Biology Studying Cells
Biology Studying Cells
Cell Structure
Contents
Studying Cells
Using a Microscope
Drawing Cells
Magnification & Resolution
Eukaryotic Cells
Eukaryotic Cells Under the Microscope
Organelles & the Production of Proteins
The Cytoskeleton
Prokaryotic & Eukaryotic Cells
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Studying Cells
Your notes
Use of microscopy
Microscopes can be used to observe and investigate cell structure
Different types of microscope can be used to study cells at different levels of detail,
e.g.
light microscopes
electron microscopes
The images generated by the different types of microscope differ significantly
Light microscopes
Light, or optical, microscopes use light to form an image
The maximum resolution of a light microscope is around 0.2 micrometres (µm),
meaning that the maximum useful magnification of optical microscopes is about ×1500
Light microscopes can only be used to observe larger structures, e.g.:
entire cells
nuclei
mitochondria and chloroplasts
While light microscopes have limited resolution, they do have advantages, such as:
they are small and relatively cheap
specimen preparation can be straightforward enough to perform in a school
laboratory
they can be used to produce colour images
they allow the observation of living specimens
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Your notes
Light microscope images allow the observation of cell shape, as well as larger internal
structures, e.g, here chloroplasts can be seen within a series of plant cells
Kelvinsong, via Wikimedia Commons
Electron microscopes
Electron microscopes use electrons to form an image
Electron microscopes have a maximum resolution of around 0.0002 µm, or 0.2 nm, and
a maximum magnification that range from around ×1,000,000 up to many millions
Electron microscopes can be used to observe small structures inside cells, such as:
cell membranes
ribosomes
the endoplasmic reticulum
lysosomes
While electron microscopes are essential tools in the study of cell biology, they do have
some limitations
They are very large and expensive
Specimens must be prepared using a highly complex process
Specimens must be viewed in a vacuum, meaning that live specimens cannot be
observed
Images are always black and white, though they can be artificially coloured during
processing
There are two types of electron microscope:
transmission electron microscopes (TEMs)
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scanning electron microscopes (SEMs)
Transmission electron microscopes
Your notes
TEMs use electromagnets to transmit a beam of electrons through a specimen; denser
parts of the specimen absorb more electrons, meaning that denser parts appear darker
on the final image
TEMs produce images that:
are high-resolution
allow the internal structures within cells, and within organelles to be seen
are two-dimensional
TEM image
TEM images allow the internal structures within cells and organelles to be studied
Klingm01, via Wikimedia Commons
Scanning electron microscopes
SEMs pass a beam of electrons across the surface of a specimen and then detect the
rate at which the electrons bounce back
This means that SEMs produce images that:
are three-dimensional
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show the surface of specimens
SEMs have a lower maximum resolution than TEMs
SEM image Your notes
SEM images are three-dimensional and show the surface of objects, e.g. here E. coli
bacteria can be seen
NIAID, via Flickr
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Using a Microscope
Your notes
Preparation of Microscope Slides
Many biological structures are too small to be seen by the naked eye
Optical microscopes are an invaluable tool for scientists as they allow for tissues, cells
and organelles to be seen and studied
For example, the movement of chromosomes during mitosis can be observed using a
microscope
Apparatus
The key components of an optical microscope are:
The eyepiece lens
The objective lenses
The stage
The light source
The coarse and fine focus
Other tools used:
Forceps
Scissors
Scalpel
Coverslip
Slides
Pipette
Staining solution
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Your notes
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This involves fixing the specimen using formaldehyde (preservative), dehydrating it
using a series of ethanol solutions, impregnating it in paraffin/resin for support then
cutting thin slices from the specimen using a microtome Your notes
The paraffin is removed from the slices/specimen, a stain is applied and the
specimen is mounted using a resin and a coverslip is applied
Or
Freeze the specimen in carbon dioxide or liquid nitrogen
Cut the specimen into thin slices using a cryostat
Place the specimen on the slide and add a stain
Gently place a coverslip on top and press down to remove any air bubbles
When using an optical microscope always start with the low power objective lens:
It is easier to find what you are looking for in the field of view
This helps to prevent damage to the lens or coverslip in case the stage has been
raised too high
Preventing the dehydration of tissue:
The thin layers of material placed on slides can dry up rapidly
Adding a drop of water to the specimen (beneath the coverslip) can prevent the
cells from being damaged by dehydration
Unclear or blurry images:
Switch to the lower power objective lens and try using the coarse focus to get a
clearer image
Consider whether the specimen sample is thin enough for light to pass through to
see the structures clearly
There could be cross-contamination with foreign cells or bodies
Using a graticule to take measurements of cells:
A graticule is a small disc that has an engraved ruler
It can be placed into the eyepiece of a microscope to act as a ruler in the field of
view
As a graticule has no fixed units it must be calibrated for the objective lens that is in
use. This is done by using a scale engraved on a microscope slide (a stage
micrometer)
By using the two scales together the number of micrometers each graticule unit is
worth can be worked out
After this is known the graticule can be used as a ruler in the field of view
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Your notes
The stage micrometer scale is used to find out how many micrometers each graticule unit
represents
Limitations
The size of cells or structures of tissues may appear inconsistent in different specimen
slides
Cell structures are 3D and the different tissue samples will have been cut at
different planes resulting in this inconsistencies when viewed on a 2D slide
Optical microscopes do not have the same magnification power as other types of
microscopes and so there are some structures that can not be seen
The treatment of specimens when preparing slides could alter the structure of cells
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The dyes used absorb specific colours of light while reflecting others; this makes the
structures within the specimen that have absorbed the dye visible
Your notes
Certain tissues absorb certain dyes, which dye they absorb depends on their chemical
nature
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
Toluidine blue and phloroglucinol are common stains used
Toluidine blue turns cells blue
Phloroglucinol turns cells red/pink
Toluidine blue and phloroglucinol have been used to stain this tissue specimen taken from
a leaf
Staining for electron microscopy
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
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Heavy-metal compounds are commonly used as dyes because they absorb electrons
well
Your notes
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 software
The internal structure of the mitochondrion can be seen using a TEM and staining
A spiracle found on the exoskeleton of an insect. No colours have been added to this
image using image-processing software.
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Your notes
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Drawing Cells
Your notes
Drawing Cells
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
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Your notes
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Magnification & Resolution
Your notes
Magnification formula
The magnification of an object can be calculated using the formula:
magnification = size of image ÷ size of real object
The magnification formula can be rearranged to allow the calculation of:
magnification (m)
size of image (i)
size of real object, often referred to as actual size (a)
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Units can be converted by multiplying or dividing by the relevant factor
Converting larger units to smaller units = multiply Your notes
Converting smaller units to larger units = divide
Note that magnification does not have units
Converting units diagram
Worked Example
An image of an animal cell is 30 mm in size and it has been magnified by a factor of
×3000.
What is the actual size of the cell?
Worked Example
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Your notes
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The ability of a microscope to magnify an object depends on the type of microscope,
and on the features of the microscope itself
Your notes
E.g. for a light microscope the magnification can be calculated by multiplying
together the magnification of the eyepiece lens and the objective lens
Resolution
Resolution can be defined as:
The ability to distinguish separate points on an image as two separate objects
The higher the resolution, the shorter the distance at which the two objects can be
clearly distinguished
The ability of a microscope to resolve two objects as separate points is dependent on
the method of image generation:
Light microscopes: the resolution is limited by the wavelength of light
As light passes close to physical structures it is diffracted, meaning that light
waves spread out
The closer the structures are to each other, the more the light waves overlap
each other as they are diffracted
Points that are closer together than half the wavelength of visible light cannot
be clearly distinguished from each other
Electron microscopes: the resolution is much higher because electrons have a
smaller wavelength than visible light
The objects past which the electrons travel can therefore be much closer
together before the diffracted beams overlap
Resolution diagram
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The resolving power of an electron microscope is much greater than that of a light
microscope; this is because electrons have a smaller wavelength than visible light
Your notes
Comparing light and electron microscopes
Light microscopes:
have a maximum resolution of 200 nm
have a maximum useful magnification of around ×1500-2000
can be used for viewing living or dead specimens
are useful for looking at whole cells, small organisms and tissues within organs such
as in leaves or skin
Electron microscopes:
have a maximum resolution of 0.5 nm (TEM) or 3-10 nm (SEM)
are capable of generating images with a magnification of more than ×500 000
TEMs are capable of higher magnification than SEMs due to their higher
resolution
can only be used for viewing dead specimens
are useful for looking at organelles and viruses, as well as looking at whole cells in
more detail
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You do not need to be able to recall the exact numbers for resolution and
magnification in different types of microscope, but you must have an appreciation of
how the values differ between light microscopes, TEMs and SEMs. Your notes
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Eukaryotic Cells
Your notes
Eukaryotic Cell Structure
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 ‘partially permeable’
The cell membrane is formed from a phospholipid bilayer of phospholipids spanning a
diameter of around 10 nm
Cell wall
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The cell wall is freely permeable to most substances (unlike the plasma membrane)
Found in plant cells but not in animal cells Your notes
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
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 (except red blood 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)
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
Mitochondria
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Your notes
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 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)
Chloroplasts
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Chloroplasts are found in the green parts of a plant – the green colour a result of the
photosynthetic pigment chlorophyll
Your notes
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
Ribosomes
Ribosomes are formed in the nucleolus and are composed of almost equal amounts of
RNA and protein
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)
Endoplasmic reticulum
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Your notes
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)
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
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Your notes
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The structure of the vacuole
A sac in plant cells surrounded by the tonoplast, selectively permeable membrane Your notes
Vacuoles in animal cells are not permanent and small
Vesicles
Lysosomes
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Used extensively by cells of the immune system and in apoptosis (programmed cell
death)
Centrioles Your notes
Microtubules
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Your notes
Microvilli
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Your notes
Cilia
Flagella
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Your notes
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Eukaryotic Cells Under the Microscope
Your notes
Photomicrographs of Eukaryotic Cells
There are some features or structures that can help to identify whether a cell shown in an
image is a plant cell or animal cell
Structures found only in animal cells: centrioles and microvilli
Structures found only in plant cells: 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.
Describing and interpreting photomicrographs, electron micrographs and drawings of
typical animal/plant cells is an important skill
The organelles and structures within cells have a characteristic shape and size which can
be helpful when having to identify and label them in an exam
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Your notes
TEM electron micrograph of an animal cell showing key features. Notice the lack of a cell
wall.
TEM electron micrograph of a plant cell showing key features. Notice the presence of a
cell wall and vacuole.
More detailed structures can be seen and identified in electron micrographs compared
to photomicrographs
This is because electron microscopes have greater maximum magnification and
resolution than light (optical) microscopes
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Your notes
Mucus producing goblet cells (found in the lining of trachea, bronchi and larger
bronchioles) are shown in a photomicrograph
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Details of the structures inside the goblet cell can be seen in an electron micrograph
Your notes
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Organelles & the Production of Proteins
Your notes
Organelles & the production of proteins
Inside cells multiple organelles are involved in the production and secretion of proteins
Organelles involved in protein production, and their roles, include:
nucleus
DNA is stored
The nucleolus manufactures ribosomes
Transcription occurs, during which an mRNA copy of DNA is produced
ribosomes
mRNA leaves the nucleus and attaches to a ribosome
Translation occurs, during which a chain of amino acids is produced; this chain
is known as a polypeptide
rough endoplasmic reticulum (RER)
Many ribosomes are attached to the surface of this organelle
After translation the polypeptides are folded and processed to produce
proteins
Golgi apparatus
Proteins are modified and prepared for secretion
vesicles
Proteins are transported from the RER to the Golgi apparatus, and from the
Golgi apparatus to the cell surface membrane inside vesicles
Vesicles fuse with the cell surface membrane to secrete proteins, e.g.
hormones, from the cell by exocytosis
Cells that produce many proteins, e.g. within hormone-producing glands, or in the
enzyme-producing cells of the digestive system, will have many of the organelles that
are involved with protein production
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Your notes
Multiple cellular structures are involved in the production and secretion of proteins
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The Cytoskeleton
Your notes
The Cytoskeleton
Within the cytoplasm of cells, there is an extensive network of protein fibres
This is known as the cytoskeleton
The cytoskeleton is made up of two main types of protein fibres: microfilaments and
microtubules
Microfilaments are solid strands that are mostly made of the protein actin. These
fibres can cause some cell movement and the movement of some organelles within
cells by moving against each other
Microtubules are tubular (hollow) strands that are mostly made of the protein
tubulin. Organelles and other cell contents are moved along these fibres using ATP
to drive this movement
Intermediate filaments (a third type of fibre) are also found within the cytoskeleton
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Your notes
The cytoskeleton provides mechanical strength to cells, aids transport within cells and
enables cell movement
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Prokaryotic & Eukaryotic Cells
Your notes
Comparison of Prokaryotic & Eukaryotic Cells
Animal and plant cells are types of eukaryotic cells, whereas bacteria are a type of
prokaryote
Prokaryotic cells are much smaller than eukaryotic cells (between 100 - 1000 times
smaller)
Prokaryotic cells also differ from eukaryotic cells in having:
A cytoplasm that lacks membrane-bound organelles
Their ribosomes are structurally smaller (70 S) in comparison to those found in
eukaryotic cells (80 S)
No nucleus (instead they have a single circular DNA molecule that is free in the
cytoplasm and is not associated with proteins)
A cell wall that contains murein (a glycoprotein)
In addition, many prokaryotic cells have a few other structures that differentiate them
from others and act as a selective advantage, examples of these are:
Plasmids
Capsules
Flagellum
Plasmids are small loops of DNA that are separate from the main circular DNA molecule
Plasmids contain genes that can be passed between prokaryotes (e.g. genes for
antibiotic resistance)
Some prokaryotes (e.g. bacteria) are surrounded by a final outer layer known as a
capsule. This is sometimes called the slime capsule
It helps to protect bacteria from drying out and from attack by cells of the immune
system of the host organism
Flagellum (plural = flagella) are long, tail-like structure that rotate, enabling the
prokaryote to move (a bit like a propeller)
Some prokaryotes have more than one
Structures unique to prokaryotic cells
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Your notes
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Your notes
Prokaryotic cells are often described as being ‘simpler’ than eukaryotic cells, and they
are believed to have emerged as the first living organisms on Earth.
There are a number of important structural and physiological differences between
prokaryotic and eukaryotic cells
These differences affect their metabolic processes and how they reproduce
Prokaryotic & Eukaryotic Cells Comparison Table
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Your notes
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