CELL

STRUCTURE &
MICROSCOPY
Module 2.1
O R G A N I S M S C A N B E P R O KA RYO T E S O R E U KA RYO T E S

Prokaryotic organisms are organisms with no nucleus

Eukaryotic organisms are organisms with a nucleus

Both types of cells contain organelles, all of which have

specific functions
P L A N T & A N I M A L C E L L S A R E E U KA RYO T I C
E U K A RYO T I C C E L L S I N D E TA I L
The cell membrane:

- 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 ‘partially permeable’

- It is a phospholipid bilayer
- The fluid mosaic model is used to
explain the bilayer structure
The nucleus:

- Found in all eukaryotic cells, with one exception

- It is separated from the cytoplasm by a double
envelope which has many pores
- Nuclear pores allow 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)
- Chromosomes are made of sections
of linear DNA tightly wound around proteins
called histones
- Usually, at least one or more darkly stained
regions can be observed – these regions are
individually termed ‘nucleolus’ (plural:
nucleoli) and are the sites of ribosome
production
The mitochondria:

- The site of aerobic respiration within all

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)
The ribosomes:

- Found in all cells

- Found freely in the cytoplasm of all
cells or as part of the rough
endoplasmic 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 ribosomes (composed of 50S and
30S subunits) in prokaryotes,
mitochondria and chloroplasts
- Site of translation (protein synthesis)
The endoplasmic reticulum:

- 2 types:
1. Rough Endoplasmic Reticulum (RER)
• Found in plant and animal cells
• Surface covered in ribosomes
• Formed from continuous folds of membrane
continuous with the nuclear envelope
• Processes proteins made by the ribosomes

2. Smooth Endoplasmic Reticulum (ER)

• Found in plant and animal cells
• 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
The Golgi
body/apparatus/complex:

- Found in plant and animal cells

- Flattened sacs of membrane
similar to the smooth
endoplasmic reticulum
- Modifies proteins and lipids
before packaging them
into Golgi vesicles
• The vesicles then transport
the proteins and lipids to
their required destination
Vesicles:

- Found in plant and

animal cells
- A membrane-bound sac
for transport and
storage
Lysosomes:

- 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)
Centrioles:

- 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
The cell wall:

- The cell wall is freely permeable to

most substances (unlike the plasma
membrane)
- Found in plant cells but not in animal
cells
- 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
Large permanent vacuole:

- A sac in plant
cells surrounded by
the tonoplast, selectively
permeable membrane
- Vacuoles in animal cells
are not permanent and
small
Chloroplasts:

- Found in plant cells

- 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
 ORGANELLES WORKING
T O G E T H E R I N E U K A RYO T E S
O R G A N E L L E S A R E I N V O LV E D I N P R O T E I N S Y N T H E S I S

• Proteins are made at the ribosomes.

• The ribosomes (80s) on the rough ER make

proteins that are excreted or attached to the cell
membrane.

• The free ribosomes make proteins that remain in

the cytoplasm.

• New proteins made at the RER are folded and

processed in the RER.

• They’re then transported to the Golgi body via

vesicles for further processing.

• The proteins enter more vesicles to then be

transported to the cell membrane.

• The vesicles can fuse with the cell membrane,

allowing the proteins to be excreted.
THE CYTOSKELETON & ITS FUNCTION

• The organelles are surrounded by cytoplasm.

• The cytoplasm, in addition to being a chemical

solution, contains a network of protein threads
running through it – the cytoskeleton.

• In eukaryotes, the proteins are arranged as

microfilaments and microtubules (thin strands)

• Microfilaments:
- made from the protein actin
- cause some cell movement and the movement of
organelles within the cell
The assembly of microtubules and microfilaments, and
the movement of materials along them, requires energy
• Microtubules: from respiration.
- hollow strands made from the protein tubulin
Respiratory inhibitors can prevent the network from
- organelles and other cell components are moved functioning.
along these fibres using ATP
T H E I M P O RTA N C E O F T H E CY T O S K E L E T O N

The cytoskeleton is important due to the many functions it carries out

1. Strength and support:

- It provides the cell with mechanical strength, forming a ‘scaffolding’ that helps to maintain
the shape of the cell
- it also supports organelles and keeps them in position (unless they need to move)

2. Intracellular movement:
- It aids transport within cells by forming ‘tracks’ which allows some organelles and
components to move along
- Ex: movement of vesicles and centrioles

3. Cellular movement:
- It enables cell movement via cilia and flagella
- Both these structures are hair-like extensions that protrude from the surface of cells and
contain microtubules
P R O K A RYO T I C C E L L S
P R O KA RYO T E S A R E A D I F F E R E N T K I N D O F C E L L

Membrane-bound organelles: cellular structures that are bound by a biological membrane. The membrane may
be a single layer or a double layer of lipids and typically with interspersed proteins. Examples of membrane-
bound organelles are nucleus, ER, Golgi, mitochondria, plastids, lysosomes, and vacuoles.
B AC T E R I A L C E L L S A R E P R O KA RYO T I C

• Bacterial cells are roughly a tenth

of the size of eukaryotic cells (1-
5um in diameter).

• Therefore, normal light

microscopes aren’t powerful
enough to look at their internal
structure.

• They should be viewed under an

electron microscope.
VIRUSES
STRUCTURE OF A BASIC VIRAL CELL

• Viruses are not living cells – they are

biological structures surrounded by
protein and lipids.
• Viruses are extremely small – in the
nanometer range.
• Viruses invade host cells – this allows
them to replicate and survive.
• Viruses have no organelles – they have
no nucleus, ribosomes, or membrane-
bound organelles.
• Viruses have a genome – they carry
genetic information in the form of
either DNA or RNA.
• Viruses are made of a protein coat
called a capsid – this protects the viral
genome from the external environment.
• Some viruses can also have a lipid coat
containing glycoproteins
M A G N I F I C AT I O N A N D H O W
MICROSCOPES WORK
M A G N I F I C AT I O N E Q U AT I O N

Magnification: how much bigger the

image is compared to the specimen’s
actual size.

• Magnification can be calculated using

a simple equation.

• This equation can be rearranged to

work out any three of these factors.

• The image size is measured using a

ruler.

• The actual size will usually be given to

you in micrometers (µm)
THREE TYPES OF MICROSCOPES

1. Light/optical microscope • Use light to form an image

• Have a low resolution – maximum of 0.2µm

• The eyepiece has a magnification of x10

• The maximum useful magnification in most basic

light microscopes is x400 (10x40)

• The total magnification of a microscope =

magnification of the lens x magnification of the
objective lens

• Some light microscopes can have a

magnification of up to x1500

• Only useful for viewing whole cells or tissues, as

detail won’t be visible.

• Some tissue samples need to be treated with

chemicals to kill/make the tissue rigid – this
involves fixing the specimen with formaldehyde
2. Electron
microscope

• Use electrons rather than light to form an image

• Have a high resolution, so detail within cells can

• SEM:
be viewed.
- Scan a beam of electrons across a specimen
• 2 main types: - this knocks off electrons from the specimen,
- scanning electron microscope (SEM) which gather at a cathode tube to form the
- transmission electron microscope (TEM) image
- image shown is 3D
- resolution is good, but TEM is higher.

• TEM:
- uses electromagnets to focus an electron
beam, which is transmitted through the
specimen.
- denser parts of the specimen absorb more
electrons; therefore, they appear darker on
the image.
- have high resolution
- however, can only be used when looking at
thin specimen
3. Laser scanning confocal
microscope • Use laser beams to scan a specimen.

• The specimen is usually tagged with a

fluorescent dye.

• The laser causes the dye to fluoresce (give off

light).

• This light is then focused through a pinhole

onto a detector.

• The detector is hooked up to a computer,

which generates an image – can be 3D.

• These images are much clearer than a light

microscope.

• LSCM can be used to look at thick specimens.

G R O U P TA S K

• Research the different microscopes and create a table comparing the

differences.

• Find images of specimen under all three microscopes.

S TA I N I N G S P E C I M E N S
S TA I N I N G I N L I G H T M I C R O S C O PY

• Many tissues that are used in microscopy are naturally transparent, they let both light and electrons pass
through them
• This makes it very diffi cult to see any detail in the tissue when using a microscope
• Stains are often used to make the tissue coloured/visible

Staining for light microscopy:

• The dyes used absorb specific colours of light while reflecting others; this makes the structures within the
specimen that have absorbed the dye visible
• Certain tissues absorb certain dyes
• Specimens or sections are sometimes stained with multiple dyes to ensure the different tissues within the
specimen show up - this is known as differential staining
• It is important to remember that most of the colours seen in photomicrographs (image taken using a light
microscope) are not natural
• Chloroplasts don't need stains as they show up green, which is their natural colour
• Some stains include:
• Toluidine blue turns cells blue – has high affi nity for acidic tissue components
• Phloroglucinol turns cells red/pink – used to detect lignin
• Ethidium bromide (+ve charge) is used to stain DNA – it is a dark red , and fluoresces orange-red under UV
light
S TA I N I N G I N E L E C T R O N M I C R O S C O P E S

• When using Transmission electron microscopes (TEMs) the specimen must be

stained in order to absorb the electrons
• Unlike light, electrons have no colour
• The dyes used for staining cause the tissues to show up black or
different shades of grey
• Heavy-metal compounds are commonly used as dyes because they absorb
electrons well
• Osmium tetroxide and ruthenium tetroxide are examples
• Any of the colour present in electron micrographs is not natural and it is also
not a result of the staining
• Colours are added to the image using an image-processing softwar
S T U DY I N G C E L L S – P RAC T I C A L
ASSESSMENT USING
MICROSCOPES
U S I N G A N E Y E P I E C E G RAT I C U L E A N D S TA G E M I C R O M E T E R
SCALE

• When using a light microscope, the

measurements are important.
• An eyepiece graticule is a small piece of glass
with a measurement scale on its surface that fits
inside the microscope eyepiece – this scale is
arbitrary and has no units.
• When you look through the eyepiece, the
measurement scale is superimposed over the
specimen.
• To calibrate the graticule (convert it into real
units), you need to find the distance that the
division on the scale represent – this is where
the micrometer comes in.
• A stage micrometer is a glass slide that also has
a precisely measured scale on its surface – the
smallest markings are usually 0.01mm (10um)
apart.
• This slide is placed under the microscope lens.
• You’ll look at this slide through the graticule and
use it to calibrate your measurements.
S T E P BY S T E P G U I D E T O C A L I B RAT I O N

1. Ensure the graticule is in place and switch your microscope to the magnification
you want.
2. Place the micrometer under your lens on the microscope stage.
3. Look down the eyepiece and bring the micrometer into focus.
4. Rotate the graticule until it’s parallel to the micrometer scale.
5. Adjust the alignment of the scales so the zero values are lined up.
6. Count the number of graticule divisions that line up with a convenient amount of
micrometer divisions.
7. Divide the value of the micrometer division in um by the number of graticule
division that were equivalent, to get the real value of the graticule division.
8. Switch out the micrometer for your sample slide and use the freshly calibrated
graticule to measure your specimen.

NOTE: As you change to a higher power objective lens, the represented value
between marks will change proportionately.