CELL STRUCTURES

1. Recognise organelles and other structures found in eukaryotic cells and outline their structure and function
Illustration and how structural features relate to Present in
of organelle Main function
function Plants? Animals?
- The cell (plasma) membrane ✓ ✓
is found on the surface of
animal cells and just inside
the cell wall of plant cells.
- It’s made mostly of lipids and
protein. May be
phospholipids in a bilayer
(double).
- The cell membrane regulates
asma) membrane the movement of substances
into and out of the cell. Has 2 The plasma membrane acts as a passageway that only
functions, keeps unwanted lets certain things in and out of the cell. Fat soluble
substances out. It also allows molecules can pass through and larger molecules are
and helps to get essential able to pass through certain protein channels. (Large
nutrients into the cells and tunnel-like passages).
get waste substances out. It’s approximately 5 - 10 nm
- Receptor molecules on the
membrane allow it to
respond to chemicals like
hormones.
- These are oval/rod shaped ✓ ✓
organelles with a double
membrane.
- The inner membrane is
folded to form cristae. Inside
is the matrix, which contains
enzymes involved in
respiration.
- Mitochondrion
(Mitochondria) are the site of
aerobic respiration where
ATP is produced.
ondria The Mitochondria's structure allows it to maximise its
- They are found in large
rate of work and production. The Mitochondria is
numbers in very active cells
made of two membranes, the outer membrane acts
and require a lot of energy.
as a skin that covers the organelle. While the inner
- They have a diameter of 1
membrane is folded many times creating the layered
µm
structures (cristae). The folding of the Mitochondria
increases the surface area inside the organelle. Since
- Contains Nucleic acid.
many of the chemical reactions occur on the inner
Contains circular naked DNA.
membrane, this allows for more reactions to take
That’s why/how it's capable
place. The matrix is the fluid within the Mitochondria.
of self-division.
Mitochondria are special due to them having their
- Has 70s Ribosomes which
own ribosomes and DNA floating around in the
allow for synthesis of
Matrix.
polypeptides.
 - A membrane bound (usually ✓ Yes but
large) permanent organelle they are
found in the cytoplasm of small and
plant cells. Animal cells temporar
occasionally have a vacuole y
but they’re small and
temporary.
- Vacuoles contain a weak
solution of sugars and salts
es called cell sap. The
membrane surrounding plant
cell vacuoles is called the
tonoplast: which controls Vacuoles are cell bound membranes that contain cell
exchange between the sap. These Vacuoles regulate the osmotic properties
vacuole and the cytoplasm. of cells. Whilst also maintaining turgor pressure
- Vacuoles help to regulate the (which maintains cell shape/stops it from collapsing)
osmotic properties of cells [through the regulation of the osmotic flow of water].
(the flow of water inwards By helping to regulate the osmotic flow, they are able
and outwards). to try and make it so the cell doesn’t plasmolyze.
- This is the largest organelle ✓ ✓
that is surrounded by a
nuclear envelope, which
contains many pores (nuclear
pores) that allow and control
exchange between the
nucleus and the cytoplasm.
- The nucleus contains
chromosomes made from
protein-bound linear DNA
and one or more structures
called nucleolus. The large size of the nucleus allows it to have space to
- The nucleus controls cell store the genetic material and chromosomes. Whilst
activity through transcription also giving a large area to allow the nucleolus to have
s
of DNA, which contains room to produce the Ribosomes. The pores allow the
instructions to make protein. exchange between the nucleus and the cytoplasm.
- The nucleus makes
ribosomes.

- Contains Nucleic acid.

Contains the DNA
(deoxyribonucleic acid). May
contain RNA (ribonucleic
acid) in the form of mRNA
(messenger RNA), tRNA
(transfer RNA) or rRNA
(ribosomal RNA).
 Rough ✓ ✓

- Rough ER has a surface

covered in ribosomes.
- RER folds and processes the
proteins that have been
produced at the ribosomes.
- The RER also synthesises
membranes that are used
throughout the cell.
- It synthesises proteins and
asmic reticulum sometimes transports them.
- Continuous with nucleus.
Smooth ✓ ✓

- Smooth ER has a smooth

surface that isn’t covered in
ribosomes.
- SER synthesises and
processes lipids.
- It is also continuous with the
nucleus.
- It also breaks down toxins.

mes - Ribosomes are the sites of ✓ ✓

protein synthesis. They can
be found free in the
cytoplasm as well as on the
rough ER. They are very
small, only about 25 nm in
diameter. They are made of
RNA (ribonucleic acid) and
protein.
- They are the smallest and
most numerous of the cell
organelles.
- Ribosomes are made up of
proteins and rRNA, are not
surrounded by a membrane
and the site where proteins
are made.
- Prokaryotes and the
chloroplasts and
mitochondria have smaller
70s ribosomes than those
found in the rest of a
eukaryotic cell.
- All of them are made of two
subunits, one of them which
is larger than the other.
- The ‘s’ stands for how quickly
the molecule moves in a
centrifuge. The larger, denser
80s eukaryotes ribosomes
 settle first.

- Contains Nucleic acid.

Ribosomes make rRNA,
however you may find mRNA
or tRNA if translation is
taking place.
- A dense, solid structure ✓ ✓
composed of crystalline
protein and nucleic acid.
They are improved in
ribosome synthesis. Function
= rRNA synthesis.
- They are where ribosomes
are made.
lus

There are 3 major structures within the Nucleolus:

the fibrillar centre (FC), the dense fibrillar component
(DFC), and the granular component (GC).
Transcription of the rDNA occurs in the FC. The DFC
contains the protein fibrillar, which is important in
rRNA processing.
odies - The Golgi body is a stack of ✓ ✓
flattened sacs. More than
one Gogli body may be
present in a cell. The stack is
constantly being formed at
one end from vesicles which
bud off from the ER, and
broken down again at the
other end to form Golgi
vesicles. The stack of sacs
together with the associated
vesicles is referred to as the
Golgi apparatus or Golgi
complex. The Golgi body
collects, processes and sorts The large surface area due to the stacked sacs allows
molecules (particularly it to perform its job/function more efficiently.
proteins from the rough ER),
ready for transport in Golgi
vesicles either to other parts
of the cell or out of the cell.
Two examples of protein
processing in the Golgi body
are the addition of sugars to
proteins to make molecules
known as glycoproteins, and
the removal of the first
amino acid, methionine,
from newly formed proteins
to make a functioning
protein. In plants, enzymes in
the Golgi body convert
 sugars into cell wall
components. Golgi vesicles
are also used to make
lysosomes.
- The Golgi vesicles also store
lipids and proteins made by
the golgi apparatus/body and
then transport them out of
the cell through the cell
membrane often by
exocytosis.
- Lysosomes are spherical sacs, ✓ ✓
surrounded by a single
membrane and having no
internal structure. They are
commonly 0.1-0.5 µm in
diameter.
- They contain digestive
(hydrolytic) enzymes which
must be kept separate from
the rest of the cell to prevent
The membrane allows for a gateway which allows
damage from being done.
molecules into the lysosome without letting the
Lysosomes are responsible
digestive enzymes escape into the cell.
for the breakdown
mes (digestion) of unwanted
structures such as old
organelles or even whole
cells, in mammary glands
after lactation (breast
feeding). In white blood cells,
lysosomes are used to digest
bacteria. Enzymes are
sometimes released outside
the cell.
- Lysosomes are types of Golgi
vesicles.
- They contain digestive
enzymes lysozymes.
plasts - Chloroplasts tend to have an ✓ NO
elongated shape and a
diameter of about 3 to 10 µm
(compared to 1 µm diameter
for mitochondria), Like
mitochondria, they are
surrounded by two
membranes, forming the
chloroplast envelope. Also
like mitochondria,
chloroplasts replicate
themselves independently of
cell division by dividing into
two.
- The main function of The chloroplast has an inner and outer membrane
chloroplasts is to carry out with an empty intermediate space in between. Inside
photosynthesis. Chloroplasts the chloroplast are stacks of thylakoids, called grana,
 are an excellent example of
how structure is related to
function, so a brief
understanding of their
function will also help you to
understand their structure.
as well as stroma, the dense fluid inside of the
chloroplast. These thylakoids contain the chlorophyll
that is necessary for the plant to go through
photosynthesis.

- Contains Nucleic acid.

Contains circular naked DNA.
That’s why it's capable of
self-division.
- The rigid structure that ✓ NO
surrounds cells in plants,
algae and fungi.
- It’s made mainly of the
carbohydrate cellulose in
plant and algae cells, In fungi;
the cell wall is made of chitin.
ll
Note - some bacteria
(prokaryote) have
peptidoglycan cell walls. The cellulose fibres, structural proteins and other
- The primary function of the polysaccharides help the cell wall perform its function
cell wall is to support cells of maintaining cell shape and supporting the cell.
and prevent them from
changing shape.
Tiny appendages that stick out of Not in ✓
eukaryotic cells that move the cells higher
around as well as moving fluid past plants
the cells.
 Flagella help organisms in movement. Not in ✓
They act as sensory organelles to higher
detect temperature and pH changes. plants
And they also aid in the movement by
pushing and directing it.

- Centrioles are paired Not in ✓

structures that lie just higher
outside the nucleus of nearly plant
all animal cells and some cells
cells of lower plants. They’re
found in an area called the
centrosome.
- They are absent in higher
plants.
- A centriole is a hollow
cylinder about 500 nm long,
oles formed from a ring of short
microtubules.
- Each centriole contains nine
triplets of microtubules.
Their exact function in most
cells is still not known but
they do act as microtubule-
organising centres (MTOC) in
the flagella and cilia of
bacteria.
 - Microtubules make up part ✓
of the cell cytoskeleton
which helps to give the cell
its shape.
- They’re very small, 25 nm in
diameter and made of alpha
(a) and beta (β) tubulin
proteins as a double
molecule or dimer.
ubules - Long protofilament
molecules line up in a ring to
form tubules.
- The spindle fibres which pull
apart chromosomes during
cell division are
microtubules.
- They’re also involved with
the movement of vesicles
and some organelles.
- The microvilli are extensions No ✓
of the villi.
- Their purpose is to increase
the surface area of the cell.
This allows them to increase
the rate of things being
absorbed into the cells.
illi

- Plasmodesmata are ✓ No
cytoplasmic bridges that
allow for intercellular
communication in plants.
- They span the cell walls,
linking the fluid cytoplasm,
plasma membranes and
desmata
endoplasmic reticulum
between adjacent cells.
- There is cell to cell
communication of both small
molecules and
macromolecules (proteins
and RNA).

P.S (NOTE) : Cytoplasm also contains nucleic acid. In the form of tRNA and possibly mRNA, however the Cytoplasm isn’t technically an
organelle.
2. Describe and interpret photomicrographs, electron micrographs and drawings of typical plant and animal cells.

Photomicrographs : A photograph of a microscopic object, taken with the aid of a microscope.

Electron Micrograph : Electron microscopy (EM) is a technique for obtaining high resolution images of biological and non-
biological specimens. It is used in biomedical research to investigate the detailed structures of tissues, cells and organelles.

Photomicrograph of root cells:

Electron micrograph of blood cells:

Drawing of typical Animal Cell:
Drawing of typical Plant Cell:
3. Define resolution and magnification and explain the differences between these terms, with reference to light microscopy
and electron microscopy.

Resolution
The resolution is how detailed the image is. The better the resolution, the better the microscope is able to distinguish between two
points that are close together.
If a microscope cannot separate two objects, more magnification will not be of help, (it will only make it harder to distinguish).

Poor resolution. Better resolution. Best resolution.

Magnification
Magnification is simply how much bigger the image appears than the specimen sample is. It’s calculated using this formula:

Magnification = Size of image / Size of real object

It’s written as x10 or 10x.

E.g Magnified image = 15000 µm wide. Actual cell size = 15 µm wide. 15000/15 = x1000
Magnification = x1000 (or 1000x) magnification

Types of Microscopes
There are 2 types of microscopes, used when studying cells. They are the optical (light) microscopes and the electron microscopes.

There are 2 electron microscope types : TEM (Transmission electron microscope [Used for surfaces])
SEM (Scanning electron microscope [Used for 3D models])
Electron microscopes can only be used on dead (unalive) objects and organisms.

Electron microscopes have higher magnifications and better resolution when compared to the light microscopes.

Light microscopes simply use lenses to magnify an image.

4. Compare the structure of typical plant and animal cells.

Diagram comparing animal and plant cells

Table comparing animal and plant cells

Basic Term Plant Cell Animal Cell

Cell shape Have a regular shape. Have an irregular or round shape.

Cell size Tend to be larger. Tend to be smaller.

Enclosed by Rigid cellulose cell wall. Thin and flexible plasma membrane.

Vacuole position One large central vacuole. Numerous and small vacuoles.

The flexibility of the cell Tend to be rigid. Hence, not prone to Tend to be flexible. Hence, cells are
changes. prone to changes in shape.

Plastids Present for exposing plant cells that Absent.

contain chloroplast to sunlight.

Nucleus position Lie on the periphery of the cytoplasm. Lie at the centre of the cell.

Centrioles Absent except in the motile cell of lower Present.

plants.

Lysosomes Quite rare. Present

Glyoxysomes Present. Absent.

 Tight junctions and desmosomes Absent. Present.

Plasmodesmata Present. Absent.

Form of food storage Starch. Glycogen.

Synthesis All amino acids, coenzymes and vitamins. Cannot synthesise all amino acids,
coenzymes, and vitamins.

Formation of spindle During cell division in anastral i.e. During cell division is amphiastral i.e has
without asters at opposite poles. an ester at each pole.

Cytokinesis occurrence Cell plate method. Construction or furrowing.

What happens in hypotonic solution Do not burst due to the presence of rigid Tend to burst due to lack of cellulose
cellulose cell walls. cell wall.

Mode of nutrition Autotrophs. Heterotrophs.

Mitochondria Present in fewer numbers. Present in larger numbers.

Chloroplast Present . Absent.

What is a plant cell?

A plant cell is a basic unit of life for multicellular eukaryotes in the kingdom Plantae. The mode of nutrition is autotrophic in
nature.
They are distinguished from animal cells by certain organelles, such as the cell wall, chloroplasts, and vacuoles. The size of plant
cells typically varies between 10-100 µm.

Types of plant cells

Phloem Cells - They are also known as sieve-tube members. They are responsible for transporting food and nutrients to the plant.

Xylem Cells - They are also known as water-conducting cells. They help in conducting water from the roots to the other part of the
plant.

Sclerenchyma - They have a cell wall that is embedded within lignin material. This helps to provide support and rigidity to the
plant.

Collenchyma - The walls are thin but some parts are thickening. The main function of the cells is to provide structural support.

Parenchyma - The cells have thin cell walls. They are responsible for the storage of organic products in plants.

What is an animal cell?

An animal cell is the fundamental unit of life for organisms that belong to the kingdom Animalia. The mode of nutrition is normally
heterotrophic in nature.
The size of the animal cell tends to vary between 10-30 µm in diameter. The key organelles in the animal cells are nerves and
muscles. They enhance locomotion and other vital functions.
Types of animal cells
Nerve Cells - These are specialised cells that send impulses or information to help the body coordinate and perform their
functions.

Skin Cells - They are responsible for the protection of internal parts and prevent an excess of loss of water through dehydration.

Blood Cells - They help in the transportation of nutrients and hormones within the body. Also, transport oxygen to different tissues
and eliminate carbon dioxide from different body tissues.

Muscle Cells - They help in the protection of the delicate parts of the body and also enhance the movement of the body.

Bone Cells - They are responsible for making the bones and skeletons of animals. The main function is to provide structural
support and help in the movement of the body.

Main difference between plant and animal cells

1. A plant cell is usually larger while the animal cell is smaller.
2. A plant cell has a rigid and regular shape while the animal cell has an irregular shape.
3. A plant cell has a permanent shape while animal cell shape is prone to changes.
4. An animal cell has a nucleus at the centre while the plant cell has a nucleus on the periphery.
5. A plant cell has a cell wall (and plasma membrane) while the animal cell has a plasma membrane.
6. Plant cell contains centrally placed vacuoles while the animal cell has smaller scattered vacuoles.
7. Plant cell cytokinesis occurs by cell plate formation method while that of an animal cell by furrowing.
8. The animal cell has centrioles while the plant cell has centrioles in lower plants only. (None in higher plants)
9. Plant cells have chloroplast for photosynthesis while animal cells do not have chloroplast.
10. The mode of nutrition of plant cells is autotrophs while that of animal cells is heterotrophs.

Similarities between plant and animal cells

1. Both have cytoplasm.
2. Both are eukaryotic cells.
3. Both have plasma membranes for the regulation of substance movement.
4. Both have nucleus.
5. Both contain Golgi apparatus.

5. State and describe the role of ATP in cells

ATP or Adenosine 5’-triphosphate is the principal molecule for storing and transporting energy in cells. It is the energy that is
produced when a cell goes through respiration.
Glucose + Oxygen —> Carbon Dioxide + Water + Energy (ATP)
C6H12O6 + 6O2 —> 6CO2 + 6H2O + Energy (ATP)

6. Outline key structural features of a prokaryotic cell as found in a typical bacterium

The features of a prokaryotic cell as found in a typical bacterium, include:

 - Unicellular.
- 1-5 µm diameter.
- Peptidoglycan cell walls.
- Circular DNA.
- 70s ribosomes.
- Absence of organelles surrounded by double membranes.

Prokaryotic (Bacteria)
- No nucleus.
- DNA is circular and lies free in the cytoplasm, naked.
- Small loops DNA (Plasmids) free in cytoplasm.
- No membrane bound organelles.
- Infolding of membrane (mesosome) or thylakoids in some.
- Smaller ribosomes (70s), no ER (Endoplasmic reticulum).
- Cell wall made of peptidoglycan. (Polysaccharides + protein).
- Capsule: Layer of polysaccharide (sometimes proteins) protects the bacteria cell and is often associated with pathogenic
bacteria.
- Size = 1 - 5 µm. Smallest = approximately 0.1 µm.

Eukaryotes
- Nucleus surrounded by an envelope.
- Contains DNA.
- DNA is not circular, associated with proteins, forming chromosomes.
- Complex cell with many organelles - double membrane (e.g nucleus) or single membrane (e.g lysosomes).
- Bigger ribosomes (80s), ER (Endoplasmic reticulum) present.
- Plants (cellulose) and fungi (chitin) have cell walls.
- No capsule.
- Size = 10 - 100 µm.

8. State that all viruses are non-cellular structures with a nucleic acid core (either DNA or RNA) and a capsid made of protein
and that some viruses have an outer envelope made of phospholipids

Viruses are acellular (they are not cells [non-living]) they lack some of the essential life characteristics.

Virus structure
- The shape of a virus particle shows considerable variation between the different types of virus but they all tend to be very
symmetrical (They are also very very small, i.e the smallest bacteria would be similar to the largest virus (approx 0.1 µm =
largest virus/smallest bacteria).
- The protein coat or capsid is made up of individual protein molecules called capsomeres.
- Viruses that contain RNA rather than DNA are known as retroviruses. E.g HIV.
Virus reproduction
- Every virus that we have discovered to date causes diseases. They are parasitic in that they can only carry out life functions
when they inhabit a host cell.
- Virus particles reproduce using the host cell DNA to synthesise the proteins needed to produce new virus particles.
- Eventually so many copies of the virus are made it causes the cell membrane to burst, huge numbers of virus are released
into the surrounding tissue fluid (+ toxins in some cases) and the cell dies.

Viral diseases
- Common viral infections include colds, flu, chicken pox, measles, Rubella (German measles), mumps, some forms of
tonsillitis, hepatitis A and hepatitis B.
- Antibiotics are ineffective against viral diseases - they only attack bacteria.
- Many viral diseases get better on their own - our bodies' immune system will eventually eradicate them. We may be given
other medication to ease the discomfort or symptoms of the disease but this isn’t a cure.

Viral disease treatments

- Antiviral drugs are available but they are usually reserved for the most serious of viral infections to avoid the issue of drug
resistance (virus may adapt and form resistance).
- Antiviral medications work by inhibiting the production of virus particles. Some interfere with the production of viral DNA,
others prevent viruses from entering host cells.
CELL MEMBRANES AND TRANSPORT
1. Describe the fluid mosaic model of membrane structure with reference to the hydrophobic and hydrophilic interactions
that account for the formation of the phospholipid bilayer and the arrangement of proteins.
2. describe the arrangement of cholesterol, glycolipids and glycoproteins in cell surface membranes
3. describe the roles of phospholipids, cholesterol, glycolipids, proteins and glycoproteins in cell surface membranes, with
reference to stability, fluidity, permeability, transport (carrier proteins and channel proteins), cell signalling (cell surface
receptors) and cell recognition (cell surface antigens – Ch.11)

Function of the cell surface membrane

The function of the cell membranes is to control the exchange of substances required for normal metabolic activity - such as the
nutrients required and the waste products produced, between the cell and its environment.

A similar principle applies to movement of materials within a cell in and out of the various organelles. By compartmentalising, the
organelles provide optimum conditions for the vast range of reactions occurring in a cell and act as a barrier to other substances
e.g pH may differ in/outside.

Membranes also have receptors which allows them to respond to hormone messages and other aspects of cell signalling.

The diagram of the cell membrane is called the ‘Fluid Mosaic Model’. It is fluid due to the fact that the membrane can move
(flexible) and that the components are able to move along the membrane. It is also a mosaic as it is made up of many different
components, like a mosaic art piece.

Diagram of fluid mosaic model of membrane structure

Roles of the components of cell membranes
Phospholipids - Acts as a barrier to most water-soluble substances/some phospholipids can be modified chemically to act as
signalling molecules. The phospholipid bilayer is approximately 10 nm in thickness. The phospholipid bilayer is what determines
the permeability of the membrane. The phospholipid bilayer is made up of hydrophilic phosphate heads and hydrophobic lipid tails.
Due to this opposing nature of the bilayer it only allows small nonpolar (not charged) molecules through, without the aid of a

protein channel. Controls permeability.

Cholesterol - At low temperatures, cholesterol increases the fluidity of the membrane, preventing it from becoming too rigid.
Cholesterol is also important for the mechanical stability of membranes.
Glycolipids and glycoproteins - The carbohydrate chains attached to glycoproteins and glycolipids help them act as receptor
molecules, which bind with particular substances at the cell surface. These chains also help form hydrogen bonds with water
(which helps to stabilise the membrane) and form a sugary coating known as the glycocalyx. In animals, this is mainly
glycoproteins, in plants it’s mainly glycolipids.
Some glycolipids and glycoproteins act as cell markers or antigens, allowing cell to cell recognition/signalling. Furthermore when
the receptor and messenger molecules bind it triggers a series of cellular reactions.
A second group of receptors bind to the molecules on surfaces that are going to be engulfed by the cell surface membrane by
endocytosis.
Glycolipid = to antigen
Glycoprotein = to receptor

A third group of receptors are involved in cell adhesion, in animal organs and tissues. The glycolipids and glycoproteins act as cell
markers or antigens which allow cell to cell recognition. Each cell type has a unique antigen e.g the different antigens found on
erythrocytes to indicate A, B or AB blood groups (groups O doesn’t have the antigens)
Proteins - Many proteins in the matrix act as transport proteins. These provide hydrophilic channels or passageways for ions and
polar molecules to pass through the membrane. There are two types of transport protein: Channel proteins and Carrier proteins.
Each transport protein is specific for a particular kind of ion or molecule. Therefore the types of substances that enter or leave the
cell can be controlled.

Other proteins in the cell surface membrane or organelle membranes may be enzymes e.g ATPas on the inner cristae of
mitochondria.

Some of the proteins on the inside of the cell membrane are attached to the cell cytoskeleton - a series of protein filaments which
help maintain cell shape and are thought to help shape changes when cells move.

Cell Membrane Structure and Functions

- All organisms generally have a similar structure of cell membrane (also called plasma membranes).
- Membranes are composed of lipids, proteins and carbohydrates.
- The fluid mosaic model, proposed in 1972 is the most accepted model for understanding the structure of a cell membrane.
- According to this model, the membrane is made up of a phospholipid bilayer where the protein molecules are scattered in
the bilayer.
- The phospholipid molecule is made up of a phospholipid head and a phospholipid tail. The bilayer is made up of phosphate
heads (Hydrophilic and Polar) and Fatty acid/lipid tails (Hydrophobic and nonpolar).
- Some protein molecules have carbohydrates attached to them and are called glycoproteins.
- Some lipids also have carbohydrate chains attached to them and are called glycolipids.
- The cell membranes are selectively permeable i.e allowing only certain molecules to pass through them.
- Some membrane proteins, also called carrier proteins, span the cell membrane and allow passage of some molecules.
- Cholesterol is a lipid that is found in the cell membrane.
4. Outline the main stages in the process of cell signalling leading to specific responses: • secretion of specific chemicals
(ligands) from cells • transport of ligands to target cells • binding of ligands to cell surface receptors on target cells.

Cell Signalling
Cell signalling is the molecular mechanism by which cells detect and respond to external stimuli e.g changes in their external
environment.
It allows communication and coordinated responses between different groups of cells in different parts of the body.
Signal pathways can be electrical (nervous system) or chemical (e.g Hormones).
Conversion of the original signal to a message that is then transmitted is called transduction.
Transmitting the message involves crossing barriers such as cell surface membranes. Signalling molecules are usually very small
for easy transport.
The cell surface membrane is a critical component of most signalling pathways because it is a barrier to the movement of
molecules and so controls what moves between the internal and external environments of the cell.

Ligand
A ligand is defined as any molecule or atom that reversibly binds to a receiving protein molecule,
otherwise known as a receptor.
When a ligand binds to its respective receptor, the shape and or activity of the ligand is altered to
initiate several different types of cellular responses. E.g they have roles in growth and
metabolism amongst many others.

Ligands are usually relatively small molecules and need a means of getting to their target cells - for
hormones, this is the blood stream.
It will bind to the cell surface receptor protein on target cells.
Any receptor has some degree of specificity towards one (or a few) ligands to bind to their ligand-binding region.
Ligand-activated receptors can be mostly found on the surface of the cell but there are some at various locations inside the cell
which are involved in different signalling pathways.
Usually, ligand binding causes a shape/conformation change in the receptor protein it’s binding with. This may activate another
pathway, or trigger the release of another ligand, to carry the message to other receptors - this is called transduction, the signal
has been converted from one method of transmission to another.

Glucagon
Glucagon is an example of a ligand.
It’s a hormone produced by the pancreas in response to a drop in blood glucose levels (i.e this is the stimulus). So it causes a
cascade reaction/chain in order to combat the drop in blood glucose.

G proteins and signal cascades

A G protein acts as a switch and causes the release of numerous
‘second messenger’ molecules which diffuse through the cell
cytoplasm.
(Called G because it binds with GTP i.e guanine instead of adenine
in ATP).
This amplifies (magnifies) the original signal
(impulse/stimulus/input).
G proteins often cause the release of an enzyme. Which then
causes the release of another. Which causes the release of
another and the signal is amplified each time until the final
enzyme is released which brings about the required action of the
cell e.g a change in metabolism.
This is known as a signal cascade.

Other ways a receptor can alter cell activity

- They may cause the opening of an ion channel and so cause a change in membrane potential.
- They can act directly as membrane bound receptors e.g the Glucagon receptor.
- They can act as an intracellular receptor - the initial signal molecule passes straight through the cell surface membrane
and binds with a receptor in the interior of the cell. e.g Hydrophobic steroid hormones like oestrogen pass through both
the cell surface and nuclear membrane and bind with a receptor in the nucleus.
Direct (cell to cell) contact is another method of cell signalling. E.g white blood cells detecting foreign antigens on other cells.

Nuclear receptors
Nuclear hormone receptors can be activated by other lipid-soluble molecules e.g thyroid hormones and vitamin D.
Each of these ligands can easily cross the plasma membrane something most of the other intracellular messengers can’t do.
When a ligand binds to a nuclear receptor, the receptor changes shape and this prevents the ligand from breaking away. The newly
formed receptor-ligand complex (similar to enzyme and active site complex but with ligands and receptors) can then bind to
specific DNA sequences known as hormone response elements (HREs).

How ligands aid the control of reactions

The ability of a ligand to activate a protein for a short amount of time and then be released and recycled allows control of many
biochemical cellular reactions.
The amount of time a ligand spends attached to its receptor is due to the affinity between the ligand and the protein.
If there is a high affinity, the ligand will tend to stick to the protein and modify its function for longer.
If the ligand has a low affinity for the protein, it will be less likely to bond in the first place and will release from the receptor
faster.

Ligand affinity
The affinity of a ligand for a particular protein is determined entirely by the amino acids exposed at the binding site.
The amino acids will match the ligand in terms of electrical activity. If the ligand is positively charged, the binding site should be
negatively charged. This creates the strongest interaction. (opposites attract)
In this way, proteins can obtain a certain degree of specificity for a ligand.

Interference with protein-ligand binding

While ligand binding processes are the basis of how cells can differentiate between different molecules, it can also cause huge
problems.
Many substances are poisonous or toxic because of their ability to interfere with the protein-ligand binding process.
Either the toxin directly binds to the protein itself, because it has a higher affinity, or the toxin otherwise prevents the normal
bonding of a ligand to its target protein. E.g Carbon monoxide binds irreversibly with the proteins that facilitate oxygen’s entry
into a cell - it has a greater affinity than oxygen for those proteins.

Some ligands have been developed which prevent the entry of heavy metals into cells. E.g BAL has been used to treat mercury
poisoning for a number of years.
Others are being developed to suppress proteins associated with cancer tumour growth.

5. Describe and explain the processes of: simple diffusion, facilitated diffusion, osmosis, active transport, endocytosis and
exocytosis.

There are four basic mechanisms in which some materials/substances are able to enter and leave the cell they are:
1. Diffusion and Facilitated Diffusion
2. Osmosis
3. Active transport
4. Bulk transport

Diffusion
Diffusion is the net movement of molecules (or ions) from a region of high concentration to a region of lower concentration.
The molecules move down a concentration gradient.
Molecules have kinetic energy, which makes them move about randomly. As a result of diffusion molecules reach an equilibrium
where they are evenly spread out. This is when there is no net movement of molecules from either side.
Diffusion is a passive process which means that no energy is used, the molecules
have a natural kinetic energy.
Determinants of the rate of diffusion: There are 4 factors
1. Steepness of the concentration gradient. The bigger the difference between the two sides of the membrane the quicker
the rate of diffusion.
2. Temperature. Higher temperatures give molecules or ions more kinetic energy. Molecules move around faster, so diffusion
is faster.
3. Surface area. The greater the surface area the faster the diffusion can take place. This is because more molecules or ions
can cross the membrane at any one moment.
4. Type of molecule or ion diffusing. Large molecules need more energy to get them to move so they tend to diffuse more
slowly. Non-polar molecules diffuse more easily than polar molecules because they are soluble in nonpolar phospholipid
tails.

Molecules that diffuse through cell membranes

1. Oxygen - Nonpolar so diffuses very quickly.
2. Carbon dioxide - Polar but very small so diffuses quickly.
3. Water - Polar but also very small so diffuses.

Facilitated Diffusion
- Large polar molecules such as glucose and amino acids, cannot diffuse across
the phospholipid bilayer. Also ions such as Na + or Cl - cannot pass.
- These molecules pass through protein channels instead. Diffusion through these
channels is called facilitated diffusion.
- Movement of molecules is still passive, just like ordinary diffusion, the only
difference is, the molecule goes through a protein channel instead of passing
between the phospholipids.
The molecules move through the protein channel passively. The molecules move from an area of high concentration to an area of
low concentration.

Carrier Proteins
Carrier proteins do not extend through the membrane. They bond and drag molecules through
the bilayer and release them on the opposite side. Uses energy, it’s active transport.

Cotransport also uses the process of diffusion. In this case a molecule that is moving naturally
into the cell through diffusion is used to drag another molecule into the cell. E.g in example
Glucose hitches a ride with sodium.

Osmosis
Osmosis is the diffusion of water from an area of high concentration of water molecules (high water potential) to an area of low
concentration of water (low water potential) across a partially permeable membrane.
Osmosis and red blood cells Osmosis in plant cells

Water potential
- Symbol 𝞇, measured in kPa.
- For pure water: 𝞇 = 0
- Adding solute to water lowers its water potential (i.e makes it more negative). Achieving pure water is very difficult, due to
particles/impurities automatically diffusing in.
- Applying more or less pressure to a solution changes its water potential.
- 𝞇p = pressure potential 𝞇s = solute potential 𝞇 = psi
- For a flaccid cell, 𝞇p = 0
- Overall equation : 𝞇 = 𝞇p + 𝞇s

Active Transport
Transport of sucrose and hydrogen ions.

How different molecules cross the membrane

Bulk Transport/Vesicle-mediated transport

Vesicles and vacuoles that fuse with the cell membrane may be utilised to release or transport chemicals out of the cell or to allow
them to enter a cell. (Bulk transport)

Endocytosis and Exocytosis Bulk transport

Endocytosis
The cell membrane can engulf structures that are much too large to fit through the pores in the membrane proteins, this process
is known as endocytosis. In this process the membrane itself wraps around the particle and pinches off a vesicle inside the cell.
Endocytosis is the case when a molecule causes the cell membrane to bulge inward, forming a vesicle.
Phagocytosis is the type of endocytosis where an entire cell or solid material is
engulfed.
Pinocytosis is when the external fluid is engulfed. Receptor mediated
endocytosis occurs when the material to be transported binds to certain
specific molecules in the membrane. Examples include the transport of insulin
and cholesterol into animal cells.

Exocytosis
Exocytosis is the opposite of endocytosis. Large molecules that are
manufactured in the cell are released through the cell membrane.

6. Explain the movement of water between cells and solutions in terms of water potential and explain the different effects of
the movement of water on plant cells and animal cells (knowledge of solute potential and pressure potential is not expected)

Osmosis, water potential and tonicity.

- Osmosis is the diffusion of water across a semi-permeable or partially permeable membrane.

- Water moves from an area of high water potential 𝞇 (low solute concentration) to an area of low water potential (higher solute
concentration) down a water potential gradient.
- This will occur until equilibrium has been reached.

- Depending on the condition of the extracellular environment, different things can happen to the cell.:
- If the cell is exposed to an isotonic environment (same concentration inside and outside the cell), the movement of water into
and out of the cell occurs at the same rate i.e no overall/net change.
- If the cell is exposed to a hypertonic environment (outside of the cell has a lower water potential [higher solute concentration]
than inside), the cell will shrivel or crenelate because of loss of water.
- If the cell is exposed to a hypotonic environment (inside the cell has lower water potential [higher solute concentration than
outside]), the cell will take up more water and become bloated and will eventually burst/lyse - if it is an animal cell.
Plant cells do not burst/lyse due to their cell wall - high turgor pressure against cell walls provides vital support for plant tissues.
E.g stems and leaves.

- A solution has a High water potential when water has few particles dissolved in it. (Pure water has the highest at 0,
solutions have a lower, negative value).
- A solution has a Low water potential when water has many particles dissolved in it. (Sea water has a low water potential as
it has various salts and ions dissolved in it).
- A weak/dilute solution is a hypotonic solution.
- A strong/concentrated solution is a hypertonic solution.
- 2 solutions with the same concentration are called isotonic solutions.

Water potential is represented by the Greek symbol 𝞇 psi. This shows the difference between the potential of water in a cell and
the potential of pure water at the same temperature and pressure.
It is demonstrated as a force acting on water molecules in a cell (or solution) separated from pure water by a membrane that is
permeable to water molecules only.
It’s expressed as the sum of the solute potential and the pressure potential by the equation: 𝞇 = 𝞇s + 𝞇p
Water potential is measured in kilopascals (kPa).
Biological Molecules

1. Explain how hydrogen bonding occurs between water molecules and relate the properties of water to its roles in living
organisms, limited to solvent action, high specific heat capacity and latent heat of vaporisation.

The structure of water (H2O)

- 2 atoms of hydrogen covalently bonded with oxygen.
- Water is a polar molecule. The electrons aren’t evenly distributed across the molecule (hydrogen
ends slightly positive, oxygen ends slightly negative.)
- Attraction between these charges forms hydrogen bonds between water molecules.

The structure of water gives it, its properties:

- High heat capacity.
- Large latent heat of vaporisation.
- Strong cohesion between water molecules.
- An important solvent.
- A metabolite in many metabolic reactions.

High Heat Capacity

The heat needed to raise the temperature of 1kg of water by 1 oC is termed the specific heat capacity.
Water has a large specific heat capacity. Which means that it can absorb large amounts of heat energy before its temperature
raises a significant amount.

Importance to living organisms?

The bodies of living organisms are mostly made of water. This water in and around our cells absorbs a lot of heat energy without its
temperature increasing much. The water ‘buffers’ the heat changes.
The importance of this high heat capacity for aquatic organisms is the idea of how large bodies of water, like seas or lakes, do not
change temperature quickly. Helping them to have a stable temperature environment.

Large latent heat of vaporisation

In a body of water some molecules of water are moving at faster speeds (have higher kinetic energy). Some have enough kinetic
energy to escape the water, moving into the air, this is called evaporation.
When these molecules evaporate their energy goes with them, leading to the average kinetic energy of the water to decrease. This
means that the water cools down. The energy that is lost is called the latent heat of vaporisation.

Importance to living organisms?

Animals that are able to sweat can keep cool as the water in sweat evaporates off the surface of the animal.
Plants are also cooled when water evaporates from their leaves.

Strong cohesion between water molecules

Due to their polarity (charges), water molecules are attracted to each other, and form hydrogen bonds.
These hydrogen bonds help hold water together, so they can flow as a continuous stream. This is known as mass flow.
Importance to living organisms?
In plants, water moves up the xylem vessels as a continuous stream. This allows water to move from the roots to the top of the
tallest tress.
Water cohesion leads to ‘surface tension’, making water behave as if there is a skin where the water meets the air. This allows
small animals to live on the surface of water bodies. (Water walking, JESUS???).

An important solvent
A solvent is a liquid that other substances (called solutes) can dissolve in. The positive and negative charges of water attract other
molecules causing them to separate from each other - dissolve.
When substances are dissolved in water they are free to move around and react with other molecules.

Importance to living organisms?

The metabolic reactions that happen inside all living organisms can only happen when the reactants are dissolved in water.
Substances being dissolved in water also allows them to be transported around the bodies of living organisms. E.g glucose, CO2,
urea in blood plasma, also mineral ions and sugars dissolved in water are transported in xylem and phloem in plants.

A metabolite
Water molecules can also be involved in chemical reactions directly.

Importance in living organisms?

Hydrolysis reactions are important in digestion of larger molecules in
animals.
Condensation reactions are important in synthesis of important molecules
such as proteins in living organisms.

Transparency
“Pure” water is transparent. It allows light to pass through, so objects can be seen clearly.
This is a vital property for aquatic plants who need light to photosynthesis. (Different plants may utilise different photosynthetic
pigments at different depths in order to maintain their ability to absorb different light wavelengths.)
The ability to see through water is a necessity for both aquatic predators and prey and often requires adaptations to deal with the
aquatic medium rather than air.

Many aquatic animals display countershading. They are coloured to maximise their ability not to be seen. E.g Sharks are dark above
and light below.

2. Describe and draw the ring forms of α-glucose and β-glucose

- Carbohydrates only contain 3 elements. Carbon, hydrogen and oxygen.
- The ratio of hydrogen to oxygen is, with a few exceptions, the same as water. 2:1.
- They are the most abundant class of biomolecules and in animals their main function is to act as an easily accessible
source of energy.
- They have this role in plants as well, but here they also have an important structural function.
 - Carbohydrates include sugars, starch, cellulose and glycogen.
- Monosaccharides are the simplest carbohydrates. They literally mean “single sugar”, they have the general formula
(CH2O)n with the n = number of carbon atoms. This can vary from 3-7 but 6 is the most common giving 6 carbon atom
sugars or hexose sugars.
- Glucose is the most abundant hexose and so has the formula C6H12O6. However this formula gives no information as to how
these atoms are arranged in 3D.
- This is shown by the structural formula which displays the ring-like structure of glucose clearly.
- Glucose exists in 2 forms. “Alpha” and “Beta”
- The alpha and beta differ in the right OH and H groups. With the H group of the alpha being above and the OH group
below. And the beta being the opposite with the OH group above and the H group below.

3. Define the terms monomer, polymer, macromolecule, mono-, di- and polysaccharide

Monomer - A monomer is a molecule of any class of compounds that can react to form polymers. A monomer is a molecule
(usually organic) that is able to link up to form a variety of polymers. E.g Glucose.

Polymer - A polymer is a molecule made up of 2 or more monomers. They have different functions depending on what monomers
make them up. E.g Cellulose.

Macromolecule - A Macromolecule is a very large molecule, usually with a diameter ranging from about 0.01 to 1µm.

Monosaccharide - A monosaccharide is the simplest sugar molecule. Such as glucose or fructose.

Disaccharide - A disaccharide is the second simplest kind of sugar molecule, it consists of 2 monosaccharides joined together
usually via an oxygen atom and by condensation reactions.
Polysaccharide - Polysaccharides are the most complex of sugars, they consist of many monosaccharides joined together in chains
or links.

Formula of sugars
- Most of the sugars (hexose etc) share the same chemical formula, but differ in their molecular structure and so are termed
isomers.
- The different structures do give slightly different properties for the isomers.
- All monosaccharides are soluble, taste sweet and form crystals.

- Additionally Glucose is so small that it can pass through the villi of our intestine and the capillaries into our bloodstream.
These molecules subsequently release energy as a result of aerobic respiration.

Disaccharides

4. state that glucose, fructose and maltose are reducing sugars and that sucrose is a non-reducing sugar

Reducing sugars have free aldehyde or ketone groups.

Whereas non-reducing sugars don’t have free aldehyde or ketone groups.

Glucose, fructose and maltose are reducing sugars and sucrose is a non-reducing sugar.

5. describe the formation of a glycosidic bond by condensation, with reference to disaccharides, including sucrose, and
polysaccharides

The process of joining 2 monomers together is one of condensation involving the loss of water, forming a glycosidic link.
This link is normally between C1 (Carbon 1) of one monomer and C4 (Carbon 4) of the other and is so called a 1-4 glycosidic bond.
The general formula of a disaccharide is C12H22O11 but again there are different isomers with this formula.
E.g

6. describe the breakage of a glycosidic bond in polysaccharides and disaccharides by hydrolysis, with reference to the non-
reducing sugar test

The reverse of this condensation reaction is the addition of water and is known as hydrolysis.
This takes place during the digestion of disaccharides and polysaccharides when they are broken back down to monosaccharides.
Like most chemical reactions that occur in cells both types of reaction are controlled by enzymes.

Benedict’s test
Benedict’s test is used to determine if the sugar sample is non-reducing or reducing in nature. If Benedict’s solution is added to the
sugar sample and we see no change in the colour, then the sugar sample is a non-reducing sugar. If we see a change in the colour
of the sugar sample then it is a reducing sugar.

Blue = No reducing sugars present in the sample.

Green = Traces of reducing sugar present in the sample.
Yellow = Low amounts of reducing sugars present in the sample.
Orange = Moderate amount of reducing sugars present in the sample.
Red = High amounts of reducing sugars present in the sample.
7. describe the molecular structure of the polysaccharides starch (amylose and amylopectin) and glycogen and relate their
structures to their functions in living organisms

Starch
The polysaccharide starch has two types: Amylose and Amylopectin.

Amylose makes up about 25 - 30% of starch and Amylopectin makes up 70 - 75% of starch.
Amylose is made from many thousands of alpha glucose monomers. It is a linear molecule which forms a helix as a result of the
angle of the alpha 1,4 glycosidic bonds. Every turn of the amylose helix requires six alpha glucose molecules.

Amylopectin consists of the same 1,4 linked glucose monomers as amylose with occasional 1,6 glycosidic bonds which provide
branching points around every 24 - 39 glucose residues. This branching allows many millions of glucose molecules to be stored in a
compact form.

Glycogen
Glycogen, like starch, is a branched polysaccharide. It is chemically similar to amylopectin, being composed of alpha glucose
molecules, but there are more alpha 1,6 glycosidic links mixed with alpha 1,4 links. This makes it more highly branched and more
water soluble than starch. Glycogen is a storage compound in animal tissues and is found mainly in liver and muscle cells. It is
readily hydrolysed by enzymes to form glucose making it an ideal energy storage molecule for active animals.

Glycogen is more soluble than starch and thus is better for animals as they are more active and require energy to be produced
faster.

Glycogen = Animals
Starch = Plants

8. describe the molecular structure of the polysaccharide cellulose and outline how the arrangement of cellulose molecules
contributes to the function of plant cell walls

Cellulose is an unbranched polymer of beta glucose molecules bonded by extremely stable beta 1,4 glycosidic bonds. The
unbranched structure of cellulose produces parallel chains which become cross linked with hydrogen bonds to form strong
microfibrils.

The microfibrils consist of between 40-70 cellulose chains joined by hydrogen bonds.

Cell walls are made from cellulose microfibrils. They provide the cell with strength and rigidity.
9. state that triglycerides are nonpolar hydrophobic molecules and describe the molecular structure of triglycerides with
reference to fatty acids (saturated and unsaturated), glycerol and the formation of ester bonds
10. relate the molecular structure of triglycerides to their functions in living organisms
11. describe the molecular structure of phospholipids with reference to their hydrophilic (polar) phosphate heads &
hydrophobic (non-polar) fatty acid tails

Lipid Presentation - James and Adam

Triglycerides
Triglycerides are the most common lipids. They are nonpolar hydrophobic molecules. A glyceride is an ester formed by a fatty acid
combining with the alcohol glycerol. The three ester bonds have a condensation reaction (it has OH [Hydroxyl] groups) with the
fatty acid tails resulting in the formation of Triglycerides. The tail varies in length depending on the fatty acids used.
Triglycerides aren’t water soluble however they can be hydrolysed by acid and heat.
- Triglycerides don’t have a hydrophilic portion.

Fatty Acids
Fatty acids are made up of a series of acids and can sometimes be found in lipids. They contain the hydroxyl group -COOH. The
larger molecules in the series have long hydrocarbon chains attached to the acid head of the molecule.

Saturated
A fatty acid is saturated if it does contain the
highest possible amount of hydrogen. Meaning
that there are no double carbon bonds. Animal
lipids are often saturated and occur as fats.

Unsaturated
A fatty acid is unsaturated if it doesn’t contain
the highest possible amount of hydrogen. This
is due to the double carbon bonds. An unsaturated fatty acid/lipid melts more easily due to the double bond. Most oils are
unsaturated. There are two kinds of unsaturated fatty acids, polyunsaturated (more than one double bond) and monounsaturated
(only one double bond). Plant lipids are often unsaturated and occur as oils.

Esters
Esters are chemicals that are formed when an acid and an alcohol react
together. Alcohols contain a hydroxyl group -OH, which is attached to a
carbon atom.
Ester bonds or ester linkages are a chemical link between the acid and
the alcohol.

Glycerol
Glycerol is seen in biological systems as an intermediate in carbohydrate
and lipid metabolism because surplus carbohydrate can be converted
into long chain fatty acids and esterified with the three hydroxyl groups.
Glycerol is essentially the medium between carbohydrates and lipids.

Triglyceride - Relation between structure and function

Triglycerides are excellent long term energy storage molecules because they are not soluble in water and so don’t break down
when mixed with water. They are also able to be consumed and broken down into energy. They are made of a glycerol backbone
with 3 fatty acid chains.

Fatty acid Phospholipids

Phospholipid molecules contain two hydrophobic tails of fatty acids and one hydrophilic head of phosphate, joined together by an
alcohol or glycerol molecule.
The opposing polarity of the hydrophobic and hydrophilic parts allow only non polar or very small and polar molecules to pass
through.

12. describe and draw the general structure of an amino acid and the formation and breakage of a peptide bond

An amino acid consists of the: Amine group, R group (represents a range of different groups), carboxyl group and hydrogen.
Like carbohydrates and lipids, proteins contain the elements carbon, hydrogen and oxygen, but in addition they also always
contain nitrogen.

The building blocks of protein are 20 amino acids. ‘R’ on the molecule represents ‘the rest’ and includes groups such as -CH3 and -
C2H5, but the simplest is just an H forming the amino acid glycine. E.g if it is -CH3 then the amino acid is alanine.

Some amino acids also contain sulphur e.g in cysteine the R is CH2SH.
Phosphorus is another common component of protein molecules and haemoglobin (one of the most important protein molecules
in our bodies) which also holds an iron based haem group between protein molecules.

Although there are over 100 naturally occuring amino acids only 20 are used in the biosynthesis of proteins.
8 of these amino acids are called essential and must be included in our diet as we cannot synthesise them.
Amino acids join to form proteins in a similar way to monosaccharides forming polysaccharides.
The first step in this involves the union of 2 amino acids.
A reaction occurs between the amino group of one amino acid and the carboxyl group of the other forming a “PEPTIDE” link or
bond, forming a “DIPEPTIDE” molecule. This is done through a condensation reaction.
Further condensation reactions lead to the addition of more and more amino acids resulting in the formation of a long chain called
a “POLYPEPTIDE”.
A polypeptide may form a protein on its own or it may associate with other polypeptides to form a functioning protein molecule.

The peptide bond can be broken through hydrolysis reactions (adding water).

13. explain the meaning of the terms primary structure, secondary structure, tertiary structure and quaternary structure of
proteins.

There are 4 levels of organisation involved in the structure of protein molecules:

1. Primary structure
This is the simple chain-like sequence of amino acids in a polypeptide or protein molecule.

2. Secondary structure
The chain of amino acids often folds or curls on itself.

Alpha helix (α-helix)

Many polypeptides coil into a regular 3D shape called an alpha helix, held in shape by hydrogen bonds between various
amino acids. The function of the alpha helix is to help maintain the shape of the molecule. This shape is a more stable and
robust structure than a straight, untwisted polypeptide chain would be. Alpha helices are found in proteins such as
enzymes and antibodies where the precise 3D shape and surface contours is an important feature of the molecule.

The protein above only displays a secondary structure as the simple α-helix polypeptides do not undergo further folding.
This is the structure of a fibrous protein. It is made of 3 α-helix polypeptides twisted together.

Beta pleated sheets/strand (ꞵ-pleated sheets)

These are formed when hydrogen bonding between parallel chains results in a flat structure which becomes folded. They
occur less frequently than alpha helices but still give strength to the protein molecule. E.g silk
3. Tertiary structure
A polypeptide chain sometimes folds around on itself to form a complex 3D shape. This is called the tertiary structure of a
protein.
Again, various bonds between amino acids at different points in the chain help to hold it in its particular 3D shape.

Hydrogen bonds are not the only bonds involved in keeping the particular shape of a protein molecule. Other bonds
involved include ionic bonds, disulphide bonds and hydrophobic interactions.

The tertiary structure of a polypeptide is maintained by different bonds when it’s folded into a precise shape.
The bonds that hold these ‘bends’ and ‘tucks’ in a permanent shape include:
- Disulphide bridges (covalent sulphur-sulphur bonds)
- Hydrogen bonds
- Ionic bonds
Specific contours of proteins have extremely significant roles in life processes.

4. Quaternary Structure
A quaternary structure occurs when a protein is made
of two or more polypeptides. It refers to the way these
polypeptides are arranged to form a biologically active
protein e.g haemoglobin has 2 α polypeptide chains
and 2 ꞵ polypeptide chains. Each of these fold around
one of the four iron haem groups needed to transport
oxygen.
 The haem group is essential for the protein to carry out its function - such groups are referred to as prosthetic groups.
The haemoglobin molecule is an example of globular protein.

14. describe the types of interaction that hold protein molecules in shape:hydrophobic interactions, hydrogen bonding, ionic
bonding, covalent bonding and disulfide bonds

There are many types of interactions or bonds that hold protein molecules in shape. They are:

Hydrophobic interactions:
- Hydrophobic interactions describe the relations between water and hydrophobes (low water-soluble molecules).
Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules.
- Hydrophobic interactions occur between 2 or more nonpolar molecules when they’re in polar environments (most
commonly water). Due to their hydrophobic nature the molecules stick together or fold in a certain way (as to “stay away”
from the water) and in order to interact with the polar environment as little as possible.

Hydrogen bonding:
- Hydrogen bonding is a special type of dipole-dipole attraction between molecules, not a covalent bond to a hydrogen
atom. It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom
such as N, O, or F atom and another very electronegative atom.
- Most often hydrogen bonds are formed between adjacent water molecules when the negative end of one water molecule
is attracted to the positive end of another water molecule.
- Hydrogen bonding is an interaction involving a hydrogen atom located between a pair of other atoms having a high affinity
for electrons; such a bond is weaker than an ionic bond or covalent bond but stronger than van der Waals forces.

Ionic bonding:
- Ionic bonding is the type of linkage formed from the electrostatic attraction between oppositely charged ions in a
chemical compound. Such a bond forms when the valence electrons of one atom are transferred permanently to another
atom.
- The passing of electrons from one atom to another makes them ions and makes them attracted to one another.

Covalent bonding:
 - Covalent bonds are the interatomic linkage that results from the sharing of an electron pair between two or more atoms.
The binding arises from the electrostatic attractions of their nuclei for the same electrons.
- The sharing of electrons between the atoms allows them to form full valence shells and become attracted to one another.

Disulfide bonds:
- Disulfide bonds function to stabilise the tertiary and/or quaternary structures of proteins and may be intra-protein
(stabilising the folding of a single polypeptide chain) or inner-protein (multi-subunit proteins such as antibodies or the A
and B chains of insulin).
- The disulfide bond is formed between 2 sulphide atoms bonded covalently. (MORE SHOULD BE ADDED)

15. state that globular proteins are generally soluble and have physiological roles and fibrous proteins are generally insoluble
and have structural roles

The functions of proteins are directly related to its shape. Proteins can be either globular or fibrous.

Globular proteins
- In globular proteins the polypeptide chains are folded to form a more or less spherical
shape. An important class of globular proteins are enzymes, and the polypeptide
chains are folded to form a more or less spherical shape.
- An important class of globular proteins are enzymes, and the functioning of enzymes
is directly related to their shape.
- Globular proteins are also used in the construction of microfilaments and
microtubules which together make up the cytoskeleton. Antibodies are also globular
proteins.
- Globular proteins are usually very soluble in aqueous solutions.
- Globular proteins often have physiological roles by activating or contributing to certain reactions in the body.

Fibrous proteins
- Fibrous proteins are insoluble and consist of long parallel polypeptide chains crossed linked at many points along their
length. Because the chains are not folded by frequently twisted around each other they have a secondary structure.
Keratin is a good example, it’s found in hooves and hair.

- Collagen is also a fibrous protein. It is the most abundant protein in vertebrates, making up a third of their protein mass. It
consists of 3 polypeptide chains coiled round each other in a triple helix. The resulting structure is like a plaited rope and
has great strength. Collagen is found in bones, cartilage, tendons, ligaments, connective tissues and skin.

Uses of proteins
- Liberate energy.
- Cell membrane proteins transport substances across the cell membrane.
- Enzymes catalyse reactions.
- Hormones.
 - Antibodies.
- Structural proteins - collagen.
- Transport proteins - haemoglobin.
- Contractile proteins - actin and myosin in muscle contraction.
- Storage - casein in milk supplies proteins to babies.
- Buffer proteins - keep the pH of plasma constant.

Test for proteins

- Add “Biuret” solution (a mixture of copper sulphate and sodium hydroxide).
- If protein is present the solution turns from a pale blue colour to a violet colour.

16. describe the structure of a molecule of haemoglobin as an example of a globular protein, including the formation of it's
quaternary structure from two alpha (α) chains (α–globin), two beta (β) chains (β–globin) and a haem group. Describe and
explain protein denaturation

Haemoglobin

Each red blood cell contains approximately 270 million haemoglobin molecules.

Structure
The 4 chains have a non-polar hydrophobic section which, when the protein is folded around the haem group, points towards the
centre of the molecule. This helps the molecule keep its 3-D shape.
The chains are folded in such a way so that hydrophilic sections are on the outside of the molecule - this arrangement makes
globular proteins soluble as water is attracted to the polar hydrophilic groups.
The haemoglobin in a sickle cell anaemia sufferer has a hydrophobic non-polar R group on the outside which makes it less soluble.
Enzymes are also examples of globular proteins.
Haemoglobin is the oxygen carrying pigment found in red blood cells. This globular protein consists of four polypeptide chains,
each chain is a globin and there are two alpha and two beta chains. There is a “haem” group in the centre of each chain which
contains an iron atom which can bind reversibly with oxygen. This haem group isn’t part of the amino acid sequence so it is known
as a prosthetic group.

Protein Denaturation

Denaturation involves the breaking of many of the weak bonds (e.g hydrogen bonds), within a protein molecule that are
responsible for the highly ordered structure of the protein in its natural (native) state. Denatured proteins have more random,
looser structures as well as most being insoluble.

The denaturation occurs due to either increased temperature, changes in pH level, adding of heavy metal salts, acids, bases and
protonation of amino acid residues, and exposure to UV light and radiation.

17. relate the structure of haemoglobin to its function, including the importance of iron in the haem group

The iron atom in the haem group is crucial to its function as the iron atom is what binds reversibly with the oxygen atoms. Without
it the haemoglobin wouldn’t be able to carry and transport oxygen so well.

18. describe the structure of a molecule of collagen as an example of a fibrous protein, and the arrangement of collagen
molecules to form collagen fibres
19.relate the structures of collagen molecules and collagen fibres to their function

25% of the mass of most mammals is made up of the insoluble fibrous protein collagen. It’s a vital structural protein found in skin,
bones and blood vessel walls.
Collagen consists of three polypeptide chains, quite loosely wound into a helix to form a rope-like triple helix structure which is
held together by hydrogen and covalent bonds between the adjacent R groups).

About every third amino acid in a collagen molecule is glycine (the smallest amino acid). This allows chains to lie close to each
other and produces the twist at each glycine.

Many collagen molecules lying side by side also make cross links to form fibrils. Fibrils running alongside each other form fibres
which give flexibility and strength.
Enzymes

Basics of Enzymes
- Enzymes are biological catalysts, regulating cell metabolism.
- An enzyme acts on a molecule called the substrate.
- Enzymes are specific for the reactions they catalyse.
- Enzyme activity depends on the enzyme’s shape and its active site (the binding site for the substrate).
- Enzymes are often unnamed for the substrate on which they work, and often include the suffix - ‘ase’ :
- E.g Lipase: breaks down lipids. Amylase: breaks down starch (amylose/amylopectin). Lactase: breaks down milk sugar
(lactose). Cholinesterase: breaks down the neurotransmitter acetylcholine in the nervous system.

1. Describe and explain the globular structure of enzymes

- Ribonuclease S is an enzyme that breaks up RNA molecules.

- The active sites are composed of certain amino acid ‘R’ groups.
- The substrate (in this case, RNA) is drawn into the active site, putting the
substrate molecule under stress, thereby causing the reaction to proceed more
readily.

Enzymes have a globular structure as a result of the interactions among the side chains
of the amino acids. Most often, the hydrophobic acid side chains are buried, closely
packed, in the interior of a globular protein, out of contact with water.

2. State that enzymes function inside and outside the cell

Enzymes function both inside and outside the cell.

Enzymes that function inside the cell naturally don’t break down proteins as proteins are what make up the enzyme. These
enzymes are often created whole and are ready to catalyse reactions.
Whereas enzymes that function outside the cell often break down things like proteins (not all the time). Due to this these enzymes
need to be created and sent out of the cell as incomplete and they join a prosthetic or coenzyme to form a working enzyme (which
due to being outside the cell, cannot harm the cell).

3. Describe the role that enzymes play in metabolic reactions

Enzymes speed up the rate of metabolic reactions by lowering the activation energy. When an enzyme binds to a substrate, it
stresses and destabilises the bonds in the substrate. This reduces the overall energy of the level of substrate transition state. The
reaction rate is the amount of reaction over time.

4. Describe the active site, enzyme-substrate complex and enzyme specificity

Functional Enzyme
- Nearly all enzymes are made of protein, although RNA can also have enzymatic
properties.
- Some enzymes contain only protein.
- Others, called conjugated protein enzymes, require additional components to
complete their catalytic properties.
- They may be permanently attached parts called prosthetic groups, or
temporarily attached non-protein coenzymes, which detach after a reaction
and may then participate with another enzyme in other reactions.

Enzyme-substrate complexes
The enzyme-substrate complex is where the enzyme and the substrate join
together at the active site of the enzyme. It is one of the phases of the
enzyme’s action.
Enzymes will only fit together with particular substrates.

Mechanism of Enzyme Action

- The degree of substrate specificity is determined by the complexity of
the binding sites.
- The wrong substrates won’t fit into the active site.
 - Some enzymes have specificity to a bond type (e.g lipases break up any chain length of lipid).
- Enzymes will catalyse catabolic reactions. I.e molecules are broken down to release energy or anabolic reactions which
synthesise larger molecules from smaller substrates.

5. Describe and explain enzyme effect on

activation energy

Enzymes are catalysts.

Catalysts increase the rate of chemical reactions by:
- Influencing the stability of bonds in the
reactants.
- Providing an alternative reaction pathway;
the binding reactants and enzymes can
weaken bonds in the reactants and allow the
reaction to proceed more easily.

- Enzymes are biological catalysts; they alter

the chemical equilibrium between the
reactant and the product.
- When the substrate attains the required
energy it is able to change into the product or products.

- Catalysts provide an alternative pathway of lower activation energy.

The activation energy is the energy required for the reaction to occur. Enzymes lower the activation energy required for reactions
to occur.

6. Explain the mode of action of enzymes (“lock and key” & “induced fit” models)

Lock and Key hypothesis:

The lock and key hypothesis is analogous (similar/like) with how a key and a lock
would function. The substrate acts like a key and will perfectly fit into an enzyme
which acts like a lock. This creates an enzyme - substrate complex.

Induced fit model:

The induced fit theory is where both the enzyme and the substrate undergoes changes during the enzyme-substrate complex in
order to obtain an optimal fit. It does this due to the enzyme and substrate complex usually never fitting perfectly.

7. Explain the effect of a reversible competitive inhibitor on the rate of enzyme activity at varying substrate concentrations
8. Explain the effect of a reversible non-competitive inhibitor on the rate of enzyme activity at varying substrate
concentrations

Enzyme Inhibition
- Enzyme inhibitors are substances that prevent the normal action of an enzyme and thereby slow the rate of enzyme
controlled reactions.
- Enzyme inhibitors may or may not act reversibly.
- In reversible inhibition, the inhibitor binds temporarily to the enzyme, thereby preventing its function.
- Reversible inhibition is often a means by which enzyme activity is regulated in the functioning cell (it is used intentionally
as a way to regulate the enzyme in the cell).
- In irreversible inhibition, the inhibitor (poison) may bind permanently to the enzyme and cause it to be permanently
deactivated.

Reversible Inhibition
Reversible inhibitors are used to control the activity of enzymes.
- There is often an interaction between the substrate or end product and the enzyme controlling the reaction.
- Buildup of the end product or a lack of substrate may deactivate the enzyme. This deactivation can occur via competitive
or noncompetitive inhibition.
- The inhibitor will unbind.

Competitive inhibitors compete with the substrate for the active site. (i.e they want to fit in there.)
Noncompetitive inhibitors bind to the enzyme, but not at the active site. The substrate can bind but enzyme function is impared.
Allosteric inhibitors are noncompetitive inhibitors that prevent the substrate from binding.

Irreversible Inhibition
Irreversible enzyme inhibitors are poisons that prevent enzyme functions.

Heavy metals: Certain heavy metals bind tightly and permanently to the active sites of enzymes, destroying their catalytic
properties.
- They’re generally non-competitive inhibitors, although an exception is mercury which deactivates papain.
- Heavy metals are retained in the body and lost very slowly.

Competitive Inhibition
- Competitive inhibitors compete with the substrate for the active site, thereby blocking it and preventing its attachment to
the substrate.
- The inhibition is reversible.
E.g : Malonate is a powerful inhibitor of cellular respiration because it is a competitive inhibitor of the enzyme succinate
dehydrogenase in the Krebs cycle, which catalyses the oxidation of succinate to fumarate.

Non-competitive Inhibition
- Non-competitive inhibitors bind to the enzyme, but not at the active site, and alter its shape. The substrate is still able to
bind, but the reaction rate is slowed because the enzyme is less able to perform its function.
- Allosteric enzyme inhibitors are non competitive inhibitors that induce a shape change that alters the active site and
prevents the substrate from binding. (in the example the enzyme ceases to function.)

Effects of pH on enzyme activity

- Like all proteins, enzymes are denatured (made non-functional) by
extremes of pH (acid/alkaline).
- Within these extremes most enzymes are still influenced by pH.
- There is a particular pH for optimum activity for each enzyme. This is
because the active sites of the enzyme can be disabled by the wrong pH
as bonds holding the active site in a particular shape are broken.

Effects of temperature on enzyme activity

- Reactions occur faster at higher temperatures, but the rate of enzyme denaturing
also increases as the temperature increases.
 - High temperatures break the disulfide bonds important for the tertiary structure of the enzyme.
- This destroys the active sites and therefore makes the enzyme non-function.

Effects of enzyme concentration on enzyme activity

- Assuming that the amount of substrate is not limiting (there is unlimited
substrate for the enzyme to use), an increase in enzyme concentration
causes an increase in the reaction rate.
- Cells may increase the amount of enzyme present by increasing the rate of its
synthesis to meet demand.

Effects of substrate concentration on enzyme activity

- Assuming that the amount of enzyme is constant and limiting (there is
not an unlimited amount of enzyme but rather a set amount), an increase in
substrate concentration causes a diminishing increase in the reaction
rate.
- A maximum rate is obtained at a certain substrate concentration where all
enzymes are occupied by substrate. The reaction rate cannot increase
further if the conditions remain the same.

Anabolism
- Anabolism is the build up or synthesis of complex molecules from simpler ones to
make chemicals required by the cell.
- This process requires energy.
- Examples: Protein synthesis - Proteins are assembled from amino acids.
Photosynthesis - Glucose is made from water and carbon dioxide with the input light
energy.
Catabolism
- Catabolism is the breakdown of complex, high energy, molecules into simpler ones
with lower energy.
- This process releases energy, including heat to keep us warm.
- Examples include: Digestion of food - Carbohydrates, proteins and fats are broken
down into their constituent parts for absorption. Cellular respiration - Glucose
molecules are broken down to release energy (as ATP).

Regulation of Metabolism
Metabolic regulation is a term used to describe the process by which metabolic pathways
(both the anabolic/biosynthetic and catabolic/degradative pathways) are regulated in
mammals.

9. Explain that the maximum rate of a reaction (Vmax) is used to derive the Michaelis-Menten constant to compare enzyme
affinities for their substrate

Initial rate of reaction

In evaluating the relative rates of several trials in an experiment, it is very important that we consider the initial rate of the
reaction, because the reaction is always fastest in the beginning because there is;
- Maximum substrate concentration
- Maximum number of active sites are available

Maximal Velocity (Vmax)

- Increasing the substrate concentration indefinitely does not increase the rate of an enzyme-catalysed reaction beyond a
certain point.
- This point is reached when there are enough substrate molecules to completely saturate the enzyme’s active sites. The
maximal velocity, or Vmax, is the rate of the reaction under these conditions.
- Vmax reflects how fast the enzyme can catalyse the reaction.
Michaelis Constant Km
- Enzymes have varying tendencies to bind their substrates (affinities).
- An enzyme’s Km describes the substrate concentration at which half the enzyme’s active sites are occupied by substrate.
- A high Km means a lot of substrate must be present to saturate the enzyme, meaning the enzyme has a low affinity for the
substrate.
- A low Km means only a small amount of substrate is needed to saturate the enzyme, indicating a high affinity for
substrate.

Km and Vmax of some common enzymes

Enzyme Km Vmax

Carbonic anhydrase 8,000 600,000

Chymotrypsin 5,000 100

Penicillinase 50 2,000
 Lysozyme 6 0.5
10. Compare and contrast the effects of immobilisation on enzyme activity

Enzyme affinities
- The rate of enzyme reactions will vary between the enzymes involved but usually it’s around 1,000 substrate molecules
being converted into products per second.
- The maximum rate is reached when all the active sites of the enzyme are occupied by substrate molecules, i.e there are no
free enzymes, they are all involved in enzyme-substrate complexes. This is referred to as the Vmax.
- We can measure Vmax by keeping the enzyme concentration the same and increasing the concentration of the substrate.
In this way we can determine the concentration that will produce the maximum rate of reaction (provided none of the
other conditions are changed).

If you have a reaction where the rate does change:

- You can use a tangent to calculate the rate at any specific moment in time.
- The tangent must only touch one tiny point on the curve/reaction rate line. You can then use the gradient of the tangent
to calculate the reaction rate at that specific moment.

Immobilised Enzymes
- Immobilised enzymes are enzymes physically confined or localised in a
certain defined region of space with retention of their catalytic
activities, and which can be used repeatedly and continuously.
E.g Lactase and how it is used to make lactose free milk.

- Immobilised enzymes are often used because controlling the rate of

reaction is easy, simply controlling the amount of reactants and the
enzyme can only react with that amount.

How Inhibitors affect the enzyme reaction rate.

Nucleic acids and protein synthesis

DNA and RNA basics

DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) are nucleic acids i.e they’re made of nucleotides.
DNA stores the genetic information of an organism, while RNA helps in the process of protein formation.
Both RNA and DNA have a sugar, nitrogenous base and phosphate group.

1. Describe the structure of nucleotides, including the phosphorylated nucleotide ATP (structural formulae are not
expected).

- Nucleic acids such as DNA and RNA are macromolecules (large molecules).
- Nucleic acids are polymers. With their subunits/monomers being nucleotides. Which means that nucleic acids are
polynucleotides.

Nucleotides
- Nucleotides are made up of three key components.
- A nitrogenous base (base containing nitrogen)
- A pentose sugar (5 carbon sugar)
- A phosphate group

Nucleotide structure table

Properties DNA RNA

Pentose sugar Deoxyribose Ribose

Bases - Adenine - Adenine

- Thymine - Uracil
- Guanine - Guanine
- Cytosine - Cytosine

Number of strands Double-stranded (double helix) Single-stranded

ATP
- Adenosine Triphosphate (ATP) is the main energy carrying molecule that provides energy to cells.
- The phosphate groups are what gives ATP the energy.
- ATP is another type of nucleic acid and therefore has a structure similar to the nucleotides of DNA and RNA.
- ATP is a phosphorylated nucleotide.
- Adenosine (a nucleotide) can be combined with one, two or three phosphate groups.
- One phosphate group = Adenosine monophosphate (AMP)
- Two phosphate groups = Adenosine diphosphate (ADP)
- Three phosphate groups = Adenosine triphosphate (ATP)
2. State that the bases adenine and guanine are purines with a double
ring structure, and that the bases cytosine, thymine and uracil are
pyrimidines with a single ring structure (structural formulae for
bases are not expected).

- The nitrogenous bases that are found in the nucleotides of DNA

(T, A, G, C) and RNA (U, A, G, C) occur in two structural forms:
Purines and Pyrimidines.
- The bases Adenine and Guanine are Purines and have a Double
Ring Structure.
- The bases Thymine, Uracil and Cytosine are Pyrimidines and
have a Single Ring Structure.

3. Describe the structure of a DNA molecule as a double helix,

including:
• The importance of complementary base pairing between the 5′ to 3′
strand and the 3′ to 5′ strand (antiparallel strands)
• Differences in hydrogen bonding between C–G and A–T base pairs
• Linking of nucleotides by phosphodiester bonds

DNA - Deoxyribonucleic acid is a polynucleotide which is made up of

many nucleotides that are bonded together in a long chain.

- DNA molecules are made of two polynucleotide strands lying

side by side, running in opposite directions. This is called
Antiparallel.
- Each DNA polynucleotide strand is made of alternating
deoxyribose sugars and phosphate groups bonded to form the
phosphate backbone. These bonds are covalent and are known
as phosphodiester bonds.
- The phosphodiester bonds link the 5-carbon of one deoxyribose sugar molecule to the phosphate group from the same
nucleotide, which is itself linked by another phosphodiester bond to the 3-carbon of the deoxyribose sugar molecule of the
next nucleotide in the strand.
- Each DNA strand is said to have a 3’ end and a 5’ end (these numbers relate to which carbon on the pentose sugar could
be bonded with another nucleotide).
- As the strands run antiparallel, one strand is known as the 5’-3’ strand and the other is known as the 3’-5’ strand.
- The nitrogenous base faces the interior of the double helix.
Hydrogen bonding
- The two antiparallel DNA strands that make up the DNA molecule are held together by hydrogen bonds between the
nitrogenous bases.
- They run antiparallel because when it's flipped they match up due to the complementary base pairing rule.
- These hydrogen bonds always occur between the same pairs of bases:
- The purine adenine (A) always pairs with the pyrimidine thymine (T) – two hydrogen bonds are formed between these
bases.
- The purine guanine (G) always pairs with the pyrimidine cytosine (C) – three hydrogen bonds are formed between these
bases.
- This is known as complementary base pairing.
- These pairs are known as DNA base pairs.
Double Helix
- The DNA molecule is in the form of a 3-dimensional double helix.

4. Describe the semi-conservative replication of DNA during the S phase of the cell cycle, including:
• The roles of DNA polymerase and DNA ligase (knowledge of other DNA replication enzymes & different types of DNA
polymerase not expected)
• The differences between leading strand and lagging strand replication as a consequence of DNA polymerase adding
nucleotides only in a 5′ to 3′ direction

Semi-conservative DNA replication

 - The DNA replication occurs during S phase (interphase), when the cell is not dividing.
- The hydrogen bonds between the base pairs of the two antiparallel strands are broken.
- The two ‘unzipped’ DNA strands (which form the double helix) [Helicase is the enzyme which unzips the DNA] each act as
a template for the formation of a new strand.
- The old and the new strand then join together in order to form a new DNA molecule.
- This method of replicating DNA is known as semi-conservative replication because half of the original DNA molecule is
kept (conserved) in each of the two new DNA molecules
- This was discovered/shown by Meselson and Stahl in 1958. They used two nitrogen isotopes (a heavy N-15 and a normal N-
14). It allowed them to show how the density of DNA changed over generations.

DNA Polymerase
- In the nucleus, there are free nucleotides to
which two extra phosphates have been added
(these free nucleotides with three phosphate
groups are known as nucleoside triphosphates or
‘activated nucleotides’).
- The extra phosphates activate the nucleotides,
enabling them to take part in DNA replication.
- The bases of the free nucleoside triphosphates
align with their complementary bases on each of
the template DNA strands.
- The enzyme DNA polymerase synthesises new
DNA strands from the two template strands.
 - It does this by catalysing condensation reactions between the deoxyribose sugar and phosphate groups of adjacent
nucleotides within the new strands, creating the sugar-phosphate backbone of the new DNA strands.
- DNA polymerase cleaves (breaks off) the two extra phosphates and uses the energy released to create the phosphodiester
bonds (between adjacent nucleotides).
- Hydrogen bonds then form between the complementary base pairs of the template and new DNA strands.

Leading and lagging strands

- The DNA polymerase can only build the new strand in the 5’ to 3’ direction.
- As DNA is ‘unzipped’ from the 3’ towards the 5’ end, DNA polymerase will attach to the 3’ end of the original strand and
move towards the replication fork (the point at which the DNA molecule is splitting into two template strands).
- This template strand that the DNA polymerase attaches to is called the leading strand.
- The other template strand created during DNA replication is called the lagging strand.
- On this strand, DNA polymerase moves away from the replication fork (from the 5’ end to the 3’ end).
- This means the DNA polymerase enzyme can only synthesise the lagging DNA strand in short segments (called Okazaki
fragments).
- A second enzyme known as DNA ligase is needed to join these lagging strand segments together to form a continuous
complementary DNA strand.
- DNA ligase does this by catalysing the formation of phosphodiester bonds between the segments to create a continuous
sugar-phosphate backbone.
5. Describe the structure of an RNA molecule, using the example of messenger RNA (mRNA)

RNA Structure
- RNA (Ribonucleic acid) is a polynucleotide.
- RNA nucleotides contain the nitrogenous bases Adenine (A), Cytosine (C), Guanine (G) and Uracil (U) in place of Thymine.
- RNA contains the pentose sugar Ribose instead of Deoxyribose.
 - RNA molecules are only single stranded (not double like DNA).
- Each polynucleotide is made of alternating ribose
sugars and phosphate groups linked together.
- The sugar-phosphate bonds are covalent bonds called
phosphodiester bonds.
- These bonds form the sugar-phosphate backbone of
the RNA.
- The phosphodiester bonds link the 5-carbon of one
ribose sugar molecule to the phosphate group from the
same nucleotide, which is itself linked by another
phosphodiester bond to the 3-carbon of the ribose
sugar molecule of the next nucleotide in the strand.

- Examples are mRNA (messenger RNA), which is the

transcript copy of a gene that encodes for a specific
polypeptide. Two other examples are tRNA (transfer
RNA); which is used in the construction of polypeptides,
it brings the amino acids over, and rRNA (ribosomal
RNA), which make up ribosomes.

6. State that a polypeptide is coded for by a gene and that a

gene is a sequence of nucleotides that forms part of a DNA molecule

- A gene is a sequence of nucleotides that forms part of a DNA molecule,

(one DNA molecule contains many genes).
- This sequence of nucleotide bases (gene) codes for the production of a specific
polypeptide (protein).
- Protein molecules are made up of a series of amino acids bonded together.
 - The shape and behaviour of a protein molecule depends on the exact sequence of these amino acids (the initial sequence
of amino acids is known as the primary structure of the protein molecule).
- The genes in DNA molecules control protein structure and as a result protein function, as they determine the exact
sequence in which the amino acids join together when proteins are synthesised in a cell.

7. Describe the principle of the universal genetic code in which different triplets of DNA bases either code for specific amino
acids or correspond to start and stop codons.

- The DNA nucleotide base code found within a gene is a three-letter,

or triplet, code.
- Each sequence of three bases codes for one amino acid.
- These triplets of bases are known as Codons (each codon codes for a
different amino acid -there are 20 different amino acids that cells
use to make up different proteins).
- E.g CAG codes for the amino acid Valine. TTC codes for the amino
acid Lysine. Etc.

- Some of these triplets of bases code for start (usually AUG -

Methionine) and stop.
- These signals tell the cell where individual genes start and stop.
- This ensures the cell reads the DNA correctly (the code is not
overlapping) and can produce the correct sequences of amino acids,
which produces the correct protein molecules that function
correctly.
- There are four bases so there are 64 different triplets possible, yet
there are only 20 amino acids that commonly occur in biological
proteins. Due to this many codons code for the same amino acids. These codes are said to be degenerate (this can limit the
effect of mutations).
- The genetic code is universal meaning that almost every organism uses the same code. Barring a few exceptions.
- This means that the same codons code for the same amino acids in all living things. So transfer of genetic information is
possible between species.

8. Describe how the information in DNA is used during transcription and translation to construct polypeptides, including the
roles of:
• RNA polymerase
• Messenger RNA (mRNA)
• Codons
• Transfer RNA (tRNA)
• Anticodons
• Ribosomes

The process of protein synthesis occurs in two stages:

- Transcription - DNA is transcribed and a mRNA molecule is produced.
- Translation - mRNA is translated and an amino acid sequence (polypeptide) is produced.
Transcription
 - The stage of protein synthesis that occurs in the nucleus of the cell.
- Part of a DNA molecule unwinds, (the hydrogen bonds between the complementary base pairs break due to helicase).
- This exposes the gene to be transcribed, the gene from which a particular polypeptide will be produced.
- A complementary copy of the code from the gene is made
by building a single stranded nucleic acid molecule known
as mRNA (messenger RNA).
- Free activated RNA nucleotides pair up with their
complementary bases on the template strand of the
‘unzipped’ DNA molecule via hydrogen bonds.
- The sugar phosphate groups of these RNA nucleotides are
then bonded together by the enzyme RNA polymerase to
form the sugar phosphate backbone of the mRNA
molecule.
- When the gene has been transcribed, the hydrogen bonds
between the mRNA and DNA strands break and the double
stranded DNA molecule re-forms. With the mRNA
detaching.
- The mRNA then leaves the nucleus via a pore in the
nuclear envelope/membrane.

Translation
- The stage of protein synthesis that occurs in the
cytoplasm of the cell.
- After leaving the nucleus, the mRNA molecule attaches to
a ribosome.
- In the cytoplasm, there are free molecules of tRNA
(transfer RNA).
 - These tRNA molecules have a triplet of unpaired bases at one end (known as the Anticodon) and a region where a specific
amino acid can attach at the other.
- There are at least 20 different tRNA molecules, each with a specific anticodon and specific amino acid binding site.
- The tRNA molecules bind with their specific amino acids (in the cytoplasm) and bring them to the mRNA molecule on the
ribosome.
- The anticodon (triplet of bases) on each tRNA molecule pairs with a complementary codon (triplet of bases) on the mRNA
molecule.
- Two tRNA molecules fit onto the ribosome at any one time, bringing the amino acid they are each carrying side by side.
- A peptide bond is formed between the two amino acids.
- This process continues until a ‘stop’ codon on the mRNA molecule is reached. This acts as a signal for translation to stop
and at this point the amino acid chain coded for by the mRNA molecule is complete.
- This amino acid chain then forms the final polypeptide.

9. State that the strand of a DNA molecule that is used in transcription is called the transcribed or template strand and that
the other strand is called the non-transcribed strand

- In the transcription stage of protein synthesis, the section of

DNA where the gene is located unwinds.
- Free activated RNA nucleotides then pair up with the exposed
bases on the DNA molecule but only with those bases on one
strand of the DNA molecule.
- This strand of the DNA molecule is called the Template
strand or the Transcribed strand.
 - This is the strand that is transcribed to form the mRNA molecule.
- This mRNA molecule will then be translated into an amino acid chain.
- The strand of the DNA molecule that is not transcribed is called the non-template strand or the non-transcribed strand.

10. Explain that, in eukaryotes, the RNA molecule formed following transcription (primary transcript) is modified by the
removal of non-coding sequences (introns) and the joining together of coding sequences (exons) to form mRNA

- Within eukaryotic genes, there are both coding and non-

coding sequences of DNA.
- The coding sequences are called Exons and these are the
sequences that will eventually be translated into the
amino acids that will form the final polypeptide.
- The non-coding sequences are called Introns and are not
translated (they don’t code for amino acids).

- When transcription of a gene occurs, both the exons and

the introns are transcribed.
- This means that the RNA molecule formed (known as the
Primary Transcript) also contains exons and introns.
- As the introns are not to be translated, they must be
removed from the RNA molecule.
- The exons are then all fused together to form a
continuous RNA molecule called mature mRNA that is
ready to be translated.
- This process is sometimes called ‘splicing’ and is part of
the process of post transcriptional modification, which
refers to the modification of the RNA molecule after
transcription but before translation occurs.

11. State that a gene mutation is a change in the sequence of base pairs in a DNA molecule that may result in an altered
polypeptide

- A gene mutation is a change in the sequence of base pairs in a DNA molecule that may result in an altered polypeptide.
- Mutations occur continuously.
- As the DNA base sequence determines the sequence of amino acids which make up a protein, mutations in a gene can lead
to a change in the polypeptide that the gene codes for.
- Most mutations do not alter the polypeptide or only alter it slightly so that its structure or function is not changed. (due to
the genetic code being degenerate).
12. Explain that a gene mutation is a result of substitution or deletion or insertion of nucleotides in DNA and outline how
each of these types of mutation may affect the polypeptide produced

Insertion of nucleotides
- A mutation that occurs when a nucleotide (with a new base) is randomly inserted into the DNA sequence is known as an
insertion mutation.
- An insertion mutation changes the amino acid that would have been coded for by the original base triplet, as it creates a
new, different triplet of bases.
- An insertion mutation has a knock-on effect of changing the triplets further in the DNA sequence.
- This is sometimes known as frameshift mutation.
- This may dramatically change the amino acid sequence produced from this gene and therefore the ability of the
polypeptide to function.

Deletion of nucleotides
- A mutation that occurs when a nucleotide (and therefore its base) is randomly deleted from the DNA sequence.
- Like an insertion mutation, a deletion mutation also changes the amino acid that it would have coded for.
- It also has the knock-on effect by changing the groups of three bases further on in the DNA sequence. Frameshift
mutation.
- This may dramatically change the amino acid sequence produced from this gene and therefore the ability of the
polypeptide to function.

Substitution of nucleotides
- A mutation that occurs when a base in the DNA sequence is randomly swapped for a different base.
- Unlike an insertion or deletion mutation, a substitution mutation will only change the amino acid for the triplet in which
the mutation occurs, it will not have a knock-on effect.

Substitution mutations can take three forms.

- Silent mutations - The mutation does not alter the amino acid sequence of the polypeptide, because some codons code
for the same amino acid as the genetic code is degenerate,
- Missense mutations - The mutation alters a single amino acid in the polypeptide chain. Sickle cell anaemia is an example
of a disease caused by a single substitution mutation changing a single amino acid in the sequence.
 - Nonsense mutations - The mutation creates a premature stop codon, causing the polypeptide chain produced to be
incomplete and therefore affecting the final protein structure and function. Cystic fibrosis is an example of a disease
caused by a nonsense mutation, although this is not always the only cause.

The effect of gene mutations on polypeptides

- Most mutations do not alter the polypeptide or only alter it slightly so that its appearance or function is not changed.
- However a small number of mutations code for a significantly altered polypeptide with a different shape.
- This may affect the ability of the protein to perform its function.
- E.g If the shape of the active site of an enzyme changes, the substrate may no longer be able to bind to the active site.
- E.g A structural protein, such as collagen, may lose its strength if its shape changes.
The mitotic cell cycle

1. Describe the structure of a chromosome, limited to:

DNA
histone proteins
sister chromatids
centromere
Telomeres

- Chromosomes are made of one very long, condensed DNA molecule associated with proteins (in eukaryotic cells).
- The main proteins present are the large positively charged, globular proteins called Histone proteins, their role is to
organise and condense the DNA tightly so that it fits into the nucleus.
- The other proteins are enzymes used in copying and repairing the DNA.
- The tightly coiled combination of DNA and proteins is called a Chromatin, chromosomes are made of the same things as
they are just chromatids but called chromosomes due to the phase they are in.

- During interphase (S phase) the DNA replicates to create two identical strands of DNA called chromatids, joined together
by a narrow region called the centromere. The two chromatids that make up the double structure of a chromosome are
known as ‘sister chromatids’.
- It is important that the sister chromatids are identical, containing the same genes, because they are the keys to cell
division, as one chromatid goes into one daughter cell and one goes into the other daughter cell during mitosis, which
makes sure that the daughter cells are genetically identical.
- Each chromatid is made up of a very long and condensed DNA molecule, which in turn is made up of a series of genes.
- The ends of the chromatids are protected with Telomeres, which aid in the longevity of a cell.
2. Explain the importance of mitosis in the production of genetically identical daughter cells during:
Growth of multicellular organisms
Replacement of damaged or dead cells
Repair of tissues by cell replacement
Asexual reproduction

- Mitosis is the process of nuclear division where two genetically identical daughter nuclei are produced that are identical to
the parent nucleus.
- The process of mitosis is of great biological importance and is fundamental to many biological processes.

Growth of multicellular organisms

- Two daughter cells produced are identical to one another (clones) and have the same number of chromosomes as the
parent cell.
- This allows unicellular zygotes to grow into multicellular organisms.
- Growth may occur across the whole body of the organism or be confined to certain regions.

Replacement of cells and repair of tissues

- Damaged tissues can be repaired by mitosis followed by cell division. E.g Dead cell, fix with 2 cells.
- As cells are constantly dying they need to be continually replaced by genetically identical cells.
- E.g In humans the cells in the skin and lining of the gut are constantly being replaced.
- Some animals can regenerate body parts. E.g Zebrafish can regenerate fins and axolotls regenerate legs and their tail, etc.

Asexual reproduction
- Asexual reproduction is the production of new individuals of a species by a single parent organism. The offspring are
genetically identical to the parent.
- For Amoeba a unicellular organism cell division results in the reproduction of an identical offspring.
- For multicellular organisms (as seen with many plant species), new individuals grow from the parent organism and then
detach (‘bud off’) from the parent in different ways. Examples include budding in Hydra and yeast and runners from
strawberries.

3. Outline the mitotic cell cycle, including:

Interphase (growth in G1 and G2 phases and DNA replication in S phase)
Mitosis
Cytokinesis

- Mitosis is part of the controlled process known as the cell cycle.

- The cell cycle is the regulated sequence of events that occurs between one cell division and the next.
- The cell cycle has three phases:
- Interphase
- Mitosis (nuclear division)
- Cytokinesis (cell division)

- The length of the cell cycle varies depending on environmental conditions, the cell type and the organism,
 - The movement from one phase to another is triggered by chemical signals called cyclins.

Interphase
- During interphase the cell increases in mass and size and carries out its normal cellular functions, such as synthesising
proteins and replicating its DNA ready for mitosis.
- Interphase consists of three phases:
- G1 phase
- S phase
- G2 phase
- It is at some point during the G1 phase a signal is received telling the cell to divide again.
- The DNA in the nucleus replicates (resulting in each chromosome consisting of two sister chromatids).
- This phase of the interphase is called the S phase. With S meaning synthesis of DNA. The S phase is relatively short.

- The gap between the previous cell division and the S phase is called the G1 phase, with G standing for gap/growth.
- Cells make the RNA, enzymes and other proteins required for growth during the G1 phase.

- Between the S phase and the next cell division the G2 phase occurs.
- During the G2 phase, the cell continues to grow and the new DNA that has been synthesised is checked for errors that are
usually repaired.
- Other preparations for cell division are made. (E.g as production of tubulin protein, which is used to make microtubules for
the mitotic spindle.)

- Interphase = G1 + S + G2

Mitosis (nuclear division)

- Follows interphase, and is referred to as the M phase with M standing for mitosis.
- Cell growth stops during the M phase.
Cytokinesis
- Follows M phase.
- Once the nucleus has divided into two genetically identical nuclei, the whole cell divides and one nucleus moves into each
cell to create two genetically identical daughter cells.
- In animal cells, cytokinesis involves the constriction of the cytoplasm between the two nuclei and in plant cells a new cell
wall is formed.

4. Describe the behaviour of chromosomes in plant and animal cells during the mitotic cell cycle and the associated
behaviour of the nuclear envelope, the cell surface membrane and the spindle (names of the main stages of mitosis are
expected: prophase, metaphase, anaphase and telophase)

- Mitosis is the process of nuclear division, with two genetically identical daughter nuclei being produced.
- Although mitosis in reality is one continuous process, it can be divided into four main stages.
- These stages in order are:
- Prophase
- Metaphase
- Anaphase
- Telophase

- Most organisms contain many chromosomes in the nuclei of their cells, (e.g humans have 46).

Prophase
- Chromosomes condense and are now visible when
stained.
- The chromosomes consist of two sister chromatids.
- The two centromeres move towards opposite poles.
- Spindle fibres (made of microtubules) begin to emerge
from the centrosomes. (consist of two centrioles in
animal cells).
- The Nuclear envelope/membrane breaks down into
small vesicles.

Metaphase
- Centrosomes reach opposite poles.
- Spindle fibres continue to extend from centrosomes.
- Chromosomes line up at the equator of the spindle (also
called the metaphase plate) so they are equal distance
from the two centrosome poles.
- Spindle fibres attach to the centromeres.
 - Each sister chromatid is attached to a spindle fibre
originating from opposing poles.

Anaphase
- The sister chromatids separate at the centromere.
Centromere divides into two.
- Spindle fibres begin to shorten.
- The separated sister chromatids (can now be called
chromosomes) are pulled to the opposite poles by the
spindle fibres.

Telophase
- Chromosomes arrive at opposite poles and begin to
decondense.
- Nuclear envelopes begin to reform around each set of
chromosomes.
- The spindle fibres break down.

5. Outline the role of telomeres in preventing the loss of genes

from the ends of chromosomes during DNA replication

- The ends of the chromatids in chromosomes are ‘sealed’

with protective structures known as telomeres.
- They are made of non-coding DNA (DNA with no genes) that is made of short base sequences that are repeated many
times.
- In telomeres, one strand is rich in the base Guanine (G) and the other strand is rich in the complementary base Cytosine
(C).
- The main function of telomeres is to ensure that the very ends of the DNA molecules included in DNA replication during
mitosis are kept safe.
- If this end part of the DNA contained an important gene, that piece of genetic information would be lost during DNA
replication.
- In each subsequent cell division a little more genetic information would be lost.
- Telomeres therefore act as buffers of non-coding (not essential) DNA and ensure that no important coding DNA sections
near the ends of the DNA molecule are left out of the replication process.
- This ensures that no genes are lost during cell division and allows the continued replication of a cell.
- To avoid the risk of losing genes most cells have the enzyme Telomerase that adds additional bases to the telomeres.
- Some cells (generally specialised ones) do not have telomerase to add bases to their telomeres and therefore after a
certain number of cell divisions the cell dies, this has been connected with the ageing process.
6. Outline the role of stem cells in cell replacement and tissue repair by mitosis

Significance of Stem Cells

- A stem cell is a cell that can divide (by mitosis) an unlimited number of times/continuously.
- Each new cell has the potential to remain a stem cell or to develop into a specialised cell such as a blood cell or a muscle
cell, (by a process known as differentiation).
- This ability of stem cells to differentiate into more specialised cell types is known as Potency.
- There are three types of potency:
- Totipotency - Totipotent stem cells are ones that can differentiate into any cell type found in an embryo, as well as
extra embryonic cells (the cells that make up the placenta). The zygote formed when a sperm cell fertilises an egg cell is
totipotent, as are the embryonic cells up to the 16-cell stage of human embryo development.
- Pluripotency - Pluripotent stem cells are embryonic stem cells that can differentiate into any cell type found in an
embryo but are not able to differentiate into extra embryonic cells (cells that make up the placenta).
- Multipotency - Multipotent stem cells are adult stem cells that have lost some of the potency associated with
embryonic stem cells and are no longer pluripotent.

Multipotent adult stem cells

- As tissues, organs and organ systems develop, cells become more and more specialised.
- Having differentiated and specialised to fulfil particular roles. Most adult cells gradually lose the ability to divide until;
eventually, they are no longer able to divide.
 - However, small numbers of stem cells (known as adult stem cells) remain to produce new cells for the essential processes
of growth, cell replacement, and tissue repair.
- Although these adult stem cells are able to divide an unlimited number of times, they are only able to produce a limited
range of cells. They are Multipotent.
- E.g stem cells found in bone marrow are multipotent adult stem cells. They can only differentiate into blood cells.
- In adults, stem cells can be found throughout the body (e.g bone marrow, skin, gut, heart and brain).
- Research is being done on stem cell therapy. Which can introduce adult stem cells into damaged tissues to treat diseases
such as Leukaemia and injuries like skin burns.

7. Explain how uncontrolled cell division can result in the formation of a tumour

- Cancers demonstrate how important it is that cell division is precisely controlled, as cancers arise due to uncontrolled
mitosis.
- Cancerous cells divide repeatedly and uncontrollably forming a Tumour (an irregular mass of cells).
- Cancers start when changes occur in the genes that control cell division. A change in a gene is known as a mutation. If the
mutated gene is one that causes cancer it is known as an Oncogene.
- Mutations are common and don’t often lead to cancer.
- Most mutations either result in early cell death or result in the cell being destroyed by the body’s immune system.
- As most cells can easily be replaced, these events usually have no harmful effect on the body. Most mutations aren’t
very harmful.

- The mutations that result in the generation of cancerous cells do not result in early cell death or in the cell being
destroyed by the body’s immune system.
- This means that the harmful mutation occurring in the original cell can be passed on to all that cell’s descendants.
- Typical tumours contain around a billion cancerous cells by the time it is detected.

- Carcinogens are any agents that may cause cancer (e.g UV light, tar in tobacco and X-rays). If the agent causes cancer it is
carcinogenic.
- Some tumours spread throughout the body, invading and destroying other tissues. These are known as Malignant tumours
and cause cancer.
- Malignant tumours interfere with the normal function of the organ/tissue that they grow on. E.g Block intestines, lungs
or blood vessels.
- Malignant tumour cells can break off the tumour and travel through the blood or lymphatic system to form secondary
growths elsewhere in the body.
- The spreading of cancers in this way is called Metastasis.
- Metastasis is very dangerous as it is very difficult to detect, locate and remove.
Mammalian Transport and the Heart

Blood Components

- The average adults has around 5 litres of blood in their system at any one time (women between 4-5, men between 5-6)
- In a healthy adult, there are usually around
- 20 – 30 trillion (or 2.5 x 1013) red blood cells
- 5 x 1011 white blood cells
- Around 6 x 1012 (6 trillion or 6,000,000,000,000) platelets
- 2.4 million new erythrocytes are produced per second in human adults!
Erythrocytes

- Erythrocytes are made in the bone marrow. As they mature they squeeze out their nucleus and most of their other
organelles.
- During the first day or two in circulation, when they are immature, they’re called a reticulocyte and will still often contain
remnants of organelles.
- Reticulocytes should make up approximately 1-2% of the erythrocyte count and this gives us a rough estimate of the rate
of RBC production.
- If the number of reticulocytes is much lower or higher than 1-2% it would indicate abnormalities in red blood cell
production which is normally around 2 billion.
- RBCs make up around 45% of the volume of blood and around 25% of the number of all cells in the body.
- At 7μm they’re much smaller than the ‘average’ cell size of around 40 μm.
White Blood Cells/Leukocytes
Leukocytes are responsible for our immune responses:
The 5 types of white blood cells can be divided into two main categories: granulocytes and agranulocytes.

Granulocytes: (produced by bone marrow)

- Eosinophils – can release toxins e.g. against a parasitic worm. They’re also involved in the inflammatory responses seen in
allergic reactions.
- Neutrophils – the most abundant type of white cells in the body. They destroy foreign bacteria that invade us. When we
are injured/get sick, neutrophils are the first cells to respond. They’re phagocytes.
- Basophils - produce histamine (helps fight allergies) and heparin (prevents blood from clotting).

Agranulocytes – don’t have visible granules.

- Monocytes: constantly ‘clean’ the circulatory (and lymphatic) system. They’re also phagocytes.
- Lymphocytes: are active agents in formation of the various immune responses. They activate when the organism detects
foreign organisms e.g. pathogens, inside the human body.
The lymphatic tissues i.e. the thymus, spleen and lymph nodes, produce lymphocytes (20-30% of white blood cells) and monocytes
(~4-8%).

Two types of white blood cells (leukocytes) are phagocytic - neutrophils (microphages) and monocytes (macrophages).
The small, granular neutrophils quickly appear at the site of a wound and ingest bacteria.
Monocytes are larger and usually appear about three days after infection. They seek out bacteria, foreign particles, dead cellular
material or protozoa.

High Altitudes
- At sea level the partial pressure of oxygen is just over 20 KPA.
- While at the top of Mt Everest (8,800m) it is 10 KPA.
- The change equally marked in the lungs alveoli is about 13 KPA at sea level to just over 5 KPA at (6,500m)

- If someone travels from sea level to a very high altitude very quickly the body does not have enough time to adjust to the
drop in the oxygen available and may suffer from altitude sickness.
- Mild altitude sickness (dizziness, fatigue and weakness) can be cured by going back to a lower altitude.

- The condition can quickly become a killer however as the dilated capillaries in the brain start leaking fluid into the brain
tissue (cerebral edema) causing retinal bleeds, vomiting, confusion, disorientation and eventual death.

- Even worse, the fluid can start leaking into the lungs (Pulmonary edema), this has disastrous effects on the individual's
ability to breathe/absorb oxygen and may lead to complete respiratory failure and death.
- However, if the body is given plenty of time to adapt, then most people can cope well at altitudes up to at least 5000m.

- As the body gradually acclimate to high altitude, a number of changes take place. Perhaps the most significant of these is
that the number of red blood cells increases. Normally RBC makes up 40-50% of blood. However after months at high
altitudes this rise is up to as much as 50-70%. However this does require a long time to occur.
 - People who live permanently at high altitudes such as the Andes or Himalayas, show a number of adaptations for their
lower oxygen level environment. E.g broader chest, larger heart (specifically the right side) and more haemoglobin in their
blood.

1. State that the mammalian circulatory system is a closed double circulation consisting of a heart, blood and blood vessels
including arteries, arterioles, capillaries, venules and veins.

Closed double circulatory system

The need for a circulatory system

- The cells of all living organisms need a constant supply of reactants for metabolism. E.g oxygen and glucose.
- Smaller organisms (single celled organisms) can gain oxygen and glucose directly from their surroundings, and the
molecules can diffuse to all parts of the cell quickly due to short diffusion distances.
- Larger organisms, however are made up of many layers of cells, meaning that there is a greater time for substances such
as glucose and oxygen to diffuse to every cell in the body, this time would be far too long.
- This is due to the diffusion distances being too great.
- To solve this problem their exchange surfaces are connected to a mass transport system, for example.
- The digestive system is connected to the circulatory system.
- The lungs are connected to the circulatory system.
- Mass transport is the bulk movement of gases or liquids in one direction, usually via a system of vessels and tubes.
- The circulatory system in mammals is a well studied example of a mass transport system. It has a one way flow of blood
within the blood vessels and carries essential nutrients and gases to all the cells of the body.

Open and closed systems

- Circulatory systems can either be open or closed.
 - In a closed circulatory system the blood is pumped around the body and is always contained within a network of blood
vessels.
- All vertebrates and many invertebrates have closed circulatory systems.
- In an open circulatory system, blood is not contained within blood vessels but is pumped directly into body cavities.
- Organisms such as arthropods and molluscs have open circulatory systems.

- Humans have a closed double circulatory system, it is a complete circuit around the body where it passes through the
heart (pump) twice.
- The right side of the heart pumps deoxygenated blood to the lungs for gas exchange, this is called the pulmonary
circulatory system.
- Blood then returns to the left side of the heart, so that oxygenated blood can be pumped efficiently (at high pressure)
around the body; this is the systemic circulatory system.

2. Describe the functions of the main blood vessels of the pulmonary and systemic circulations, limited to pulmonary artery,
pulmonary vein, aorta and vena cava.

- The pulmonary and systemic circulations are features of a double circulatory system.
- The pulmonary circulatory system transports deoxygenated blood to the lungs for gas exchange.
 - The systemic circulatory system transports oxygenated blood to the rest of the body.

- The diffusion of oxygen is reliant on:

- The concentration gradients that exist between oxygen in the air in the alveoli of the lungs and the oxygen in the
blood (it's a net diffusion into red blood cells).
- The concentration gradient that exists between oxygen in the red blood cells and the respiring tissues of the body.
(the net diffusion of oxygen into the mitochondria of the cells from the blood).

3. explain how the structure of muscular arteries, elastic arteries, veins and capillaries are each related to their functions

- Arteries, veins and capillaries all have varying structural features.

'

- The walls of arteries are much thicker

(more smooth muscle) than veins as they need to be able to handle the high pressure of the blood as it flows from the
heart. Additionally they must also have more elastin/elastic fibres in order to accommodate said high pressure.
 - The veins have valves in order to prevent backflow and they have less smooth muscle and elastin as they have no need for
it.
- Capillaries have very thin walls, one cell thick, in order to allow for diffusion to occur quickly due to the reduced diffusion
distance.

4. State that water is the main component of blood and tissue fluid and relate the properties of water to its role in transport
in mammals, limited to:
- Solvent action
- High specific heat capacity

Solvent action
- Water is the main component of blood, where it constitutes 95% of plasma, a straw coloured liquid. It is also the main
component of tissue fluid.
- Tissue fluid is formed when plasma passes through capillaries and some of it leaks into the spaces between the cells in the
walls of the capillaries. Tissue fluid is therefore mainly water.
- Water’s properties as a solvent (the universal solvent) make it ideal for transport in mammals.
E.g Glucose is transported in solution from the small intestine to every cell of the human body for respiration. In addition,
urea is transported in solution from the liver to the kidneys.

Specific heat capacity

- Specific heat capacity is a measure of the energy required to raise the temperature of 1 kg of a substance by 1 degrees
celsius.
- Water has a high specific heat capacity of 4200 J/Kg℃. A relatively large amount of energy is required to raise its
temperature.
- This means that water is able to absorb a lot of heat without big temperature fluctuations.
- This is vital in maintaining temperatures that are optimal for enzyme activity.
- Water in blood plasma is also vital in transferring heat around the body, helping to maintain a fairly constant temperature.
- As blood flows from a more active/”warmer” area of the body, heat energy is absorbed but the temperature
remains fairly constant.
- Water in tissue fluid also plays an important role in the regulation of maintaining a constant temperature.

5. State the functions of tissue fluid and describe the formation of tissue fluid in a capillary network.

Blood, Tissue Fluid and Lymph

 - Plasma is a straw coloured liquid that makes up around 55% of blood.
- Due to plasma being mainly 95% composed of water, it can transport many substances around the body.
- As blood passes through capillaries, some plasma leaks out through the gaps in the walls of the capillaries to surround the
cells of the body.
- This results in the formation of tissue fluid

- The composition of plasma and tissue fluid are virtually the same, although tissue fluid contains far fewer proteins.
- This is due to the proteins being far too large to fit through the gaps in the capillary walls and so remain in the
blood.

- Tissue fluid bathes almost all of the cells of the body outside of the circulatory system.
- Exchange of substances between cells and the blood occurs via the tissue fluid.
E.g, Carbon dioxide produced in aerobic respiration will leave a cell, dissolve into the tissue fluid surrounding it, and then
diffuse into the capillary.

Tissue fluid formation

- How much of the liquid that leaves the plasma to form tissue fluid depends on the 2 opposing forces.

- When blood is at the arterial end of a capillary, the hydrostatic pressure is great enough to push molecules out of the
capillary.
- Proteins remain in the blood; the increased protein content creates a water potential between the capillary and the tissue
fluid.
- However, overall movement of water is out of the capillary into the tissue fluid.

- When blood is at the venous end of the capillary, less fluid is pushed out of the capillary as pressure within the capillary is
reduced.
- The water potential gradient of the capillary and the tissue fluid stays the same as the arterial end. So water begins to flow
back into the capillary from the tissue fluid.
- Overall, more fluid leaves the capillary than returns,
leaving tissue fluid behind to bathe the cells.

- If blood pressure is high (hypertension) then the pressure

at the arterial end is even greater.
- This pushes more fluid out of the capillary and
fluid begins to accumulate around the tissues.
This is called oedema.

Formation of lymph
- Some tissue fluid re enters the capillaries while some
enters the lymph capillaries.
- The lymph capillaries are separate from the circulatory system.
- They have closed ends and large pores that allow large molecules to pass through.
- Larger molecules that are not able to pass through the capillary wall enter the lymphatic system as lymph.
- There are small valves in the vessel walls that act as the entry point to the lymphatic system.

- The liquid moves along the larger vessels of this system by compression caused by body movement. Any backflow is
prevented by valves.
- This is why people who have been sedentary on planes can experience swollen lower limbs.

- The lymph eventually re enters the bloodstream through veins near the heart.
- Any plasma proteins that have escaped from the blood are returned to the blood via lymph capillaries.
- If plasma proteins were not removed from tissue fluid they could lower the water potential of the tissue fluid and
prevent the reabsorption of water into the blood in the capillaries.
- After digestion lipids are transported from the intestines to the bloodstream via the lymph system.

6. Describe the role of red blood cells in transporting

oxygen and carbon dioxide with reference to the roles
of:
- Haemoglobin.
- Carbonic anhydrase.
- The formation of haemoglobinic acid.
- The formation of carbaminohemoglobin.

Transport of oxygen
- The majority of oxygen that is transported around the body is bound to the protein haemoglobin in red blood cells.
- Red blood cells (RBCs) are more formally known as erythrocytes.
- Each molecule of haemoglobin (polypeptide) contains four haem groups, each able to bond with one molecule of oxygen.
- This means that each molecule of haemoglobin can carry four oxygen molecules, or eight oxygen atoms in total.

- When oxygen binds to haemoglobin, oxyhaemoglobin is formed.

Oxygen + Haemoglobin ⇌ Oxyhaemoglobin

4O2 + Hb ⇌ Hb4O2

- Oxygen binds to the haemoglobin present in red blood cells. This binding takes place inside the lungs near the alveoli and
blood vessels through diffusion of oxygen.
- The binding of the first oxygen molecule results in a conformational change in the structure of the haemoglobin molecule,
making it easier for each successive oxygen molecule to bind; this is cooperative binding.
- The reverse of this process happens when oxygen dissociates in the tissues.
 1. Oxygen enters into blood capillaries from alveoli of the lungs through diffusion.
2. As continuous inspiration is going on, alveoli have a high pO2. Therefore, oxygen diffuses from higher concentration to
lower concentration or simply loads upon or binds to haemoglobin thus forming oxyhaemoglobin.
3. When cells undergo respiration, the oxygen diffuses from capillaries to respiring tissues.
4. As a result, pO2 decreases and unloading or unbinding of oxygen from haemoglobin takes place.
5. The haemoglobin then binds to CO2 as pCO2 is more now and returns to the lungs to release CO2 at the alveolar level and
to rebind with new oxygen molecules.

- Binding of one oxygen makes it easier to bind the rest of the oxygen to the haemoglobin by changing the structure of
haemoglobin.
- At higher pCO2, haemoglobin loses its oxygen quickly.
- As a result, the rate of oxygen unloading increases.
- Rate of oxygen unloading means dissociation of oxyhaemoglobin (to give off the oxygen being carried) is greater.
- This phenomenon is known as the Bohr effect.

Carbon dioxide carriage in the blood

Carbon dioxide is continually produced by respiring cells. It diffuses from the cells and into blood plasma, from where some of it
diffuses into the red blood cells. In the cytoplasmic red blood cells there is an enzyme, carbonic anhydrase, that catalyses the
following reaction.

Carbonic Anhydrase
CO2 + H2O ⇌ H2CO3 (carbonic acid)

The carbonic acid dissociates:

H2CO3 ⇌ H+ + HCO3 (hydrogencarbonate ion)

- Haemoglobin readily combines with the hydrogen ions, forming haemoglobinic acid, HHb. In doing so, it releases the
oxygen which it is carrying.
- This has 2 effects - Haemoglobin acts as a buffer by removing the hydrogen ions from solution and maintaining the pH of
the blood to close to neutral. And - the Bohr effect.
- One product of the dissociation of dissolved CO2 is hydrogen carbonate ions.
- The accumulation of Hydrogen ions would increase the acidity and kill the cell. However due to the haemoglobin acting as
a buffer the presence of the ions. Causes the oxyhaemoglobin to split up into haemoglobin and oxygen. The O2 diffuses
out of the red blood cell and into the tissues while the haemoglobin takes up the hydrogen ions to form a very weak acid.
Haemoglobinic acid.
- These are initially formed in the cytoplasm of the red blood cell (that’s where the carbonic anhydrase is found). Most of
the hydrogencarbonate ions then diffuse out of the red blood cell into the blood plasma where they are carried in solution.
About 85% of the CO2 transported by the blood is carried in this way.

- Some CO2 however, does not dissociate, but remains as carbon dioxide molecules.
- Some of these just dissolve in the blood plasma; about 5% of the total is carried in this form.
- Other carbon dioxide molecules diffuse into the red blood cells, but instead of undergoing the reaction catalysed by
carbonic anhydrase, they combine directly with the terminal groups (-NH2) of some of the haemoglobin molecules.
- This forms carbaminohemoglobin. About 10% of carbon dioxide is carried in this way.

7. Describe the chloride shift and explain the importance of the chloride shift.

- The chloride shift is the movement of chloride ions into red blood cells that occurs when hydrogen carbonate ions are
formed.
- Hydrogen carbonate ions are formed by the process of:
- Carbon dioxide diffuses into red blood cells.
- The enzyme carbonic anhydrase catalysing the combining of carbon dioxide and water to form carbonic acid
(H2CO3).
CO2 + H2O ⇌ H2CO3
- Carbonic acid dissociates to form hydrogen carbonate ions + hydrogen ions.
H2CO3 ⇌ HCO3 + H

- Negatively charged hydrogencarbonate ions formed from the dissociation of carbonic acid are transported out of the red
blood cells through a transport protein in the membrane.
- To prevent an electrical imbalance, negative charged chloride ions are transported into the red blood cells via the same
transport protein.
- This is important because if it didn’t occur then red blood cells would become positively charged as a result of a buildup of
hydrogen ions formed from the dissociation of carbonic acid.
8. Describe the role of plasma in the transport of carbon dioxide.

- Waste carbon dioxide produced during respiration diffuses from the tissues into the blood.
- This waste carbon dioxide is transported around the body in different ways:
- In the blood plasma in the form of hydrogen carbonate ions (HCO3). Around 85% of carbon dioxide is transported
in this way.
- Around 5% of carbon dioxide dissolves directly in the blood plasma.
- Bound to haemoglobin as carbaminohaemoglobin. 10% of carbon dioxide is transported in the blood.

Carbon dioxide in the plasma

- Carbon dioxide released as a waste product from respiring cells diffuses into the cytoplasm of red blood cells.
- Inside the RBCs, carbon dioxide combines with water to form H2CO3

CO2 + H2O ⇌ H2CO3

- Red blood cells contain the enzyme carbonic anhydrase which catalyses the reaction above.
- Without carbonic anhydrase this reaction is much slower.
- The plasma contains very little carbonic anhydrase, therefore H2CO3 forms much more slowly in plasma than in
the cytoplasm of the red blood cells.
- Carbonic acid dissociates readily into hydrogen ions (H) and hydrogen carbonate ions (HCO3)

H2CO3 ⇌ HCO3 + H

- Hydrogen ions can combine with haemoglobin forming haemoglobinic acid and preventing the hydrogen ions from
lowering the pH of the red blood cells. The haemoglobin acts as a buffer.
- The hydrogen carbonate ions diffuse out of the red blood cells and into the plasma, where they are then transported in
solution.
9. Describe and explain the oxygen dissociation curve of adult
haemoglobin.

The Oxygen Dissociation Curve

- The oxygen dissociation curve shows the rate of oxygen association as
well as dissociation with haemoglobin at different partial pressures of
oxygen (pO2).
- Partial pressure of oxygen refers to the pressure exerted by
oxygen within a mixture of gases; it is a measure of oxygen
concentration.
- Haemoglobin is referred to as being saturated when all of its
oxygen binding sites are taken up with oxygen (4 oxygen
molecules/8 oxygen atoms).
- The ease with which haemoglobin binds and dissociates with oxygen
can be described as its affinity for oxygen.
- When haemoglobin has a high affinity binds easily and
dissociates slowly.
- When haemoglobin has a low affinity for oxygen it binds slowly and dissociates easily.
- In other liquids, such as water, we would expect oxygen to become associated with water/dissolve at a constant rate.
Providing a straight line on a graph, however with haemoglobin Oxygen binds at different rates as the pO2 changes,
therefore the resulting curve.

- It can be said that haemoglobin’s affinity for oxygen changes at different partial pressures of oxygen.
Interpreting the Oxygen Dissociation Curve
- When the curve is read from left to right, it provides information about the rate at which haemoglobin binds to oxygen at
different partial pressures of oxygen.
- At low pO2 (bottom left of the graph), oxygen binds slowly to haemoglobin; this means that haemoglobin cannot
pick up oxygen and has become saturated as blood passes through the oxygen depleted tissues.
- Haemoglobin has a low affinity for oxygen at low pO2,, so the saturation percentage is low.
- At medium pO2 (central region of the graph), oxygen binds more easily to haemoglobin and saturation increases
quickly; at this point on the graph a small increase in pO2 causes a large increase in haemoglobin saturation.
- At high pO2 (top right of the graph), oxygen binds easily to haemoglobin; this means that haemoglobin can pick up
oxygen and become saturated as blood passes through the lungs.
- Haemoglobin has a high affinity for oxygen at high pO2, so the saturation percentage is high.
- At this point on the graph increasing the pO2 by a large amount only has a small effect on the percentage
saturation of the haemoglobin. This is due to the fact that most of the oxygen binding sites on
haemoglobin are already occupied.

- When read from right to left, the curve provides information about the rate at which haemoglobin dissociates with
oxygen at different partial pressures of oxygen
- In the lungs, where pO2 is high, there is very little dissociation of oxygen from haemoglobin
- At medium pO2, oxygen dissociates readily from haemoglobin, as shown by the steep region of the curve; this
region corresponds with the partial pressures of oxygen present in the respiring tissues of the body, so ready
release of oxygen is important for cellular respiration
- At this point on the graph a small decrease in pO2 causes a large decrease in percentage saturation of
haemoglobin, leading to easy release of plenty of oxygen to the cells
- At low pO2 dissociation slows again; there are few oxygen molecules left on the binding sites, and the release of the final
oxygen molecule becomes more difficult, in a similar way to the slow binding of the first oxygen molecule

Explaining the Oxygen Dissociation Curve

- The curved shape of the oxygen dissociation curve for haemoglobin can be explained:
- Due to the shape of the haemoglobin molecule it will be difficult for the first oxygen molecule to bind to the
haemoglobin. This means that binding of the first oxygen occurs slowly, explaining the shallow curve at the
bottom left corner of the graph.
- After the first oxygen molecule binds to haemoglobin, the haemoglobin protein changes shape, conforming,
making it easier for the next oxygen molecules to bind; this speeds up the binding of the remaining oxygen
molecules and explains the steeper part of the curve in the middle of the graph.
- The shape change of haemoglobin leading to easier oxygen binding is known as cooperative binding.
- As the haemoglobin molecule approaches saturation it takes longer for the fourth oxygen molecule to bind due to
the shortage of remaining binding sites, explaining the levelling off of the curve in the top right corner of the
graph.
10. Explain the importance of the oxygen dissociation curve at partial pressures of oxygen in the lungs and in respiring
tissues.

The oxygen dissociation curve is important as it shows how at places of lower partial pressures of oxygen such as the respiring
tissues (lower left corner), there is little oxygen gained as the oxygen is instead diffusing out of the red blood cell and into the
respiring tissue.

It is also important as it shows how at higher partial pressures of oxygen such as the lungs (the middle to upper right), there is
lots of oxygen gained as the oxygen is able to diffuse into the red blood cells due to its “cooperative binding nature” meaning
that as it binds it gets easier due to the shape of the haemoglobin changing to make it easier. Additionally it shows how once
almost all the binding sites of oxygen on the haemoglobin have been taken up, the rate at which haemoglobin saturation increases
is a very minimal increase.

11. Describe the Bohr shift and explain the importance of the Bohr shift.

- Changes in the oxygen dissociation curve as a result of carbon dioxide levels are known as the Bohr effect, or Bohr shift. It
explains how the ability of haemoglobin to bind to oxygen then release it changes according to CO2 levels.
- When the partial pressure of carbon dioxide in the blood is high (respiring tissues), haemoglobin’s affinity for oxygen is
reduced - This is helpful because it means that haemoglobin gives up its oxygen much more easily.
- This is especially true in respiring tissues, where cells are producing carbon dioxide as a waste product of
respiration.
- This occurs because CO2 lowers the pH of the blood (by forming carbonic acid), which causes haemoglobin to
release its oxygen..
- CO2 combines with water to form carbonic acid.
- Carbonic acid dissociates into hydrogen carbonate ions and hydrogen ions.
- Hydrogen ions bind to haemoglobin, causing the release of oxygen.
- This is a helpful change because it means that haemoglobin gives up its oxygen more readily in the respiring tissues where
it is needed.
- Carbon dioxide levels in the lungs are very low compared to what is being carried in the blood) so haemoglobin’s affinity
for oxygen is increased - thus making it easier for oxygen to bind to haemoglobin.
- On a graph showing the dissociation curve, the curve shifts to the right when CO2 levels increase.
- This means that at any given partial pressure of oxygen, the percentage saturation of haemoglobin is lower at
higher levels of CO2.

- The higher the partial pressure of oxygen, the greater the saturation of haemoglobin with oxygen, and vice versa
- The more CO2 there is, causes the line to shift to the right (the lower of the two lines) - showing more dissociation has
occurred, as the percentage saturation of oxygen is lower
- This is an important change, as it means that where there is a lot of carbon dioxide, such as at respiring tissues,
oxyhaemoglobin readily breaks down and gives up its oxygen to the nearby tissues.
12. Describe the external and internal structure of the mammalian heart.

Mammalian Heart Structure

General structure of blood circulation in mammals
- The circulatory system consists of heart + blood vessels.
- Mammals possess a double circulation.
- Systemic circulation: Oxygenated blood is pumped out of the heart through the aorta and carried by further
arteries, arterioles and capillaries to all parts of the body and deoxygenated blood comes back to heart via
superior vena cava and inferior vena cava.
- Pulmonary circulation: Deoxygenated blood from heart is pumped out through pulmonary artery into lungs and
oxygenated blood comes back to heart from lungs via pulmonary veins.

- There are also specialised blood vessels dealing with the flow of blood to and from the liver.
- The hepatic artery and hepatic vein enter and leave the liver respectively. Also there is a special circulation between the
gut and the liver through the Hepatic Portal Vein which carries waste from the gut to the liver.
- The Renal artery and Renal vein enter and leave the kidney respectively.

- Along with all these types of arteries and veins the heart itself has a blood supply - the right and left coronary arteries.

Heart structure

- The human heart has a mass of around 300g and is roughly the size of a closed fist.
- The heart is a hollow, muscular organ located in the chest cavity,
- It is protected in the chest cavity by the pericardium, a tough and fibrous sac.

- The heart consists of four chambers: 2 auricles (atria) and 2 ventricles

- The atria (or auricles) are located above the ventricles.
- In between the two atria there is an intra auricular septum and in between the two ventricles there is an
intra ventricular septum and the atrioventricular septum between the atria and ventricles.
 - Valves:
- Open when the pressure of blood behind them is greater than the pressure in front of them.
- Close when the pressure of blood in front of them is greater than the pressure behind them.
- Valves are important for keeping blood flowing forward in the right direction and stopping it flowing
backwards. They are also important for maintaining the correct pressure in the chambers of the heart.
- The right atrium and right ventricle are separated by the atrioventricular valve, which is otherwise
known as the tricuspid valve.
- The right ventricle and the pulmonary artery are separated by the pulmonary valve.
- The left atrium and left ventricle are separated by the mitral valve, which is otherwise known as the
bicuspid valve.
- The left ventricle and aorta are separated by the aortic valve.
- There are two blood vessels bringing blood to the heart; the vena cava and pulmonary vein.
- There are two blood vessels taking blood away from the heart; the pulmonary artery and aorta.

- Ventricles:
- The ventricles are more muscular than auricles and have chordae tendineae (held in place by papillary
muscles).
panda

- Coronary arteries:
- The heart is a muscle and so requires its own blood supply for aerobic respiration.
- The heart receives blood through arteries on its surface, called coronary arteries.
- It’s important that these arteries remain clear of plaques, as this could lead to angina or a heart attack
(myocardial infarction).

- The mammalian heart is a double pump: the right side pumps blood, at low pressure, to the lungs and the left side pumps
blood, at high pressure, to the rest of the body.
- The atria receive blood from the major veins. Deoxygenated blood from the body flows through the superior/inferior vena
cava into the right atrium.
- Oxygenated blood from the lungs flows through the pulmonary vein into the left ventricle. From the atria, blood flows
down through the atrioventricular valves into the ventricles.

- Attached to the valves are tendinous cords which prevent the valves from turning inside out when both ventricular walls
contract.
- The septum ensures that oxygenated blood (on the left side) and deoxygenated blood (on the right side) are kept
separate.
- Deoxygenated blood leaves the right ventricle in the pulmonary artery to the lungs where it is oxygenated.
- Oxygenated blood leaves the lungs through the pulmonary vein, through the left atria and ventricle, and is pumped
around the body via the aorta.
- The aorta supplies blood to a number of arteries that supply all parts of the body.
- At the base of the major arteries (e.g aorta/pulmonary artery), where they exit the heart, there are semilunar valves. These
prevent blood from returning to the heart as the ventricles relax (diastole).
13. Explain the differences in the thickness of the walls of the:
- atria and ventricles.
- left ventricle and right ventricle.

The Walls of the Heart

- The muscular walls of the atria are thinner than those of the ventricles.
- When the atria contracts, the thin muscular walls do not generate much pressure, but enough to force blood down into
the ventricles, through the atrioventricular valves.
- In contrast, the walls of the ventricles are thicker and much more muscular than the atrial walls.
- Following the contraction of the atria, the ventricles contract and squeeze blood inwards, increasing its pressure and
pushing it out of the heart through right and left semilunar valves.

Left and right ventricles

- The muscles of the left ventricle are significantly thicker than the right ventricle.
- This is because the blood leaving the right ventricle travels less distance than the blood leaving the left ventricle.
- The blood pumped out from the right ventricle travels to the lungs, whereas the blood leaving the left ventricle has to
travel to the rest of the body to deliver oxygen for respiration.
- To reach the rest of the body, the blood leaving the left ventricle must be under high pressure.
- This is generated by the contraction of the muscular walls of the left ventricle.
- The right ventricle generates less pressure from the contraction of its thinner walls, as blood only has to reach the
lungs.

14. Describe the cardiac cycle, with reference to the relationship between blood pressure changes during systole and diastole
and the opening and closing of valves.

Pressure and volume changes associated with valve movement during the cardiac cycle to maintain a unidirectional flow of
blood.

- The valves open in one way only or the opening of the heart valves are unidirectional.
- Whether they will be open or closed depends upon the relative pressure of the heart chambers.
- If the pressure created by blood is more after the valve, then it is forced open, but if the pressure is before the valve, then
the valve must be closed.
- Therefore the flow of blood is unidirectional.

The cardiac cycle (diastole and systole meanings)

 - The contraction of the heart is called systole (squeeze), while the relaxation of the heart is called diastole.
- Atrial systole is the period when the atria are contracting and the ventricular systole is when the ventricles are
contracting.
- Ventricular systole occurs around 0.13 seconds after atrial systole.
- During ventricular systole, blood is forced out of the pulmonary artery (to the lungs) and aorta (to the rest of the body).
- One systole and diastole makes up a heartbeat and lasts around 0.8 seconds in humans, this is the cardiac cycle.

Pressure changes
- During systole and diastole, heart valves open and close as a result of pressure changes.
- Valves are an important mechanism to stop blood flowing backwards.
- During diastole, the heart is relaxing.
- The atrioventricular valves open and the semilunar valves are closed.
- During systole, the heart contracts and pushes blood out of the heart.
- During this time, the atrioventricular valves are closed and the semilunar valves are open.

Cardiac cycle
The cardiac cycle takes place in 3 steps:
1. Auricles contract (systole) and ventricles relax (diastole).
2. Ventricles contract (systole) and auricles relax (diastole).
3. Both auricles and ventricles relax (joint diastole).
Changes in pressure (mmHg) and volume (ml) during the cardiac cycle.
1. Auricles contract and ventricles relax:
- Auricular pressure increases gradually due to contraction and slight increase in ventricular pressure due to passive
filling or slow filling of blood from auricles to ventricle.
- Bicuspid and tricuspid valves open.
- Volume decreases because of contraction and stretching of ventricles.

2. Ventricles contract and auricles relax:

- Bicuspid and tricuspid valves close, producing the first heart sound ‘lub’.
- Ventricular pressure increases gradually due to contraction and pressure decrease in auricles due to relaxation.
- Semilunar valves open.
- Volume decreases because of contraction and expansion of auricles (atria).

3. Both ventricles and auricles relax:

- Semilunar Valves close producing a second heart sound ‘dub’.
- Ventricular pressure decreases due to relaxation.
- Auricular pressure starts increasing due to entry of blood but also falls a little as some blood falls into the
ventricles passively (gravity assists with this).
- Pressure increases slowly in both auricles and ventricles as blood is filling.
- Volume increases in both auricles and ventricles due to filling of blood and extension of heart muscles.

The cardiac cycle can also be recorded using an ECG (electrocardiogram). Each ECG cycle consists of 5 waves: P, Q, R, S, T
corresponding to different phases of the heart activities. Both in terms of electrical stimulation and contractions. The shapes
produced can be used to diagnose heart irregularities.
Myogenic nature of Cardiac Muscle and Control of Heart Rate
Regular heart beat is due to the contraction of cardiac muscles. These muscles are myogenic. Myogenic means it can contract and
relax without impulse from the nervous system.
15. Explain the roles of the sinoatrial node, the atrioventricular node & Purkyne tissue in the cardiac cycle (knowledge of
nervous and hormonal control is not expected).

Heart action: initiation and Control

- Control of the basic heartbeat is myogenic, which means the heart will beat without any external stimulus.
- The heart will beat around 60 times a minute.
- The sinoatrial node (SAN) is a group of cells in the wall of the right atrium, it is often called the pacemaker of the heart
and sets the rhythm for heartbeat and initiates the cardiac cycle. The SAN initiates a wave of depolarisation that causes
the atria to contract. SAN sends out regular electrical impulses to atrial walls causing the left and right atria to contract
simultaneously
- The “Annulus fibrosus” is a region of non-conducting tissue which prevents the depolarisation spreading straight to the
ventricles.
- Instead the depolarization is carried to the atrioventricular node (AVN).
 - This is a region of conducting tissue between the atriums and ventricles.

- After a slight delay, the AVN is stimulated and passes the stimulation along the bundle of His via the median septum
- This delay means that only the ventricles contract after the atria.

- The bundle of His is a collection of conducting tissue in the septum (middle) of the heart. The bundle of His divides into
two conducting fibres, called Purkyne tissue, and carries the wave of excitation along them.
- The Purkyne fibres spread around the ventricles and initiate the depolarization of the ventricles from the apex (bottom)
of the heart.
- This makes the ventricles contract and blood is forced out of the pulmonary artery and aorta.

Practical work:

1. Recognise arteries, veins & capillaries from microscope slides, photomicrographs and electron micrographs & make plan
diagrams showing the structure of arteries and veins in transverse section (TS) and longitudinal section (LS)

Reference Diagrams.
2. Recognise & draw red blood cells, monocytes, neutrophils and lymphocytes from microscope slides, photomicrographs and
electron micrographs
Gas Exchange

1. describe the structure of the human gas exchange system, limited to:
- lungs
- trachea
- bronchi
- bronchioles
- alveoli
- capillary network

Gas exchange takes place in the human thorax. A collection of organs and tissues in the chest cavity.

2. Describe the distribution in the gas exchange system of cartilage, ciliated epithelium, goblet cells, squamous epithelium of
alveoli, smooth muscle and capillaries

3. Describe the functions of ciliated epithelial cells, goblet cells and mucous glands in maintaining the health of the gas
exchange system

- Cartilage is a strong and flexible tissue found in various places around the body.
 - One place is in rings along the trachea, called Tracheal rings.
- These rings help to support the trachea and ensure it stays open. Whilst allowing movement and flexing whilst we
breathe.

- Ciliated epithelium is a specialised tissue found along the trachea down to the bronchi. Each cell has small projections of
cilia which sweep mucus, dust and bacteria upwards and away from the lungs and the epithelium itself

- Goblet cells can be found scattered throughout the ciliated epithelium of the trachea.
- They are mucus producing cells that secrete viscous mucus which traps dust, bacteria and other microorganisms
and prevents them from reaching the lungs.
- The mucus is then swept along by the cilia of the ciliated epithelium upwards and is swallowed.
- The mucus and any microorganisms will then be destroyed by the acid in the stomach.

- The alveoli have a thin lining of squamous epithelium that allows for gas exchange.
- The squamous epithelium forms the structure of the alveolar wall, which is very thin and permeable for the easy
diffusion of gases.

- Smooth muscle can be found throughout the walls of the bronchi and bronchioles.
- It helps to regulate the flow of air into the lungs by dilating when more air is needed and constricting when less air
is needed.

- Each alveolus is surrounded by an extensive network of capillaries.

- Carbon dioxide diffuses out of the capillaries and into the alveoli to be exhaled, while oxygen diffuses the other
way from alveoli and into the capillaries to be carried around the body.

- These capillaries have a diameter of around 3-4µm, which is only wide enough for one red blood cell to travel through at
any one time.
- This ensures that there is sufficient time and opportunity for gas exchange to occur.

4. Describe the functions in the gas exchange system of cartilage, smooth muscle, elastic fibres and squamous epithelium

- Ciliated epithelial cells, goblet cells and mucous glands play different yet vital roles in maintaining the health of the gas
exchange system.
- Cartilage, smooth muscle, elastic fibres and squamous epithelial tissue all play important structural roles in maintaining
the gas exchange system.
5. Describe gas exchange between air in the alveoli and blood in the capillaries

- The exchange of oxygen and carbon dioxide occurs between the alveoli and the capillaries in the lungs.
- Oxygen and carbon dioxide are exchanged in the process of diffusion; the passive movement of the particles from a high
concentration to a low concentration.
- The air in the alveoli contains a high concentration of oxygen. The oxygen diffuses from the alveoli and into the blood
capillaries, before being carried away to the rest of the body for aerobic respiration.
- The blood in the capillaries has a relatively low concentration of oxygen and a high concentration of carbon dioxide. This
carbon dioxide diffuses into the alveoli from the blood and is then exhaled. Whilst the oxygen diffuses out of the alveoli
and into the blood stream.

Structures of the respiratory system

Trachea
- Trachea = windpipe; approx 1.8 cm diameter.
- Leads from mouth/nose to bronchi.
- Surrounded by C-shaped rings of cartilage, connected by smooth muscle.
- Lined with goblet cells and ciliated epithelial cells.
- Has smooth muscle.

Bronchi
- Left and right bronchi (singular: bronchus).
- Leads from trachea to bronchioles.
- Narrower lumen than trachea.
- Surrounded by blocks of cartilage.
- Lined with goblet cells and ciliated epithelial cells.
- Composed of smooth muscle.

Bronchioles
- Terminal bronchioles (around 48,000)
- 1.0 mm diameter.
- No cartilage, goblet cells, but do still have smooth muscle and cilia.
- Respiratory bronchioles (around 300,000)
- 0.5 mm diameter.
- No cartilage, goblet cells, smooth muscle, but do have a few cilia.
Practical Work:

1. Recognise cartilage, ciliated epithelium, goblet cells, squamous epithelium of alveoli, smooth muscle and capillaries in
microscope slides, photomicrographs and electron micrographs

- The cartilage in the trachea has a “glassy appearance due to its translucent protoplasm.
- It also contains no nerves or blood vessels.
- Ciliated epithelial cells are distinctive due to their narrow cell bodies and hair like cilia located along the apical layer.
- The cilia are tiny projections which greatly increase the surface area of the cell.

-
Goblet cells can be found scattered among the ciliated epithelium of the trachea
and bronchi.
- They are distinctive in the epithelium due to their lack of cilia. Although they do
still have some microvilli projecting outwards.
- The nucleus is found towards the basal (bottom) layer of the cell, with a large
Golgi apparatus and mucus granules found towards the apical layer.
- Squamous epithelium is made of thin, flat squamous cells.

- The cells of smooth muscle are tightly packed and are found beneath the
ciliated epithelium.
- Unlike the skeletal muscles, they are not striated and as such don’t show any cross stripes under a microscope.

- Capillaries are distinctive from other blood cells due to their tiny diameter (approximately 4 μm)
- Their walls consist of a single layer of epithelial cells.
2. Recognise trachea, bronchi, bronchioles and alveoli in microscope slides, photomicrographs and electron micrographs and
make plan diagrams of transverse sections of the walls of the trachea and bronchus

- A trachea cross section shows the large lumen which air has to travel through.
- The innermost cells of the trachea are the ciliated epithelium which projections called cilia.

- The cells of the ciliated epithelium are present above - the cells are tightly packed and interspersed with goblet cells,
which are shown in the white.

- The density of the cilia are shown in this electron micrograph.

- The cilia are essential for preventing bacteria and dust filled
mucus from entering the lungs, by pushing it up the trachea and ,
into the back of the mouth.
- The mucus is then swallowed and any pathogens would
hopefully be destroyed by stomach acid.
- Bronchi are distinctive from the trachea because their lumen is narrower; 8.7 mm instead of 18mm.
- However, like the trachea they are lined by ciliated epithelium.

- Bronchioles are approximately 1 mm or less in diameter.

- Smooth muscle and cuboidal epithelium are present in their walls.

- Alveoli have a sponge-like appearance under microscopes due to their air

spaces.
- They are surrounded by an extensive capillary network and are lined by
squamous epithelium.
- The tracheal lumen is around 15 to 20 mm and is lined with ciliated epithelia.
- The tracheal walls are surrounded by strong and flexible cartilage which flexes during breathing.
- The smooth muscle of the trachea constricts and allows air

- Like the trachea, the bronchus is lined with ciliated epithelium.

- The cartilage hoops provide structural support to the bronchi
and the gland ducts secrete mucus in the bronchial tubes.
Infectious Diseases

1. State that infectious diseases are caused by pathogens & are transmissible

Disease - A disease is an illness or a disorder of the body or mind that leads to poor health; each is associated with a set of signs
and symptoms.

Infectious Diseases - Diseases that are caused by organisms known as pathogens, sometimes they are called communicable
diseases as they are passed from infected to uninfected people. Some also affect animals and are passed from animals to humans.

Non-infectious Diseases - These are long term degenerative diseases. They are not caused by pathogens and may have other
causes such as genetic disorders or exposure to environmental pollutants e.g sickle cell anaemia and lung cancer.

Some infectious diseases such as malaria (which is caused by Plasmodium) are transmitted via other “vectors”, other are
transmitted through infected water and food or during direct contact/sexual activity.

2. State the name and type of pathogen that causes each of the following:
● Cholera – caused by the bacterium Vibrio cholerae
● Malaria – caused by the protoctists Plasmodium falciparum, P. malariae, P. ovale and P. vivax
● Tuberculosis (TB) – caused by the bacteria Mycobacterium tuberculosis and Mycobacterium bovis
● HIV/AIDS – caused by the human immunodeficiency virus (HIV)

- Four infectious diseases of international and worldwide importance are: cholera, malaria, tuberculosis (TB) and HIV/AIDS.
- Throughout the world many are infected with these diseases and the chance of being infected remains very high as well.
These diseases pose serious public health problems, currently and as well as in the foreseeable future.
- In order to restrict and control a disease, it is vital to know what causes it (known as the causative agent or pathogen).

3. Explain how cholera, malaria, TB and HIV are

transmitted
Transmission of cholera:
- Cholera is caused by the bacterium Vibrio cholerae.
- The disease is water-borne and food-borne. (i.e the bacterium lives in water and food)
- This means the disease occurs where people do not have access to proper sanitation (a clean water supply) and
uncontaminated food.
- Cholera can be transmitted when people bathe or wash in contaminated water, drink contaminated water or eat food
which has been exposed to contaminated water.
- Infected people egest large numbers of the bacteria in their faeces.
- If these faeces contaminate the water supply, or if infected people handle food or cooking utensils without washing their
hands, then the bacteria are transmitted to uninfected people.

Transmission of malaria:
- Malaria is caused by one of the four species of the protoctist
Plasmodium.
- These protoctists are transmitted to humans by an insect
vector:
- Female “Anopheles mosquitoes” feed on human blood
to obtain the protein they need to develop their eggs.
- If the person they bite is infected with Plasmodium, the
mosquito will take up some of the pathogen with the
blood meal.
- Then when feeding on the next human. The
Plasmodium passes from the mosquito to the new
human’s blood.
- Malaria may also be transmitted during blood transfusion and
when unsterile needles are used.
- Plasmodium can also pass from mother to child across the placenta.

Transmission of tuberculosis (TB):

- When infected people with the active form of the disease cough or sneeze, the Mycobacterium tuberculosis bacteria enter
the air in tiny droplets of liquid.
- TB is transmitted when uninfected people inhale these droplets of the Mycobacterium tuberculosis.
- TB therefore spreads more quickly among people living in overcrowded conditions.
- The form of TB caused by Mycobacterium bovis occurs in cattle but is spread to humans through contaminated meat and
unpasteurised milk.
- Very few people in developing countries acquire TB in this manner, although meat and milk can still be a source of
infection in some developing countries.

Transmission of HIV/AIDS:
- Human Immunodeficiency Virus is a retrovirus,
- The HIV virus is not transmitted by a vector (unlike malaria).
- The virus is unable to survive outside the human body.
- The virus is spread through intimate human contact and can only be transmitted by direct exchange of bodily fluids.
- This means HIV can be transmitted in the following ways:
- Sexual intercourse.
 - Blood donations.
- Sharing of needles used by intravenous drug users.
- Mother to child across the placenta.
- Mixing of blood between mother and child during birth.
- Mother to child through breast milk.

Summary table:

4. Discuss the biological, social and economic factors that need to be considered in the prevention and control of cholera,
malaria, TB and HIV (details of the life cycle of the malarial parasite are not expected)

Prevention and control of cholera:

Biological factors:
 - Cholera can be prevented/controlled by ensuring that there is a clean and sanitary water supply. This is needed because
Cholera lives/thrives in water as it is a waterborne bacteria.
- Therefore ensuring a clean and sanitary environment with a clean water supply would help prevent cholera.

Social factors:
- Cholera affects developing countries the most. This is because these countries have lots of overcrowding which results in
the accidental sharing of contaminated equipment/utensils/water. This results in the rapid spreading of the disease.
- Therefore reduction of overcrowding would reduce the amount of cholera cases as there wouldn’t be as much
spreading/sharing of contaminated water and items.

Economical factors:
- Developing countries are also heavily affected by cholera due to not possessing or having access to effective sanitation
facilities which means that they would lack access to clean water. Additionally those who live in poorer/developing
countries would also be more at risk because they wouldn’t be able to afford treatment or an abundance of supplies,
meaning that they would have to share them with others. This would only encourage the spreading of cholera as infected
people wouldn’t be able to treat their disease and the sharing of contaminated items would only encourage the spreading
of the disease.
- Additionally the provision of clean, piped water that has been “chlorinated” to kill bacteria, vaccination programs, a good
sewage treatment infrastructure and a steady supply of usable antibiotics in severe cases would all help prevent cholera.

Prevention and control of malaria:

Biological factors:
- Due to malaria being spread mainly via insect vectors (“Anopheles mosquitoes”), reducing the number of these
mosquitoes in an area would reduce the chance of being bitten which would help prevent the disease.
- Additionally, using repellents/insecticides and mosquito nets would help to keep them away from humans.

Social factors:
- The widespread use of insecticides in homes/living spaces would kill off many mosquitoes. Additionally spreading oil over
the surfaces of water bodies that the mosquitoes breed in such as ponds and irrigation or even drainage ditches would kill
off their larvae as they wouldn’t be able to breathe due to the oil layer.
- Draining of marshes and other unnecessary bodies of water would also help. And if not having fishes or animals that fed off
of these larvae would also help, as it would be near impossible to kill off the mosquitoes in this way due to them being
able to lay eggs in puddles as well.
- Also the prevention of sharing of blood (unless necessary) and uncleaned medical equipment; specifically syringes, would
help.

Economical factors:
- “Prophylactic” drugs (drugs that prevent diseases such as chloroquine mefloquine) should be taken before, during and
after a visit to a location where malaria is prevalent. However, the use of these drugs has resulted in drug resistant strains
of the Plasmodium. Despite this the drugs are a key part of the prevention and making them more economically accessible
would be helpful.
- Additionally bed nets can be used to protect people whilst they sleep during the night when mosquitos are the most
active. If these nets could be freely distributed or at least at a low price it would be very beneficial for the protection
against malaria.
 - Additionally having good treatment centres and places where those with malaria can be helped would be extremely
beneficial.

Prevention and control of Tuberculosis (TB):

Biological factors:
- TB spreads quickly from person to person when droplets are released by coughing or sneezing of an infected person. When
the active form of the illness is inhaled by an uninfected person.
- Due to this a good way of prevention is isolating if you get the disease.
- Additionally taking the “BCG vaccine” (the only vaccine for TB). This vaccine protects up to 70-80% of those who receive
it. Although its effectiveness decreases with age unless the person is exposed to TB.
- The form that can be transmitted between cattle and humans (caused by Mycobacterium b ovis) can be prevented by.
Routinely testing cattle for TB and destroying those that test positive, pasteurising milk (kills any TB-causing bacteria in
the milk), ensuring the meat is cooked properly.

Social factors:
- Preventing the transmission of the disease by isolating.
- Prevention of contaminated cattle products from being consumed/used by humans.
- Ensuring everyone near a contaminated person has been vaccinated against the disease.

Economical factors:
- Ensuring that countries have full inventories of the vaccine as well as ensuring that there are treatment drugs (although
these may want to be used sparingly as it may cause mutations in the bacterium).
- Additionally ensuring that there are enough treatment centres where people who have gotten the disease are able to be
treated.
- Ensuring that there is a through checking of cattle products would allow for their safe consumption.

Prevention and control of HIV/AIDS:

Biological factors:
- Preventing the spread of HIV is very difficult as the virus has a long latent stage, which results in it being transmitted by
people who have the virus but show no symptoms and do not know they are infected.
- This occurs because the virus can change its surface proteins, making it difficult for the human immune system to
recognise it and for a vaccine to be developed.
- In order to prevent the transmission of HIV the following procedures should be used:
- Blood donations should be screened. And if the virus is found it should be heated to kill them.
- HIV-positive mothers and their babies can be treated with drugs (as HIV can be transmitted across the placenta,
during birth and through breast milk).
- Condoms, femidoms and dental dams should be used to decrease the risk of infection during sexual intercourse,
by forming a physical barrier between body and fluids.

Social factors:
- Education programmes about how the virus is transmitted can be released into the community in order to inform the
people and encourage a change in their behaviours in order to protect themselves and others.
- Intravenous drug users are encouraged not to share needles.
 - People should also try to be more wary of who they have sexual intercourse with as to not unknowingly get the disease.
- Contact tracing should be used for the virus.
- Public health measures. Blood screening and needle exchange programs to exchange old needles for new sterile ones
should be put in place.
- Encouraging high-risk groups such as male homosexuals, prostitutes, injecting drug users to be tested.
- The use and supply of retroviral drugs.

Economic factors:
- The socio-economic status of a person or country with HIV can determine how it is controlled. For example, HIV-positive
mothers are advised not to breastfeed in high-income countries, however, in low- and middle-income countries
breastfeeding offers protection against other diseases (eg. cholera).
- Ensuring that there are contraceptive devices that form a physical barrier being readily available to the public at low
prices.
- The facilities needed in order to screen/treat those with the virus.

5. Outline how penicillin acts on bacteria & why antibiotics don’t affect viruses.

Antimicrobial
- Fungi and viruses can also be a danger to humans, and they are targeted by antifungals and antivirals.
- The term antimicrobial is an umbrella term for anything that inhibits or kills microbial cells including antibiotics,
antifungals, antivirals and chemicals such as antiseptics (used to sterilise body surfaces) or disinfectants (used to sterilise
nonliving surfaces e.g benches.)

Penicillin and why it affects bacteria and not viruses:

- Antibiotics are drugs that kill or stop the growth of bacteria (prokaryotes) but do not harm the cells of the infected
organism.
- Some antibiotics are derived from living organisms such as penicillin which is produced by certain fungi in the genus
“Penicillium” whilst others are made synthetically in a laboratory.
- Antibiotics work by interfering with the growth or metabolism of the target bacterium. Antibiotics target a variety of
processes including:
- The synthesis of bacterial cell walls (THE MAIN ONE).
- Activity of proteins in bacterial cell surface membranes.
- Bacterial enzyme action.
- Bacterial DNA synthesis.
- Bacterial protein synthesis.

How penicillin affects bacteria.

- Bacterial cell walls are composed of peptidoglycans.

- These peptidoglycan molecules are held together by cross-links that form between them.
 - When a new bacterial cell is growing, it secretes enzymes known as “autolysins” that create small holes in the bacterial
cell wall.
- These holes allow the bacterial cell wall to stretch, with new peptidoglycan molecules then joining up via the cross links.
- The Penicillin interferes with cross linking between the peptidoglycan molecules properly in the last stages of cell wall
synthesis when the bacterium is dividing. This essentially prevents the bacterium from forming the peptidoglycan cell
walls.
- It does this through inhibiting the enzymes that catalyse their formation.
- However, the autolysins keep creating the holes in the bacterial cell walls, making the walls weaker.
- As bacteria live in water environments and take up water by osmosis, their weakened cell walls eventually burst as they
can no longer withstand the pressure exerted on them from within the cell.
- This means penicillin is only effective against bacteria that are still growing (Autolysins are no longer creating holes
and no more cross links between the peptidoglycan molecules are formed once the growth of a bacterium is complete, as
the bacterial cell wall no longer needs to expand.

- Penicillin (and other antibiotics) do not affect viruses as they do not have cells (or cell walls) and therefore cannot be
targeted in any of the ways that an antibiotic targets a bacterial cell.
- When a virus replicates, it uses the host cell’s mechanisms for transcription and translation, so not even these processes
can be targeted as antibiotics do not bind to the proteins that host cells use in these processes.
- Penicillin is not effective against all bacterial strains. One example is tuberculosis, because the bacteria may have:
- Thick cell walls which reduce permeability.
- Enzymes which break down penicillin.

Penicillin facts
 - It was discovered by Alexander Fleming (a Scottish biochemist) in 1928 but wasn’t usable until other chemists (Florey and
Chain) had developed upon his work.

Gram positive and Gram negative bacteria

Gram positive bacteria:

- Bacteria can be divided into two basic groups. Gram positive and gram
negative (after Hans Christian Gram in the 1800’s).
- Gram positive bacteria have a thick wall composed almost exclusively of
peptidoglycan and they absorb crystal violet dye very well. So they appear
purple. E.g Listeria, Streptococcus and Staphylococcus.

Gram negative bacteria:

- Gram negative bacteria have a layer of lipoproteins over a thin peptidoglycan
layer. This makes them much harder to stain and much harder for antibiotics to
destroy as the peptidoglycan layer is simply harder to “get at”.
- Gram negative bacteria stain red or pink. E.g Yersinia pestis (beware the silent
marmot) and E.coli.

6. Discuss the consequences of antibiotic resistance and the steps that can be taken to reduce its impact.

Resistance to Antibiotics:
- Within a bacterial population, there is a variation caused by mutations (as occurs in populations of all species).
- A chance mutation might cause some bacteria to become resistant to an antibiotic e.g penicillin.
- When the population is treated with this antibiotic the non-resistant bacteria die. Whilst the resistant bacteria don’t die.
- This means that the resistant bacteria can continue to reproduce with less competition from the non-resistant bacteria,
which are now dead.
- Therefore the genes for antibiotic resistance are passed on with a much greater frequency to the next generation.
- Due to bacteria only having one copy of each gene. A mutant gene will have an immediate effect on any bacteria
possessing it.
- Over time the whole population of bacteria becomes antibiotic-resistant because the antibiotic-resistant bacteria are best
suited to their environment.
- This is an example of natural selection where only those that are strong survive and the whole species evolves.
- Some pathogenic bacterium have become resistant to penicillin as the have acquired the genes that are required to code
for the production of the enzyme β-lactamase (also known as penicillinase), which breaks down penicillin.
Vertical transmission
- Bacteria reproduce asexually by binary fission; the DNA of the bacterial chromosome is replicated and the bacterial cell
divides in two, with each daughter cell receiving a copy of the chromosome.
- Bacteria reproduce like this very rapidly (on average, every 20 minutes).
- If one bacterium contains a mutant gene that gives it antibiotic resistance. All of its descendants will also have antibiotic
resistance.
- This method of spreading antibiotic resistance within a bacterial population is known as vertical transmission.

Horizontal transmission
- Plasmids (the small rings of DNA present in bacterial cells) often contain antibiotic resistant genes.
- These plasmids are frequently transferred between the bacteria.
- This occurs during “conjugation”; when a thin tube forms between two bacteria allowing them to exchange DNA. DNA
from the bacterial chromosome is also transferred in this way.
- In this way, a bacterium containing a mutant gene that gives it antibiotic resistance could pass this gene on to other
bacteria (even those of a different species). This is how “superbugs”, with multiple resistances, have been developed. E.g
Methicillin-resistant Staphylococcus aureus.
- This method of spreading antibiotic resistance is known as horizontal transmission.
 - Antibiotic resistance in bacteria is an example of natural selection that humans have helped to develop. This is due to the
overuse of antibiotics in situations where they were not really necessary or the incorrect use of antibiotics. E.g
- For treatment of non-serious infections.
- Routine treatment to animals in agriculture.
- Failure to finish the prescribed course of antibiotics.

Consequences of antibiotic resistance

- Commonly prescribed antibiotics are becoming less effective for many reasons, the main being:
- Overuse of antibiotics and antibiotics being prescribed when not necessary.
- Large scale use of antibiotics in farming to prevent disease when livestock are kept in close quarters, even when
animals are not sick.
- Patients failing to complete the full course of antibiotics prescribed by doctors.
- These factors have led to an increase in antibiotic resistance in bacteria.
- These bacteria become “superbugs”
- The most common example is a strain of “Staphylococcus aureus” which has developed a resistance to the power
antibiotic methicillin and is known as MRSA. It is also resistant to other antibiotics like penicillin.
- Bacteria living where there is a widespread use of different antibiotics may have plasmids containing resistance genes for
several different antibiotics, giving them multiple resistances and presenting a significant problem for doctors.
- Additionally resistance may first appear in a non-pathogenic bacterium but then be passed onto a pathogenic species via
horizontal transmission.

Reducing antibiotic resistance and its impacts

- Ways to prevent the incidence of antibiotic resistance increasing include:
- Tighter controls in countries where antibiotics are able to be sold without a prescription.
 - Doctors avoid the overuse of antibiotics. Only giving prescriptions when they’re needed.
- Antibiotics not being used in non-serious infections which the immune system can handle.
- The enforcement of finishing the entire course of the antibiotics to ensure the bacteria is dead.
- Antibiotics not being used for viral infections.
- The use of wider-spectrum antibiotics being reduced and using higher specificity towards certain
bacteria/infections.
- The type of antibiotics being prescribed is being changed so the same antibiotic is not always prescribed for the
same infections and diseases (this reduces the chance of a resistant strain developing).
- The use of antibiotics being reduced and more tightly controlled in industries such as agriculture.

- The spread of existing resistant strains can be limited by:

- Ensuring good hygiene practices such as handwashing and use of hand sanitisers.
- Isolating infected patients to prevent the spread of resistant strains.

Endotoxins and Exotoxins

Endotoxins:
- An endotoxin is the toxin within a bacterial cell (pathogen), which is only released when the cell dies/lyses.

Exotoxin:
- An exotoxin is the toxin within a bacterial cell (pathogen), which releases whilst the cell is growing/existing.
Immunity

Key Vocab
- Immune response: A complex series of responses of the body to the entry
of foreign antigen; it involves the activity of lymphocytes and phagocytes.
- Antigen: A substance/protein that is foreign to the body and stimulates an
immune response.
- Non-self: Refers to any substance or cell that is recognised by the immune
system as being foreign and so will stimulate an immune response.
- Self: Refers to substances produced by the body so that the immune
system does not recognise body cells as foreign, so they do not stimulate
an immune response. This involves cell signalling.
- The immune system: The immune system is what fights against antigens
and pathogens, protecting the body from invading cells. It has non-specific
and specific responses to pathogens.
- Autoimmune diseases: These are the result of failures in the immune system to distinguish between self and non-self.
Examples include lupus, coeliac disease and type 1 diabetes amongst many others.

1. Describe the mode of action of phagocytes (macrophages & neutrophils)

- Phagocytes are white blood cells that are produced

continuously in the bone marrow.
- They are stored in the bone marrow before being distributed
around the body in the flood.
- They are responsible for removing dead cells and invasive
microorganisms.
- They carry out what is known as the non-specific immune
response.
- There are two types of phagocytes, each with a specific
mode of action. The two types are:
- Neutrophils.
- Macrophages.
- Phagocytes recognise the foreign antigen on the surface
membrane of a pathogen and engulf them by extending
pseudopodia (false arms) around them.
- The pathogen is contained in a vesicle called a phagosome.
- This fuses with a lysosome, which contains hydrolytic enzymes to digest the contents of the phagosome.

Neutrophils
 - Neutrophils travel throughout the body and often leave the blood by squeezing through capillary walls to ‘patrol’ the
body tissues.
- During an infection, they are released in large numbers from their stores.
- However they are short-lived cells (i.e they have a short lifespan).
- Modes of action:
- Chemicals that are released by pathogens, as well as chemicals released by the body cells which are under attack
(e.g histamine), attract neutrophils to the site where the pathogens are located (this response to chemical stimuli
is called Chemotaxis).
- Neutrophils move towards pathogens (which may be covered in antibodies).
- The antibodies are another trigger to stimulate neutrophils to attack the pathogen (neutrophils have receptor
proteins on their surfaces that recognise antibody molecules and attach to them).
- Once attached to a pathogen, the cell surface membrane of a neutrophil extends out and around the pathogen,
engulfing it and trapping the pathogen within a “phagocytic vacuole”.
- This part of the process is known as endocytosis.
- The neutrophil then secretes digestive enzymes into the vacuole (these enzymes are released from the lysosomes
which fuse with the phagocytic vacuole).
- These digestive enzymes destroy the pathogen.
- After killing and digesting the pathogens, the neutrophils die.
- Pus is a sign that this has occurred as it shows dead neutrophils.

Macrophages
 - Macrophages are larger than neutrophils and are long-lived cells (i.e they have a long lifespan).
- Rather than remaining in the blood, they move into organs including the lungs, liver, spleen, kidney and lymph nodes.
- After being produced in the bone marrow, macrophages travel in the blood as monocytes, which then develop into
macrophages once they leave the blood to settle in the various organs (the ones above).
- Modes of action:
- Macrophages play a very important role in initiating an immune response.
- Although they carry out phagocytosis, they do not destroy pathogens completely.
- They cut the pathogens up so that they can display the antigens of the pathogen on their surface (through a
structure called the major histocompatibility complex).
- These displayed antigens (the cell is now called an “Antigen-presenting cell”) can then be recognised by
lymphocytes; another type of white blood cell.

2. Explain what is meant by an antigen and state the difference between self antigens and non-self antigens

- Every cell in the human body has markers that identify it.
- Microorganisms (both pathogenic and nonpathogenic) such as bacteria and viruses also have their own unique markers.
- These markers are called antigens (which are macromolecules) and they allow cell-to-cell recognition.
- Antigens are found on cell surface membranes, bacterial cell walls, or the surfaces of viruses.
- Some glycolipids and glycoproteins on the outer surface cell surface membranes act as antigens.

- Antigens can either be self antigens or non-self antigens.

- Antigens produced by the organism’s own body; those that the immune system does not recognise as foreign
antigens, are known as self antigens.
- Self antigens do not stimulate the immune system, and as such don’t cause an immune response.
- Antigens not produced by the organism’s own body; those that the immune system recognises as being foreign,
e.g the antigens found on pathogenic bacteria and viruses or if a person receives a different blood type during a
transfusion, are known as non-self antigens.
- Non-self antigens do stimulate the immune system, and as such cause an immune response.

3. Describe the sequence of events that occurs during a primary immune response with reference to the roles of:
• Macrophages
• B-lymphocytes, including plasma cells
• T-lymphocytes, limited to T-helper cells and T-killer cells

Primary immune response

- Lymphocytes are another type of white blood cell.
- They play an important role in the “specific immune response”
- They are smaller than phagocytes.
- They have a large nucleus that fills most of the cell.
- They are produced in the bone marrow before birth.
- There are two types of lymphocytes (with different modes of action):
 - B-lymphocytes (B cells)
- T-lymphocytes (T cells)

B-lymphocytes
- B-lymphocytes remain in the bone marrow until they mature and then spread throughout the body. Concentrating in
lymph nodes and the spleen.
- Millions of types of B-lymphocyte cells are produced within us because as they mature the genes coding for antibodies are
changed to code for different antibodies.
- Once mature, each type of B-lymphocyte cell can make one type of antibody.
- At this stage, the antibody molecules do not leave the B-lymphocyte but remain in the cell surface membrane.
- Part of each antibody molecule forms a glycoprotein receptor that can combine specifically with one type of antigen.

- When an antigen enters the body for the first time, the small number of b-lymphocytes with receptors complementary to
that antigen are stimulated to divide by mitosis.
- This is known as clonal selection.
- As these clones divide repeatedly by mitosis (the clonal expansion stage) the result is large numbers of identical B-
lymphocytes being produced over a few weeks.
- During an immune response, these B-lymphocytes then for two types of cells:
- Some of these B-lymphocytes become “plasma cells” that secrete lots of antibody molecules (specific to the
antigen) into the blood, lymph or linings of the lungs and the gut.
- These plasma cells are short lived (short life span); their numbers drop off after several weeks. But the antibodies
they have secreted stay in the blood for a longer time.
- The other B-lymphocytes become “Memory cells” that remain circulating in the blood for a long time (potentially
even decades).
- This response to a newly encountered antigen is relatively slow and is known as the primary immune response.
T-lymphocytes
- Immature T-lymphocytes leave the bone marrow to mature in the thymus.
- Mature t-lymphocytes have specific cell surface receptors called T cell receptors.
- These receptors have a similar structure to antibodies and each are specific to one antigen.

- T-lymphocytes are “activated” when they encounter and bind to their specific antigen that is being presented by one of
the host’s cells. Usually macrophages.
- This antigen presenting cell is likely to be a macrophage or maybe a body cell that has been invaded by a pathogen and is
displaying the antigen on its cell surface membrane.
- These activated T-lymphocytes, those that have receptors specific to the antigen. Divide by mitosis to increase in numbers
(similar to the clonal selection and clonal expansion of B-lymphocytes).
- These T-lymphocytes then differentiate into two main types of T-cells:
- Helper T cells
- Killer T cells
- Helper T cells release cytokines (hormone-like signals) that stimulate B-lymphocytes to divide and develop into antibody
secreting plasma cells. Some helper T cells secrete cytokines that stimulate macrophages to increase their rates of
phagocytosis.
- Killer T cells attach to the antigens on the cell surface membrane of infected cells and secrete toxic substances that kill
both the body cells, along with the pathogen inside.
4. Explain the role of memory cells in the secondary immune response and in long-term immunity

Memory cells and long term immunity

- During an immune response. B-lymphocytes form two types of cells: plasma and memory cells.
- Memory cells form the basis of immunological memory. These cells can last for many years and often a lifetime.
- There are two types of immune response:
- Primary immune response (responding to a newly encountered antigen).
- Secondary immune response (responding to a previously encountered antigen).

Primary immune response

- When an antigen enters the body for the first time, the small number of B-lymphocytes with receptors complementary to
that antigen are stimulated to divide via mitosis.
- This is called clonal selection.
- As these clones divide repeatedly by mitosis (the clonal expansion stage) the result is large numbers of identical B-
lymphocytes being produced over a few weeks.
- Some of these B-lymphocytes become plasma cells that secrete lots of antibody molecules (specific to the antigen) into
the blood, lymph or linings of the lungs and the gut.
- These plasma cells are short-lived (their numbers drop off after several weeks) but the antibodies they have secreted stay
in the blood for a longer time.
- The other B-lymphocytes become memory cells that remain circulating in the blood for a long time.
 - This response to a newly encountered pathogen is relatively slow.

Secondary immune response

- If the same antigen is found in the body a second time, the memory cells recognise the antigen, divide very quickly and
differentiate into plasma cells; to produce antibodies and more memory cells.
- This response is very quick, meaning that the infection can be destroyed and removed before the pathogen population
increases too much and symptoms of the disease develop.
- This response to a previously encountered pathogen is extremely fast when compared to the primary immune response,

- T-lymphocytes also play a part in the secondary immune response.

- They differentiate into memory cells, producing two main types:
- Memory helper T-cells
- Memory killer T-cells
- Just like the memory cells formed from B-lymphocytes, these memory T cells remain in the body for a long time.
- If the same antigen is found in the body a second time, these memory T cells become active very quickly.
5. Relate the molecular structure of antibodies to their functions

Structure
- Antibodies are globular glycoproteins called immunoglobulins.
- Antibodies have a quaternary structure; which is represented as Y shaped. With two ‘heavy/long’ polypeptide chains
bonded by disulfide bonds to two ‘light/short’ polypeptide chains.
- Each polypeptide chain has a constant region and a variable region.
- The constant regions do not vary within a class (isotype) of antibodies but do vary between the classes. The constant
region determines the mechanism used to destroy the antigens.
- There are 5 classes of mammalian antibodies each with different roles.

- The amino acid sequence in the variable regions of the antibodies; the tips of the “Y”, are different for each antibody. The
variable region is where the antibody attaches to the antigen to form an “antigen-antibody complex”.
- At the end of the variable region is a site called the antigen binding site. Each antigen binding site is generally composed
of 110 to 130 amino acids and includes both the ends of the light and heavy chains.
- The antigen binding sites vary greatly which gives the antibody specificity for binding to antigens. The sites are specific to
the epitope (the part of the antigen that binds to the antibody).
- A pathogen or virus may also have multiple different antigens meaning that multiple different antibodies must be
produced.
- The ‘hinge’ region (where the disulfide bonds join the heavy chains) gives flexibility to the antibody molecule which allows
the antigen binding site to be placed at different angles when binding to antigens.
- This region is not present in all classes of antibodies.
- Disulfide bonds are covalent bonds so they provide strength and stability to the antibody.

Function
- Antibodies are produced by B-lymphocytes.
- Antibodies bind to specific antigens which triggers the specific immune response. Every antigen has one antibody.
- Antibodies are divided into five major classes (isotypes), each with a different role
- The function of antibodies differ:
- Antibodies can combine with viruses and toxins of pathogens (e.g bacteria) to block them from entering or
damaging cells.
- Antibodies can act as anti-toxins by binding to toxins produced by pathogens (e.g the bacteria that causes
diphtheria and tetanus) which neutralises them making them harmless. They can also prevent the toxins from
entering the cells.
- Antibodies can attach to bacteria making them readily identifiable to phagocytes, this is called opsonization.
Once identified, the phagocytes has receptor proteins for the heavy polypeptide chains of the antibodies, which
makes it easier for phagocytes to do phagocytosis.
- Antibodies act as agglutinins causing pathogens carrying antigen-antibody complexes to clump together, this is
known as agglutination. This reduces the chance that the pathogens will spread through the body and makes it
possible for phagocytes to engulf a number of pathogens at one time.
- Antibodies together with other molecules can create holes in the cell walls of pathogens causing them to burst
(lyse) when water is absorbed by osmosis, (similar to antibiotics and peptidoglycan).
6. Outline the hybridoma method for the production of monoclonal antibodies

The Hybridoma Method

- Monoclonal antibodies are artificially produced antibodies produced from a single B-cell clone.
- The hybridoma method is a method used to make monoclonal antibodies (Mabs).
- The method enables large quantities of identical antibodies to be produced.
- The hybridoma method solved the problem of having B-cells that could divide by mitosis but not produce antibodies and
plasma cells that could produce antibodies but not divide.
- This method was established/discovered in the 1970s.
- Monoclonal antibodies bind antigens, in the same way naturally produced antibodies do.

- They are produced by injecting mice with an antigen that stimulates the production of antibody producing plasma cells.
- Isolated plasma cells from the mice fused with immortal tumour cells (cultured myeloma cells), which resulted in
hybridoma cells.
- These hybrid cells are grown in a selective growth medium and screened for the production of the desired antibody.
 - They are cultured to produce large numbers of monoclonal antibodies.
- Monoclonal antibodies have multiple applications to include diagnostics, treating disease, food safety testing and
pregnancy testing.

7. Outline the principles of using monoclonal antibodies in the diagnosis

of disease and in the treatment of disease

Diagnostic uses of monoclonal antibodies

- Monoclonal antibodies can be used diagnostically for:
- Pregnancy tests
- Diagnosing HIV
- Detecting the presence of pathogens such as Streptococcus bacteria
- Distinguishing between Herpes I and Herpes II
- Blood typing before transfusions and tissue typing before transplants
- Detecting the presence of antibiotics in milk
- Detecting cancer cells

- Monoclonal antibodies can be used to test whether or not somebody is pregnant. This is done through a pregnancy kit.
 - The kit contains a dipstick with an absorbent pad.
- On the surface of the pad are hCG-specific monoclonal antibodies bound to particles of gold (one of the reasons
they’re not cheap).
- When the pad is dipped into a urine sample any hCG will bind to the antibodies and be carried upwards as the
urines seeps up the stick.
- Further up the dipstick is a line of immobilised hCG antibodies. When the hCG-antibody-gold complexes reach this
area they bind and are held fast.
- As more and more complexes arrive they form a coloured line. This is a positive result.
- Further along the dipstick is a second line of immobilised antibodies (the procedural control region).
- This second line binds with any hCG antibodies without the hormone hCG.
- A coloured line in this second region (but no coloured line in the first area) will confirm that the woman is not
pregnant.

- Monoclonal antibodies can also be used to locate the position of blood clots for patients thought to have deep vein
thrombosis. This occurs by:
- Injecting a mouse with human fibrin (the main protein found in blood clots).
- This activates the plasma cells to produce antibodies against fibrin.
- These cells are collected from the mouse spleen.
- The plasma cells are then fused with tumour cells forming hybridomas that produce antifibrin antibodies.
- To detect where the antibodies are binding to fibrin molecules, a radioactive chemical (producing gamma
radiation) is attached to the antibodies making them radioactively labelled.
- A gamma-ray camera is used to detect where these radioactively labelled antibodies have attached to a fibrin
molecule, hence indicating where blood clots can be found.
- Monoclonal antibodies in treatment. The monoclonal antibodies can be used to deliver drugs to cancer cells.
- They have been called ‘magic bullets’, because they can pick out just the cancer cells, avoiding harm to other
body cells.
- Once monoclonals have been made to match up with a protein on the surface of the cancer cells, molecules of an
anti-cancer drug are attached.

- Disadvantages:
- It can be very difficult (and incredibly expensive) to develop specific procedures that produce antibodies
that only bind to cancer cells.
- Monoclonals produce by mice can be sometimes be recognised as ‘foreign’ by the patient’s body and be
destroyed by the immune system.

- Advantages:
- Monoclonal antibodies are usually specific to only the cancerous cells and therefore there are few or no
side effects which is much better for the patient compared to chemotherapy alone.
- They are often used in combination with other forms of treatment to increase their effectiveness and
reduce side effects.
 - Example:
- Herceptin is a monoclonal antibody that is used as part of a regime of treatment for breast cancer.
- Herceptin works on the surface of the cancer cells that register as HER2 receptor positive on the surface
by blocking the chemical signals that can stimulate this uncontrolled growth.
- By binding to the receptor it slows down the rate of cell division. The antibody-antigen complex makes it
easier for the immune system to identify the complex as foreign and so be ingested by phagocytosis.

- Therapeutic uses of monoclonal antibodies. Therapeutically monoclonal antibodies have multiple applications to include:
- Treatment for the rabies virus, (which can be potentially fatal), by injecting purified antibodies.
- The prevention of transplanted organ rejection, achieved by intervening with the T cells involved in the rejection
process.
- Autoimmune therapies for allergic asthma and rheumatoid arthritis; here monoclonal antibodies are able to bind
and deactivate factors involved in the inflammatory response.
- Treatment for diseases caused by the overproduction or inappropriate production of B-cells (eg. leukaemia,
multiple sclerosis and myasthenia gravis); the antibody (rituximab) binds to cell surface receptor proteins on B-
cells (not plasma cells) and causes the death of the cells.
- Prevention of blood clotting following angioplasty procedures; here monoclonal antibodies bind to receptors on
the platelet surface thereby inhibiting fibrinogen from binding and subsequent clotting from ensuing.
- Targeted treatment of breast cancer; Herceptin (trastuzumab) is a monoclonal antibody used to treat breast
cancer, it recognises receptor proteins on the surface of cancer cells and binds to them allowing the immune
system to identify and destroy them.
- Treatment of melanoma (a type of skin cancer); the antibody (ipilimumab) binds to a protein produced by T-cells
(whose role is to reduce the immune response) which results in the immune system remaining active against the
cancer cells.

- Using monoclonal antibodies as a treatment requires multiple administrations and this can cause problems.
- Initially the monoclonal antibodies were produced by mice, rabbits or other laboratory animals (as these were easier to
produce), however this triggered an immune response when they were introduced to humans.
- Scientists have largely overcome this by:
- Genetically modifying the antibody polypeptide chains so that the amino acid sequences are now human not
mouse or rabbit sequences.
- Altering the type and position of the sugar groups (antibodies are glycoproteins) attached to the heavy
polypeptide chains to reflect those found on human antibodies.

8. Describe the differences between active immunity and passive immunity and between natural immunity and artificial
immunity

Active immunity
- Active immunity is acquired when an antigen enters the body triggering a specific immune response (antibodies are
produced).
- Active immunity is naturally acquired through exposure to microbes or artificially acquired through vaccinations.
- The body produces memory cells, along with plasma cells, in both types of active immunity giving the person long-term
immunity.
 - In active immunity, during the primary response to a pathogen (natural) or to a vaccination (artificial), the antibody
concentration in the blood takes one to two weeks to increase. If the body is invaded by the same pathogen again or by
the pathogen that the person was vaccinated against then, during the secondary response, the antibody concentration in
the blood takes a much shorter time to increase and is higher than after the vaccination or the first infection.

Passive immunity
- Passive immunity is acquired without an immune response. Antibodies are not produced by the infected person.
- As the person’s immune system has not been activated then there are no memory cells that can produce antibodies in a
secondary response. If a person is reinfected they would need another infusion of antibodies.
- Depending on the disease a person is infected with (e.g tetanus) they may not have time to actively acquire the immunity,
that is, there is no time for active immunity. So passive immunity occurs either artificially or naturally.
- Artificial passive immunity occurs when people are given an injection/transfusion of the antibodies. In the case of
tetanus this is an antitoxin. The antibodies were collected from people whose immune system had been triggered by a
vaccination to produce tetanus antibodies.
- Natural passive immunity occurs when:
- Foetuses receive antibodies across the placenta from their mothers.
- Babies receive the initial breast milk from mothers (the colostrum) which delivers a certain isotype of antibody
(IgA).
9. Explain that vaccines contain antigens that stimulate immune responses to provide long-term immunity

- A vaccine is a suspension of antigens that are intentionally put into the body to induce artificial active immunity. A
specific immune response where antibodies are released by plasma cells.
- There are two main types of vaccines:
- Live attenuated vaccines
- Inactivated vaccines.

- Vaccines are administered either by injection or orally.

- The vaccinations given by injection can be into a vein or muscle.
- Vaccinations produce long term immunity as they cause memory cells to be created. The immune system remembers the
antigen when reencountered and produces antibodies to it, in what is a faster and stronger secondary response.
 - Vaccines can be:
- Highly effective with one vaccination giving a lifetime’s protection (although less effective ones will require
booster/subsequent injections).
- Generally harmless as they do not cause the disease they protect against because the pathogen is killed by the
primary immune response.

- Unfortunately there can be problems with vaccines:

- People can have a poor response (e.g they are malnourished and cannot produce the antibodies - proteins or their
immune system may be defective).
- A live pathogen may be transmitted to others in the population (ideally enough people are vaccinated at the same
time to give herd immunity; where even if one gets it lots of others are vaccinated which means that these
vaccinated people cannot pass it to non vaccinated people as they themselves are protected.)
- Antigenic variation : The variation (due to major changes) in the antigens of pathogens causes the vaccines to
not trigger an immune response or diseases caused by eukaryotes (e.g malaria) have too many antigens on their
cell surface membranes making it difficult to produce vaccines that would prompt the immune system quickly
enough.
- Antigenic concealment - This occurs when the pathogen ‘hides’ from the immune system by living inside cells or
when the pathogen coats their bodies in host proteins or by parasites immune cells such as macrophages and T
cells (e.g HIV). Or by remaining in parts of the body that are difficult for vaccines to reach (e.g Vibrio cholerae
which remains in the small intestine).
- Edward Jenner was the one who discovered the underpinning principles of vaccinations back in the 1700s where he created
the first smallpox vaccine.

Live attenuated vaccines

- Live attenuated vaccines contain whole pathogens (e.g bacteria and viruses) that have been ‘weakened’
- These weakened pathogens multiply slowly allowing the body to recognise the antigens and trigger the primary immune
response. Where the plasma cells produce antibodies.
- These vaccines tend to produce a stronger and longer lasting immune response.
- They can be unsuitable for people with weak immune systems as the pathogen may divide before sufficient antibodies can
be produced.
- An example of this type of vaccine is the MMR (Measles, Mumps and Rubella).

Inactivated vaccines
- Inactivated vaccines contain whole pathogens that have been killed (‘whole killed’) or small parts (‘subunit’) of the
pathogens (e.g proteins or sugars or harmless forms of the toxins - toxoids).
- As inactivated vaccines do not contain living pathogens they cannot cause disease, even for those with weak immune
systems.
- However these vaccines do not trigger a strong or long lasting immune response, unlike the live attenuated vaccines.
Repeated doses and or booster doses are often required.
- Some people may have allergic reactions or local reactions (e.g sore arm) to inactivated vaccines as adjuvants may be
conjugated with the subunits of the pathogen to strengthen and lengthen the immune response.
- An example of a whole killed vaccine is polio vaccine. An example of a toxoid subunit vaccine; where inactivated versions
of the toxins produced by pathogens are used), is Diphtheria.
10. Explain how vaccination programmes can help to control the spread of infectious diseases

- With the exception of the great success story surrounding the eradication of Smallpox following a ten year global initiative
in 1980 no other pathogen has been eradicated globally since then.
- Smallpox was able to be eradicated because a ‘live attenuated’ vaccine was used against the only strain of the virus. There
was also a programme of surveillance, contact tracing and ‘ring’ vaccinations.
- There are many safe and effective vaccines that do exist against many pathogens and these have managed to push a
number of childhood diseases to the verge of extinction.
- Vaccines against such diseases as mumps, chicken pox and whooping cough are administered to children as part of an
immunisation schedule and they successfully confer immunity.
- As a result many childhood diseases are kept at low levels within populations due to herd immunity.
- Herd immunity arises when a sufficiently large proportion of the population has been vaccinated (and are therefore
immune) which makes it difficult for a pathogen to spread within that population, as those not immunised are protected
and unlikely to contract it as the levels of the disease are so low.
- Although most vaccinations are given to children there are some vaccines that are provided at later stages in life, for
example vaccinations for tuberculosis (TB) and Hepatitis B are offered to frontline medical workers who have a higher risk
of coming into contact with such diseases in the hospital setting;

- Travellers may be advised to take particular vaccines if travelling to areas where certain diseases are endemic
such as Yellow Fever in parts of Africa.
Transport in Plants

Plant Transverse Sections

Dicotyledonous (dicots) plants:

- Dicotyledonous (dicots) plants have:
- Seeds that contain two cotyledons (seed leaves).
- Network of veins.
- Leaves that typically have broad blades (leaf surface) and petioles (stalks).
- Tap root with lateral branches.

Transport systems
- Plants need transport systems to meet their metabolic demands (glucose, hormones, mineral ions are required for various
processes within plants), to efficiently move substances up and down and to compensate for their relatively small
surface area to volume ratio (generally plants are unable to rely on diffusion alone).
- Plants have a vascular system which involves a network of vessels (vascular tissue) running through the leaves, stem and
roots. These three parts are the main organs involved in transport.
- The vascular system is comprised of two distinct types:
- Xylem (transports water and mineral ions from the roots to the rest of the plant).
- Phloem (transports substances from the source (e.g leaf) to the sink (e.g root).
- The xylem and phloem are arranged together in vascular bundles.
- The bundles are laid out differently in the leaves, stem and roots.

1. Describe the distribution of xylem and phloem in transverse sections of stems, roots and leaves of herbaceous
dicotyledonous plants.

Xylem
- The functions of xylem tissue in a plant are:
 - Vascular tissue that carries dissolved minerals and water up the plant.
- Structural support.
- Food storage.

- Xylem tissue is found, along with phloem tissue and other tissues, in vascular bundles.
- The location of the vascular bundles is dependent on which organ they are in as the different organs are under different
stresses:
- In the roots the vascular bundle is found in the centre and the centre core of this is xylem tissue. This helps the
roots withstand the pulling strains they are subjected to as the plant transports water upwards and grows.
- In the stems the vascular bundles are located around the outside and the xylem tissue is found on the inside
(closest to the centre of the stem) to help support the plant.
- In the leaves the vascular bundles form the midrib and veins and therefore spread from the centre of the leaf in a
parallel line. This xylem tissue is found on the upper side of the bundles (closest to the upper epidermis).

Phloem
- The function of phloem tissue in a plant is to:
- Transport organic compounds, particularly sucrose, from the source (e.g leaf) to the sink (e.g roots). The
transport of these compounds can occur up and down the plant.

- Phloem is a complex tissue also made up of various cell types; its bulk is made up of sieve tube elements which are the
main conducting cells and the companion cells.
- Other cell types of phloem tissue also include parenchyma for storage and strengthening fibres.
- The location of the vascular bundles is dependent on which organ they are in as the different organs are under different
stresses:
- In the roots the vascular bundle is found in the centre and on the edge of the centre core is the phloem tissue.
- In the stems, the vascular bundles are located around the outside and the phloem tissue is found on the outside
(closest to the epidermis).
- In the leaves, the vascular bundles form the midrib and veins and therefore spread from the centre of the leaf in a
parallel line. The phloem tissue is found on the lower side of the bundles (closest to the lower epidermis).
2. Relate the structure of xylem vessel elements, phloem sieve tube elements and companion cells to their functions.

Xylem Vessel Elements: Structure and Function

- The functions of xylem tissue in a plant are:

- Vascular tissue that transports dissolved minerals and water around the plant.
- Structural support.
- Food storage.
- Xylem tissue is made up of four cell types that function together:
1. Tracheids (long, narrow tapered cells with pits).
2. Vessel elements (large with thickened cell walls and no end plates when mature).
3. Xylem parenchyma.
4. Sclerenchyma cells (fibres and sclereids).

- Most of the xylem tissue is made up of tracheids and vessel elements, which are both types of water-conducting cells.
Phloem Sieve Tube Elements and Companion Cells: Structure and Function
- The function of phloem tissue in a plant is to:
- Transport organic compounds (assimilates), particularly sucrose, from the source (e.g leaf) to the sink (e.g roots).
The transport of these compounds can occur up and down the plant.

- The organic compounds are dissolved in water to form sap.

- Phloem is a complex tissue made up of various cell types; its bulk is made up of sieve tube elements which are the main
conducting cells and companion cells.
- Other cell types of phloem tissue also include the parenchyma for storage and strengthening fibres.
- Mature phloem tissue contains living cells, unlike xylem tissue.
Sieve tube elements
- Sieve tube elements line up end to end to form a continuous tube.

Companion cells
- Each sieve tube element has a companion cell associated with it as companion cells control the metabolism of their
associated sieve tube member.
- They also play a role in loading and unloading of sugars into the phloem.
3. State that some mineral ions and organic compounds can be transported within plants dissolved in water.
4. describe the transport of water from the soil to the xylem through the:
• apoplast pathway, including reference to lignin and cellulose
• symplast pathway, inc. ref. to the endodermis, Casparian strip and suberin

Water and mineral ion transport: Pathways and Mechanisms

- Within a plant mineral ions and organic compounds (e.g sucrose) are transported around by being dissolved in water.
The dissolved mineral ions are transported in the xylem tissue and the dissolved organic compounds are transported in
the phloem tissue.
- The plant roots are responsible for the uptake of water and mineral ions and can have root hairs to increase the surface
area for absorption of the substances.
- The uptake of water is a passive process and occurs by osmosis.
- The uptake of minerals can be passive or active and occurs by diffusion or active transport respectively.
- Plants must take in a constant supply of water and dissolved minerals to compensate for the continuous loss of water via
transpiration in the leaves, and so that they can photosynthesise and produce proteins.
- There are two pathways that water (and the dissolved solutes) can take to move across the cortex (and the molecules can
change between routes at any time):
- Apoplastic
- Symplastic

Apoplastic pathway
- Most water travels via the apoplastic pathway (when transpiration rates are high), which is the series of spaces running
through the cellulose cell walls, dead cells, and the hollow tubes of the xylem.
- The water moves by diffusion (as it is not crossing a partially permeable membrane).
- The water is able to move from cell wall to cell wall directly or through the intercellular spaces.
- The movement of water through the apoplastic pathway occurs more rapidly than the symplastic pathway.
- When the water reaches the endodermis the presence of a thick, waterproof, waxy band of suberin within the cell walls
blocks the apoplastic pathway.
- This band is called the Casparian strip and forms an impassable barrier for the water.
- When the water and dissolved minerals reach the Casparian strip they must take the symplastic pathway. While the
presence of the strip is not fully understood it is thought that it may help the plant control which mineral ions reach the
xylem and generate root pressure.
- As the plant ages the Casparian strip thickens (as more suberin is deposited) except in cells called the passage cells,
allowing for further control of the mineral ions.

Symplastic pathway
- A smaller amount of water via the symplastic pathway. Which is the cytoplasm and plasmodesmata or vacuole of the
cells.
- The water moves by osmosis into the cells (across the partially permeable cell surface membrane), possibly into the
vacuole (through the tonoplast by osmosis) and between cells through the plasmodesmata.
 - The movement of water in the symplastic pathway is slower than the apoplastic pathway.

5. Explain that transpiration involves the evaporation of water from the internal surfaces of leaves followed by diffusion of
water vapour to the atmosphere.

Transpiration
- Summary Description:
Transpiration is the loss of water vapour (water) from a plant to its environment by diffusion. The main site of transpiration
is the internal surfaces of the plant’s leaves, mainly occurring at the stomata. Transpiration makes up for approximately
99% of the plant’s total water loss. Transpiration is also a method of cooling for plants and it also allows for the
transpiration stream to exist which aids in the uptake of mineral ions.

- The movement of water through a plant's xylem is largely due to the evaporation of water vapour from the leaves and
the cohesive and adhesive properties exhibited by molecules.
- It is the gradient in water potential that is the driving force permitting the movement of water from the soil (higher water
potential) to the atmosphere (lower water potential), via the plant’s cells.
- Plants are constantly taking water in at their roots and losing water via the stomata (in the leaves).
- Around 99% of the water absorbed is lost through evaporation from the plant’s stem and its leaves in a process called
transpiration.
- Transpiration refers to the loss of water vapour from a plant to its environment by diffusion and the transpiration
stream refers to the movement of water from the roots to the leaves.
 - The advantage of transpiration is that:
- It provides a method of cooling the plant via evaporative cooling.
- The transpiration stream is helpful in the uptake of mineral ions.
- The turgor pressure of the cells (due to the presence of water as it moves up the plant) provides support to leaves
(enabling an increased surface area of the leaf blade) and the stem of non-woody plants.

Movement of water through leaves

- Certain environmental conditions (e.g low humidity, high temperatures) can cause a water potential gradient between the
air inside the leaves (higher water potential) and the air outside (lower water potential) which results in water vapour
diffusing out of the leaves through the stomata (Transpiration).
- The water vapour lost by transpiration lowers the water potential in the air spaces surrounding the mesophyll cells.
- The water within the mesophyll cell walls evaporates into these air spaces resulting in a transpiration pull.
- This transpiration pull results in water moving through the mesophyll cell wall (Apoplastic pathway) or out of the
mesophyll cytoplasm (Symplastic pathway) into the cell wall.
- The pull from the water moving through the mesophyll cells results in water leaving the xylem vessels through pits (non-
lignified areas), which then cause water to move up the xylem vessels (due to the cohesive and adhesive properties of the
water). This movement is called the transpiration stream.
- When rates of transpiration are high the walls of the xylem are pulled inwards by the faster flow of water.

The role of the stomata

- Transpiration is mainly controlled by the pairs of guard cells that surround the stomata (plural, stoma is singular).
- Guard cells open the stomata when they are turgid and close the stomata when they lose water.
- When the stomata are open there is a greater rate of transpiration and of gaseous exchange.
- When the stomata close transpiration and gaseous exchange decreases.
- As stomata allow gaseous exchange (CO2 in and O2 out) they are generally open during the day.
6. Explain how hydrogen bonding of water molecules is involved with movement of water in the xylem by cohesion-tension in
transpiration pull and by adhesion to cellulose in cell walls.

The movement of water:

- Water has unique properties:

- It is polar
- Hydrogen bonds form between the water molecules

- Water moves from the roots to the leaves because of a difference in the water potential gradient between the top and
bottom of the plant. This gradient is created because of different events occurring within the plant and due to the
properties of water.
- In the leaves, water evaporates from the mesophyll cells resulting in the water (and any dissolved solutes) being pulled
from the xylem vessels (transpiration pull) into the mesophyll cells.
- The water that is pulled into the mesophyll cells moves across them passively (either via apoplastic diffusion or symplastic
osmosis pathways) lowering the hydrostatic pressure within the xylem vessels which creates a tension on these vessels.
- Xylem vessels have lignified walls to prevent them from collapsing due to the pressure differences being created from the
mass flow (all the water molecules and any dissolved solutes move together) of water upwards.
- The mass flow is helped by the polar nature of water and the hydrogen bonds that form between water molecules which
results in cohesion between water molecules and adhesion between the cellulose in the cell walls and the water
molecules.
- So due to the evaporation of water from the mesophyll cells in the leaves a tension is created in the xylem tissue which is
transmitted all the way down the plant because of the cohesiveness of water molecules. The cohesive force results in a
continuous column of water with high tensile strength and the adhesive force stops the water column from pulling away
from the walls of the xylem vessels so the water is pulled up the xylem tissue from the roots to replace what was lost in
the leaves, This mechanism is called the cohesion-tension theory.

The transpiration stream

- The pathway of the water from the soil through the roots up the xylem tissue to the leaves is the transpiration stream.
- Plants aid the movement of water upwards by raising the water pressure in the roots (root pressure).
- This is raised by actively secreting solutes (e.g mineral ions) into the xylem vessels in the root which lowers the
water potential in the xylem.
- This results in the water from the surrounding cells being drawn into the xylem by osmosis thus increasing the
water pressure/root pressure.

- Root pressure helps move water into the xylem vessels in the roots however the volume moved does not contribute
greatly to the mass flow of water to the leaves in the transpiration stream.
7. State that assimilates dissolved in water, such as sucrose and amino acids, move from sources to sinks in phloem sieve
tubes.

Movement in the Phloem

- Although translocation could refer to the transport of substances in the xylem and phloem, as it means ‘moving from one
place to another,’ it is more commonly connected with the transport of assimilates in the phloem tissue.
- Thus translocation within phloem tissue can be defined as the transport of assimilates from source to sink and requires
the input of metabolic energy (ATP).
- The liquid that is being transported (found within phloem sieve tubes) is called phloem sap.
- This phloem sap consists not only of sugars (mainly sucrose) but also of water and other dissolved substances such as
amino acids, hormones and minerals.

- The source of the assimilates could be:

- Green leaves and green stem (photosynthesis produces glucose which is transported as sucrose, as sucrose has
less of an osmotic effect than glucose).
- Storage organs e.g tubers and tap roots (unloading their stored substances at the beginning of a growth period).
- Food stores in seeds.

- The sinks (where the assimilates are required) could be:

- Meristems (apical or lateral) that are actively dividing.
- Roots that are growing and / or actively absorbing mineral ions.
- Any part of the plant where the assimilates are being stored (eg. developing seeds, fruits or storage organs).

- The loading and unloading of the sucrose from the source to the phloem, and from the phloem to the sink is an active
process.
- It can be slowed down or even stopped at high temperatures or by respiratory inhibitors.
- Translocation of assimilates is not fully understood yet by scientists. The understanding they do have come from studies
such as:
- On plants whose sap does ‘clot’ so that it is still possible to collect and study the sap (eg. castor oil plants).
- Using aphids to collect the sap – after the aphid inserts its stylet (tubular mouthpart) scientists remove the
aphid's head and collect the sap that continues to flow.
- Using radioactively labelled metabolites (eg. Carbon-14 labelled sugars) which can be traced during translocation.
- Advances in microscopes enabling the adaptations of companion cells to be seen.
- Observations about the importance of mitochondria to the process of translocation.
8. Explain how companion cells transfer assimilates to phloem sieve tubes, with reference to proton pumps and
cotransporter proteins.

The Sucrose Loading Mechanism

- Assimilates such as sucrose are transported from source to sink through phloem sieve tubes.
- Carbohydrates are generally transported in plants in the form of sucrose because:
- It allows for efficient energy transfer and increased energy storage (sucrose is a disaccharide and therefore
contains more energy).
- It is less reactive than glucose as it is a non-reducing sugar and therefore no intermediate reactions occur as it is
being transported.

Loading of assimilates (e.g Sucrose)

- The pathway that sucrose molecules use to travel to the sieve tubes is not fully understood yet. The molecules move by
the:
- symplastic pathway (through the cytoplasm and plasmodesmata) which is a passive process as the sucrose
molecules move by diffusion.
- apoplastic pathway (through the cell walls) which is an active process.

- If the sucrose molecules are taking the apoplastic pathway then modified companion cells (Called transfer cells) pump
hydrogen ions out of the cytoplasm via a proton pump and into their cell walls. This is an active process and therefore
requires ATP as an energy source.
- The large concentration of hydrogen ions in the cell wall of the companion cell results in the hydrogen ions moving down
the concentration gradient back to the cytoplasm of the companion cell.
- The hydrogen ions move through a cotransporter protein. While transporting the hydrogen ions this protein also carries
sucrose molecules into the companion cell against the concentration gradient for sucrose.
 - Companion cells have infolding in their cell surface membrane to increase the available surface area for the active
transport of solutes and many mitochondria to provide the energy for the proton pump.
- This mechanism permits some plants to build up the sucrose in the phloem to up to three times the concentration of that
in the mesophyll.

Unloading of assimilates (e.g Sucrose).

- The unloading of assimilates (e.g sucrose) occurs at the sinks.
- Scientists believe that the unloading of sucrose is similar to the loading of sucrose, with the sucrose being actively
transported out of the companion cells and then moving out of the phloem tissue via the apoplastic or symplastic
pathways.
- To maintain a concentration gradient in the sink tissue, sucrose is converted into other molecules. This is a metabolic
reaction so requires enzymes (e.g invertase which hydrolyses sucrose into glucose and fructose)

9. Explain mass flow in phloem sieve tubes down a hydrostatic pressure gradient from source to sink.

Phloem: Mass Flow

 - The Mass Flow hypothesis was the model initially used to explain the movement of assimilates in the phloem tissue.
- The mass flow hypothesis was modelled by Ernst Münch in 1930. His simple model consisted of:
- Two partially permeable membranes containing solutions with different concentrations of ions (one dilute the
other concentrated).
- These two membranes were placed into two chambers containing water and were connected via a passageway.
- The two membranes were joined via a tube.
- As the membranes were surrounded by water, the water moved by osmosis across the membrane containing the
more concentrated solution which forced the solution towards the membrane containing the more dilute solution
(where water was being forced out due to hydrostatic pressure).

- Scientists now support a modified version of this hypothesis - the Pressure Flow Gradient.

Pressure (hydrostatic) flow gradient

- Phloem sap (containing sucrose and other organic solutes) moves by mass flow up and down the plant.
- Carbohydrates are generally transported in plants in the form of sucrose due to:
- It allows for efficient energy transfer and increased energy storage (sucrose is a disaccharide and therefore
contains more energy).
- It is less reactive than glucose as it is a non-reducing sugar and therefore no intermediate reactions occur as it is
being transported.

- The advantage of mass flow is that it moves the organic solutes faster than diffusion.
- In xylem tissue the pressure difference that causes mass flow occurs because of a water potential gradient between the
soil and leaf (this requires no energy).
- However in phloem tissue energy is required in order to create pressure differences for the mass flow of the organic
solutes.
 - The pressure difference is generated by actively loading sucrose into the sieve elements at the source (usually a
photosynthesising leaf or storage organ) which lowers the water potential in the sap.
- This results in water moving into the sieve elements as it travels down the water potential gradient by osmosis.
- The presence of water within the sieve elements increases the hydrostatic/turgor pressure at the source and as solutes
(e.g sucrose) are removed/unloaded from the sieve elements causing water to follow by osmosis at the sink creating a low
hydrostatic pressure, therefore a pressure gradient occurs.
- The pressure difference between the source and the sink results in the mass flow of water (containing the dissolved
organic solutes) from the high hydrostatic pressure area to the low hydrostatic pressure area.
- The mass flow of organic solutes within the phloem tissue occurs above and below the sources (which is typically
photosynthesising leaves). Therefore sap flows upwards and downwards within a plant.

Xerophytic Plant Leaf Adaptations

- Xerophytes (from the Greek xero for ‘dry’) are plants that are adapted to dry and arid conditions.
- Xerophytes have physiological and structural (xeromorphic) adaptations to maximise water conservation.