BIO 101 (Biology): Preliminaries

Text books: Prescribed (P) & Recommended (R)

• Taylor, D.J., Green, N.P.O, and Stout, G.W. (1997). Biological Science
1 & 2. Cambridge University Press, London. ISBN 0-521-63923-9.
(P)
• Kent, M. (2000). Advanced biology. Oxford University Press, London.
ISBN 0-19-914195-9. (P)
• Jones, M., Fosberg, R., Gregory, J., and Taylor, D. (2017). Cambridge
International AS and A Level Biology Course book. Cambridge
University Press. ISBN 9781316637708. (R)

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Textbooks (continuation)

• Clegg, C. J. (2014). Cambridge International AS and A Level Biology.

Hodder Education. ISBN 9781444175349. (R)
• Elliot, W.H, and Elliot, D.C. (2004). Biochemistry and molecular
biology. 3rd ed. Oxford Press, Oxford. ISBN 0-19-927199-2. (R)
Course delivery
• Lectures: 4 hours per week
• Tutorials: 2 hours (one session per week)
• Laboratory/practicals: 2 hours (one session per week)
• Self-study, group work, discussions, etc

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Course assessment
1. Continuous assessment 40%
(a) 3 (6) Tests 20%
(b) 3 Assignments 3%
(c) 6 Quizzes 7%
(d) Practicals (labs) 10%
2. Final Examinations 60%
(a) Theory 40%
(b) Practical 20%

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Course outline (topics to be covered)
1. Cells
• Microscopes
• Prokaryotic cell parts
• Eukaryotic cell parts
2. Cell membranes
• Fluid mosaic model
• Carrier proteins and channel proteins
• Receptors and antigens
• Diffusion, osmosis, active transport and Bulk transport
3.Biomolecules
• Carbohydrates
• Lipids
• Proteins
• water
• Food tests
4. Enzymes
• Active site, substrate, intracellular, extracellular
• Lock and key, and induced fit hypotheses
• Factors affecting enzyme action
• Enzyme inhibition
5. Protein synthesis
• Transcription
• Translation
• Genetic code
6. Prokaryotic gene regulation
• Structural and regulatory genes
• Repressible and inducible enzymes
• Lac operon
7. Cell division
• Cell cycle
• Mitosis
• Meiosis
• Importance of mitosis and meiosis
8. DNA structure, function and chromosomes
• Structure of chromosome (histones, telomeres)
• Function of chromosome
• DNA replication
• Nucleic acids
9. Variations and selections
• Continuous and discontinuous variations
• How environmental factors stabilize, disrupt and direct natural
selections
• Hardy-Weinberg principle
10. Genetics
• History/origin, Definitions, sex linkage
• Monohybrid crosses
• Dihybrid crosses, gene interaction
• Multiple alleles, penetrance, expressivity
11. Energy and respiration
• Need for energy
• ATP: formation, structure and function
• Stages of respiration
• Roles of NAD, FAD and Coenzyme A
• Electron transport system in mitochondria & chloroplasts
• Why lipids are energy-rich
• Respiratory quotient
• Oxidative phosphorylation
12. Biodiversity, Classification and Conservation
• Kingdoms: Protoctista, Fungi, Plantae, and Animalia
• Definitions
• Importance of random sampling
• Species diversity
• Levels of classification
• The three domains: Archaea, Bacteria and Eukarya
• Why viruses are independent
• Threats to biodiversity
• Why maintain biodiversity
• Methods of protecting endangered species
• Methods of preventing overpopulation
• Alien species
• NGOs involved in conservation
• Restoration of degraded habitats
Unit 1: Cells
1.1: Microscopes
Lesson objectives:
At the end of the lesson, students should be able to:
a) Know the different types of microscopes
b) Use a microscope at the Laboratory
c) State the function of each part of a simple microscope
d) Calculate magnification
Microscopes
▪ A microscope is an instrument used to magnify (enlarge, make big a
small object) objects.
▪ It is used to magnify the fine details of a large object in order to
examine minute specimens that cannot be seen by the naked eye.
▪ A compound microscope consists of structural and optical components.
▪ Besides a compound (light, simple) microscope, other types of
microscopes include transmission electron microscope and scanning
electron microscope
▪ It is called a compound microscope because it has a pair of lenses,
namely: ocular lenses (eye piece) and objective lenses

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▪ Cells are too small to be seen by the naked eye

▪ The light microscope is the most common instrument used in the

laboratory, capable of revealing the general feature of the cell, such as
the cytoplasm and the nucleus.
▪ The compound light microscope was inverted by Jansen in 1590
▪ The electron microscope, developed in the 1950s,can reveal much
finer detail (or ultra-structure) of the cell.
▪ The electron microscope floods the specimens with a beam of
electrons

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Main features of microscopes
▪ The two main features of the microscope are: magnification and
resolving power.
▪ Magnification is the ability of the microscope to enlarge specimens for
the viewer.
▪ The light microscope can magnify the cell structure to about 1,000
times the normal size.
▪ The electron microscope can magnify the image to about 250,000
times or more.

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Laboratory microscopes
▪ The resolving power is the ability of the microscope to reveal fine
details of the specimen.
▪ The resolving power is the ability to separate minimum distance
between two points.
▪ Resolving power is the ability of a microscope to view separately two
objects that are close.
▪ Two types of microscopes used in the laboratory are the transmission
types and the dissecting types.

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Dissecting Microscope
(SEM opened sample chamber)
Transmission Microscope
• The electron source of the TEM
is at the top, where the lensing
system (4,7 and 8) focuses the
beam on the specimen and then
projects it onto the viewing
screen (10). The beam control is
on the right (13 and 14)
 OPERATIONS OF MICROSCOPES
▪ In transmission microscopes the light waves are transmitted through the
specimen,
▪ Whereas in electron microscopes electrons are transmitted through the
specimen.
▪ In dissecting microscopes the light is reflected on the surface of the
specimen to reveal surface features
▪ A variant of a dissecting microscope is the scanning electron microscope
(SEM) designed to reveal the surface features of the specimen.
▪ A variant of the transmission microscope is the transmission electron
microscope (TEM) designed to reveal internal structures of the specimen.
Hooke’s microscope

• English scientist Robert Hooke

built this microscope in the 17th
century
• He discovered the cell structure
of plants by observing a thin
slice of cork.
Structure of a compound microscope

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A scanning electron microscope

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Structural components of a compound microscope
The three basic structural components of a compound microscope are
the head, base and arm.
▪ Head or body tube houses the optical parts in the upper parts of the
microscope
▪ The base of the microscope supports the microscope and houses the
illuminator
▪ The arm connects to the base and supports the microscope head. It is
also used to carry the microscope.

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 Optical components of a compound microscope
▪ There are two optical systems in a compound microscope: eyepiece
lenses and objective lenses.
▪ Eyepiece lenses or ocular lenses is what you look through at the top of
the microscope.
▪ Most eyepiece lenses have magnifying power of x10. Other eyepiece
lenses have magnifying powers ranging from x5 to x30.

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Eyepiece tube
▪ Holds the eyepiece lenses in place.
▪ The lens the viewer looks through to see the specimen. The eyepiece
usually contains a 10X or 15X power lens.
▪ Binocular microscope heads typically incorporate a diopter adjustment
ring that allows for the possible inconsistencies of our sight in one or
both eyes.
▪ Diopter Adjustment: used to change focus on one eyepiece so as to
correct for any difference in vision between the two eyes.

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Body tube (head)
▪ The body tube connects the eyepiece to the objective lenses.
▪ Arm: The arm connects the body tube to the base of the microscope.
▪ Coarse adjustment: Brings the specimen into general focus.
▪ Objective lenses. They are the primary optical lenses on a microscope.
They range from 4x to 100x.
▪ Standard objectives include 4x, 10x, 40x and 100x

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Nose piece
▪ The nose piece houses the objective lenses. The objective lenses are
exposed and are mounted on a rotating nose piece
▪ Fine adjustment: Fine tunes the focus and increases the detail of the
specimen.
▪ The fine and course adjusting knobs are coaxial knobs: they are built
on the same axis with the fine focus knob on the outside.

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Stage
▪ This is where the specimen to be viewed is placed.
▪ Stage clips are used when there is no mechanical stage. The viewer is
required to move the slide manually to view different sections of the
specimen.
▪ Aperture is the hole in the stage through which the base (transmitted)
light reaches the stage.
▪ Illuminator is the light source for a microscope, typically located in
the base of the microscope.
▪ It is used to ensure that enough light reaches the object to be
magnified for proper focussing

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Iris Diaphragm
▪ It controls the amount of light reaching the specimen. It is located
above the condenser and below the stage.
▪ The iris diaphragm control both the focus and the quantity of light
reaching the specimen.
▪ Condenser focus knob moves the condenser up or down to control the
lighting focus on the specimen.

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How a compound microscope works
▪ The light from the illuminator passes through the aperture, through the
slide, and through the objective lens,
▪ The objective lens is optical part where the image of the specimen is
magnified.
▪ The magnified image is then transmitted to the eyepiece where it is
further magnified.
▪ The following steps should be followed when using a
compound/light/simple microscope:

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1. Turn on the illuminator. Slowly increase the light intensity because
the lamp heats up quickly
2. Place the slide or specimen on the stage with the sample directly
above the aperture and, if possible, fasten it to the stage clips. A cover
slip improves the quality of image formed.
3. Ensure the iris diaphragm is completely open, allowing the maximum
amount of light to reach the slide and the lenses.
4. Rotate the nosepiece so that the objective lens with lowest level of
magnification is directly above the specimen. This helps to select the
part of the specimen of interest and then adjust to higher objective
lenses.

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5. Look through the eyepiece and adjust the
iris diaphragm until the required amount of light is used. Sufficient amount
of light should be used to the comfort of the viewer.
6. Turn the course adjusting knob until the specimen comes into broad
focus. In some microscopes, the course adjusting knob moves the stage
closer to the objective lenses. It is advisable to be careful when using the
course adjusting knob so that neither the sample nor the objective lenses
are broken.
7. Turn fine adjusting knob to get a clear focus of the specimen

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Magnification
▪ Magnification is the apparent enlargement of an object by an optical
instrument
▪ It is the ratio of the dimensions of an image formed by the instrument to
the corresponding dimensions of the object.
▪ To calculate total magnification simply multiply the ocular lens (eye
piece) magnifying power by the magnifying power of the objective lens.
▪ Therefore, a 10x eyepiece used with a 40x objective lens will produce a
magnification of 400x. This means that the naked eye has seen an image
that has been enlarged 400x.

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Magnification of a drawing or photograph
▪ First determine the actual size of the object being viewed.
▪ This is normally done by calibrating the microscope when viewing an
object of known size, such as a graduated scale on a slide.
▪ Once the actual size is determined, the magnification of a drawing or
illustration can be calculated using the following formula:
Magnification of the illustration = Size of the illustration / Actual size
(size of drawing or image/size of object or specimen)

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The final answer obtained from magnification should be rounded off to
the nearest whole number e.g. x2 or 2x

▪ An estimated magnification is then calculated by including a third

factor (number of times the investigator thinks the image from the
microscope has been magnified on the drawing)
▪ Hence, total magnification is written as (for example) x10x10x4
meaning: x10 eyepiece was used and a x10 objective lens was used
and the person has magnified the microscope image four times.

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Resolution
▪ It is the ability to distinguish objects that are close together.
▪ The shortest distance between two points on a specimen that can still
be distinguished by the observer or camera system as separate entities.
▪ The primary factor in determining resolution is the aperture of the
specimen, type of specimen, illumination

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Oil immersion Procedure
▪ Some monocular microscopes and all binocular compound
microscopes have 100x oil immersion lenses.
▪ These lenses are identified by a red or white band around the lens. At
magnifications greater than 500x, light is refracted too much as it
passes through air to yield good resolving power.
▪ Thus, optics for these higher magnifications are able to use high grade
mineral oil as the medium for transmitting light. The procedure
involved
1. Locate the region of interest on your slide and centre it at 400x.

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2. Raise the objective lens to its limit (maximise the distance between
the stage and the objectives)

swing the lens out of the way about half way to the next position.
3. Carefully place a small drop of immersion oil directly on the
slide over the centre of the region of interest.
4. Rotate the oil immersion objective into position and, carefully,
while looking from the side, lower it using the course focus knob
until the lens just makes contact with the oil drop.
5. Using the fine adjusting knob while looking through the ocular
lens (eye piece), focus on the specimen.
6. After focussing, clean the lens with the lens paper until no
more oil comes off and clean the slide if it is to be saved.

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 Specimen preparation (How should I prepare my specimen?)
▪ The specimen must be thin enough to allow enough light to pass through
it.
▪ The examined specimen is usually examined while immersed in water to
prevent the protoplasm from being deformed.
▪ The following procedure when making a temporary wet mount:
1. Place the specimen to be magnified in the centre of a clean, grease-free
microscope slide.
2. Cover the specimen with a small drop of water, or other suitable
mountant (e.g. lugol’s solution, iodine solution).
3. Using the thumb of the forefinger of the left hand, hold a clean, grease-
free microscope cover slip so that its bottom edge just comes into contact
with the left-hand side of the drop on the microscope slide.

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The microscope cover slip needs to be held at an angle of between 45
and 60֯ (45 to 60 degrees angle) in order to exclude air bubbles.

4. While supporting the microscope cover slip at its upper edge with a
needle held in the right hand, gently lower the microscope cover slip on
the microscope slide containing the specimen.
▪ This method avoids the inclusion of air bubbles in the mount.
▪ Bring into focus the objective lenses beginning with the lowest. Turn
the course and fine adjusting knobs to get a clear image of the
specimen.
▪ This type of focus is called parfocal meaning that when you switch
from the low to high power, a focussed image is produced.

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Calculating the size of cells
▪ Diameter of x10 objective field of view is 2mm. This is the field of
view when using the 10x objective lens (100x total magnification).
▪ To determine the length of one cell when 8 cells are seen in the field of
view, you divide 2mm by the number of cells (2mm / 8 cells = 0.25mm
for example).
mm = 1000 um
0.25 mm = 1000x0.25
= 250um
▪ The diameter of the field of view changes depending on the objective
lens used according to the table below.

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Objective lens Field of view diameter Total magnification
using x10 ocular lens
(eyepiece)

x4 4.0 mm (4.45) x40

x10 2.0 mm (1.78) x100

x40 0.4 mm (0.45) x400

x100 0.2 mm (0.178) x1000

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Transmission electron microscope (TEM)
▪ Use a particle beam of electrons to visualize specimens and generate a
highly-magnified black and white image.
▪ TEMs can magnify objects up to Two million times
▪ Air needs to be pumped out of the vacuum chamber, creating a space
where electrons are able to move.
▪ It fires a beam of electrons through a specimen to produce a magnified
image of an object.
▪ Used to view thin specimens (tissue sections, molecules) through
which electrons can pass generating a projection image.

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Disadvantages of a TEM
▪ Electron and electromagnetic fields and must be housed in an area that
isolates them from possible exposure.
▪ Requires constant upkeep including maintaining voltage, currents to
the electromagnetic coils and cooling water.
▪ Differences between a transmission electron microscope and a
scanning electron microscope (SEM) are: Rather than the broad static
beam used in TEM, the SEM beam is focused to a fine point and scans
line by line over the sample surface in a rectangular raster pattern.
▪ Lesson self-help questions:
(1) What is the difference between resolution and magnification?
(2) Compare and contrast TEM, SEM and simple microscopes.

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