to scan & detect
the area of mitosis then the high power lens to view mitotic features.

56
Precautions
› Cut away from yourself to avoid cutting your skin.
› Wear safety goggles to protect your eyes from the HCl used in the investigation.
› Wear a lab coat to prevent the stain from affecting your clothes.
Value of the experiment

› To observe the mitotic features.
› To calculate mitotic index =
(Number of cells undergoing mitosis / Total no. of cells viewed) x 100
› To estimate the duration of each phase of mitosis; the number of cells in a certain phase is
proportionate to the duration of the phase. The larger the number, the larger the phase .
Homogenous short interlacing cells aligned V-shaped 2 nuclei are

nucleus threads at the equator chromosomes seen

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2) Investigating tensile strength of plant fibers
Tensile strength: The maximum stress a plant fiber can withstand without breaking.
Investigation design
1) Select plant fibers of the same initial length
& diameter.
2) Suspend gradually increasing masses to the
plant fiber.
3) Record the mass at which the fiber breaks.
4) Convert the mass into force then convert the
force into tensile strength.
5) To ensure accuracy, repeat with narrower
intervals between the last 2 masses added.
6) To ensure validity, keep other factors
constant such as temperature & humidity.
7) To ensure reliability, repeat for each type of
fiber & calculate the average tensile strength.
How to control variables
› Initial length: Use a measuring tape to ensure all fibers have the same initial length.
› Initial diameter: Use a micrometer or Vernier caliper.
› Temperature: Use a temperature controlled room with AC.
› Humidity: Same closed chamber (with humidifier).
Vernier caliper

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Safety precaution
› Wear safety goggles to protect your eyes from the fiber after it breaks.
› Use a soft matt (wet fabric) under the suspended mass to protect your feet.
› Tie a rope around your waist while collecting fibers from plants to protect yourself from
falling down.
Advantages of plant fibers (plant based products VS. oil based products)
› Sustainable: As plants can be regrown unlimited number of times so they never run out
like oil based products
› Biodegradable: Broken down by bacterial enzymes in decomposition so they don’t
accumulate in nature.
3) Investigating the effect of mineral ion deficiency

Investigation design
1) Select maze seedlings of the same species, age &
original mass/length.
2) Place a seedling in a beaker containing a solution of
all mineral ions except nitrate ions.
3) Close the beaker with cotton wool. This allows the
entry of air supplying oxygen & reduces entry of
pathogens.
4) Wrap aluminum foil around the beaker to prevent
entry of sunlight. This stimulates(mimics) soil
conditions & prevents overgrowth of algae.
5) Leave for 4 weeks then measure the final mass of the
seedling.
6) Calculate the change in mass.
7) Repeat the whole process using another seedling placed in a solution containing all mineral
ions including nitrates. This is a control for comparison.
8) To ensure validity, keep all other variables constant such as temperature, light intensity,
humidity, pH of solution and concentration of mineral ions.
9) To ensure reliability, repeat 3 times for each type of solution and calculate the average
change in mass.

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How to control variables
› Temperature: temperature controlled room with AC/thermostatic water bath
› Light intensity: use light bulbs of the same voltage (wattage) at the same distance
› Humidity: same closed chamber/tie a clear plastic bag around the shoot
› Solution pH: use buffer solution to keep constant pH
› Mineral ion concentration: add known mass of each mineral ion to a known volume of
water
Importance of mineral ions
› Nitrate ions Amino acids Proteins Enzymes Photosynthesis Better growth
› Magnesium ions Chlorophyll pigment Traps sunlight Photosynthesis Better
growth
› Calcium ions Calcium pectate in the middle lamella Holds microfibrils of adjacent
cell walls together Higher tensile strength Better growth
› Phosphate ions ATP energy Better growth
DNA} more mitosis Better growth
RNA} more protein synthesis

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4) Investigating antimicrobial properties of plant extracts
Practical steps
1) Spread the bacterial culture evenly over the surface
of agar. (lawn distribution using pipette or
streaking method using inoculating loop)
2) Make 2 equal sized holes in agar.
3) Use a pipette to add 0.1cm3 of maize extract to one
hole & 0.1cm3 of water to the other hole. (control
for comparison)
4) Cover the petri dish by a vertically fixed lid.
5) Incubate at temperature of 28°C for 24 hours.
6) Measure the surface area of inhibition zone around
the wells/ holes using graph paper tracing.
7) The larger the inhibition zone, the higher the antibacterial properties.
8) Repeat 3 times for each extract & calculate the average area of inhibition zone.
What is meant by inhibition zone?
A clear area around the plant extract in which it kills bacteria (bactericidal) or inhibits its growth
(bacteriostatic)
How to prepare the petri dish?
› Get a sterile petri dish.
› Add agar.
› Spread bacteria evenly over the surface of agar.
Why temperature 28°C?
High enough for proper enzyme activity of bacterial enzymes but still lower than core body
temperature of 37°C at which pathogenic bacteria can grow.
Why a vertically fixed lid?
To reduce entry of foreign bacteria & also to avoid creating anaerobic conditions that encourage
growth of anaerobic bacteria.

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How to handle bacteria safely in the lab?
› Flame the inoculating loop & the neck of the flask containing bacterial culture using a
bunsen burner.
› Use a harmless bacteria strain such as E.coli.
› Sterilize the laboratory bench before & after the investigation using cotton soaked in
ethanol.
› Incubate at temperature of 28°C to reduce entry of foreign bacteria & also to avoid
creating anaerobic conditions that encourage growth of anaerobic bacteria.
› Vertically fix the lid to reduce entry of foreign bacteria & also to avoid creating anaerobic
conditions that encourage growth of anaerobic bacteria.
› Autoclave all the used equipment before & after the investigation.
› Safe disposal of agar after the investigation.
Flask containing bacterial culture
Bunsen burner Inoculating loop

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5) Understanding microscopy
Magnification Vs Resolution
Magnification is how many bigger is the image compared with actual size while Resolution is the
smallest distance that two objects can be apart while still appearing as two objects.
In other words, resolution allows us to see more fine details.
› Human eyes have limited magnification & resolution so to observe biology we need to
increase magnification and resolution using microscopes.
› The resolution of the human eye is 0.1 mm.
› The eukaryotic cells are roughly 1- 20 um in size while prokaryotic cells are 0.1 – 5 um
in size.

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The Light Microscope (The Optical microscope)
› The first microscope by mankind and the most commonly used.

› Light is sent from a light source then passes through the specimen and then the image is
magnified by glass lenses.
› They are the most common as:

• They are cheap.
• They are Easy to use.
• They can be used to study Living cells so can view processes occurring in real
time.
› However,
• Light microscopes produce 2D images.
• They use visible light to create an image, this limits their
resolution to 200nm and magnification to 2000x.

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The Electron Microscope
› Instead of using light beams, the electron microscopes use beam of electrons to study
specimens.
› Electrons have a shorter wavelength so they can create images with higher resolution.
› There are two types of electron microscopes: scanning electron microscope (SEM) and
transmission electron microscope (TEM)
› In both types a beam of electrons is focused by a magnet towards the specimen.
› Specimen must be coated with metal and placed in vacuum. This preparation means
electron microscopy can only be used to study dead specimens.
SEM: After the electrons hit the specimen they become scattered on a detector.
This scattering allows to determine how far away are structures in the specimen
from each other and thus it produces a 3D image. However, the scattering of
electrons reduces magnification and resolution.
TEM: Electron beam travels through the specimen to a detector below with no
scattering. This allows for higher resolution and magnification, but produces a 2D
image.

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Comparing Microscopes
P.O.C. Light Microscope SEM TEM

Medium Light beam Electron beam Electron beam
Dimensions 2D 3D 2D
Max.
X1500- 2000 X200,000 X2,000,000
Magnification
Max
200nm 20nm 0.1nm
Resolution
Specimen Living or dead Dead only Dead only
Micrographs

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Size Units
To make proper use of magnification calculations we need to know how to convert between size
units. The SI unit for distance is a meter.
The units we are interested in are the: meter, centimeter, millimeter, micrometer and nanometer.
1m = 100 cm
1cm = 10 mm
So 1m= 1000 mm
1mm= 1000 um
1um= 1000 nm
Calculating Magnification
1) Write down the equation:

2) Image = Actual X Magnification
3) Covert given into the same units
4) Substitute in the equation
Practice: Calculate the magnification of the image below
Practice: If a plan drawing shows a leaf cross section, magnification 400x, and a nucleus
on it measures 0.5mm width, what is the actual nucleus width?

67
Staining cells for Microscopy
What is staining?
› Staining is a technique where dye is used to highlight cells in the

microscope.
› Some structures already modify light as it passes through them so
there is no need to stain them as they are colorful. Example: Algae
that contain chlorophyll pigment.
› We only stain when we need to view structures that we wouldn’t
normally be able to see as they are transparent.
How stains work
Stains work by collecting around particular types of molecules. For

example, acetic orcein is a stain that collects around DNA producing a red
colour.
Metachromatic stains: They are differential stains that highlight different components of the cell
with different colours. Iodine stains starch grains blue black while other cellular components
appear yellow. The all purpose metachromatic stain is Toluidine blue O (TBO). For example, TBO
stains lignin blue, pectin pinkish & nucleic acids purple.
Cells stained by Iodine
Lignin Pectin DNA

68
Core Practical: Using Light Microscope
Microscopes can be used to observe many types of specimens, from animal, plants and
microorganisms.
Laboratory prepared slides usually undergo:

› Dehydration
› Staining
› Slicing
› Embedded in wax to prevent sliding
Observing the slide occurs through the following steps:
› Examine by naked eye first to be able to position the slide

correctly on the microscope stage.
› Select the lower power lens first.
› Place the slide on the stage of the light microscope and
move it so the specimen is directly under the lens.
› Switch on the microscope light to shine through the
specimen.
› Use focus wheel to bring into focus.
› Scroll the stage around to view different areas of the
specimen.
› Move to the next power lens to view things more
specifically.
› Use the highest power lens to observe in more details and the shift to the lower power
whenever you need to reposition the specimen.

69
Plant Tissue preparation: (Stem, Root or Leaves)
› Lay the stem on a chopping board.
› Use a scalpel to cut transvers sections of the stem.
› (Make sure that the sharp end of the scalpel is facing
away from you to avoid cutting yourself & wet the
scalpel to reduce friction so that you don’t damage the
tissue)
› Ensure that you cut thin sections so that you become
able to see their components clearly.
› Place a drop of water onto the slide to house your
section.
› Place the stem section onto the slide.
› Use a mounted needle/forceps to lower the coverslip
onto it gently.
› Use absorbent tissue to mop up any leaked water at the
edges.
› Observe under microscope.
Observing samples of Animal/Plant cells:
N.B. Always wear gloves when handling samples to prevent bacteria on the hand from
infecting the specimen. Also use a sterile forceps to transfer the specimen to the slide as
this prevents pathogens reaching the sample & also prevents distortion of the sample.

70
Plan Drawings
› These drawings can be made when observing tissue or cell structures.

› To draw a tissue, we use the low or the medium power, to draw a cell we use the high
power.
› Always draw with a sharp HB pencil.
› Make a title explaining what the drawing is and what is the magnification used.
› Drawings should never include shading or colouring.
› Lines in a tissue drawing separate cell types.
› Draw to cover at least half the space provided and leave space for labels/annotations.
› Label tissue regions with sharp clear lines. Label lines shouldn’t intersect.
› Make it proportional to the sizes of structures in the real specimen.
› If italics needed, underline instead.
N.B. If you are drawing cells, only show structures visible inside cells such as cell wall, cell
membrane, cytoplasm & nucleus. Make sure to draw what you see not what you expected
to see!

71

72
Drawing Practice
Draw a low power plan for the tissues shown in the following micrographs
1) TS of a leaf

73
2) TS of a root

74
3) TS of a leaf

75
4) TS of a leaf

76
Draw a high power plans for 4 of the cells shown in this photomicrograph
1) Blood cells sample

77
2) Onion cells sample

78
3) Cheek cells sample

79
Graticule to make measurements
› Light/optical microscope enlarges in a linear fashion, so 100x magnification means that
the image is 100x wider & longer than the real object.
› The magnification is a product of the objective lens magnification and eyepiece
magnification.
› They eyepiece in a microscope can be fitted with a graticule – a transparent device acting
as a ruler.
› This means dimensions of what we see can be measured in eyepiece units (EPU).
› At different magnifications, EPUs represent different lengths, so we have to calibrate the
graticule for each objective lens.
› We use a stage graticule which is placed on the stage of the light microscope, to calibrate
the eyepiece graticule.
› This stage graticule is usually 1mm (1000um) long.
How to calibrate the EPUs:

› Place the eyepiece graticule into the 10x eyepiece of the microscope.
› Use the 4x objective lens and focus on the stage graticule.
› Use these 2 rulers aligned to work out how much distance one EPU represents at the
magnification of 40x. For example, if you found that 40 EPUs correspond to the stage
graticule which is 1000um in length, then 1 EPU = 25um.
› You can repeat this for any other objective lens.
Practice: If the smallest division in the stage micrometer is 10um. Calculate the size of the
smallest division of the eyepiece graticule.
N.B. Remember standard forms from your mathematics course.

80
Microscopy Evaluation
Conclusions: Through microscopy we can conclude:

› The type of cell or tissue present under the microscope.
› The presence or absence of certain pathogens, tissue damage, tumour invasion or foreign
bodies.
› The size of certain features using graticules.
Errors:
› Errors in preparation of the slide:
• Contaminating the sample with fingers or other objects.
• Damage to the sample during preparation (by crushing for example)
• Improper use of stains
• Dirty slides/ lenses.
› Error in identifying histological features leading to misdiagnosis of pathogens or cancers.
› Error in size calculations or improper use of graticules.
Limitations:
› Bad preparation, staining or preservation of the specimens.
› Some features are difficult or impossible to stain so can’t be visualized.
› Poor resolution or magnification of the used microscope.
› Improper focus on the slides leading to blurring of the image.
› We only view a sample of a tissue not the whole tissue, so we can miss diagnosis of
abnormalities such as cancers or pathogens present.
› Some features appear differently in a transverse cut than longitudinal cut or in a 2D
image than in a 3D image. This might cause confusion.
Improvements:
› Careful preparation of the specimen.
› Examine more than one tissue sample.
› Double check calculations to ensure reliability.

81
Practice Question 1
A researcher is examining a crop which maybe exposed to a recent bacterial endemic. The
bacteria are thought to invade the epidermis of the leaves within the crop.
a) Describe a method the researcher could use to prepare the epidermis for inspection under
a light microscope. (4)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
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………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
b) One disadvantage of light microscopes is that their magnification is limited. State an

instrument the researcher could use with higher magnification, if the source of infection
was a very small virus. (1)
………………………………………………………………………………………………………………………………………..
c) In preparing the slide for the light microscope, what 2 actions could the researcher take to
minimise contamination of the slide? Explain your reasoning for each. (4)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..

82
d) The researcher begins observing slides with an objective lens, magnification 4x. The
overall magnification is 40x. What is the magnification of the eyepiece lens? (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
e) Under 40x magnification, the bacterium found within the epidermis measures 100mm in
his plan drawing. What is the actual size of the bacterium in micrometers? (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
f) With a 10x eyepiece lens and 4x objective lens, the stage graticule covers 20 EPU on the
eyepiece graticule. How much distance does 1 EPU represent? (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
g) Across several slides, the bacteria appear to take on different shapes. They are all of the
same stain – what explanation would clarify the different shapes observed? (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
h) Suggest an error in the procedure the scientist could have made, to explain different
measurements in cell size across the slides. (1)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..

83
Practice question 2
Vaccinerators is a biotech company which has developed a micropatch needle out of a

biosynthetic material which can be used to administer pain-free vaccines. The company is
concerned that the needles in the patch they have produced are too far apart, they require the
distance between the needles to be less than 100nm.
a) Suggest to the company whether an electron or a light microscope should be used to

check whether the needles are close enough. Explain your answer. (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
The disease that vaccinerators are attempting to target is a bacterial disease known as
meningitis. The vaccine causes damage to the plasma membrane of bacterial cells. The first
stage of this damage causes bumps to appear in the cell membrane.
b) Suggest, with a reason, what sort of microscope should be used to monitor the first stage
of vaccine action. (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
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c) Explain the difference between magnification & resolution. (2)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..

84
d) Below is a cross section of 2 flagella, calculate the magnification and state what sort of
microscope was used to obtain it. (3)
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
………………………………………………………………………………………………………………………………………..
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85
6) Investigating the effect of sucrose concentration on pollen tube growth
› Prepare pollen culture medium and add to it a known sucrose concentration.
› Add a drop of the solution you prepared to the center of a clean slide.
› To add pollen, use a low power microscope and knock pollen off the anthers of a flower
using a mounted needle.
› Observe under the microscope to note when pollen tubes start to grow,
this usually occurs after about 15 – 30 minutes depending on the used
plant species.
› At this point, use the eye piece and stage graticules to record the
pollen tube length every 3 minutes for half an hour.
› Repeat the same process with other slides using pollen from the same
anther and the same culture medium but with a range of different
sucrose concentrations.

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Topic 3: Cell structure, Reproduction and Development

Dr. Mohab Megahed

N.B: For a structure to be called a cell it must have:-

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

› There are two types of ribosomes:

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© Dr. Mohab Megahed

© Dr. Mohab Megahed

Same organelles as the animal cell plus:

1. Chloroplasts: Double membrane bound

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Double membrane Single membrane bound Non-membrane

© Dr. Mohab Megahed

Structures that must be present in the bacterial cell:

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Comparison between Eukaryotic & Prokaryotic cells

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2. S phase: Synthesis of DNA

3. G2 phase: 2nd phase of growth

N.B Interphase summary:

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© Dr. Mohab Megahed

4) Telophase (Reverse of prophase)

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N.B Significance of Mitosis:

N.B Significance of the cell cycle:

DNA content graph

N.B Homologous chromosomes

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

Gametogenesis and Embryonic Development

• 2 male nuclei:: • 1 egg nucleus: fertilized by one of the

© Dr. Mohab Megahed

© Dr. Mohab Megahed

Spermatogenesis in Males Oogenesis in Females

© Dr. Mohab Megahed

› Sperms are: Many to increase chances of fertilization.

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

© Dr. Mohab Megahed

Sources of stem cells:

How cells specialize

Evaluation of stem cells:

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© Dr. Mohab Megahed

N.B Important definitions:

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© Dr. Mohab Megahed