2.1.

1 Cell Structure
Microscopes

Magnification: The degree to which the size of an image is larger than the object itself (linear magnification
– length and width)
Resolution: The degree to which it is possible to distinguish between two objects that are very close
together. The higher the resolution the greater detail you can see.

Optical (light) Microscopes:

Pros: Relatively cheap, easy to use, portable, able to study living organisms.
Cons: Only able to see larger organelles within cells (i.e. not ribosomes/ER, diameter 20nm).
Max Magnification: x1500
Max Resolution: 200nm
• Staining of the specimen is required, beam is focused by condenser, objective and eyepiece lenses.
• Used to show biological activity (movement, food uptake and cell division). Also, larger cellular
structures (cell wall, nuclei, vacuoles, occasionally mitochondria).
• Optical microscope slides can be used to view living organisms (amoeba), smear of human
blood/cheek calls, and thins sections of animal/fungal/ plant tissue (leaf, root, hyphae, muscle).
• Photomicrograph: A photograph of an image seen using an optical microscope (modern digital
microscopes display the image on a screen)

Electron Microscopes:
Beam of electrons used to create the image, electrons are fired from the cathode and focused by magnets,
rather than glass lenses. Fast-travelling electrons have a smaller wavelength than visible light. This accounts
for the electron microscopes better resolution compared to optical microscope.

Pros: Can see smaller specimens due to higher magnification and in more detail due to higher resolution.
Cons: Extremely expensive, live specimens can’t be used by either, need lots of training to use.
When an image from an electron microscope is photographed it is called an electron micrograph.

Transmission Electron Microscope (TEM):

2D black-and-white image created.
Max Magnification: x500,000
Max Resolution: 0.2nm
• Image created by beam of electrons passing through specimen and being focused by electromagnet
on photographic plate/ screen.
• Denser parts of the specimen absorb more electrons and look darker.
• Sample must be dehydrated (chemically fixed) and stained – so live specimens cannot be used.
• Used to view smaller organelles (e.g. Endoplasmic reticulum and ribosomes).

Scanning Electron microscope (SEM):

3D Image created (black-and-white but given false colouring by computer).
Max Magnification: x100,000
Max Resolution: 10nm (some say 0.2)
• Electrons ‘bounce’ off the specimen’s surface and are focused onto a screen. Specimen is placed in a
vacuum (so cannot be live) and is often coated with thin layer of metal.

Laser Scanning Confocal Microscopes:

• Use laser light (beam) to scan an object point by point to assemble a digital image (3D).
• High resolution and show high contrast
• Can be used to clearly observe whole living specimens, as well as cells.
 • Used in medical profession (e.g. observing fugal corneal infection, faster more effective treatment).
• Specimens are stained with fluorescent dyes, which reflect the laser beams.
• Laser beam scanned at different depths: the laser beam can be focused at a specific depth
eliminating the blur of optical microscopes; or images can be taken at successive depths and fed into
a computer to construct a 3D image. Can focus on structures of different depths – depth sensitivity.

Graticules:
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(eyepiece x10, objective x40, total x400).

Using an eyepiece graticule and a stage micrometer/graticule to calibrate the eyepiece graticule to measure
whatever is being viewed under the microscope:

Example question:
1 micrometer slide division = 0.5mm

40 Eyepiece divisions = 1 micrometer division

= 0.5mm
So 1 eyepiece division = 0.5/20
= 0.025mm
= 25 μm
The eyepiece can be fitted with a graticule with a small ruler etched onto it. As the specimen is viewed the
eyepiece graticule is superimposed so the dimensions can be measured.
The stage graticule is used to calibrate the eyepiece graticule (it is on a slide). At different magnifications the
stage graticule is different sizes.
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𝑀𝑎𝑔𝑛𝑖𝑓𝑖𝑐𝑎𝑡𝑖𝑜𝑛 = (M=I/A)
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Staining:
Many biological structures are colourless and transparent, viewed using dark backgrounds with bright light
Stains are coloured chemicals that bind molecules in or on the specimen making it easy to see (e.g.
Methylene-blue). Stains colour parts of the cell when they react.

For TEMs Stains used that absorb electrons – objects are dipped in solutions of heavy metals (e.g. lead). The
metal ions scatter the electrons creating contrast

Differential staining: Some stains bind to specific cell structures, staining each one differently so the
structures can be easily identified within a single preparation.
• Acetic orcein binds to DNA and stains chromosomes dark red.
• Eosin stains cytoplasm; Sudan red stains lipids.
• Iodine in potassium iodide stains cellulose in plant cell walls yellow, and starch granules blue/black
(looks violet under microscope).

Preparing slides:
- Dry mount – specimen placed in middle of slide with tweezers and cover lip placed on top.
- Wet mount – drop of water on slide with pipette, specimen placed on top. Cover slip placed on slide
and slowly tilted to cover specimen. Once cover slip is in position, stain is dropped on one side and
drawn with a tissue to the other.
Prepared slides:
Made by dehydrating specimens, embedding them in wax to prevent distortion during slicing, and using a
special instrument (cryostat) to make very thin slices called sections – these are stained and mounted in a
special chemical to preserve them.
The Ultrastructure of Eukaryotic Cells

Membrane-bound organelles (TEM used for electron micrographs):

Nucleus, nuclear envelope and nucleolus:
Structure Function
Nucleus surrounded by double membrane called Nuclear envelope separates contents of nucleus
the nuclear envelope. from rest of cell.
Nucleolus has no membrane, it contains RNA. In some regions outer and inner membranes fuse
Chromatin threads are the genetic material, together – dissolved substances can pass through.
consisting of DNA wound around histone proteins. Nuclear pores enable larger substances (mRNA/
When about to divide, chromatin condenses and ribosomes) to leave nucleus and some substances
coils tightly into chromosomes, normally is spread (steroid hormones) to enter from cytoplasm.
out or extended. Ribosomes are made in nucleolus.
Chromosomes contain organism’s genes.
Summary: Stores genome, transmits genetic info,
provides instructions for protein synthesis.

Rough endoplasmic reticulum (RER):

Structure Function
System of membranes, fluid filled cavities Intracellular transport system: cisternae form
(cisternae) that continue channels for transporting substances.
from nuclear membrane. It provides large SA for ribosomes, which assemble
Studded with ribosomes. amino acids into proteins (protein synthesis). These
proteins then actively pass through the membrane
into the cisternae and are transported to the Golgi
apparatus for further modification and packaging.

Smooth endoplasmic reticulum (SER):

Structure Function
System of membranes Contains enzymes that catalyse reactions involved
etc… with lipid metabolism (e.g. synthesis of cholesterol,
synthesis of lipids/phospholipids needed by the cell,
No ribosomes synthesis of steroid hormones).
Involved with absorption, synthesis and transport
of lipids.

Golgi apparatus:
Structure Function
Stack of membrane-bound flattened sacs called Proteins are modified by:
cisternae. • Adding sugar molecules – glycoproteins.
Secretory • Adding lipid molecules – lipoproteins.
vesicles bring • Being folded into their 3D shape.
materials to Proteins are packaged into
and from. vesicles that are pinched off
then: stored in the cell, or
moved to plasma membrane to
be incorporated into it or
exported out of the cell.
Golgi is also responsible for
making lysosomes.
Mitochondrion:
Structure Function
Spherical, rod-shaped or branched, 2-5 μm long. The site of ATP production during aerobic
Double membrane with fluid-filled cavity in- respiration.
between. The inner membrane is highly folded into Self-replicating so can be made if cell’s energy
cristae. needs to increase.
The inner part of the mitochondrion is the fluid- Abundant in cells where
filled mitochondrial matrix. much metabolic activity takes
They possess place (e.g. liver cells,
70S ribosomes synapses between neurons
– prokaryotic where neurotransmitters are
origins. synthesised and released).

Chloroplasts:
Structure Function
Large organelles, 4-10 μm long. Chloroplasts are the site of photosynthesis.
In plant cells and some protoctists. 1st stage of photosynthesis: light energy trapped by
Double membrane, inner membrane is continuous chlorophyll and used to make ATP – occurs in
with stacks of flattened membrane sacs called grana. Water is also split to make hydrogen ions
thylakoids (plates) which contain chlorophyll. (light dependent reaction).
Each stack of thylakoids is called a granum (grana 2nd stage of photosynthesis: hydrogen reduces CO2
pl). Joined by the intergranal lamallae. using energy from ATP, to
The fluid-filled matrix is called the stroma. make carbohydrates –
Chloroplasts occurs in the stroma (light
contain loops independent).
of DNA and Chloroplasts are abundant
starch grains. in leaf cells, particularly to
They also palisade mesophyll layer.
possess 70S
ribosomes.

Vacuole:
Structure Function
Surrounded by a membrane called the tonoplast, Only plant cells have large permanent vacuole.
and it contains fluid (water, waste products & other Filled with water and solutes, maintains cell stability
substances). by pushing against cell wall when full – turgor.
If plant cells are turgid this helps support the plant
(especially non- woody plants).

Lysosomes:
Structure Function
Small bags formed from the Golgi apparatus, each Keep powerful hydrolytic enzymes separate from
surrounded by a single membrane. rest of the cell.
Contain powerful hydrolytic (digestive) enzymes. Can engulf old cell organelles and foreign matter
Abundant in phagocytic cells that can ingest and (e.g. bacteria), digest them and return digested
digest invading pathogens. components to cell for reuse. Can also digest self
for self-destruction (autolysis).
Cilia and Undulipodia (flagella in prokaryotes):
Structure Function
Protrusions from the cell. The epithelial cells lining your airways each have
Each composed of many hundreds of cilia that beat and move the
microtubules and are formed band of mucus.
from centrioles. Most cell types have one cilia that acts as an
Structured by a ring of 9 pairs antenna. It contains receptors that allow it to
of microtubules surrounding 2 detect signals about its immediate environment.
central pairs, surrounded by Only human cell with undulipodium (longer cilium)
cell surface membrane. is spermatozoon, to enable it to move.
Called ‘9 + 2’ formation.

Organelles without membranes:

Ribosomes:
Structure Function
Small spherical organelles (20nm diameter). Ribosomes bound to exterior of RER are for
Made of ribosomal RNA (rRNA) in the nucleolus as synthesising proteins to be exported out of the cell.
two separate subunits that pass through the Ones that are free in cell (singly/clusters) are for
nuclear envelope into the cytoplasm, then the assembly of proteins for use in the cell.
combine, when protein synthesis is about to begin. Eukaryotes have 80S, prokaryotes have 70S
Remain free in cytoplasm or attach to RER. generally.

Centrioles:
Structure Function
Centrosomes consist of two bundles of Before cell division the spindle, made of threads of
microtubules (2 centrioles) at right angles. tubulin, forms from the centrioles.
Microtubules are made of tubulin protein subunits Chromosomes attach to the middle part of the
and are arranged in nine triplets to form a cylinder spindle, and motor proteins walk along the tubulin
– a centriole. threads, pulling chromosomes to opposite ends of
the cell – in cell division.
Centrioles are involved in the formation of cilia and
undulipodia:
• Before cilia form, centrioles multiply and
line up beneath the cell surface membrane.
• Microtubules then sprout outwards from
each centriole, forming a
cilium/undulipodium.
Centrioles are usually absent from cells of more
complicated plants.

Cellulose cell wall:

Structure Function
The cell wall in plant cells is The cell wall is strong and can prevent plant cells
made from bundles of from bursting when turgid.
cellulose fibres. The cell wall of plant cells: provides
Some have plasmodesmata – strength/support, maintains cell’s shape, contribute
channels for exchanging to strength and support of whole plant, and are
substances with adjacent permeable and allow solutions (solutes dissolved in
cells. solvents) to pass through.
Fungi’s cell walls are made of chitin.
Cytoskeleton:
Structure Function
Network of protein structures within cytoplasm, Microtubules and Microfilaments:
consists of: • Provide shape and support/mechanical
Rod-like microfilaments made of subunits of strength to cells.
protein actin. • Help substances and organelles move
Intermediate filaments slightly bigger. through the cytoplasm within the cell.
Straight, cylindrical microtubules, made of protein • Microtubules form the track along with
subunits called tubulin. Larger than filaments. motor proteins (dynein and kinesin) walk
The cytoskeletal motor proteins, myosins, kinesins and ‘drag’ organelles.
and dyneins, are molecular motors. They are also • Microtubules form the spindle before cell
enzymes and have a site that binds to and allow division – move chromosomes.
hydrolysis of ATP as their energy source. • Make up cilia (microfilaments allow
movement – movement of cell),
undulipodia and centrioles.
Intermediate filaments are made of a variety of
proteins. They:
• Anchor the nucleus within the cytoplasm.
• Extend between cells in some tissues,
between special junctions, enabling cell-cell
signalling and allowing cells to adhere (stick)
to a basement membrane, therefore
stabilising tissues.
Need to be able to recognise photo micrographs of different organelles and label plant/animal cells.

Interrelationship between organelles making/secreting proteins:

• The gene that has coded instructions for a protein (e.g. insulin), housed on chromatin in the nucleus,
is transcribed into a length of messenger RNA (mRNA).
• Many copies of this mRNA are made, and they pass out of the nuclear pores to the ribosomes.
• At the ribosomes, the instructions are translated, and insulin molecules are assembled.
• The insulin molecules pass into the cisternae of the RER and along these hollow sacs.
• Vesicles with insulin inside are ‘pinched off’ from the RER and pass, via microtubules and motor
proteins, to the Golgi apparatus.
• The vesicles fuse with the Golgi apparatus, where insulin protein molecules may be modified for
release.
• Inside vesicles pinched off from the Golgi apparatus, these molecules then pass to the plasma
membrane.
• The vesicles and the
plasma membrane fuse,
and the insulin is
released to the outside
of the cell.
Differences between Prokaryotic cells and Eukaryotic cells
Prokaryotes Eukaryotes
Contain plasma membrane, cytoplasm, ribosomes for assembling proteins and DNA/RNA
Extremely small cells (2 μm diameter) Larger cells (10-100 μm diameter)
70S ribosomes (smaller) 80S ribosomes
Less well-developed cytoskeleton, no centrioles More developed cytoskeleton, contain centrioles
No nucleus Nucleus
Naked circular DNA loops in cytoplasm Linear DNA wound round histone proteins or
enclosed by nuclear envelope
No membrane-bound organelles (e.g. Many organelles, membrane and non-membrane
mitochondria, ER). Do have non-membrane bound bound.
organelles (e.g. ribosomes)
Have Memosomes which carry out respiration Mitochondria carry out respiration
Peptidoglycan cell wall Chitin or cellulose cell wall, or no cell wall (animals)
Divide by binary fission Divide by mitosis/meiosis (have linear
chromosomes required)
Flagella (when present) simpler, made of protein Flagella (when present) complex, made of
flagellin, arranged in a helix microtubule proteins in ‘9 + 2’ formation
Some have waxy capsule surrounding cell and
plasmids (small loops of DNA)
Some have Pili – smaller hair-like projections that
allow the bacteria to adhere to host cells/each
other, and transfer plasmid DNA.

Bacteria Cell Diagram: