2022-24 syllabus By: Sultan ALShehri

Cell structure
 The microscope in cell studies
 Microscope Slide Preparation
 In order to observe cellular material in more detail, specimens can be
prepared for viewing under a light microscope
 Samples need to be thin enough to allow light to pass through
 The type of preparation that is appropriate is dependent on the cellular
material that needs to be viewed
 Slide preparation methods table

 Samples sometimes need to be stained, as the cytosol and other cell

structures may be transparent or difficult to distinguish
 To stain a slide the sample needs to be first air-dried and then heated by
passing it through a Bunsen burner flame – this will allow the sample to
be fixed to the slide and to take up the stain
 As with the type of preparation required, the type of stain used is
dependent on what type of specimen is being used
 Common microscope stains & uses table

 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
 The conventions are:
o The drawing must have a title

1|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

o The magnification under which the observations shown by the drawing are made must
be recorded
o A sharp HB pencil should be used (and a good eraser!)
o Drawings should be on plain white paper
o Lines should be clear, single lines (no thick shading)
o No shading
o The drawing should take up as much of the space on the page as possible
o Well-defined structures should be drawn
o The drawing should be made with proper proportions
o Label lines should not cross or have arrowheads and should connect directly to the
part of the drawing being labelled
o Label lines should be kept to one side of the drawing (in parallel to the top of the page)
and drawn with a ruler
 Drawings of cells are typically made when visualizing cells at a higher
magnification power, whereas plan drawings are typically made of
tissues viewed under lower magnifications (individual cells are never
drawn in a plan diagram)
o When producing a biological drawing, it is vital that you only ever draw what you see
and not what you think you see.
o To accurately reflect the size and proportions of structures you see under the
microscope, you should get used to using the eyepiece graticule.

 Magnification Calculations
 Magnification is how many times bigger the image of a specimen
observed is in comparison to the actual (real-life) size of the specimen
 The magnification (M) of an object can be calculated if both the size of
the image (I), and the actual size of the specimen (A), is known

An equation triangle for calculating magnification

Worked Example
An image of an animal cell is 30 mm in size and it has been magnified by a
factor of X 3000. What is the actual size of the cell?
To find the actual size of the cell:

2|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

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

 Converting units of measurement

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

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

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

Remember that 1mm = 1000µm
2000 / 1000 = 2, so the actual thickness of the leaf is 2 mm and the drawing
thickness is 50 mm
Step 2: Calculate Magnification
Magnification = image size / actual size = 50 / 2 = 25
So the magnification is x25

3|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Eyepiece Graticules & Stage Micrometers

 An eyepiece graticule and stage micrometer are used to measure the

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

 Using stage micrometer & eyepiece graticule

 In the diagram, the stage micrometer has three lines each 10 µm apart
 Each 10 µm division has 40 eyepiece graticule divisions
 40 graticule divisions = 10 µm
1 graticule division = number of micrometres ÷ number of graticule division
 1 graticule division = 10 ÷ 40 = 0.25 µm this is the magnification factor
 The specimen slide would be used to replace the stage micrometer and
the eyepiece graticule at the same magnification, and would be used to
measure the length of the object
 The number of graticule divisions can then be multiplied by the
magnification factor:
graticule divisions x magnification factor = measurement (µm)
o The calculations involving stage micrometers and eyepiece graticules are often seen in
exam questions, so make sure that you are comfortable with how to calibrate the
graticule and calculate the length of an object on the slide.

4|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Resolution & Magnification

Magnification
 Magnification is how many times bigger the image of a specimen
observed is in compared to the actual (real-life) size of the specimen
 A light microscope has two types of lens:
o An eyepiece lens, which often has a magnification of x10
o A series of (usually 3) objective lenses, each with a different magnification
 To calculate the total magnification the magnification of
the eyepiece lens and the objective lens are multiplied together:
eyepiece lens magnification x objective lens magnification
= total magnification
Resolution
 Resolution is the ability to distinguish between two separate points
 If two separate points cannot be resolved, they will be observed as one
point
 The resolution of a light microscope is limited by the wavelength of light
 As light passes through the specimen, it will be diffracted
 The longer the wavelength of light, the more it is diffracted and the
more that this diffraction will overlap as the points get closer together
 Electron microscopes have a much higher resolution and magnification
than a light microscope as electrons have a much smaller wavelength
than visible light
o This means that they can be much closer before the diffracted beams overlap
 The concept of resolution is why the phospholipid bilayer structure of
the cell membrane cannot be observed under a light microscope
o The width of the phospholipid bilayer is about 10nm
o The maximum resolution of a light microscope is 200nm (half the smallest wavelength
of visible light, 400nm)
o Any points that are separated by a distance less than 200nm (such as the 10nm
phospholipid bilayer) cannot be resolved by a light microscope and therefore will not
be distinguishable as “separate”

5|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

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

 Comparison of the electron microscope & light microscope

 Light microscopes are used for specimens above 200 nm
o Light microscopes shine light through the specimen, this light is then passed through
an objective lens (which can be changed) and an eyepiece lens (x10) which magnify
the specimen to give an image that can be seen by the naked eye
o The specimens can be living (and therefore can be moving), or dead
o Light microscopes are useful for looking at whole cells, small plant and
animal organisms, tissues within organs such as in leaves or skin
 Electron microscopes, both scanning and transmission, are used for
specimens above 0.5 nm
o Electron microscopes fire a beam of electrons at the specimen either a broad static
beam (transmission) or a small beam that moves across the specimen (scanning)
o The electrons are picked up by an electromagnetic lens which then shows the image

o Due to the higher frequency of electron waves (a much shorter wavelength) compared
to visible light, the magnification and resolution of an electron microscope is much
better than a light microscope
o Electron microscopes are useful for looking at organelles, viruses and DNA as well as
looking at whole cells in more detail
o Electron microscopy requires the specimen to be dead however this can provide
a snapshot in time of what is occurring in a cell eg. DNA can be seen replicating and
chromosome position within the stages of mitosis are visible
Light v Electron Microscope Table

Uses electron radiation Uses light radiation

 Calculating Actual Size

 When investigating the size of organisms and biological structures you
will use a microscope of a specific magnification to produce an image
 Photomicrographs are images obtained from a light microscope, these
are used for specimens above 200 nm (a bacteria cell is about 1000 nm)

6|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Electron micrographs are images obtained from electron microscopes,

both scanning and transmission, these are used for specimens above 0.5
nm
o Electron microscopes are useful for looking at organelles and biological molecules, eg.
DNA can be seen replicating
 To better understand the images we produce using microscopes we need
to know the actual size of the specimen
Worked example: Calculating the actual size of a specimen
A scientist looks at a sample of red blood cells under a light microscope.
The eyepiece lens of the microscope has a magnification of x10 and an
objective lens of x40 was used to view the blood cells. The scientist takes a
photomicrograph of the blood cells, in which the average size of each cell is 3
mm.
What is the average size of the red blood cells in the sample? Give your answer
in micrometres.
Known values:
 Eyepiece lens magnification: x10
 Objective lens magnification: x40
 Image size: 3 mm
Step 1: Calculate the total magnification of the specimen
eyepiece lens magnification x objective lens magnification
= total magnification
x10 x x40 = x400
Step 2: Calculate the image size in the units asked for (micrometres)
1 mm = 1000 μm
3 mm = 3000 μm
Step 3: Calculate the actual size of the red blood cell

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

7|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Cells as the basic units of living organisms

 Eukaryotic Cell Structures & Functions

 Cell surface membrane

The structure of the cell surface membrane – although the structure looks static the
phospholipids and proteins forming the bilayer are constantly in motion
 All cells are surrounded by a cell surface membrane which controls the
exchange of materials between the internal cell environment and the
external environment
o 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

The cell wall is freely permeable to most substances (unlike the plasma membrane)
 Cell walls are formed outside of the cell membrane and offer structural
support to cell
 Structural support is provided by the polysaccharide cellulose in plants,
and peptidoglycan in most bacterial cells
 Narrow threads of cytoplasm (surrounded by a cell membrane)
called plasmodesmata(singular:plasmodesma) connects the cytoplasm
of neighbouring plant cells

8|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

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

 Mitochondria

9|Page Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

A single mitochondrion is shown – the inner membrane has protein complexes vital for the
later stages of aerobic respiration embedded within it
 The site of aerobic respiration within eukaryotic cells; mitochondria are
just visible with a light microscope
 Surrounded by double-membrane with the inner membrane folded to
form cristae
 The matrix formed by the cristae contains enzymes needed for aerobic
respiration, producing ATP
 Small circular pieces of DNA (mitochondrial DNA) and ribosomes are also
found in the matrix (needed for replication)

 Chloroplast

Chloroplasts are found in the green parts of a plant – the green colour a result of the
photosynthetic pigment chlorophyll
 Larger than mitochondria, also surrounded by a double-membrane
 Membrane-bound compartments called thylakoids
containing chlorophyll stack to form structures called grana
 Grana are joined together by lamellae (thin and flat thylakoid
membranes)
 Chloroplasts are the site of photosynthesis:
o The light-dependent stage takes place in the thylakoids
o 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

10 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Ribosome

Ribosomes are formed in the nucleolus and are composed of almost equal amounts of RNA
and protein
 Site of translation (protein synthesis)
 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
cytoplasm
 70S (composed of 50S and 30S subunits) ribosomes in mitochondria and
chloroplasts

 Endoplasmic reticulum

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

11 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Rough Endoplasmic Reticulum (RER)

o Surface covered in ribosomes
o Formed from continuous folds of membrane continuous with the nuclear envelope
o Processes proteins made by the ribosomes
 Smooth Endoplasmic Reticulum (SER)
o Does not have ribosomes on the surface, its function is distinct to the RER
o Involved in the production, processing and storage of lipids,
carbohydrates and steroids

 Golgi apparatus (golgi complex or golgi body)

The structure of the Golgi apparatus

 Flattened sacs of membrane similar to the smooth endoplasmic
reticulum
 Modifies proteins and packages them into vesicles or lysosomes

 Large permanent vacuole

The structure of the vacuole

 Sac in plant cells surrounded by the tonoplast, a selectively permeable
membrane(it’s function is surrounding the permanent vacuole)
 Vacuoles in animal cells are not permanent and small

12 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Vesicle

The structure of the vesicle

 Membrane-bound sac for transport and storage

 Lysosome

The structure of the lysosome

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

13 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Centriole

The structure of the centriole

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

 centriole: one of two small, cylindrical structures, made from

microtubules, found just outside the nucleus in animal cells, in a region
known as the centrosome; they are also found at the bases of cilia and
flagella
 centrosome: the main microtubule organising centre (MTOC) in animal
cells
 A centriole is a hollow cylinder about 500 nm long, formed from a ring of
short microtubules. Each centriole contains nine triplets of microtubules

14 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Microtubules

The structure of the microtubule

 Makes up the cytoskeleton of the cell about 25 nm in diameter
 Made of α and β tubulin combined to form dimers, the dimers are then
joined into protofilaments. Thirteen protofilaments in a cylinder make a
microtubule
 The cytoskeleton is used to provide support and movement of the cell
and that’s microtubule’s function

 Microvilli

The structure of the microvilli

 Cell membrane projections that increase the surface area for absorption

15 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Cilia

The structure of the cilia

 Hair-like projections made from microtubules
 Allows the movement of substances over the cell surface

 Flagella

The structure of the flagella

 Similar in structure to cilia, made of longer microtubules
 Contracts to provide cell movement for example in sperm cells

16 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Electron Micrographs: Animal Cells

TEM electron micrograph of an animal cell showing key features

 Electron Micrographs: Plant Cells

TEM electron micrograph of a plant cell showing key features

17 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Structure of Animal & Plant Cells

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

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

18 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

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

 The Vital Role of ATP

 All organisms require a constant supply of energy to maintain their cells
and stay alive
 This energy is required:
o In anabolic reactions – building larger molecules from smaller molecules
o To move substances across the cell membrane (active transport) or to move
substances within the cell
o In animals, energy is required:
 For muscle contraction – to coordinate movement at the whole-organism
level
 In the conduction of nerve impulses, as well as many other cellular
processes
 Adenosine Triphosphate (ATP) is a nucleotide
o The monomers of DNA and RNA are also nucleotide
 In all known forms of life, ATP from respiration is used to transfer energy
in all energy-requiring processes in cells
 This is why ATP is known as the universal energy currency

19 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Structural Features of Typical Prokaryotic Cells

 Animal and plant cells are types of eukaryotic cells, whereas bacteria are
a type of prokaryote
 Prokaryotes have a cellular structure distinct from eukaryotes:
o They’re unicellular and have peptidoglycan cell walls
o Their genetic material (DNA) is not packaged within a membrane-bound nucleus and is
usually circular (eukaryotic genetic material is packaged as linear chromosomes)
o Prokaryotes lack membrane-bound organelles, in other words, they’re absent.
o They are many (100s/1000s) of times smaller than eukaryotic cells(generally 1-5 μm
diameter)
o Their ribosomes are structurally smaller (70 S) in comparison to those found in
eukaryotic cells (80 S)

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

20 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

 Prokaryotic v Eukaryotic Cell Structures

Prokaryotic & eukaryotic cells comparison table

 Key Features of Viruses

 Viruses are non-cellular infectious particles that straddle the boundary
between ‘living’ and ‘non-living’
 They are relatively simple in structure; much smaller than prokaryotic
cells (with diameters between 20 and 300 nm)
 Structurally they have:
o A nucleic acid core (their genomes are either DNA or RNA, and can be single or double-
stranded)
o A protein coat called a ‘capsid’
o (some viruses only) a membrane-like outer layer, called the envelope, that is made of
phospholipids. (The structure of phospholipids is described in Chapter 2.) Proteins
may project from the envelope.
 All viruses are parasitic in that they can only reproduce by infecting living
cells and using their protein-building machinery (ribosomes) to produce
new viral particles

21 | P a g e Contact no.: +966 50 888 8580

2022-24 syllabus By: Sultan ALShehri

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

22 | P a g e Contact no.: +966 50 888 8580