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YOUR NOTES

1. Cell Structure

1.1 The Microscope in Cell Studies

1.1.1 The Microscope in Cell Studies
1.1.2 Magnification Calculations
1.1.3 Eyepiece Graticules & Stage Micrometers
1.1.4 Resolution & Magnification
1.1.5 Calculating Actual Size
1.2 Cells as the Basic Units of Living Organisms
1.2.1 Eukaryotic Cell Structures & Functions
1.2.2 Animal & Plant Cells
1.2.3 The Vital Role of ATP
1.2.4 Prokaryotic v Eukaryotic Cells
1.2.5 Viruses

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1.1 The Microscope in Cell Studies YOUR NOTES

1.1.1 The Microscope in Cell Studies

In order to observe cellular material in more detail, specimens can be prepared for
viewing under a light microscope
Samples need to be thin enough to allow light to pass through
The type of preparation that is appropriate is dependent on the cellular material
that needs to be viewed

Slide preparation methods table

Samples sometimes need to be stained, as the cytosol and other cell structures
may be transparent or difficult to distinguish
To stain a slide the sample needs to be first air-dried and then heated by passing
it through a Bunsen burner flame – this will allow the sample to be fixed to the
slide and to take up the stain
As with the type of preparation required, the type of stain used is dependent on
what type of specimen is being used

Common microscope stains & uses table

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YOUR NOTES
To record the observations seen under the microscope (or from photomicrographs
taken) a labelled biological drawing is often made
Biological drawings are line pictures which show specific features that have been
observed when the specimen was viewed
There are a number of rules/conventions that are followed when making a
biological drawing

The conventions are:

The drawing must have a title
The magnification under which the observations shown by the drawing are
made must be recorded
A sharp HB pencil should be used (and a good eraser!)
Drawings should be on plain white paper
Lines should be clear, single lines (no thick shading)
No shading
The drawing should take up as much of the space on the page as possible
Well-defined structures should be drawn
The drawing should be made with proper proportions
Label lines should not cross or have arrowheads and should connect directly
to the part of the drawing being labelled
Label lines should be kept to one side of the drawing (in parallel to the top of
the page) and drawn with a ruler

Drawings of cells are typically made when visualizing cells at a higher

magnification power, whereas plan drawings are typically made of tissues viewed
under lower magnifications (individual cells are never drawn in a plan diagram)

Exam Tip
When producing a biological drawing, it is vital that you only ever draw what
you see and not what you think you see.To accurately reflect the size and
proportions of structures you see under the microscope, you should get
used to using the eyepiece graticule.

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1.1.2 Magnification Calculations YOUR NOTES

Magnification is how many times bigger the image of a specimen observed is in

comparison to the actual (real-life) size of the specimen
The magnification (M) of an object can be calculated if both the size of the image
(I), and the actual size of the specimen (A), is known

An equation triangle for calculating magnification

Worked Example
An image of an animal cell is 30 mm in size and it has been magnified by a
factor of X 3000.

What is the actual size of the cell?

To find the actual size of the cell:

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The size of cells is typically measured using the micrometre (μm) scale, with YOUR NOTES
cellular structures measured in either micrometers (μm) or nanometers (nm)
When doing calculations all measurements must be in the same units . It is best to
use the smallest unit of measurement shown in the question
To convert units, multiply or divide depending if the units are increasing or
decreasing
Magnifi cation does not have units

Converting units of measurement

There are 1000 nanometers (nm) in a micrometre (µm)

There are 1000 micrometres ( µm) in a millimetre (mm)
There are 1000 millimetres (mm) in a metre (m)

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Worked Example YOUR NOTES

Step 1: Check that units in magnification questions are the same

Remember that 1mm = 1000µm

2000 / 1000 = 2, so the actual thickness of the leaf is 2 mm and the drawing thickness
is 50 mm
Step 2: Calculate Magnification

Magnification = image size / actual size = 50 / 2 = 25

So the magnification is x 25

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1.1.3 Eyepiece Graticules & Stage Micrometers YOUR NOTES

An eyepiece graticule and stage micrometer are used to measure the size of the
object when viewed under a microscope
Each microscope can vary slightly so needs to be calibrated when used
The calibration is done with a stage micrometer, this is a slide with a very accurate
scale in micrometres (µm), it is usually in 10 µm divisions, so 1 mm divided into
100 divisions
The eyepiece graticule is a disc placed in the eyepiece with 100 divisions, this has
no scale
To know what the divisions equal at each magni fication the eyepiece graticule is
calibrated to the stage micrometer at each magni fication

Using stage micrometer & eyepiece graticule

In the diagram, the stage micrometer has three lines each 10 µ m apart
Each 10 µ m division has 40 eyepiece graticule divisions
40 graticule divisions = 10 µm

1 graticule division = number of micrometres ÷ number of graticule division

1 graticule division = 10 ÷ 40 = 0.25 µm this is the magnification factor

The specimen slide would be used to replace the stage micrometer and the
eyepiece graticule at the same magni fication would be used to measure the length
of the object
The number of graticule divisions can then be multiplied by the magni fication
factor:

graticule divisions x magnification factor = measurement (µm)

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Exam Tip YOUR NOTES

The calculations involving stage micrometers and eyepiece graticules are
often seen in exam questions, so make sure that you are comfortable with
how to calibrate the graticule and calculate the length of an object on the
slide.

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1.1.4 Resolution & Magnification YOUR NOTES

Magnification
Magnifi cation is how many times bigger the image of a specimen observed is in
compared to the actual (real-life) size of the specimen
A light microscope has two types of lens:
An eyepiece lens, which often has a magnification of x10
A series of (usually 3) objective lenses, each with a different magnification
To calculate the total magnification the magnification of the eyepiece lens and the
objective lens are multiplied together:

eyepiece lens magnification x objective lens magnification = total magnification

Resolution
Resolution is the ability to distinguish between two separate points
If two separate points cannot be resolved, they will be observed as one point
The resolution of a light microscope is limited by the wavelength of light
As light passes through the specimen, it will be diffracted
The longer the wavelength of light, the more it is diffracted and the more that
this diffraction will overlap as the points get closer together
Electron microscopes have a much higher resolution and magnification than a
light microscope as electrons have a much smaller wavelength than visible light
This means that they can be much closer before the di ffracted beams overlap

The concept of resolution is why the phospholipid bilayer structure of the cell
membrane cannot be observed under a light microscope
The width of the phospholipid bilayer is about 10nm
The maximum resolution of a light microscope is 200nm (half the smallest
wavelength of visible light, 400nm)
Any points that are separated by a distance less than 200nm (such as the
10nm phospholipid bilayer) cannot be resolved by a light microscope and
therefore will not be distinguishable as “separate”

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YOUR NOTES

The resolving power of an electron microscope is much greater than that of the light
microscope, as structures much smaller than the wavelength of light will interfere
with a beam of electrons

Comparison of the electron microscope & light microscope

Light microscopes are used for specimens above 200 nm
Light microscopes shine light through the specimen, this light is then passed
through an objective lens (which can be changed) and an eyepiece lens (x10)
which magnify the specimen to give an image that can be seen by the naked
eye
The specimens can be living (and therefore can be moving), or dead
Light microscopes are useful for looking at whole cells , small plant and animal
organisms, tissues within organs such as in leaves or skin

Electron microscopes, both scanning and transmission, are used for specimens
above 0.5 nm
Electron microscopes fire a beam of electrons at the specimen either a broad
static beam (transmission) or a small beam that moves across the specimen
(scanning)
The electrons are picked up by an electromagnetic lens which then shows the
image
Due to the higher frequency of electron waves (a much shorter wavelength)
compared to visible light, the magni fication and resolution of an electron
microscope is much better than a light microscope
Electron microscopes are useful for looking at organelles, viruses and DNA as
well as looking at whole cells in more detail
Electron microscopy requires the specimen to be dead however this can
provide a snapshot in time of what is occurring in a cell eg. DNA can be seen

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replicating and chromosome position within the stages of mitosis are visible YOUR NOTES
Light v Electron Microscope Table

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1.1.5 Calculating Actual Size YOUR NOTES

When investigating the size of organisms and biological structures you will use a
microscope of a specific magnification to produce an image
Photomicrographs are images obtained from a light microscope, these are used
for specimens above 200 nm (a bacteria cell is about 1000 nm)
Electron micrographs are images obtained from electron microscopes, both
scanning and transmission, these are used for specimens above 0.5 nm
Electron microscopes are useful for looking at organelles and biological
molecules, eg. DNA can be seen replicating

To better understand the images we produce using microscopes we need to know

the actual size of the specimen

Worked example: Calculating the actual size of a specimen

A scientist looks at a sample of red blood cells under a light microscope.

The eyepiece lens of the microscope has a magnification of x10 and an objective
lens of x40 was used to view the blood cells. The scientist takes a
photomicrograph of the blood cells, in which the average size of each cell is 3 mm.

What is the average size of the red blood cells in the sample? Give your answer in
micrometres.
Known values:

Eyepiece lens magnification: x10

Objective lens magni fication: x40
Image size: 3 mm

Step 1: Calculate the total magnification of the specimen

eyepiece lens magnification x objective lens magnification

= total magnification

x10 x x40 = x400

Step 2: Calculate the image size in the units asked for (micrometres)

1 mm = 1000 μm

3 mm = 3000 μm

Step 3: Calculate the actual size of the red blood cell

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Therefore, the average size of a red blood cell in this sample is 7.5 micrometres YOUR NOTES

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1.2 Cells as the Basic Units of Living Organisms YOUR NOTES

1.2.1 Eukaryotic Cell Structures & Functions

Cell surface membrane

The structure of the cell surface membrane – although the structure looks static the
phospholipids and proteins forming the bilayer are constantly in motion

All cells are surrounded by a cell surface membrane which controls the exchange
of materials between the internal cell environment and the external environment
The membrane is described as being ʻpartially permeableʼ

The cell membrane is formed from a phospholipid bilayer of phospholipids

spanning a diameter of around 10 nm

Cell wall

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YOUR NOTES

The cell wall is freely permeable to most substances (unlike the plasma membrane)

Cell walls are formed outside of the cell membrane and offer structural support to
cell
Structural support is provided by the polysaccharide cellulose in plants, and
peptidoglycan in most bacterial cells
Narrow threads of cytoplasm (surrounded by a cell membrane) called
plasmodesmata connect the cytoplasm of neighbouring plant cells

Nucleus

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YOUR NOTES
The nucleus of a cell contains chromatin (a complex of DNA and histone proteins)
which is the genetic material of the cell

Present in all eukaryotic cells, the nucleus is relatively large and separated from
the cytoplasm by a double membrane (the nuclear envelope) which has many
pores
Nuclear pores are important channels for allowing mRNA and ribosomes to travel
out of the nucleus, as well as allowing enzymes (eg. DNA polymerases) and
signalling molecules to travel in
The nucleus contains chromatin (the material from which chromosomes are made)
Usually, at least one or more darkly stained regions can be observed – these
regions are individually termed ʻnucleolusʼ and are the sites of ribosome
production

Mitochondria

A single mitochondrion is shown – the inner membrane has protein complexes vital
for the later stages of aerobic respiration embedded within it

The site of aerobic respiration within eukaryotic cells, mitochondria are just visible
with a light microscope
Surrounded by double-membrane with the inner membrane folded to form cristae
The matrix formed by the cristae contains enzymes needed for aerobic
respiration, producing ATP
Small circular pieces of DNA (mitochondrial DNA) and ribosomes are also found in
the matrix (needed for replication)

Chloroplast

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YOUR NOTES

Chloroplasts are found in the green parts of a plant – the green colour a result of the
photosynthetic pigment chlorophyll

Larger than mitochondria, also surrounded by a double-membrane

Membrane-bound compartments called thylakoids containing chlorophyll stack to
form structures called grana
Grana are joined together by lamellae (thin and flat thylakoid membranes)
Chloroplasts are the site of photosynthesis:
The light-dependent stage takes place in the thylakoids
The light-independent stage (Calvin Cycle) takes place in the stroma

Also contain small circular pieces of DNA and ribosomes used to synthesise
proteins needed in chloroplast replication and photosynthesis

Ribosome

Ribosomes are formed in the nucleolus and are composed of almost equal amounts
of RNA and protein

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Found freely in the cytoplasm of all cells or as part of the rough endoplasmic YOUR NOTES
reticulum in eukaryotic cells
Each ribosome is a complex of ribosomal RNA (rRNA) and proteins
80S ribosomes (composed of 60S and 40S subunits) are found in eukaryotic cells
70S (composed of 50S and 30S subunits) ribosomes in prokaryotes, mitochondria
and chloroplasts
Site of translation (protein synthesis)

Endoplasmic reticulum

The RER and ER are visible under the electron microscope - the presence or absence
of ribosomes helps to distinguish between them

Rough Endoplasmic Reticulum (RER)

Surface covered in ribosomes

Formed from continuous folds of membrane continuous with the nuclear envelope
Processes proteins made by the ribosomes

Smooth Endoplasmic Reticulum (ER)

Does not have ribosomes on the surface, its function is distinct to the RER
Involved in the production, processing and storage of lipids, carbohydrates and
steroids

Golgi apparatus (golgi complex)

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YOUR NOTES

The structure of the Golgi apparatus

Flattened sacs of membrane similar to the smooth endoplasmic reticulum

Modifies proteins and packages them into vesicles or lysosomes

Large permanent vacuole

The structure of the vacuole

Sac in plant cells surrounded by the tonoplast , selectively permeable membrane

Vacuoles in animal cells are not permanent and small

Vesicle

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YOUR NOTES

The structure of the vesicle

Membrane-bound sac for transport and storage

Lysosome

The structure of the lysosome

Specialist forms of vesicles which contain hydrolytic enzymes (enzymes that break
biological molecules down)
Break down waste materials such as worn-out organelles, used extensively by cells
of the immune system and in apoptosis (programmed cell death)

Centriole

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YOUR NOTES

The structure of the centriole

Hollow fibres made of microtubules, two centrioles at right angles to each other
form a centrosome, which organises the spindle fibres during cell division
Not found in flowering plants and fungi

Microtubules

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YOUR NOTES

The structure of the microtubule

Makes up the cytoskeleton of the cell about 25 nm in diameter

Made of α and β tubulin combined to form dimers, the dimers are then joined into
protofilaments. Thirteen protofilaments in a cylinder make a microtubule
The cytoskeleton is used to provide support and movement of the cell

Microvilli

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The structure of the microvilli

YOUR NOTES
Cell membrane projections that increase the surface area for absorption

Cilia

The structure of the cilia

Hair-like projections made from microtubules

Allows the movement of substances over the cell surface

Flagella

The structure of the flagella

Similar in structure to cilia , made of longer microtubules

Contract to provide cell movement for example in sperm cells

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1.2.2 Animal & Plant Cells YOUR NOTES

TEM electron micrograph of an animal cell showing key features

Exam Tip
You should be able to describe and interpret photomicrographs, electron
micrographs and drawings of typical animal cells.

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YOUR NOTES

TEM electron micrograph of a plant cell showing key features

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YOUR NOTES
The only structures found in animal cells but not plant cells are the centrioles and
microvilli
Plant cells also have additional structures: the cellulose cell wall, large permanent
vacuoles and chloroplasts

The ultrastructure of an animal cell shows a densely packed cell – the ER and RER and
ribosomes form extensive networks throughout the cell in reality

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YOUR NOTES

Plant cells have a larger, more regular structure in comparison to animal cells

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1.2.3 The Vital Role of ATP YOUR NOTES

All organisms require a constant supply of energy to maintain their cells and stay
alive
This energy is required:
In anabolic reactions – building larger molecules from smaller molecules
To move substances across the cell membrane (active transport) or to move
substances within the cell
In animals, energy is required:
For muscle contraction – to coordinate movement at the whole-organism
level
In the conduction of nerve impulses, as well as many other cellular
processes

In all known forms of life, ATP from respiration is used to transfer energy in all
energy-requiring processes in cells
This is why ATP is known as the universal energy currency
Adenosine Triphosphate (ATP) is a nucleotide
The monomers of DNA and RNA are also nucleotides

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1.2.4 Prokaryotic v Eukaryotic Cells YOUR NOTES

Animal and plant cells are types of eukaryotic cells, whereas bacteria are a type of
prokaryote
Prokaryotes have a cellular structure distinct from eukaryotes:
Their genetic material is not packaged within a membrane-bound nucleus and
is usually circular (eukaryotic genetic material is packaged as linear
chromosomes)
Prokaryotes lack membrane-bound organelles
They are many (100s/1000s) of times smaller than eukaryotic cells
Their ribosomes are structurally smaller (70 S) in comparison to those found
in eukaryotic cells (80 S)

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Prokaryotic cells are often described as being ʻsimplerʼ than eukaryotic cells, and they
YOUR NOTES
are believed to have emerged as the first living organisms on Earth

Prokaryotic & Eukaryotic Cells Comparison Table

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1.2.5 Viruses YOUR NOTES

Viruses are non-cellular infectious particles that straddle the boundary between
ʻlivingʼ and ʻnon-livingʼ
They are relatively simple in structure; much smaller than prokaryotic cells (with
diameters between 20 and 300 nm)
Structurally they have:
A nucleic acid core (their genomes are either DNA or RNA, and can be single
or double-stranded)
A protein coat called a ʻcapsidʼ

Some viruses have an outer layer called an envelope formed usually from the
membrane-phospholipids of a cell they were made in
All viruses are parasitic in that they can only reproduce by infecting living cells
and using their protein-building machinery (ribosomes) to produce new viral
particles

Viruses are not cellular like prokaryotes and eukaryotes – this is just one example of
a virus structure

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