Topic 2: Cells

Cell Membranes
Fluid mosaic model

The structure of the plasma membrane is made up of a bilayer of phospholipids with proteins and
cholesterol interspersed throughout the structure. The fluid mosaic model is used to describe the
arrangement of molecules in the membrane - ‘fluid’ because the phospholipids are constantly
moving around and ‘mosaic’ because protein molecules are scattered throughout the
phospholipids like tiles in a mosaic.

We refer to this concept as a ‘model’ because it is the best representation of membrane structure
based on the evidence which is currently available. As we learn more about the structure of the
plasma membrane, the fluid mosaic model may be updated.

Components of the plasma membrane

• Phospholipids: consist of a hydrophilic head group which faces the intracellular /

extracellular fluid and two hydrophobic tails which point towards each other, away from
water. They are the main component of the plasma membrane and form a barrier to
anything which is not lipid-soluble (such as ions and glucose).
• Glycoproteins: these are proteins with sugar molecules attached. They act as recognition
sites and antigens - antigens are like little ‘flags’ on the surface of our cells which allows our
body to detect which cells are our own and which cells are foreign.
• Glycolipids: these are phospholipids with sugar molecules attached. They have a similar
function to glycoproteins - they also act as recognition sites and antigens. They also
increase membrane stability by forming hydrogen bonds with water molecules.
• Cholesterol: cholesterol is a lipid which slots in between the phospholipid tails, pushing them
closer together. It regulates the stability and fluidity of the plasma membrane.
• Intrinsic proteins: these are proteins which span both bilayers of the plasma membrane.
They act as channels or carrier proteins to transport water-soluble molecules.
• Extrinsic proteins: these are proteins which are found on the surface of the plasma
membrane. They usually function as enzymes and catalyse chemical reactions inside the
cell.
Investigating cell membrane structure

The permeability of cell membranes is affected by things like temperature, pH and ethanol. You may
be asked to describe an experiment to determine the effect of one of these factors on membrane
permeability. These experiments using involve plant cells which contain a coloured pigment, such as
beetroot, since we can measure the amount of membrane permeability depending on how much
pigment leaks out of the cells and into the surrounding solution. The method for this type of
experiment is outlined below:

• Prepare eight cylinders of beetroot of equal size. Make these samples as similar as
possible, e.g. by cutting from the same part of each plant. Rinse each piece to remove any
pigment released during cutting.
• If you are investigating the effect of temperature, prepare eight water baths of varying
temperatures ranging from 0-70oC.
• Prepare a series of test tubes containing the same volume of water (e.g. 10 cm3). Place the
tubes in different water for five minutes.
• Place a single sample of beetroot into each of the eight test tubes. Leave for 15 minutes.
• Use forceps to remove the pieces of beetroot from each tube. Keep the coloured liquid and
transfer into a cuvette.
• Use a colorimeter to measure how much light is absorbed by each liquid. The darker the
solution (i.e. the more permeable the membrane), the more light is absorbed.
• Draw a graph plotting absorbance against temperature.
Temperature and membrane permeability

• At temperatures below freezing, the

permeability of cell membranes increases
since the proteins in the membrane unfold
and become deformed. The molecules in the
membrane have low amounts of energy so
cannot move around much. The
phospholipids become closely packed
together which makes the membrane rigid.
When temperatures fall low enough for ice
crystals to form, these can puncture the
membrane which increases its permeability when the cell membrane re-thaws, damaging the
cell.
• Between temperatures of 0oC and 45oC, membranes are partially permeable. As
temperature increases, the components in the membrane gain kinetic energy and move
around more. The more fluid the membrane is, the more substances it allows through.
• As temperatures exceed 45oC, permeability increases rapidly because proteins in the
membrane become denatured and start to unravel. In addition, water inside the cell
cytoplasm expands, putting pressure on the cell membrane and creating gaps within the
bilayer.

Transport across cell membranes

Molecules can make their way across the plasma membrane in one of three ways: osmosis (if the
molecule is water), diffusion (if it is a molecule moving down its concentration gradient) or active
transport (if it is a molecule moving against its concentration gradient. For larger substances to
get into or out of the cell, such as proteins or carbohydrates, they will rely on processes called
endocytosis and exocytosis.

Simple diffusion

Diffusion is the movement of molecules down their concentration gradients. When molecules move
by simple diffusion, they pass directly through the phospholipid bilayer. It is a passive process
which means that no energy is required. Oxygen and carbon dioxide move by simple diffusion when
they pass from the alveoli into the bloodstream during gas exchange.

The rate of simple diffusion depends on:

• The concentration gradient – the steeper the gradient, the faster the rate of diffusion
 • The thickness of the exchange surface – thicker exchange surfaces mean a longer
diffusion distance
• Surface area – larger surface areas mean more space for diffusion to take place. Adaptations
like microvilli in the small intestine increase surface area.

Facilitated diffusion

Facilitated diffusion involves the movement of molecules down their concentration gradients. It
differs from simple diffusion in the fact that a carrier protein or a channel protein within the cell
membrane helps them get from one side to the other. This is also a passive process. An example of
facilitated diffusion is the movement of glucose molecules into liver cells through glucose transporter
proteins embedded in the plasma membrane.

The rate of facilitated diffusion depends on:

• The concentration gradient – the steeper the gradient, the faster the rate of diffusion
• The number of channel/carrier proteins – the more transport proteins, the faster
substances can be moved across the membrane

Osmosis

Osmosis is the movement of water molecules

down its concentration gradient across a
partially permeable membrane. It is a passive
process so does not require energy in the form of
ATP. Osmosis is responsible for the movement of
water molecules into the root hair cells of plants,
for example.

You can think of it as how ‘pure’ the water it. Pure

water has the highest water potential – all other solutions will have lower water potentials in
comparison, with the more solute dissolved in it, the lower the water potential. Two solutions with the
same water potential are isotonic.

Rate of osmosis depends on:

• The water potential gradient – the steeper the gradient, the faster the rate of osmosis
• The surface area – the larger the surface area, the more space there is for osmosis to take
place
• The thickness of the exchange surface – thinner surfaces mean a shorter diffusion
distance
Determining the water potential of potato cells

You can set up an experiment to determine the water potential inside potato cells. If potato is placed
in a solution of higher water potential, water will move into the cells and the potato gains mass. If it is
placed in a solution of lower water potential, it will lose mass. When there is no change in mass, the
solution and the potato’s cytoplasm are isotonic and you have found the water potential inside the
cells.

Method:

• Prepare cylinders of potato using a cork borer and cut into three.
• Measure the mass of the potato pieces using a mass balance.
• Prepare serial dilutions of sucrose solution. First, make a 2M solution with a volume of 10
cm3. Transfer half (5 cm3) to another test tube, with an equal volume of water. Repeat three
more times so that you end up with solutions of 2M, 1M, 0.5M, 0.25M and 0.125M.
• Place the potato pieces in each solution and leave for 30 minutes.
• Remove from solution and dry with a paper towel.
• Record the mass of each potato piece and calculate the percentage change in mass.
• Draw a graph with percentage change in mass on the y-axis and concentration of sucrose
solution on the x-axis. Read off the sucrose concentration where the change in mass = 0.
Look up the water potential for this sucrose concentration – it’s the same as the water
potential of the potato cells.

Active transport

• Active transport moves molecules against

their gradient, from low to high
concentration.
• This involves a carrier protein which
carries the molecule from one side of the
membrane to the other.
• It is an active process and uses ATP to
release energy.
• An example is the transport of glucose
from the villi of the intestine into the bloodstream.
• Cotransporters are a special type of carrier protein which can bind to two molecules at a
time. The concentration gradient of one molecule is used to transport the other molecule
against its gradient.
Rate of active transport depends on:

• The number of carrier proteins in the membrane – more proteins means faster rate of
transport
• The speed of each carrier protein – the faster carrier proteins work, the faster the rate of
active transport
• The rate of respiration – the faster respiration is taking place, the more ATP is generated.
Inhibition of respiration will also inhibit active transport

Cotransport of glucose and sodium ions in the intestine

Inside our intestine, carbohydrates are

digested into glucose which needs to be
absorbed into the bloodstream. To
maximise the number of glucose molecules
taken into our body, the gut relies on active
transport. In the epithelial cells lining the
ileum, a sodium-potassium ion pump
actively transports sodium ions out of the
cell, creating a sodium ion gradient
between the ileum cell and the intestinal
lumen. A co-transporter protein uses the
sodium ion gradient to transport glucose against its gradient. It picks up both molecules on the
lumen side and transports them both into the ileum cell. Glucose can then move into the bloodstream
by facilitated diffusion, through a glucose channel.
Topic 2: Cells
Eukaryotic and Prokaryotic Cells
Ultrastructure of eukaryotic cells

All organisms are divided into two different domains: eukaryotes and prokaryotes. Eukaryotes
include any organism whose cells contain a nucleus, while prokaryotes lack a nucleus and any other
membrane-bound organelles.

Eukaryotic cells, such as the cells of animals, plants and fungi may contain the following organelles:

• Nucleus - contains DNA which controls the activities of the cell by containing the base
sequences (the ‘instructions’ needed to make proteins. The DNA is associated with histone
proteins and referred to as chromatin which is wound into structures called chromosomes.
• Nucleolus - this is a region within the nucleus where ribosomes are made.
• Nuclear envelope - a double membrane which surrounds the nucleus. It contains pores
which allows small molecules (like single stranded RNA) to pass into the cytoplasm but keeps
hefty chromosomes safely inside its walls.
• Rough endoplasmic reticulum (RER) - the RER is an extension of the nuclear envelope
and is coated with ribosomes. It facilitates protein synthesis by providing a large surface area
for ribosomes. It then transports the newly synthesised proteins to the Golgi apparatus for
modification.
• Smooth endoplasmic reticulum (SER) - synthesises lipids including cholesterol and steroid
hormones (such as oestrogen).
• Golgi apparatus - made up of a
group of fluid-filled membrane-
bound flattened sacs surrounded
by vesicles. It receives proteins
from the RER and lipids from the
SER. It modifies the proteins and
lipids and repackages them into
vesicles. The Golgi apparatus is
also the site of lysosome
synthesis.
• Ribosomes - ribosomes are responsible for the translation of RNA into protein (protein
synthesis). They either float freely in the cytoplasm or are stuck onto the rough endoplasmic
reticulum.
• Mitochondria - site of ATP production during
aerobic respiration. It is self-replicating so can
become numerous in cells with high energy
requirements. It contains a double membrane
with folds called cristae, which provides a large
surface area for respiration.
• Lysosomes - phospholipid rings which contain
digestive enzymes separate from the rest of the
cytoplasm. Lysosomes engulf and destroy old organelles or foreign material.
• Chloroplasts - the site of photosynthesis. It is enclosed by a double membrane and has
internal thylakoid membranes arranged in
stacks to form grana linked by lamellae.
These structures are found only in plants and
certain types of photosynthesising bacteria or
protoctists.
• Plasma membrane - consists of a
phospholipid bilayer with additional proteins to
serve as carriers. It also contains cholesterol
to regulate membrane fluidity. The plasma
membrane contains the cell contents and
holds the cell together, whilst controlling the movement of substances into and out of the cell.
• Centrioles - these are bundles of microtubules which form spindle fibres during mitosis in
order to pull sister chromatids apart. They are also important for the formation of cilia and
flagella. They are not found in plant and bacterial cells.
• Cell wall - a rigid structure made of cellulose (in plants), chitin (in fungi) and murein (in
prokaryotes) which provide support to the cell.
 • Flagella - a tail-like structure which are made up of bundles of microtubules. The
microtubules contract to make the flagellum move and propel the cell forward. Cells with a
flagellum include sperm cells, which use it to swim up the fallopian tubes to fertilise the egg
cell.
• Cilia - finger-like projections found on the surface of some cells. These also contain bundles
of microtubules which contract to make the cilia move. Cilia are found on epithelial cells lining
the trachea and move to sweep mucus up the windpipe.
• Vacuole - the vacuole is an organelle which stores cell sap and may also store nutrients and
proteins. It helps to keep plant cells turgid. Some vacuoles can perform a similar function to
lysosomes and digest large molecules.
• Plasmodesmata - channels (threads of cytoplasm) found between plant cells that enable
them to communicate

Levels of organisation

The cell is the ‘basic building block of life’ and

is the smallest functioning part of an
organism. A group of cells working together is
called a tissue and a collection of tissues all
performing a specific function is called an
organ. Multiple organs which are connected
together are referred to as an organ system.

The lungs are an example of an organ found

in animals and is made up of the following
tissues:

• Endothelium – forms the capillary

walls which supply alveoli with
oxygen and nutrients.
• Fibrous connective tissue – helps to push air out of the lungs during exhalation.
• Squamous epithelial tissue – makes up the walls of the alveoli.

Examples of organ systems include the respiratory system, circulatory system, reproductive system
and digestive system.
Comparing eukaryotic and prokaryotic cells

Prokaryotes and eukaryotes share

some of the same organelles
(cytoplasm, cell membrane,
ribosomes) but there are some
important differences:

• Prokaryotes have no membrane-

bound organelles (so no
mitochondria, Golgi, endoplasmic
reticulum, nucleus etc.). Their
DNA floats freely in the cytoplasm.
• Their DNA consists of a single
circular chromosome whereas
DNA in eukaryotes is linear and
wrapped around chromosomes.
• Prokaryotes have extra bits of DNA in the form of small circular plasmids.
• Prokaryotes have smaller ribosomes (70S) compared to eukaryotic ribosomes (80S).
• Eukaryotes like plants and fungi have cell walls made of cellulose and chitin. Bacterial cell walls
are made of murein (a type of glycoprotein).
• Prokaryotic cells are much smaller than eukaryotic cells.
• Both prokaryotes and eukaryotes can have flagella but those found in prokaryotes are made of a
protein called flagellin whereas in eukaryotes they are formed from microtubules.

Prokaryotes have some organelles that are absent from eukaryotic cells. These include:

• Pili - pili are hair-like structures which stick out from the plasma membrane. They are used to
communicate with other cells (including the transfer of plasmids between bacteria).
• Mesosomes - the mesosome is a folded portion of the inner membrane. While some scientists
believe that it plays a role in chemical reactions, such as respiration, other scientists doubt
whether it even exists and think that it may just be an artefact produced during the preparation of
bacterial samples for microscopy.
• Plasmids - plasmids are small, circular rings of DNA which are separate from the main
chromosome. They house genes which are not crucial for survival but might prove useful - such
as antibiotic-resistance genes, for example. Plasmids can replicate independently from the main
chromosomal DNA.
• Slime capsule - in addition to a cell wall, some bacteria also have a capsule which is made of
slime. The main function of the capsule is to protect the bacterium against an immune system
attack.
Bacterial replication

Bacteria replicate by binary fission, which is where the cell replicates its DNA then splits to form two
genetically identical daughter cells.

• The large loop of chromosomal DNA replicates once. Plasmids also replicate (sometimes
more than once). DNA moves to opposite ends of the cell.
• The cell grows bigger and cytoplasm divides. New cell wall is synthesised.
• The cytoplasm completely splits in two (cytokinesis) and two new cells are formed that are
clones of each other (except they may have different numbers of plasmids).

Virus structure

• Technically, viruses are not alive

because they cannot reproduce on
their own (they need to get inside the
cells of other organisms to make
more copies of themselves).
• Contain nucleic acid (either DNA or
RNA) and enzymes surrounded by a
protein coat called a capsid.
• This is enclosed in a viral envelope
with attachment proteins sticking out.
• Unlike eukaryotic and prokaryotic
cells, they do not contain cytoplasm,
a cell membrane or ribosomes.

Viral replication

• Viruses get inside host cells by binding to receptors on the membranes of host cells using
their attachment proteins. This means that viruses can only infect one cell type (which have
the complementary shaped receptor on their plasma membrane).
• The virus releases its capsid (containing nucleic acids and enzymes) into the cell.
• The single strand of nucleic acid is converted into double-stranded DNA and integrated into
the host cell’s genome.
• The host cell’s ribosomes are used to translate the viral DNA into viral proteins, which are
assembled into new viral particles.
Topic 2: Cells
Microscopy and Mitosis
Microscopy

The light microscope uses light to magnify objects up to

1,500x their actual size. They have a resolution of
approximately 0.2 μm which isn’t large enough to visualise
any of the smaller organelles, such as ribosomes and
lysosomes. They are more commonly used for visualising
whole cells or tissues. An advantage of light microscopy
is that it can visualise living cells so we can watch
behaviours such as cell division in real time.

The transmission electron microscope (TEM) is more

powerful than a light microscope and has a high enough resolution (around 0.0002 μm) to visualise
individual organelles. A TEM uses electromagnets to focus a beam of electrons at a sample.
Electrons have a much shorter wavelength compared to visible light which means higher-resolution,
detailed images can be produced. A disadvantage of TEM is that the sample needs to be fixed and
placed in a vacuum, which means that live cells cannot be used.

The scanning electron microscope (SEM) has a lower resolution (around 0.002 μm) than the TEM
but they can produce 3D images of cells and organelles. They emit a beam of electrons towards a
sample, knocking electrons off it which are used to build an image. Like TEMs, SEMs cannot be used
with live cells. Both types of electron microscope are pretty big and expensive so you’ll only find them
in specialised research facilities and hospitals.

Light microscope TEM SEM

Maximum 1500 x 1,000,000 x 500,000 x
magnification
Maximum resolution 0.2 μm 0.0002 μm 0.002 μm

Magnification

Magnification is how enlarged the image is compared to the original object. Resolution is defined as
how well a microscope distinguishes between two points that are close together (i.e. how much detail
it can make out). Light microscopes have a much lower resolution, so produce less detailed images,
compared to electron microscopes.
You can work out the magnification of a specimen viewed under a microscope using the equation:

Let’s say we magnify a 2 μm bacterial cell to form an image which is 16 cm long. The magnification
we must have used is:

• Convert both into the same units. 16 cm = 160 mm = 160,000 μm

• 160,000 / 2 = 80,000 x magnification

Calibrating the eyepiece graticule and the stage micrometer

If you wanted to measure the size of your

specimen, you’ll first need to align the
eyepiece graticule and the stage
micrometer which are little rulers which are
found on the lens and the stage respectively.
To do the calibration you need to carry out
the following steps:

• Place the stage micrometer on the stage

and focus the lens so that you can
clearly see the divisions.
• Align the eyepiece graticule with the
stage micrometer.
• Each division of the stage micrometer is 0.1 mm. If the eyepiece graticule spans a total of three
divisions, then we know that the total length of the eyepiece graticule is 0.2 mm.
• The graticule is divided by a scale from 0 to 100, which means that each individual division is a
length of 0.002 mm.
• Now we can take away the stage micrometer and add our sample, using the eyepiece graticule to
measure its size.
Viewing specimens under an optical microscope

• Pipette a drop of water onto a microscope slide then place your specimen on top (this needs
to be just a thin layer of cells so that light can pass through).
• Add a drop of stain e.g. oesin stains the cell’s cytoplasm. This creates contrast and enables
organelles to be visualised.
• Add a cover slip to protect the specimen by carefully tilting and lowering down, taking care not
to trap any air bubbles.
• Place the slide onto the microscope stage and select the lowest-powered objective lens.
• Look down the eyepiece and use the coarse adjustment knob to focus the specimen.
• Select increasingly higher magnifications until you can visualise the cell structures you’re
interested in.

Cell fractionation

Cell fractionation is a technique which separates organelles according to their density - you might
want to do this if you want to visualise certain organelles under the microscope separately. It involves
bursting the cell surface membrane to release the organelles and spinning the cell solution at really
high speeds.

Homogenisation - the first step of cell fractionation is homogenisation. This is where you break apart
the plasma membrane to release the organelles. This can be done by vibrating the cells or by
breaking them apart in a blender. It is important that this cells are placed into a solution which is ice-
cold, isotonic and buffered.

• Ice-cold - the solution needs to be ice-cold to slow down the activity of enzymes. This is
important because some enzymes will degrade organelles (such as the enzymes found inside
lysosomes) so we need to reduce their activity to preserve the
cell’s organelles.
• Isotonic - the solute concentration (and therefore water
potential) of the solution needs to be the same as the cells that
have been broken down, otherwise water would move into the
organelles by osmosis, resulting in damage
• Buffered - adding a buffer to a solution ensures the pH stays
constant. This is important because proteins are denatured by
changes in pH - remember that proteins are a key component of
various organelles.

Filtration - the homogenised solution is filtered to remove any tissue

debris. The organelles are small enough to pass through the holes of
the filter paper so will be present in the filtrate.
Ultracentrifugation - this is where we spin the filtrate at increasing speeds. The heaviest organelles
will sink to the bottom of the test-tube, forming a pellet. We can transfer the remaining solution (the
supernatant) to a separate test tube, which will be spun at a slightly higher speed. This is repeated
until you obtain the organelle that you want. Remember that the organelles will be separated from the
solution from the heaviest to the lightest. Nuclei will come out of the solution first, followed by
mitochondria, then lysosomes, then the endoplasmic reticulum. Ribosomes will be the last organelles
to form a pellet, since these are the lightest organelles in a cell.

Mitosis and the Cell Cycle

Mitosis is a type of cell division where cells produce identical copies of themselves and is used for
growth and repair and asexual reproduction. It differs from meiosis, which is the type of cell
division used to produce gametes.

Mitosis occurs as part of the cell cycle which

consists of four distinct phases. First,
interphase takes place which is made up of
three growth phases (called G1 phase, S phase
and G2 phase), followed by mitosis.

• Gap Phase 1 (G1) - cell grows bigger and

replicates its organelles. A high amount of
protein synthesis is taking place in order
to build new organelles.
• Synthesis Phase (S) - the cell replicates its DNA
• Gap Phase 2 (G2) - the cell keeps growing until all of the
organelles have duplicated.

Once the DNA has replicated, each chromosome now consists

of two sister chromatids, connected by a structure called the
centromere. The mitochondria produce more ATP which will
provide the energy for cell division and the ribosomes will be
synthesising a high level of proteins to replicate organelles.

There are two ‘checkpoints’ in the cell cycle - one before S

phase and one straight after S phase. During these
checkpoints, the cell is checking its DNA for errors. This
minimises the chances of duplicating any mutated DNA into the
replicated cell.
The Stages of Mitosis

Mitosis can be divided into a series of stages depending on what’s going on with the chromosomes in
the cell. You can use the acronym PMAT (pass me another tequila) to help you remember the order.

• Prophase - the chromosomes condense (they become shorter and fatter) and the nuclear
envelope disintegrates. The centrioles move to opposite poles of the cell and form spindle
fibres.
• Metaphase - the chromosomes line up along the middle of the cell. They attach to the
spindle fibre by their centromere.
• Anaphase - the centromere splits and the chromatids are pulled to opposite poles of the
cell.
• Telophase & cytokinesis - the two groups of chromsomes decondense (they become long
and thin) and a nuclear envelope reforms around them, forming two new nuclei. The
cytoplasm divides (cytokinesis) and the plasma membrane pinches off to form two new,
genetically-identical cells.

Cancer = uncontrolled mitosis

Mitosis is genetically controlled and stops once the cell has divided enough times to make the cells
that you need. If the genes that control mitosis mutate, mitosis can occur unchecked, resulting in the
formation of a tumour. If this invades the surrounding tissue, this leads to cancer.

Some cancer drugs work by disrupting the cell cycle to kill the tumour cells:

• Some prevent the synthesis of enzymes involved in DNA replication. This prevents the
cell cycle progressing past S phase and the cell is forced to undergo apoptosis (programmed
cell death).
• Radiotherapy works by damaging DNA using radiation. The cell cycle is stalled during the
DNA checkpoint stages (either before or immediately after interphase). Prolonged pausing of
the cell cycle causes the cell to initiate apoptosis.
The problem is that they have the same effect on healthy cells, which is why chemotherapy produces
such unpleasant side-effects.

Mitotic Index

The mitotic index is a measure of the proportion of cells which are undergoing mitosis. You may be
asked to calculate it in the exam. To do this, you need to count the number of cells with visible
chromosomes and divide this by the total number of cells.
Investigating mitosis in squashed root tips

You can see mitosis happening in root tip cells by staining the chromosomes and observing under the
microscope. We use cells right from the tips of the roots because this is where mitosis is taking place
(in the meristem tissue).

Method:

• Cut a thin section of tissue from the tip of a growing root.

• Pipette a set volume of 1M hydrochloric acid into a boiling tube and place in a 60oC water
bath.
• Place the plant tissue in the boiling tube and leave for five minutes.
• Rinse the root tip with cold water and dry using a paper towel.
• Cut the root tip so that you have a thin layer of cells (about 2 mm) and spread out onto a
microscope slide using a mounted needle.
• Add a drop of Toluidine blue O stain to the tissue and place a cover slip on top. Push down
on the cover slip to squash the cells and allow light to pass through. Be careful not to push
sideways otherwise the chromosomes will become damaged.
• Use a light microscope to visualise the cells and identify the stages of mitosis. Any cells with
visible chromosomes will be undergoing mitosis (as the chromosomes are condensed).
Topic 2: Cells
The Immune System
Pathogens and antigens

Pathogens are organisms which cause disease. They possess molecules (usually proteins) on their
cell surface called antigens which trigger an immune response when detected by our immune
system. When an antigen is detected, the immune response undergoes four main stages:
phagocytosis of pathogen, activation of T lymphocytes, activation of B lymphocytes and
production of antibodies by plasma cells.

Phagocytosis

Phagocytes are a type of white blood cell which can destroy pathogens - types of phagocyte include
macrophages, monocytes and neutrophils. They first detect the presence of the pathogen when
receptors on its cell surface bind to antigens on the pathogen. The phagocyte then wraps its
cytoplasm around the pathogen and engulfs it. The pathogen is contained within a type of vesicle
called a phagosome. Another type of vesicle, called a lysosome, which contains digestive
enzymes (lysozymes) will fuse with the phagosome to form a phagolysosome. Lysozymes digest
the pathogen and destroy it. The digested pathogen will be removed from the phagocyte by
exocytosis but they will keep some antigen molecules to present on the surface of their cells - this
serves to alert other cells of the immune system to the presence of a foreign antigen. The phagocyte
is now referred to as an antigen-presenting cell (APC).
T lymphocyte response

T lymphocytes are white blood cells which contain receptors on their cell surface. Different T cells
have different shaped receptors on their surface (so they will each bind to a different-shaped
antigen). When a particular T cell binds to a complementary antigen (e.g. on a antigen-presenting
cell or on a pathogen), the T cell will become activated - this is called clonal selection. Once it is
activated, the T cell divides by mitosis to produce clones - this is called clonal expansion. There are
different types of T cell which play different roles in the immune response:

• T helper cells release chemicals (they release a type of cytokine called interleukins) to activate B
lymphocytes.
• T killer cells (aka cytotoxic T cells) destroy any cells which have been infected with the
pathogen.
• T regulatory cells suppress other immune cells and prevent them from attacking our own (host)
cells.
• T memory cells remain in the bloodstream in low levels in case reinfection occurs. If the antigen
is detected again at a later date, they will divide into T helper, T killer and T regulatory cells.
B lymphocyte response

B cells are activated when chemicals are released from T helper cells. They are also activated when
the antibody molecules on their cell surface bind to a complementary antigen. Different B cells
have different shaped antibodies on their surface, so only the B cells with the correct-shaped
antibodies will be activated. Once they are activated, the B cells divide by mitosis and differentiate
into two kinds of cell - plasma cells and memory cells.

• Plasma cells produce antibodies with a complementary shape to the antigen.

• Memory cells remain in the bloodstream in low levels in case reinfection occurs. If the antigen is
detected again at a later date, they will quickly divide into plasma cells.
Antibody structure

Antibodies have a quaternary structure made up of four polypeptide chains (two heavy chains
and two light chains) held together by disulfide bridges. They are composed of a variable region
(which is different in different antibodies) where the antigen-binding site is located. The antigen-
binding site has a complementary shape to the antigen which makes it specific to that particular
antigen. There is also the constant region which is the same for all antibodies. The constant region
contains another binding site which allows the antibody to bind to immune system cells, such as B
cells or phagocytes. In between the variable region and the constant region is the hinge region which
provides the antibody with flexibility.

How antibodies work

Antibodies work to destroy pathogens in three different ways.

1. Agglutination - antibodies each contain two antigen-

binding sites which means they can bind to two
pathogens at the same time. This causes pathogens
to become clumped together. Phagocytes can then
engulf and digest lots of pathogens at the same time,
which makes phagocytosis more efficient.
2. Neutralising toxins - certain pathogens, such as bacteria, make us feel ill by releasing
toxins. Antibodies can bind to toxins which renders them harmless (it neutralises them). The
antibody-toxin complex can then be destroyed by phagocytes.
3. Blocking access to human cells - pathogens enter host cells when their antigens bind to
receptor molecules on host cells (like a key opening a lock). When antibodies bind to
antigens, it prevents the antigen from fitting in the receptor which means it can’t get inside the
cell.
Cellular vs humoral immune response

The immune response can be split into two types of response which interact with each other:

• Cellular immune response – includes phagocytosis and T-cell response

• Humoral immune response – includes B-cells and the antibodies they produce

Primary and Secondary Immune Response

• The primary immune response occurs when you are infected with a pathogen for the first
time. It is composed of the non-specific and the specific immune response. This process is
slow because it takes time for the correct B cell to be activated (clonal selection) and divide
into lots of plasma cells (clonal expansion) in order to produce antibodies with a
complementary shape to the antigen. The infected person will experience symptoms while
the T and B cells mount an immune response. As part of the primary response, both T and B
cells produce memory cells.
• If you are re-infected with the same pathogen in the future, the T and B memory cells will
recognise the antigen and start dividing. T memory cells will divide into the correct type of T
killer cell to kill any cells that are infected with the pathogen. B memory cells will divide into
plasma cells to produce a large number of antibodies which is complementary to the antigen
molecules on the pathogen. This is the secondary immune response and is much quicker
than the primary response. It happens so quickly that the pathogen is suppressed before you
are able to experience symptoms - you are immune to the pathogen.
Vaccines

Vaccines contain a dead or weakened form of a pathogen which is injected into the bloodstream.
Sometimes vaccines contain just the antigen proteins without the rest of the pathogen. Other
vaccines might contain a variety of different antigens to protect against different strains of pathogens
which vary in the shape of the proteins on their cell surface membranes (antigenic variation). The
injection of weakened antigens stimulates a primary immune response and the production of
memory T cells and memory B cells, resulting in immunity without becoming ill from the disease.

Antigenic variation

Pathogens are continually evolving to evade the immune system. One way in which they do this is by
switching up the shape of their antigens, a process known as antigenic variation. Viruses like
influenza and HIV have a high rate of mutation in the genes which code for its antigens. This means
that different strains of the virus will show slight differences in the shape of their antigens. Memory
cells that have formed from one viral strain may not detect the presence of antigens from other
strains, so the person has to go through the primary immune response all over again. Antigenic
variation makes it difficult to develop a vaccine for these pathogens and it’s why a new flu vaccine
is released each year.

Active vs Passive Immunity

Active immunity occurs when your body makes its own antibodies after being stimulated by an
antigen. This process can be natural (e.g. if you catch a cold, your body will make its own antibodies
against the common cold virus) or it can be artificial (e.g. if you are vaccinated with a harmless form
of an antigen).

Passive immunity occurs when you are given ready-made antibodies that have been produced by
another organism. This process can be natural (e.g. babies receive antibodies from their mother
when they breastfeed) or artificial (e.g. antibody injections can be given for some diseases - e.g. this
is being tested as a treatment for Ebola).
Active immunity lasts longer since memory cells will remain in the body for years but it takes time to
develop. Passive immunity provides immediate protection against pathogens but is short-lived
(antibodies that are transferred from mother to child during breastfeeding only remain in the body for
about 18 months).

Uses of monoclonal antibodies

Monoclonal antibodies are antibodies produced from a single B-cell clone so they all have the exact
same structure. Monoclonal antibodies can be developed to bind to anything, not just antigens on a
pathogen. For example, they can be engineered to bind to antigens on the surface of cancer cells to
deliver a chemotherapy drug to the site of a tumour, minimising the impact on healthy cells. This
works because tumour cells have different antigens compared to normal body cells.

Monoclonal antibodies are also used in pregnancy tests:

• On the application area of pregnancy tests (the part that is urinated on), there are antibodies
for human chorionic gonadotropin (hCG) hormone. The hCG hormone is released by
foetuses, so is only found in the urine of pregnant women. The antibodies are bound to a blue
bead.
• If there is any hCG present in the urine, this will bind to the antibody on the beads.
• The urine moves up the stick to the test strip, carrying the beads with it. The test strip
contains immobilised hCG antibodies, fixed in position on the test strip
• If hCG is present, the immobilised antibodies bind to the hormone that is already attached to
the mobile hCG antibody and the blue bead. This causes the strip to turn blue, only if the
hormone is present.
• If hCG is absent, the beads pass through the test area without binding to anything so the test
strip remains white.

ELISA test

The ELISA (enzyme-linked immunosorbent assay) test is used in medical diagnosis to see if
someone has antibodies against a certain pathogen. There are two types: direct ELISA uses a single
antibody that is complementary to the disease antigen. Indirect ELISA uses two different antibodies:

• Antigens for a particular disease (e.g. HIV antigens) are bound to the surface of a dish.
• A patient’s blood sample is added to the dish. If they possess complementary antibodies
(e.g. HIV antibodies), these will bind to the antigens fixed on the bottom of the plate.
• The blood sample is then washed off.
• A solution containing secondary antibody is applied. These will bind to any HIV antibody
that is bound to the plate. The secondary antibody is attached to an enzyme.
• The solution is washed off to remove any unbound secondary antibody.
 • A substrate is added which will be converted into a coloured product if the enzyme is
present. Since the enzyme is only present if the blood sample contained HIV antibodies, the
colour change indicates a positive result for HIV infection. If the person does not possess HIV
antibodies, no colour change will take place.

HIV and AIDS

Human immunodeficiency virus (HIV) is a deadly virus which can weaken a person’s immune
system by destroying a type of immune cell called T helper cells. It is spread through the
transmission of infected bodily fluids (e.g. during sexual intercourse, sharing of needles or blood
transfusion). HIV doesn’t kill the patient directly, but weakens the immune system to an extent that the
patient is unable to fight off other infections which normally would not pose a threat - these are known
as opportunistic infections.

When the patient’s immune system has weakened to a particularly low level (this is seen by a low T
helper cell count in hospital blood tests), the patient has developed a disease called acquired
immunodeficiency syndrome (AIDS). The time between the initial infection and the onset of AIDS
symptoms (the latency period) varies greatly between individuals but is usually around 10 years. The
length of the latency period depends on the individual’s age, strength of their immune system and
access to healthcare.

The symptoms of AIDS follow a series of

stages:

1. The person will first develop less

serious, minor infections which will
gradually become more and more severe.
2. As the patient’s body tries to fight off
more infections, the lower their T cell
levels drop.
3. Eventually their immune system will be so
weak that they will die of an
opportunistic infection because they do
not have enough immune cells to defend
themselves.

HIV Replication

The HIV virus consists of a core of RNA and enzymes (reverse transcriptase and integrase) which
is enclosed in a protein coat called a capsid. Surrounding the capsid is an outer layer called the
envelope which contains attachment proteins - these proteins are crucial for the virus to enter host
cells (they act like little keys to access our cells).
If a person with HIV exchanges bodily fluid with another person, HIV can infect the second individual
and will be present in their bloodstream. The HIV virus uses its attachment proteins to enter human
immune cells (specifically the T helper cell) by binding to receptors on the T cell. The capsid is
released into the cell, where it breaks apart to release the RNA and enzymes. The enzyme reverse
transcriptase converts the RNA into DNA. The single-stranded DNA is converted into double-
stranded DNA which the enzyme integrase can insert into the DNA of the T cell. The T cell now
has the ‘instructions’ (genes) to produce viral proteins. The viral DNA is transcribed and translated
and the viral proteins are used to build new virus particles, which move out of the T cell and infect
other cells.

Antibiotics

Antibiotics work by interfering with bacterial cell walls and ribosomes, either killing the bacteria or
stopping its growth. They have no effect on viruses or our own cells because:

• Viruses do not have ribosomes or cell walls, which means that antibiotic treatment is
completely ineffective against viral infections
• Human cells do not have cell walls. We do have ribosomes, but these are bigger than those
found in bacteria and unaffected by antibiotics. This is useful, because it means we can take
antibiotics without worrying about it interfering with our own cells.