A.

Unit and diversity

2. Cells
Cell Structure 2.2.1 - 2.2.11
 A.2.2 Cell estructure
What are the features common to all cells and the features that differ?

Figure 1 shows a hot spring extremophile community. This

community thrives in 75°C water in the hills of New Mexico. The
community in the picture is made up of sulfur bacteria (purple), algae
and protozoa, all one celled organisms. How does the cell theory take
into account the diversity of cell structure? What features of cells are
universal? What are some examples of features that are unique to
certain cells? What are the implications of the cell theory? What are Figure 1. Scanning electron
micrograph of a hot spring
the limits to what the cell theory predicts or explains? extremophile communitv
 A.2.2 Cell estructure
How is microscopy used to investigate cell structure?

The human eye has limited resolving power. What does resolution
refer to with respect to optical devices? What is the actual limit to the
resolving power of the human eye? How does this compare to a bird
of prey like an eagle? How large are cells? Organelles? Membranes?
What is the resolving power of the different type of microscopes like
light and electron microscopes? A scanning electron microscope was
used to prepare the image shown in Figure 2, which is an embryo on
the head of a pin. What is the value of a SEM over a transmission
Figure 2. Coloured scanning electron
electron microscope? micrograph (SEM) of a human embryo on
the tip of a pin
 A.2.2.1 Cells as the basic structural unit of all living organisms

Individual cells are fundamental units of life. Some small organisms consist of a
single cell but larger organisms are multicellular. It has been estimated that a 70
kg human consists of 3.8 × 1013 cells-that is nearly 40 trillion cells. Large
multicellular organisms have many different cell types, each specialized for a
particular role.
The statement that living organisms consist of cells is an example of a
theory.This theory was developed when Robert Hooke and other biologists from
the 17th century onwards used microscopes to look at the structure of living
organisms. Plant cells are relatively easy to view with a microscope. By the 19th
Figure 3. Robert Hooke's drawing of cork
century, animal tissues could also be examined. Both types of tissue were found cells

to consist of cells.
 A.2.2.1 Cells as the basic structural unit of all living organisms

From this, scientists concluded that all organisms are made of cells. They had not looked at all parts of all
organisms but they had found a trend that allowed them to make general predictions about the structure of
organisms.
Since the development of the cell theory, researchers have discovered some structures in living organisms that do
not consist of typical cells; some of these structures are described later. Despite these exceptions, however, the cell
theory is still useful and it has not been rejected. If a new organism is discovered, we can be reasonably confident
that some or all of it will consist of cells.
 Observations, theories and inductive reasoning

Biologists are interested in the natural world and look

carefully at it they act as observers and make
observations. Sometimes biologists notice a trend or
pattern in their observations and from this they develop
a general theory. Theories developed from specific.
observations are an example of inductive reasoning-
going from the specific to the general. In the case of the
cell theory, the specific discovery that parts of diverse
organisms consisted of cells led to the generalization that
all organisms consist of cells.
Figure 4. The cell theory was developed by inductive reasoning
Figure 5. A team of researchers at Monterey Bay Aquarium Research Institute (MBARI), led by Kakani Katija, has been researching marine
organisms called larvaceans. The photograph on the left shows a larvacean's "house" which consists of two non-cellular mucus structures. The
large coarse-mesh outer structure excludes coarse non-food particles. The inner fine-mesh structure captures smaller food particles. The larvacean
itself is too small to be seen in this image. The photograph on the right shows a magnified view of a larvacean (the blue tadpole-like organism)
adjacent to the inner part of its mucus house. By beating its tail, the larvacean pumps water through the inner and outer mucus filters to extract
food particles from the surrounding seawater. The actual organism is about 3 to 5 centimetres long but the non-cellular house it makes and lives
inside can be up to a metre in diameter. The MBARI research shows there are still exciting discoveries to be made about the natural world. It also
shows that there are some exceptions to the theory that living organisms make everything out of cells
 A.2.2.2 Microscopy skills

Lenses allow us to look at structures that are too small to see with the naked eye-anything smaller than about 0.1
millimetres. A single convex lens is useful for magnifying up to 20 times (20x). However, this is not enough for
studying the structure of cells. Microscopes with two or more lenses make much smaller structures visible because
the magnification of the lenses is multiplied. For example, a 10x eyepiece lens combined with a 40× high-power
objective lens gives a total magnification of 400x. This allows us to see structures as small as 0.0001 millimetres
(0.1 micrometres). Using a microscope is an essential skill for biologists.
 A.2.2.2 Using a light microscope

Try to improve your skill at using microscopes as much as you can.

• Learn the names of parts of the microscope.
• Understand how to focus the microscope to get the best possible image.
• Look after your microscope so it stays in perfect working order.
• Know how to troubleshoot problems.
Look after your microscope by following these guidelines:
• Always focus by moving the lens and the specimen further apart. Never move
them closer to each other.
• Make sure the upper and lower surfaces of the slide are clean and dry before
putting it on the stage.
• Never touch the surfaces of the lenses with your fingers or anything else. Figure 6. Parts of a light microscope

• Carry the microscope carefully with a hand under it to support its weight securely.
 A.2.2.2 Using a light microscope

Use these hints to troubleshoot when you are focusing:

Course and fine focusing
Problem Solution
• Put the slide on the stage, with the most promising Nothing is visible when Make sure the specimen is actually under the
region in the centre of the window in the stage that the you try to focus lens, by carefully positioning the slide and using
low power first.
light comes up through.
You can see a circle with a There is an air bubble on the slide. Ignore it and
• Always focus at low power first, even if you need thick black rim. try to improve your technique for making slides
high-power magnification eventually. so there are no air bubbles.

• Focus with the larger coarse-focusing knobs first. There are parts of Either the lenses or the slide have
When you have nearly got the image in focus, use the the image even dirt on them. Ask your teacher to
when you focus it clean them.
smaller fine-focusing knobs to make it really sharp.
as well as you can.
• If you want to increase the magnification, move the
The image is very Adjust the diaphragm to increase
slide so the most promising region is exactly in the dark. the amount of light passing through
middle of the field of view and then change to a higher the specimen.

magnification lens. The image looks Adjust the diaphragm to decrease

rather bleached. the amount of light passing through
Table 1. the specimen.
 A.2.2.2 Using a light microscope

Making temporary mounts of cells and tissues and using stains

The slides you examine with a microscope can be permanent or temporary. Making
permanent slides is very skilled and takes a long time, so these slides are normally made
by experts. Permanent slides of tissues are made using very thin slices of tissue.
Making temporary slides is quicker and easier, so you can do this for yourself.
• Place the cells on the slide, in a layer not more than one cell thick.
• Add a drop of water or stain. Stains help structures that are pale or transparent to show
up more clearly.
• Carefully lower a cover slip onto the drop. Try to avoid trapping any air bubbles.
• Remove excess fluid or stain by putting the slide inside a folded piece of paper towel
and pressing lightly on the cover slip.
Figure 7. Making a temporary Mount
 A.2.2.2 Using a light microscope

Sketches and instructions for six different cell types are shown in Table 2.

1. Moss Leaf 2. Banana fruit cell 3. Mammalian liver cell

Use Moss plant with very this leaves. Scrape a small amount of the soft Scrape cells from a freshly cut surface of liver (not
Mount a single leaf in a drop of water or tissue from a banana and place on previously frozen). Smear onto a slide and add
methylene blue stain. a slide. Mount in a drop of iodine methylene blue to stain.
solution.

Table 2
 A.2.2.2 Using a light microscope

Sketches and instructions for six different cell types are shown in Table 2.

4. Leaf lower epidermisf 5. Human cheek cell 6. White blood cell

Peel the lower epidermis off a leaf. The Use a cotton bud to scrape cells Smear a thin layer of mammalian blood over a
cell drawn here was from Centranthus. from the inside of your cheek. slide and stain with Leishman's stain.
Mount in water or in methylene blue. Smear them on a and add
methylene blue to stain.

Table 2
 A.2.2.2 Using a light microscope

Observing, drawing and photographing cells

When you have focused at high power on plant or animal cells, it is
useful to record your observations by drawing a typical cell.
Alternatively, you could use a smartphone to take a photo through
the microscope.
A biological drawing of a cell is a type of diagram because cell
structure is shown with some features only, such as the nucleus.
Usually the lines on a drawing represent the edges of structures. Do
not show unnecessary detail and only use faint shading. The cell
Figure 8. Onion epidermis cells photographed with a smartphone.
membrane is too thin to see, but you can deduce its position and you Some of the cells have a red pigment in their cytoplasm. The black-
edged circles are air bubbles; this is a common fault in temporary
should include it in your drawing. For example, it forms the outer microscope slides. They are a type of artefact something not naturally
present that was introduced during preparation of the slide.
edae of a blood cell.
 A.2.2.2 Using a light microscope

Observing, drawing and photographing cells

Drawings and diagrams are more informative if they are annotated. Use a ruler to draw a straight line from each
structure of interest to a position off the diagram. Then add notes there. You might simply identify the structure with a
name, or you can add other details such as the function.
Drawings of structures seen using a microscope are larger than the actual size the drawing shows structures magnified.
Everything on a drawing should be shown to the same magnification and the magnification should be calculated and
indicated. Photography is an alternative to drawings. The advantage of photographs is that they contain real data rather
than one biologist's subjective interpretation of it. Digital microscopes are increasingly common and they make it very
easy to take photos.

Figure 9. Qualities of drawings.

 A.2.2.2 Using a light microscope

Measuring sizes using an eyepiece graticule

You can measure the actual sizes of structures visible through a microscope
by using a scale inside the eyepiece called a graticule. The graticule has to
be calibrated so you know what size each unit on the scale indicates. This
will be different for each objective lens. For example, if one unit on the
scale represents 2.5 micrometres at 400× magnification (high power), it
will represent 25 micrometres at 40× magnification (low power).Drawings
and diagrams are more informative if they are annotated. Use a ruler to
draw a straight line from each structure of interest to a position off the
Figure 10. Microscope image photographed
diagram. Then add notes there. You might simply identify the structure using a smartphone, showing a fruit of
Centranthus ruber and a graticule scale. 100
with a name, or you can add other details such as the function. graticule units = 5 millimetres or 5,000
micrometres
 A.2.2.2 Using a light microscope

Calculating actual size, magnification and scale

Structures seen using a microscope appear larger than they actually are. Most microscopes have more than one
objective lens, so you can magnify specimens by different factors. A typical school microscope has three levels of
magnification:
• 40× (low power)
• 100x (medium power)
• 400× (high power)
If you take a photo down a microscope, you can magnity the image even more. A photo of a microscope image is called
a photomicrograph, often abbreviated to micrograph. Electron micrographs are taken using an electron microscope.
When you draw a specimen, you can make the drawing larger or smaller, so the magnification of the drawing is not
necessarily the same as the magnification of the microscope.
 A.2.2.2 Using a light microscope

Calculating actual size, magnification and scale

To find the magnification of a micrograph or a drawing, you need to know two things: the size of the image (in the
drawing or the micrograph) and the actual size of the specimen. Then you use this formula:

magnification = size of image

actual size of specimen

If you know the size of the image and the magnification, you can calculate the actual size of a specimen.
When using this formula, you must make sure you use the same units for the size of the image and the actual size of the
specimen. They could both be millimetres (mm) or micrometres (um) but they must not be different, otherwise the
calculation will be wrong. You can convert millimetres to micrometres by multiplying by 1,000. You can convert
micrometres to millimetres by dividing by 1,000.
 A.2.2.2 Using a light microscope

Calculating actual size, magnification and scale Worked example

Scale bars may be put on micrographs or drawings, or The length of an image is 30 mm. It represents a structure
shown alongside them. A scale bar is a straight line, that has an actual size of 3 µm. Determine the
labelled with the actual size that the bar represents. For magnification of the image.
example, a 10mm long scale bar on a micrograph with Either:
a magnification of x10,000 would be labelled 1 µm. 30mm = 30×10-3 m
3µm = 3×10-6 m
Magnification = 30×10-3
3x10-6 = 10,000 x
Or:
30mm = 30,000 µm
Magnification = 30,000 = 10,000 x
3
 Data-based questions: Size, magnification and scale

1. a. Determine the magnification of the Thiomargarita 2. In Figure 12, the actual length of the mitochondrion is 8 um.
cells in Figure 11. [3] a. Determine the magnification of the electron micrograph. [2]

b. Determine the maximum diameter of the whole cell b. Calculate the length of a 5 um scale bar on this electron

in the micrograph. [2] micrograph. [2]

c. Determine the width of the mitochondrion. [1]

Figure 11. Thiomargarita cells (one whole cell

and two in part). The scale bar represents 0.2
µm

Figure 12. Mitochondrion with false colour (red)

 Data-based questions: Size, magnification and scale

3. The magnification of the human cheek cell from a
compound microscope (Figure 13) is 2,000×.
a. Calculate the length of a 20 um scale bar on the image. [2]
b. Determine the maximum length of the cheek cell. [2]
4. a. Using the width of the hen's egg as a guide,
estimate the actual length of the ostrich egg in Figure
14. [2]
b. Estimate the magnification of the image. [2]

Figure 13. Human cheek cell stained with

methylene blue
Figure 14. Ostrich egg.
 Data-based questions: Size, magnification and scale

5. Caenorhabditis elegans has been widely used as a model

organism in research. Most adults are hermaphrodite and have
exactly 959 cells.
a. Measure the maximum width and total length of the worm, in
eyepiece units (EPU). [2]
b. One unit on the scale indicates 9.5 micrometres. Calculate the
actual dimensions of the worm in micrometres. [3]
c. Convert the dimensions from micrometres to millimetres. Which Figure 15. Caenorhabditis elegans together
with an eyepiece scale
length units are more convenient with an organism of this size? [3]
 A.2.2.2 Using a light microscope

Quantitative versus qualitative observations

Quantitative data is numerical and is usually obtained with a measuring
instrument. An eyepiece scale (graticule) in a microscope is an example of a
measuring instrument.
Sometimes quantitative data can be obtained simply by counting. For example,
we might count how many legs a centipede has, to see if it is 100.
In contrast, qualitative observations involve descriptions that are likely to be
more subjective. Consider the micrograph of pond water in Figure 16. An
Figure 16. A micrograph of pond water
example of a qualitative observation is that the copepod larva (centre right) is
transparent. Two types of algae are visible: Synura appears yellow and Pandorina
morum appears green.
 A.2.2.2 Using a light microscope

Quantitative versus qualitative observations

1. Create a data table with two columns headed "qualitative observations"
and "quantitative observations”
2. Make observations about the organisms in the micrograph and record
them in your table.
3. Compare your observations with those of a classmate.
4. Discuss the advantages of qualitative and quantitative observations.
Figure 16. A micrograph of pond water
5. Do all quantitative observations involve a measuring instrument? Or
numbers? Or units?
 A.2.2.3 Developments in microscopy

Microscopes were first invented in the 17th century. Since then, there have
been many technological developments in microscopy, which have made
new and more detailed observations possible. Improved light microscopes in
the second half of the 19th century allowed the discovery of bacteria and
other unicellular organisms. Chromosomes were seen for the first time and
the processes of mitosis, meiosis and gamete formation and fertilization
were discovered. More advanced microscopes also revealed the complexity
of organs such as the kidney, and the presence of mitochondria, chloroplasts
and other structures in cells.
Figure 17. Leeuwenhoek microscope of about 1670 (left)
and Zeiss microscope of 2020 (right)
 A.2.2.3 Developments in microscopy

At magnifications of more than 400x, it becomes increasingly difficult to produce a focused image with a light
microscope. Imagine a pair of dots that appear closer together as they become smaller. Eventually, it will be
impossible to see them as separate dots. A hand lens or microscope allows smaller details to be distinguished but
there is a limit because of distortions caused by the wavelength of light.
This problem was overcome by the development of microscopes that use beams of electrons instead of light. The
wavelength of electrons is much shorter than the wavelength of visible light. The first electron microscopes were
designed and constructed in Germany during the 1930s. They came into use in research laboratories in the 1940s
and 50s. Some electron microscopes can give magnifications up to 1,000,000x.
 A.2.2.3 Developments in microscopy

Making the separate parts of an object distinguishable by eye is called resolution.

Table 3 shows the maximum resolution of the unaided eye, the light microscope and
the electron microscope, using three different SI size units.

Resolution Resolution Resolution

milimitres/mm micrometres/µm nanometres/nm

Unaided eyes 0.1 100 100,000

Light microscopes 0.0002 0.2 200

Electron
0.000 001 1 1
Microscopes
Figure 18. Size of printed periods (full stops) used for punctuation can
Table 3. be used to test the resolution of the naked eye, and of the eye aided by
one or more lenses. Font size is the maximum height of letters and is
measured in "points". In desktop publishing fonts, 1 point is 0.353
mm. The diameter of a period is just less than one-tenth of the overall
font size, so a period at font size 30 has a diameter of approximately 1
mm. The table shows a row of 10 periods at font sizes from 30 to 1.
Which sizes of period can you distinguish as individual dots?
 A.2.2.3 Developments in microscopy

Because electron microscopes have better resolution, they can give much higher magnification.
This means much smaller structures can be seen than with a light microscope. Electron
microscopes have allowed scientists to investigate the detailed structure (ultrastructure) of cells.
Variations in ultrastructure between different cell types are described later.
Electron microscopes do have some disadvantages. They can only give black and white images,
so any colour in electron micrographs has to be added artificially. The methods used to prepare
material for the electron microscope always kill the cells. In any case, cells would die inside an
electron microscope because there is a vacuum and the beams of electrons are very destructive. Figure 19. An electron microscope in use
at the Max-Planck Institut in Halle,
In contrast, light microscopes can be used to examine living material and produce images in Germany. Three of the many technological
developments in microscopy are described
colour. Therefore, both types of microscope are very useful in research and continue to be here
widely used.
 A.2.2.3 Developments in microscopy

1. Fluorescent stains and immunofluorescence

Most of the chemicals in cells are white or colourless so they are difficult to distinguish unless stained. Stains used in microscopy are
coloured substances that bind to some chemicals but not others. For example, methylene blue binds to DNA and RNA so it stains the
nucleus dark blue and cytoplasm a lighter blue.
Fluorescence is when a substance absorbs light and then re-emits it at a longer wavelength. Fluorescent stains have been used for
over 100 years. Some absorb ultraviolet light and re-emit it as blue light, for example. Special fluorescence microscopes have been
designed and built with intense light sources such as high power LEDs or lasers that emit a single wavelength. This light is absorbed
and re-emitted by the sample, generating particularly bright images.
Immunofluorescence is a development of fluorescent staining. Antibodies that bind to particular chemicals (antigens) in the cell are
produced. Then fluorescent markers of different colours are linked to these antibodies. A multicoloured fluorescent image can then be
produced showing where the chemicals are located. There are many research applications of this technique; for example, it can be
used to find out if one specific type of protein is being produced in a cell.
 A.2.2.3 Developments in microscopy

Figure 20. The fluorescent stain (yellow) may be linked directly to the
antibody that binds to the target antigen (green).
Alternatively, it may be linked indirectly by an antibody that binds to the
primary antibody
Figure 21. In this image produced by immunofluorescence, DNA in the nuclei
is stained cyan.
Microtubule proteins of the cytoskeleton, which are normally invisible, are
stained magenta. This image was produced using a Nikon RTS2000MP
custom laser scanning microscope
 A.2.2.3 Developments in microscopy

2. Freeze-fracture electron microscopy

This technique is used to produce images of surfaces within cells. A sample is plunged into liquefied propane at -
190°C so it rapidly freezes. A steel blade is then used to fracture the frozen sample. The fracture goes through the
weakest points of the cells. Some of the ice at the fractured surface is removed by vaporization, to enhance the
texture of the surface. This is called etching. Then a vapour of platinum or carbon is fired onto the fracture surface
at an angle of about 35° to form a coating. This creates a replica of the fracture surface.

Figure 22. The freeze-fracture process

 A.2.2.3 Developments in microscopy

The replica is removed from the frozen sample and can be examined
using an electron microscope. It is about 2 nanometres thick on
average but the thickness varies because of the angle at which the
coating is applied. This gives the impression of a 3D image through
shadowing
The weakest point in cells is usually the middle of membranes,
between the two lavers of phospholipid. The freeze-fracture process
gives a unique image of this part of cells. When these images were
first produced, they led to a fundamental change in theories about
membrane structure. This is described in Topic B2.1. Figure 23. ThFreeze-fracture image of a yeast cell, showing a large vacuole,
smaller vesicles (unlabelled), plasma membrane (PM), cell wall (CW) and a
lipid droplet (LD). The vacuole, vesicles and plasma membrane appear
convex or concave because the fracture followed the centre of the
membrane, which was curved. The lipid droplet is cross-fractured because it
is not surrounded by a membrane
 A.2.2.3 Developments in microscopy

3. Cryogenic electron microscopy

This technique is often called cryo-EM. It is principally used for researching the structure of proteins. A thin layer of a
pure protein solution is applied to a grid. The solution is flash-frozen, to create smooth vitreous ice and prevent the
formation of water crystals. Liquid ethane just above its melting point of-182.6°C is usually used as the coolant.
The grid with the frozen protein solution is placed in an electron microscope and detectors record the pattern of
electrons transmitted by individual protein molecules. Because the protein molecules are randomly orientated in the
layer of frozen solution, many different patterns are produced. Using computational algorithms, these patterns are
combined to produce a 3D image of the protein molecules.
Previous methods for analysing protein structure only produced images of a protein in its most stable form. However,
cryo-EM analyses proteins at the instant in time when the water around them froze. This allows scientists to research
proteins that change from one form to another as they carry out their function
 A.2.2.3 Developments in microscopy

3. Cryogenic electron microscopy

Since 2010, cryo-EM techniques have improved rapidly. They can
now give resolutions of 0.12 nanometres. This allows the
generation of images of individual atoms in a protein or other
molecule. Over 10,000 protein structures have now been shared in
the Electron Microscopy Data Bank (EMDB). The 2017 Nobel
Prize in Chemistry was awarded to Jacques Dubochet, Joachim
Frank and Richard Henderson for their work in developing cryo-
EM. Figures 24 and 25 show an example of this.
Figure 24. Pyocin is a protein produced by bacteria to kill other bacteria
by bursting their cell wall and membrane. The cryo-EM image (a) shows
pyocin pre-contraction and post-contraction. The scale bar represents 30
nm. Two computer-generated coloured images of pyocin (b and c) show
components of the protein before and after it contracts
 A.2.2.3 Developments in microscopy

Figure 25. This sequence of diagrams shows how pyocin binds to and then pierces its target
 A.2.2.4 Structures common to cells in all living organisms

Cells vary considerably in size, shape and structure, but they share some common features:
1. Plasma membrane
This is the outer boundary of the cell and encloses all of its contents. The plasma membrane controls the entry and exit
of substances. It can pump substances in, even if the concentration outside the cell is very low. It is also very effective
at preventing entry of unwanted or even toxic substances. It allows a cell to maintain concentrations of substances that
are very different from those in the surrounding environment. The permeability of the plasma membrane relies on a
structure based on lipids.
Occasionally the plasma membrane of a cell bursts. This is known as lysis and can be caused by excess pressure or by
viruses. It can even be carried out by the cell itself (autolysis). Lysis always leads to the death of the cell; this shows
that the plasma membrane is a vital structure.
 A.2.2.4 Structures common to cells in all living organisms

2. Cytoplasm
Water is the main component of cytoplasm and there are many substances dissolved or suspended in this water.
Enzymes in the cytoplasm catalyse hundreds or even thousands of different chemical reactions. These reactions are the
metabolism of the cell.
Metabolism provides a cell with energy and produces all the proteins and other substances that make up the structure
of a cell. Proteins are quite easily damaged, so even when a cell is not growing the cytoplasm must continuously break
down and replace its proteins.
 A.2.2.4 Structures common to cells in all living organisms

3. DNA
Genes, made of DNA, contain the information needed for a cell to carry out all its functions. Many genes hold the
instructions for making a protein. Some proteins are structural so are needed for growth and repair. Others act as
enzymes, without which a cell cannot control chemical reactions and does not have a functioning metabolism.
DNA can be copied and passed on to daughter cells, so the information it stores is heritable. Plant and animal cells
have a nucleus that contains almost all their DNA. Bacteria do not have a nucleus and their DNA is in the cytoplasm
instead.
Use of DNA as a genetic material is therefore common to all cells, but the location of this DNA is not universal.
 A.2.2.5 Prokaryote cell structure

Organisms can be divided into two groups, prokaryotes and eukaryotes. Bacteria are prokaryotic. Plants, animals, fungi
and a variety of other organisms (such as Amoeba) are eukaryotic. The key feature of eukaryotic cells is the nucleus,
which contains chromosomes. This is bounded by a nuclear envelope consisting of a double layer of membrane.
Prokaryotic cells do not have a nucleus.
Prokaryotes were the first organisms to evolve on Earth and they still have the simplest cell structure. They are mostly
small in size and are found almost everywhere in soil, in water, on our skin, in our intestines and even in pools of hot
water in volcanic areas.
All cells have a plasma membrane. Some cels, including prokaryotic cells, also have a cell wall outside the cell
membrane. This structure is thicker and stronger than the membrane. It protects the cell, maintains its shape and
supports the plasma membrane to prevent it from bursting. In prokaryotes, the cell wall contains peptidoglycan.
 A.2.2.5 Prokaryote cell structure

There is no nucleus in a prokaryotic cell so the interior is entirely filled with cytoplasm. The cytoplasm is not divided
into compartments by membranes; instead, it is one uninterrupted chamber. Prokaryotic cells are therefore structurally
simpler than eukaryotic cells-although they still contain a very complex mixture of biochemicals including many
enzymes.
The cytoplasm of eukaryotic cells contains organelles that are analogous to the organs of multicellular organisms. Both
organs and organelles are distinct structures with specialized functions. Prokaryotes do not have cytoplasmic
organelles apart from ribosomes. Prokaryote ribosomes are smaller than those of eukaryotes: they are 70S whereas
eukaryote ribosomes are 80S. The S stands for Svedberg units, which are a measure of the rate at which a particle sinks
during centrifugation.
 A.2.2.5 Prokaryote cell structure

In many electron micrographs of prokaryotes, part of the cytoplasm appears lighter than the rest. This region contains
DNA. There is usually only a single molecule of DNA that forms a loop or circle. The DNA is "naked": unlike
eukaryotic DNA, it is not associated with proteins. The lighter region of the cytoplasm is called the nucleoid. It is
similar to a nucleus because it contains DNA, but it is not a true nucleus. Other parts of the cytoplasm appear darker in
electron micrographs. They contain ribosomes, enzymes and other proteins.
 A.2.2.5 Prokaryote cell structure

Data-based questions: Ultrastructure of Clostridium

Figure 26 shows an electron micrograph of the Gram-positive
bacterium Clostridium botulinum. This bacterium produces a
neurotoxin that is the most poisonous protein so far discovered. This
neurotoxin is used in cosmetic treatments under the brand name
Botox®.
1. What causes the cytoplasm of Clostridium to appear so dark in
the electron micrograph? [2]
2. This image is a longitudinal section: you can see a thin slice of
the bacterium going from end to end. What shape would you see in
Figure 26.
a transverse section (going from side to side)? [1]
 A.2.2.5 Prokaryote cell structure

Data-based questions: Ultrastructure of Clostridium

Figure 26 shows an electron micrograph of the Gram-positive bacterium
Clostridium botulinum. This bacterium produces a neurotoxin that is the
most poisonous protein so far discovered. This neurotoxin is used in
cosmetic treatments under the brand name Botox®.
3. There are two nucleoids visible in the cytoplasm of this cell. What
does this suggest it is getting ready to do? [2]
4. There is a scale bar on the micrograph. Use this to calculate the
magnification of the micrograph. [3]
5. Use the magnification to calculate the actual length of the cell.[2]
Figure 26.
 A.2.2.5 Prokaryote cell structure

Research skills: Using search engines effectively

Your task is to research the connection between
Clostridium botulinum and cosmetic facial injections. What cellular processes
are affected?
Your primary purpose is to use web-based sources to find information. You
should use precise language in your search terms, including scientific language.
For example, you might search "Clostridium botulinum" and "cosmetic facial
injections". However, this is likely to return results for businesses offering
cosmetic treatments. These will be sites with domain names ending in ".com".
For this task, you want information from organizations whose primary purpose
is education. Such sites have domains ending in "edu". To filter your search Figure 27. Injecting Botox®
results, include the search term "site: edu".
 A.2.2.5 Prokaryote cell structure

Research skills: Using search engines effectively

Enter the following terms in your search engine. Compare the results of
the different searches.
a. Botox® treatment
b. Clostridium botulinum and cosmetic facial injections
c. Clostridium botulinum and cosmetic facial iniections site:edu
Which search terms enabled you to answer the questions:
"What is the connection between Clostridium botulinum and cosmetic
facial injections?" and "What cellular processes are affected by
Clostridium botulinum?"

Figure 27. Injecting Botox®

 A.2.2.6 Eukaryote cell structure

Eukaryotes, like all other living organisms, have a basic cell structure with cytoplasm inside a plasma membrane. In some
eukaryotes, there is also a cell wall outside the membrane. Whereas the cytoplasm of a prokaryotic cell is one undivided
space, eukaryotic cells are compartmentalized. Areas are separated from the rest of the cytoplasm by single or double
membranes. The advantages of having compartments are described in Topic B2.2. Three other fundamental features
distinguish eukaryotic cells from prokaryotic cells:
Nucleus
This compartment holds the cell's chromosomes. The nucleus has a double membrane with pores through it. Each
chromosome consists of one long
DNA molecule attached to proteins, except when a cell is preparing to divide and the DNA is replicated. The DNA
molecules are linear rather than circular.
The proteins are histones, arranged in globular groups like small beads, with the DNA wound around the outside.
 A.2.2.6 Eukaryote cell structure

80S ribosomes
Ribosomes in eukaryotic cells synthesize proteins, as in prokaryotes, but there are structural differences and they are
larger in size. This causes them to sink more quickly than prokaryotic ribosomes when centrifuged; this is quantified
using Svedberg units (S). Eukaryotic ribosomes are 80S whereas those of a prokaryote are 70S.

Mitochondria
The cytoplasm of a eukaryotic cell contains mitochondria. A mitochondrion is surrounded by a double membrane. The
inner membrane is usually folded inwards to increase the surface area. Mitochondria carry out aerobic cell respiration,
so in eukaryotes they are only lacking in cells that never respire aerobically.
Nuclei, mitochondria and ribosomes are examples of organelles. All the important organelles of eukaryotic cells are
described in Section A2.2.10.
 A.2.2.6 Eukaryote cell structure

Figure 28. Whereas the DNA of prokaryotes is naked, DNA in eukaryotes is Figure 29. An electron micrograph of the unicellular fungus, Saccharomyces cerevisiae
attached to groups of proteins called histones. There are many of these histones (baker's yeast). The nucleus (N), mitochondria (m) and vacuole (V) are easily visible. The
along the chromosome, giving the overall appearance of a string of beads. cell wall (CW) is the thicker pale outer layer. The plasma membrane (PM) is the thinner
Source: Caputi, Francesca & Candeletti, Sanzio & Romualdi, Patrizia. (2017). dark line inside the cell wall. 80S ribosomes (R) are smaller and more difficult to see, but
Epigenetic Approaches in Neuroblastoma Disease Pathogenesis. many are present.
10.5772/intechopen.69566 The labelled ribosomes look like a string of beads. This cell is 8 µm long. What is the
magnification of the micrograph?
Remember that 1 µm = 1,000 nm
 A.2.2.7 Processes of life in unicellular organisms

Living organisms are very diverse in their activities. However, some vital processes are either universal or very
widespread:
• Homeostasis: maintenance of a constant internal environment in an organism.
• Metabolism: the sum of all the biochemical reactions that occur in a living organism.
• Nutrition: supplying the nutrients required for energy, growth and repair in an organism
• Excretion: removal of waste products of metabolism from an organism
• Growth: an increase in size or number of cells
• Response to stimuli: perception of stimuli and carrying out appropriate actions in response
• Reproduction: production of offspring, either sexually or asexually.
In a multicellular organism, different cell types are specialized to perform these functions, but the single cell of a
unicellular organism must perform them all.
The annotated diagrams of Paramecium and Chlamydomonas (Figure 30 and Figure 31) show how two unicellular
organisms perform the functions of life.
A.2.2.7 Processes of life in unicellular organisms
A.2.2.7 Processes of life in unicellular organisms
 A.2.2.7 Processes of life in unicellular organisms

Making careful observations:

Examining a community of life under a microscope

To see unicellular organisms, follow this procedure.

1. Collect some pond water.
2. If possible, centrifuge the sample to concentrate the organisms in it.
3. Place a drop of the concentrated pond water on a microscope slide.
4. Add a cover slip and view with a microscope.
You will almost certainly be able to see unicellular organisms.
Alternatively, you could obtain a pure culture of unicellular organisms such as
Paramecium or Chlamydomonas.
 A.2.2.7 Processes of life in unicellular organisms

Data-based questions: Processes of life in a testate amoeba

Arcella gibbosa is a unicellular testate amoeba that lives in freshwater
habitats. It has a hard outer coat made of chitin, with a light but strong
structure resembling honeycomb. This is called the test. There is a
circular aperture in the test and finger-like protrusions of cytoplasm
can push out through this, then retract again. In Figure 32, five
structures are labelled: nuclear membrane (nm), outer surface of test
(to), plasma membrane (pm), contractile vacuole (cv) and aperture in
the test (at). The unlabelled coloured structures are food vacuoles. A
scale bar is shown lower right.
Figure 32. Arcella gibbosa
 A.2.2.7 Processes of life in unicellular organisms

Data-based questions: Processes of life in a testate amoeba

A scale bar is shown lower right.
1. Calculate the diameter of the cell and the magnification of the
micrograph. [3]
2. Deduce the maximum size of food particle that could be ingested. [2]
3. Explain the need for a contractile vacuole in this organism. [3]
4. Predict whether this cell was:
a. Growing. [2]
b. Preparing to divide. [2]
5. Suggest a hypothesis for whether the cell has mitochondria in its
Figure 32. Arcella gibbosa
cytoplasm. Give reasons and suggest how your hypothesis could be
tested. [3]
 A.2.2.8 Differences in eukaryotic cell structure between animals, fungi and plants

Feature Animals Fungi Plants

Plastids None Plastids of varied types such as

A family of organelles with two chloroplasts (for photosynthesis) and
amyloplasts (to store starch)
outer membranes and internal
membrane sacs.
Cell wall None Cells of fungi and plants have walls, composed of
A rigid layer outside the plasma chitin in fungi and cellulose in plants.

membrane to strengthen and

protect the cell.
Vacuole Small temporary vacuoles expel excess There is often a large permanent vacuole in cells
A flexible fluid-filled compartment water or digest food or pathogens taken in of fungi and plants, used for storage of
by endocytosis. substances and pressurizing the cell.
surrounded by a single membrane

Centrioles Used to construct the spindle that moves Absent, except in fungi and plants with
Cylindrical organelles that organise chromosomes in mitosis and the 9 + 2 swimming male gametes, which have a centriole
microtubules in cilia and flagella. at the base of the flagellum.
the assembly of structures
composed of microtubules.
Undulipodia Cilia and flagella are present in many Absent except in fungi and plants with male
Cilia and flagella used to generate animal cells, including the tail of male gametes that swim using flagella (tails).
gametes.
movement of a cell or movement of.
 A.2.2.7 Processes of life in unicellular organisms

Thinking skills: Reflecting on the reasonableness of results

It is claimed that, for every one of your human cells, there are 10 prokaryotic cells living in your
body. Does this seem a reasonable claim? One way to test this claim is to model it using artist's
clay.
1. Obtain some modelling clay.
2. Construct a model of a prokaryotic cell, with dimensions 10mm × 5 mm × 5 mm.
3. Construct a model of a eukaryotic cell that is 10 times larger in every dimension: 100 mm × 50
mm x 50 mm.
4. Using these models, does the claim seem reasonable?
 A.2.2.9 Atypical cell structure in eukaryotes

According to the cell theory, all living organisms are made of cells. Each cell is expected to have one nucleus (unless it
is preparing to divide, when there may be two). However, some structures in organisms do not follow the typical
patterns. Some examples are red blood cells, phloem sieve tube elements, skeletal muscle and aseptate fungal hyphae.

Red blood cells

In mammals, these cells do not have a nucleus. At a late stage in their development in bone marrow, the nucleus is
moved to the edge of the cytoplasm and the small part of the cell containing it is pinched off and destroyed by a
phagocyte. Removal of the nucleus makes red blood cells smaller and more flexible, but they cannot repair themselves
if they are damaged. For this reason, they have a lifespan of only 100 to 120 days.
 A.2.2.9 Atypical cell structure in eukaryotes

Phloem sieve tube elements

Plants move sap through tubular vessels, made from columns of cylindrical cells. The flow of sap would be impeded if
these cells had a typical structure. In xylem vessels, which conduct watery sap from the roots to the leaves, all the
dividing walls between adjacent cells are removed and the plasma membrane and all of the cell contents break down.
This creates a hollow tube that no longer consists of cells.
In phloem, which conducts sugary sap from the leaves to other parts, the conducting vessels are called sieve tubes. The
dividing walls between adjacent cells are sieve-like, with large pores for the sap to pass through. During development
of sieve tubes, the nucleus and most of the other cell contents break down, but the plasma membrane remains as it is
essential for phloem transport. The subunits in a sieve tube are usually called elements rather than cells because of
their atypical structure. Sieve tube elements are connected to adjacent companion cells, which have a nucleus and
mitochondria. These companion cells help the sieve tube elements to survive and carry out their function.
 A.2.2.9 Atypical cell structure in eukaryotes

Skeletal muscle
Figure 33 .The human sartorius
Some large multinucleate structures are formed when groups of cells fuse muscle can be as much as 600
mm long. It contains muscle
together. This type of structure is a syncytium. Muscle fibres develop in
fibres that extend from one end to
this way. the other. Are these the longest
cells in the human body?
Columns of cells, each with a nucleus, are formed by cell division. These
cells then fuse together to form long muscle fibres.
Aseptate fungal hyphae
In some growing cells, the nucleus divides repeatedly without any Figure 34. A micrograph of
aseptate hyphae of the fungus
subsequent cell division. This results in an unusually large multinucleate Rhizopus arrhizus, which is the
most frequent cause of
structure, known as a coenocyte. The thread-like hyphae of some fungi mucormycosis. Spores and the
develop in this way. Walls that divide the hyphae of other types of fungi sporangia that produced them are
also visible
into uninucleate cells are called septa so hyphae without these divisions
are aseptate.
 A.2.2.10 Cell types and cell structures viewed in light andelectron micrographs

In light micrographs, these features help us to identify whether a cell is from a prokaryote, a plant or an animal.

Prokaryotic cells Plant cells Animal cells

• Single cells, sometimes arranged in chains. • Always multicellular apart from gametes and • Always multicellular apart from gametes,
• Amall size- cells usually less than 5 µm. zygotes. zygotes and blood cells.
• Often rod-shaped (bacilli), spheroidal (cocci) • Larger size cells usually more than 5 µm. • Larger size cells usually more than 5 µm.
or helical (spirilli). • Shape tends to be regular with flat sides and • Shape tends to be rounded with junctions
• Cell wall present. cell junctions easily visible in tissues. between cells often hard to see in tissues.
• No nucleus; instead there isa paler region of • Cell wall present. • No cell wall.
cytoplasm (nucleoid). • Nucleus normally present but not always • Nucleus normally present but not always
• Simple internal structure with no membrane- visible. visible.
bound organelles. • Plastids present, such as chloroplasts, or • No chloroplasts or stored starch but cytoplasm
• No vacuoles or other internal membranes. amyloplasts storing starch. contains many other organelles.
• Large vacuole often presente. • Only small vacuoles are present.
 A.2.2.10 Cell types and cell structures viewed in light andelectron micrographs

Table 5 describes the structure and functions of all the main organelles of eukaryotic cells.

The nuclear membrane is double and has pores through it. The nucleus
contains the chromosomes, consisting of DNA associated with histone
proteins. Uncoiled chromosomes are spread through the nucleus in the
areas that appear pale and grainy. The small areas that are more
densely stained, mostly around the edge of the nucleus, contain parts
of chromsomes that have remained coiled up (condensed). The nucleus
is where DNA is replicated and transcribed to form mRNA, which is
exported via the nuclear pores to the cytoplasm.
The rER consists of flattened membrane sacs, called cisternae.
Ribosomes are attached to the outside of these cisternae. They are
larger than in prokaryotes and are classified as 80S. The main function
of the rER is to synthesize protein for secretion from the cell. Protein
synthesized by the ribosomes of the rER passes into its cisternae. It is
then carried by vesicles, which bud off and are moved to the Golgi
apparatus.
Smooth endoplasmic reticulum consists of a branched network of
tubular membranes. In electron micrographs, it appears as circles or
ovals of membrane. The membrane is smooth because there are no
ribosomes attached. Smooth ER has a variety of functions. It is used to
 A.2.2.10 Cell types and cell structures viewed in light andelectron micrographs

Table 5 describes the structure and functions of all the main organelles of eukaryotic cells.

This organelle consists of flattened membrane sacs called cisternae

(as in rER). However, these cisternae are not as long, are often curved,
do not have attached ribosomes and have many vesicles nearby. The
Golgi apparatus processes proteins brought in vesicles from the rER.
Most of these proteins are then carried in vesicles to the plasma
membrane for secretion.

These are approximately spherical with a single membrane. They are

formed from Golgi vesicles. They contain high concentrations of
protein, which makes them densely staining in electron micrographs.
They contain digestive enzymes, which can be used to break down
ingested food in vesicles. These enzymes can also break down
organelles or even whole cells.
A double membrane surrounds mitochondria. The inner membrane is
invaginated to form structures called cristae. The fluid inside is called
the matrix. The shape of mitochondria is variable but usually spherical
or ovoid. They produce ATP for the cell by aerobic cell respiration. Fat
is digested here if it is being used as an energy source in the cell.
 A.2.2.10 Cell types and cell structures viewed in light andelectron micrographs

Table 5 describes the structure and functions of all the main organelles of eukaryotic cells.

These appear as dark granules in the cytoplasm and are not

surrounded by a membrane. They have the same size as ribosomes
attached to the rER-about 20 nm in diameter (known as 80S). Free
ribosomes synthesize protein, releasing it to work in the cytoplasm, as
enzymes or in other ways. Ribosomes are constructed in a region of
the nucleus called the nucleolus.
A double membrane surrounds the chloroplast. Inside are stacks of
thylakoids, which are flattened sacs of membrane. The shape of
chloroplasts is variable but usually spherical or ovoid. They produce
glucose and a wide variety of other organic compounds by
photosynthesis. If chloroplasts have been photosynthesizing rapidly,
they may contain starch grains.
These organelles consist of a single membrane with fluid inside. Many
plant cells have large vacuoles that occupy more than half of the cell
volume. Some animals absorb foods from outside and digest them
inside vacuoles.
Some unicellular organisms use vacuoles to expel excess water.
Vesicles are very small vacuoles used to transport materials inside the
cell.
 A.2.2.10 Cell types and cell structures viewed in light andelectron micrographs

Table 5 describes the structure and functions of all the main organelles of eukaryotic cells.

The cytoplasm of cells contains small cylindrical fibres called

microtubules. They have a variety of roles, including moving
chromosomes during cell division.
Animal cells have structures called centrioles, which consist of two
groups of nine triple microtubules.
Centrioles form an anchor point for microtubules during cell division
and also for microtubules inside cilia and flagella.
The cytoskeleton is constructed from several types of protein fibre.
Tubulin is used to make microtubules and actin is used to make
microfilaments. These structures can easily be constructed or
deconstructed, so the cytoskeleton is dynamic. Microtubules guide the
movement of components within the cell. They help plant cells to
construct cell walls.
A layer of microfilaments just inside the plasma membrane helps
animal cells to maintain their shape.
These are whip-like structures projecting from the cell surface. They
contain a ring of nine double microtubules plus two central ones.
Flagella are larger and usually only one is present, as in a sperm. Cilia
are smaller and many are present. Cilia and flagella can be used for
locomotion.
Cilia can also be used to create a current in the fluid next to a cell.
 A.2.2.11 Drawing and annotation based on electron micrographs

Electron micrographs show cell structure in great detail. However, they sometimes include artefacts as well. (An
artefact is something that is not naturally present but was introduced as the specimen was prepared by staining and
sectioning.) Therefore, a drawing of an electron micrograph may show the structure more clearly. Basic drawing skills
were described earlier and Table 5 shows how the structure of organelles can be shown in drawings.
Electron micrographs of a prokaryotic cell (Figure 35) and a eukaryotic cell (Figure 36) are shown. A drawing of the
prokaryotic cell is also included, to show how its structure can be interpreted. Organelles in the electron micrograph
of a eukaryotic cell are labelled. Using your knowledge of these organelles, you should be able to draw the whole cell
to show its ultrastructure.
 A.2.2.11 Drawing and annotation based on electron micrographs

Figure 35. Electron micrograph of Escherichia coli (1-2 um in

length), with a drawing to help interpret the micrograph
Figure 36. Electron micrograph of a liver cell. The plasma membrane is
visible as a dark line. Part of the cell on the right is not visible