Unit 4: The Natural Environment and Species

Survival
Topic 6: Infection, Immunity and Forensics
Decay and Decomposition
Microorganisms (fungi. bacteria, other decomposers) decompose organic matter and are an important
part of the carbon cycle. They secrete enzymes that decompose the dead organic matter into smaller
molecules during respiration. Scientists can estimate time of death of a body based on things like
degree of decay and this can give them a lot of information about the circumstances of the death.
 All mammals produce heat from metabolic
reactions (respiration), so from TOD these
reactions slow down and eventually stop
causing body temperature to fall until it equals
the temperature of the environment.
Body
 Forensic scientists know that the human body
Temperature
cools at a rate of 1.5-2.0°C per hour, so can
work out an estimate of TOD. Useful for first
24hrs post mortem.
 Different conditions such as air temp, clothing,
body weight, body position, air movement, and humidity can affect cooling rate.
 Muscles relax, then contract (rigor mortis), then relax again.
 Rigor mortis (stiffening of the muscles) sets in about 2-6 hours after death.
Degree of
muscle  Occurs due to muscle cells becoming deprived of O2 and is affected by body
contraction composition and temperature. Respiration still occurs, but lactic acid is produced
(Rigor due to anaerobic respiration. pH of the cell decreases due to lactic acid, inhibiting
enzymes from working, Therefore no ATP is produced and bonds between actin
Mortis)
and myosin become fixed.
 Small muscles in head contract first, large muscles in lower body contract last.
 After death different microorganisms start colonising
the body. TOD can be estimated by type of insect
present in/on the body.
 Identifying stage of lifecycle of the insects can help
Forensic estimate TOD. Different conditions affect an insect’s
entomology lifecycle (drugs, humidity, oxygen, temperature).
 Flies are first (a few hours after death). Other
insects (beetles) arrive later.

 Immediately after death, bacteria and enzymes start to decompose the body. This
extent of decomposition can be used to estimate TOD.
 Different conditions affect the rate of decomposition (e.g. temp, O2 availability).
Approximate time
Extent of decomposition
since death
Cells and tissues are broken down by the body’s own enzymes
Hours – a few days and bacteria that were present before death (autolysis). The
Extent of skin turns greenish (putrefaction at 36-72 hours).
decompositi Microorganisms decompose tissues and organs. This
Few days – a few
on produces gases, which causes the body to smell and become
weeks
bloated. The skin begins to blister and fall off.
Tissue begins to liquefy and seep out into the areas around
A few weeks
the body. Gas is released and the body deflates.
Few months – a
Only skeleton remains.
few years
Decades to The skeleton begins to disintegrate until there is nothing left of
centuries the body.
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  Types of organisms found in/on a
body change over time. TOD can
be established from the stage of
succession that the body is in. The
stages are:
1. Immediately after death the body
Stages is most favourable to bacteria.
(waves) of 2. Bacteria decompose tissue making
succession conditions favourable for flies and
larvae.
3. Fly larvae feed on a dead tissue making conditions favourable for beetles.
4. As the body dries out conditions become less favourable for flies, so they leave.
Beetles remain and decompose dry tissue, leaving only the skeleton.
 The stages of succession of a dead body are affected by things such as location
of the body, left above/below ground, under water, sealed away, etc.

Identifying the body

 Fingerprints: are unique to an individual and last a life time.
Fingerprints are taken using fine aluminium powders or protein
stains (ninhydrin) that stick to sebum oil and sweat left behind. The
four main type of finger print can be classified (Henry classification)
as: an arch (common), a tented arch, a whorl, a loop (common).
 Dental records: the best way for people with no fingerprint files.
Teeth and fillings decay slowly so a forensic dentist can make a
chart of the teeth (development of teeth, dental work, fillings, missing
teeth) which is compared with dental records of the missing person.
 Identity papers
 Genetic fingerprint: using DNA.

DNA Profiling
Forensic scientists use DNA profiling to compare samples of DNA from
crime scenes and possible suspects (to link them to crimes). DNA is
isolated from the collected samples, and each one is amplified using
PCR. PCR products are run through electrophoresis gel and the DNA
profiles are compared.
We inherit our DNA from our parents, ± half from each, so the more
bands of the two DNA profiles that match, the closer the relation
between the two people. In animals and plants, DNA profiling is used to
stop inbreeding which can cause health, productivity and reproductive
problems. Inbreeding decreases the gene pool of alleles; leading to an
increase in genetic disorders.

DNA profile: a unique genetic fingerprint of an organisms DNA.

Everyone’s DNA is different (apart from identical twins), so DNA
profiling can be used to identify people and determine a genetic
relationship between plants, animals and between humans.
DNA profiling is a multistage process:
1. DNA has to be collected in a sample (e.g. blood, saliva) and
extracted.
2. DNA sample is treated with a restriction enzyme which cuts the DNA
into fragments of different length double stranded DNA.
3. PCR is used to copy DNA numerous times.
4. The DNA fragments are separated according to size (measured in
base pairs/satellites) using gel electrophoresis to create a DNA
ladder/marker. Smaller fragments pass through the gel quicker.
5. Fragments are visualised by transferring them to a nylon membrane; Southern Blotting. The
membrane is washed with a DNA probe that binds to the repeated sequence producing visible

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 bands. A single band appears where the maternal and paternal chromosomes have the same
number of satellite repeats at the locus. If the 2 chromosomes each have a different number of
repeats there will be 2 bands.
STR’s (sort tandem repeats/satellites): within introns, short DNA sequences of repeated bases.
- Minisatellites contain 20-50 base pairs.
- Microsatellites contain 2-4 base pairs.

Non-coding protein blocks called

introns are regions of DNA present
on a gene.
They are separated by DNA coding
blocks called exons which are
expressed in an amino acid sequence
of proteins.

PCR
The Polymerase Chain Reaction (PCR) is used
to amplify DNA and make millions of copies of
specific regions of the DNA in just a few hours.
There are several stages:
1. A reaction mixture containing the DNA
sample, free nucleotides, primers (short DNA
sequences that are complimentary to DNA
adjacent to the STR) and the DNA
polymerase enzyme is made up.
2. The DNA mixture is heated to 95oCto break
down H bonds between the two strands of
DNA.
3. Mixture is cooled to 50-65oC so primers
(marked with fluorescent tags) can bind to
DNA strands.
4. Reaction mixture is again heated to 72oC so
the DNA polymerase can work.
5. DNA polymerase makes strands of new DNA
by complement strand synthesis and lines up
free DNA nucleotides alongside each template
strand. Two new copies of the fragment of
DNA are now formed and one cycle of PCR is
complete. Each cycle doubles amount of DNA
present in sample.
6. The cycle starts again with the mixture being
heated to 95oC and this time all four strands
are used as template strands.

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Gel Electrophoresis
Once DNA has been amplified a florescent tag is added to the
fragments for viewing under UV light.
Gel Electrophoresis is then used to separate out the DNA fragments
according to their length:
1. DNA is placed into a well of gel and covered in a buffer solution so
that it conducts electricity.
2. An electrical current is passed through the gel – DNA fragments
are negatively charged and so move towards the positive
electrode.
3. Shorter fragments move faster and further through the gel;
fragments separate according to length.
4. The gel is viewed under UV light; DNA fragments appear in
bands. When two DNA profiles are the same they provide the
same bands at the same place.

Summary of forensics:
 When: rigor mortis, decomposition, forensic entomology,
temperature
 Who: personal ID, finger prints, dental records, DNA profiling

Bacteria and Viruses

A pathogen is any organism that can cause disease, and a disease caused by a pathogen is called an
infectious disease. Pathogenic microorganisms include all viruses, and some bacteria and fungi.

Infectious diseases can be transmitted and are caused by the spread of pathogens or natural flora
(bacteria on skin and gut) mutating and becoming pathogenic.

Bacteria:
 Bacteria grow and reproduce in the body; producing toxins
which make people feel poorly.
 Single celled, prokaryotic microorganisms (prokaryotic means
no nucleus) that lack membrane bound organelles.
 Have a single strand of free floating DNA found in the
cytoplasm. Cytoplasm also sometimes contains plasmids
(small, circular loops of DNA).
 Some have a flagellum to aid movement by rapid rotations
(e.g. sperm) – like a rudder.
 Some have a slime capsule which protects them from attack
(e.g. phagocytosis by WBCs and blocks their receptors so
cells don’t recognise them as non-self).
 Respiration occurs on folds of cell membrane called
mesosomes (which increase surface area).
 Some have pilli (protein tubes) which help them attach to host
cells, and are also used for sexual reproduction.
 Most bacteria are only a few micrometers long.
 Bacteria cells have a plasma membrane (cell wall), cytoplasm
and ribosomes (produce proteins).
 Reproduce asexually by binary fission; replication of DNA, they
divide identically. They do not produce a spindle during cell
division.
 Bacteria can be cocci (spherical), bacilli (rod shaped), spirilli
(twisted) or vibrious (comma shaped).
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Structure of Bacteria:
 Plasma Membrane / Cell Wall: rigid wall
protects against rupture due to osmosis and
keeps shape.
 Cytoplasm: about 75% water. Contains
dissolved proteins (mainly enzymes),
lipoproteins, sugars, amino acids, fatty acids,
inorganic salts, and the waste products of
metabolism.
 Slime Capsule: a layer or capsule made up
of materials that are laid down on the outer
surface of the wall. Capsules are firmly
attached, whereas slime layers may diffuse
into the surrounding medium.
 Mesosomes: in-folding of the plasma
membrane found in some bacterial cells. In
photosynthetic bacteria, they are where the
photosynthetic pigments are housed.
 Plasmids: additional hereditary material.
Small rings of DNA present in cytoplasm of
some (not all) bacteria.
 Ribosomes: sites of protein synthesis, are
known as 70S ribosomes because they are
smaller than those in the cytoplasm of plant
and animal cells, and fungi (called 80S
ribosomes).
 Flagella: rigid protein strands that arise from
basal bodies in the plasma membrane in
some bacteria. They bring about movement
by rotating from their base, driven by the basal
body.
 Pilli: tiny tubular structures that arise from the
cell membrane of some bacteria. They enable
bacteria to attach to surfaces and to other
bacteria.

There are two types of bacterial cell walls, distinguished by Gram Staining.
- Gram positive bacteria have a thick layer of peptidoglycan containing chemicals
(acids). The crystal violet in the stain binds to the acid & resists decolouring, leaving
the positive PURPLE/BLUE in colour.
- Gram negative bacteria have a thinner layer of peptidogylcan with no teichoic acid.
- Any crystal violet which binda is readily decolourised & replaced with red safranine
in the stain, so cells appear RED in colour.

Endotoxins: lipopolysaccharides (part of the outer layer of gram

negative bacteria). They are rarely fatal (however symptoms may
indirectly lead to death). Cause symptoms such as fever, vomiting
& diarrhea (e.g. salmonella & E.coli).

Exotoxins: soluble proteins produced & released into the body by

bacteria as they metabolise and reproduce. Different types: some
damage cell membranes causing internal bleeding, some act as
competitive inhibitors to neurotransmitters, others directly poison
cells. Rarely cause fevers but include some of the most dangerous
bacterial diseases (e.g. clostridium botulinum produces one of the
most toxic substances known, botulinum toxin).
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Reproduction of Bacteria:
Bacteria can reproduce in two ways:

 Asexual Reproduction: the most common way in which a

bacterium reproduces is by binary fission (splitting into two).
One the bacterium reaches a certain size, the DNA is
replicated and the old cell wall begins to break down around
the middle of the cell. Enzymes break open the circular
piece of DNA allowing the strands to unwind and be
replicated. New cell walls are laid down in the middle of the
cell and a new cell membrane and cell walls are created.
The cell eventually divides to produce two identical cells.

 Sexual reproduction: in very rare conditions, bacteria can

reproduce using what appear to be different forms of sexual
reproduction. There are 3 ways in which genetic material
from one bacterium can be taken in and used as part of
DNA of another bacterium:

1. Transformation: a short piece of DNA is

released by a donor and actively taken up by
a recipient where it replaces a similar piece of
DNA. Only occurs in certain types of bacteria.

2. Transduction: a small amount of DNA is

transferred from one bacterium to another by
a bacteriophage. Bacteriophage attaches to
bacterial cell wall. Enzymes are released to
break down cell wall. New bacteriophage
forms and some bacteria DNA is included by mistake.

3. Conjugation: genetic information is transferred from one

bacterium to another by direct contact. The donor cell is similar to
a male cell and this produces a sex pillus, a cytoplasmic bridge
between the two cells through which DNA is transferred to the
recipient cell, similar to the female cell

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Beneficial Bacteria:
- Many bacteria in the body (skin and gut flora) are
beneficial, helping to break down food and keeping
pathogens at bay by outcompeting them. The normal
growth of bacteria on your skin or in your gut is
referred to as the ‘skin flora’ or ‘gut flora.’ Probiotic
drinks and foods contain cultures of these ‘good’
bacteria to help support the normal healthy bacterial
flora of the gut.
- Bacteria also play a vital role in the ecosystems of the
natural world. The majority of bacteria are
decomposers. They break down organic material to
produce simple inorganic molecules such as CO2 and
H2O.
They release inorganic nitrogen which returns to the soil in the nitrogen cycle.
- Another important aspect of bacteria in the carbon cycle is the fact that some microorganisms
produce the enzyme cellulase. This enzyme breaks down the cellulose produced in plant cell
walls to give sugars which can then be used as food by a wide range of other microorganisms.

Viruses:
 The smallest type of microorganism. They aren’t cells; they
are nucleic acids surrounded by protein.
 Composed of a strand of viral DNA and proteins enclosed
in a capsid (viral protein coat made up of individual
capsomeres).
 Sometimes have a lipid envelope surrounding them (taken
from a host cell; it allows them to pass from cell to cell).
 Contain a core of nucleic acid; viral genetic material
(DNA/RNA/single/double stranded) to create proteins and
reproduce.
 Viral RNA directs the synthesis of a special
enzyme called reverse transcriptase
which proceeds to make DNA molecules
corresponding to the viral genome.
 Invade living organisms and manipulate the
cells biochemistry to reproduce/create more
viruses.
 Have receptors on their surface to help
them attach to hosts; each antigen
(glycoprotein) only attaches to a specific
host membrane.
 Smaller than bacteria.
 Have no plasma membrane, no cytoplasm
and no ribosomes.
 There are very few drugs that can kill
viruses – anti viral drugs.

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How viruses enter a cell:
- Some enter cells by endocytosis and the host cell digests
the capsid releasing the genetic material.
- Some enter the cell by fusing the lipid envelope with the
phospholipid bilayer of a cell and releasing its contents
inside the cell.

Reproduction of Viruses:
1. If the virus contains DNA, the viral DNA is inserted into
the host DNA and can be replicated by DNA polymerase
and then used to make more viral proteins by protein
synthesis.
2. If the virus contains RNA, DNA reverse transcriptase is
used to translate the RNA into DNA. The DNA then
inserts itself into the hosts DNA and the host cell creates
viral proteins during protein synthesis. This is called reverse transcription. The new viruses then
exit the cell by exocytosis and go on to infect other cells.
Viral infections are specific to tissues e.g. some viruses will only infect the respiratory tract.

Retroviruses:
Retroviruses have a more complex life cycle. Their genetic material is viral RNA and this cannot be
used as mRNA but is instead translated into DNA using reverse transcriptase (e.g. HIV).
1. The retrovirus attacks an animal cell. viral genome RNA, mRNA and coat proteins.
2. Viral RNA enters the host cell. This RNA 5. New viral particles are assembled and leave
cannot be used as mRNA. the host cell by exocytosis. Viral DNA remains
3. Viral RNA is translated into viral DNA by in the nucleus so the process is repeated.
reverse transcriptase in cytoplasm. 6. The host cell continues to function as a virus
4. Viral DNA is incorporated into the host DNA in making factory, while the new viruses move
the nucleus. It directs the production of new on to infect other cells.

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Barriers to Entry:
Pathogens are transmitted in a variety of ways:
- Open routes such as eyes, nose, ears, mouth, anus, penis, etc.
- Vectors: living organism that transmit infections from one host to another (e.g. mosquitoes –
malaria).
- Fomites: travelling by inanimate objects that carry pathogens from one host to another (e.g.
hospital towels and bedding).
- Direct Contact: shaking hands, direct contact of genital organs (e.g. gonorrhea, syphilis).
- Inhalation: coughing, sneezing, and talking release pathogen containing droplets which can be
inhaled (e.g. TB, influenza).
- Ingestion: contaminated food – the risk is greatest in raw or undercooked food (e.g. salmonella).
- Inoculation: directly through a break in the skin either through contaminated medical instruments or
shared needles in drug abuse. An infected animal may also bite or lick you. (e.g. HIV, rabies).

Pathogens can enter our bodies through four major routes:

1. Cuts in the skin 3. Through the respiratory system
2. Through the digestive system via 4. Through other mucosal surfaces (inside the
contaminated food nose, mouth and genitals)

But there are several barriers which humans have to prevent entry and infection:
Stomach The acidic environment of the stomach kills most of the pathogens that enter through the
Acid digestive system; but some may survive and get passed into the gut wall.
A fibrous structural protein layer toughened by keratin that forms a physical barrier between
the pathogen laden environment and the blood rich tissues beneath the skin. The skin is made
Skin from 2 layers: the outer epidermis layer (provides a physical barrier to invading pathogens;
blood clots seal wounds, skin flora prevents colonisation of bacteria), and the inner dermis
layer.
Sebum (oily substance with a pH 3-5 which makes the skin acidic) contains chemicals which
inhibit the growth of microorganisms.
Skin Flora Natural skin flora prevent disease by competing with pathogens for nutrients and space and
produce substances that inhibit the growth of other microorganisms. This restricts pathogens
from infecting the body.
Our intestines are naturally covered by harmless microorganisms called flora that compete
Gut Flora with pathogens for nutrients and space. This restricts pathogens from infecting the body.
Surfaces of internal tubes and ducts are more vulnerable than the skin; however these
epithelial layers also produce defensive secretions (e.g. mucus). Part of the non-specific
defense of the body.
Mucus contains lysozymes: enzymes which kill pathogens by destroying microbial cell walls.
Lysosomes Sebaceous glands secrete the enzyme lysozyme which is a natural antibiotic that destroys
bacterial cell walls.
Lysozymes are also present in tears; to keep eyes moist and protect them from entry of
pathogens.

- Saliva in the mouth has bacterial properties. Some polypeptides produced in the salivary glands
destroy bacteria while others slow down bacterial growth.
- Vomitting is effectively removing many of the microorganisms physically from the system when the
body is infected.

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Immune Response:

The immune system enables the body

to recognize anything that is non-self
(pathogens) and to remove it from the
body as efficiently as possible.
Antigens are used to identify a cell as
self or non-self. The more antigens two
people have in common the more closely
related they (identical twins have exactly
the same antigens).
White blood cells are classified as
follows:
- Granulocytes which have granules in
their cytoplasm that can be stained.
- Agranulocytes which have no
granules.

There are 2 main types of white blood cells (WBC’s) involved in the immune systems;
1. Lymphocytes: agranulocytes made in bone marrow. Involved in specific immune responses.
- T cells: T lymphocytes, a type of lymphocyte found
in the blood and lymph. Mature and become active
in the thymus.
- B cells: B lymphocytes, a type of lymphocyte found
in the lymph and blood. Mature in blood.

2. Phagocytes: a general term for WBC’s involved in

non-specific immune responses which engulf and
digest pathogens and any other foreign material in the
blood and tissues. Phagocytes can sometimes be seen
as pus which may ooze out of the wound or it may be
reabsorbed into the body. There are two types of phagocytes:
- Macrophages: agranulocytes which move freely through the
tissue after leaving the bloodstream, make up about 4% of
WBC’s. They accumulate at the site of infection to attack
invading pathogens.
- Neutrophils: granulocytes, make up 70% of the white blood cells.

Characteristics of immune system:

1. Recognise self and non-self cells.
2. Immunological memory – if a pathogen tries to re-
invade the body, the immune system will be able
to react to it faster since it has T and B memory
cells.
3. Diverse – recognises over 10 million different
antigens.

Pathogens reproduce inside the body and cause

symptoms of disease.
Objective evidence of infection: symptoms of
infection that are visible on the outside e.g. a rash.
Subjective evidence of infection: symptoms of
infection that are felt by the patient e.g. headache.

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1. Non-specific (Humoral) Immune Response: help to destroy any invading pathogen
Some of these responses rely on cell recognition systems. These responses occur when a pathogen
is outside of the body’s cells.
Each cell has a unique marker on its surface such as gp120 (a glycoprotein). These sites bind to each
other if they are the same to form tissues. These markers act as antigens (a substance that stimulates
the production of antibodies; antibody generator = antigen) that are recognised by white blood cells
during specific responses.
Occurs at the site of infection. The site where the pathogen enters the body usually
becomes red, warm, swollen and painful. Processes of inflammation:
1. Mast cells in connective tissue and damaged WBC’s recognise foreign antigens on the
surface of pathogens and release chemicals (histamines) triggering inflammation.
2. Histamines cause vasodilation around site of infection, which increases the
Inflammation permeability of the capillary walls (cells separate slightly).
(aimed at bacteria) 3. This increases blood flow and brings fluid and immune cells to the area of infection.
This fluid includes plasma, white blood cells, antibodies etc. so the specific responses
can be carried out effectively e.g. WBC’s and antibodies can kill pathogens.
This causing swelling, redness/rash, heat (reduces the effectiveness of the
reproduction of pathogens) and pain in the area that is infected. Pathogen is washed
away/removed by lymph and blood.
When a cell is infected with a virus it produces anti-viral proteins/chemicals (interferons)
which help to prevent viruses spreading to uninfected cells. They do this by:
Antimicrobial
- Preventing viral replication by inhibiting the production of viral proteins.
Proteins
- Activating T and B lymphocytes (involved in specific immune response) to kill the
(aimed at viruses)
infected cells.
- Activating other mechanisms of the non-specific immune response (e.g. inflammation).
1. Thromboplastin is released from the damaged blood vessels.
2. This triggers the conversion of prothrombin into thrombin.
3. Thrombin catalyses the conversion of fibrinogen (soluble proteins) into fibrin which
Blood Clotting
creates a mesh of insoluble fibres.
4. Platelets and RBC’s get trapped in the mesh, producing a blood clot. Platelets tighten
the clot.
Occurs when a pathogen infects the body and causes the hypothalamus to reset/increase
to a higher temperature. This helps in 2 ways:
- A raised temperature reduces the ability of pathogens to function and reproduce
effectively.
Fever
- Specific response works better at a higher temperature and will be more successful at
combating the infection.
However, if the temperature gets too high, various proteins inside the body could
denature as their bonds break and they change shape; this could be fatal.
Found in the blood and in tissue, phagocytes are the first cells to respond to pathogens.
1. Phagocytes (type of WBC) recognise cells as being non-self due to the antigens on the
cell surface.
2. Phagocyte engulfs the non-self cell (pathogen) by endocytosis (phagocytosis).
Phagocytosis
3. The macrophage fuses the phagocytic vacuole with its lysosomes. Digestive enzymes
(aimed at bacteria)
in the lysosome destroy the pathogen leaving behind only antigens of the pathogen.
4. The pathogenic antigen complex is then presented on the cell surface of the
macrophage in order to activate other immune system cells (T and B cells); thus
producing an antigen-presenting cell which is destroyed during the specific response.

Interferons: a group of chemicals produced when cells are

invaded by viruses. Interferons are proteins that inhibit viral
replication within the cells. They bind to receptors in the surface
membranes on uninfected cells, stimulating a pathway which
makes the cells resistant to infection by viruses by preventing
viruses reproducing.

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 2. Specific Immune Response: help to destroy a specific invading pathogen
Kinds of Lymphocytes:
 B cells: found in lymph glands and free in the body. They have
membrane bound globular receptor proteins on their cell surface
membrane which are identical to the antibodies they will later produce.
All antibodies are known as immunoglobulins (IgM). The two types are:
1. Effector B cells which are responsible for producing antigen-
antibody complexes, and helping to clear infection by agglutination,
neutralization and preventing pathogen infection; antibodies.
2. Memory B cells are produced similarly to memory T cells, they
produce plasma cells.
 T cells: their surface of each T cell displays thousands of identical T cell receptors. There are 3
main types of T cells:
1. T killer cells which produce chemicals that destroy/kill pathogens.
2. T helper cells which are involved in the process that produces antibodies against the antigens
on particular pathogen.
3. T memory cells are produced after exposure to antigens and remain in circulation until after
the pathogen has been killed. These are activated in secondary immune response if the
pathogen enters the body again.

The working of these cells depend on special proteins known as major histocompatibility complex (MHC) proteins, which display antigens in the cell
surface membranes. MHC proteins are the proteins that display antigens on the surface of cells to make them antigen presenting cells.

The Primary Immune Response (10-17 days)

Activation of T cells by macrophages:
1. Phagocytes (macrophages) activate T cells by
binding of their antigens to complementary CD4
receptors on the T cells. Each T cell has a
different shaped receptor on its surface so
when it meets the complementary antigen it
binds to it, activating the T cell.
2. This causes the T cell to divide and differentiate
into other types of T cell. These include T
helper cells (secrete substances that activate B
cells, T killer cells, and macrophages), T killer
cells (attach to antigens on a pathogen-infected
cell and kill the cell), and T memory cells
(immunological memory; responsible for
secondary immune response).
B cell activation and plasma cells:
1. T helper cells activate B cells (WBC covered
with proteins - antibodies).
2. Antibodies bind to complementary antigens on
the pathogen to form an antigen-antibody
complex. Each B cell has a different shape
antibody on its surface that binds with its
complementary antigen. This together with
substances released from the T cells help
activate the B cells.
3. The B cell that is specific to the antigen (has a
specific antibody on its surface) engulfs the pathogen, fuses the vesicle with a lysosome and
digests the pathogen leaving behind the antigens. These antigens are presented on the surface of
the B cell.
T helper cells recognise the antigens and bind to them. They release cytokines which cause the
activated B cells to divide by mitosis and form clones called B memory cells and B effector cells.
4. The B effector cells differentiate into plasma cells and produce large amounts of antibodies which
circulate around the body in the blood and attack pathogens. Plasma cells secrete antibodies for
specific antigens on the surface of the pathogen to form antigen-antibody complexes.
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Antibodies: help to clear the body of infection; they do various jobs these include:
 Agglutinating pathogens – they clump pathogens together to prevent them from functioning.
 Neutralising toxins – antibodies bind to the toxins produced by pathogens. They prevent toxins
from affecting human cells, so the toxins are neutralised.
 Preventing the pathogen from binding to human cells – antibodies bind to antigens on pathogens,
blocking the cell surface receptors so that pathogens cannot attach to a host cell.

The role of T killer cells (occurs when a pathogen has

invaded a body cell):
1. The pathogen is digested by the cells lysosomes and
the antigens along with the MHC proteins are
presented on the surface of the host cell.
2. T killer cells present in the blood that have
complementary receptors bind to the APC/host cell.
3. If the T killer cells are exposed to cytokines from a T
helper cell that is complementary to the antigen, they
divide by mitosis to form clones of identical T killer
cells and T killer memory cells which stay in the blood
for use in the future if the same antigen is spotted.
4. These T killer cells bind to the antigens on infected
body cells and release enzymes that make pores
appear in the membrane of infected cells so water and
ions can travel into the cell causing it to die or break
down by lysis (swells and bursts).
5. Any pathogens which are released intact are then
attacked by the antibodies produced by B effector
cells.

The Secondary Immune Response (2-7 days)

If infected by the same bacterium or virus again, the immune
system responds much faster.
The secondary immune response involves memory cells; the B
memory cells produced in the primary response can differentiate
immediately to produce plasma cells and release antibodies.
There is greater production of antibodies and the response lasts
longer. The invading pathogens are often destroyed so rapidly
that the person is unaware of any symptoms; the person is said to
be immune.

Apoptosis: programmed cell death which occurs as a normal, controlled part of an organism's growth
or development.

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 Immunity
The production of memory cells gives a person immunity; when a pathogen enters the body for the
first time, the antigens on its surface activate the immune system (slow primary immune response
in which B cells are made, producing antibodies needed to bind to the antigen and overcome
infection).
After exposure, both T cells (remember the specific antigen) and B cells (remember the specific
antibody required for the antigen) produce memory cells which remain in the body.
If the same pathogen enters the body again, the immune system produces a quick, stronger
secondary immune response in which B memory cells divide into plasma cells that produce the
right antibody for the antigen, and memory T cells divide into the correct type of T cell to kill the cell.
You can become immune to a specific disease in a number of ways:
 Active immunity: Immune system makes its  Passive immunity: You get given antibodies
own antibodies after being stimulated. made by a different organism.
Active Natural Immunity Passive Natural Immunity
When a baby/fetus becomes immune by receiving
When you become immune after catching the
preformed antibodies from the mother through the
disease; the body comes into contact with a
placenta or breast milk. Both provide temporary
foreign antigen and the immune system is
immunity until baby’s own immune system
activated. The body actively makes antibodies and
becomes active; not a long term solution as the
the pathogen is destroyed.
antibodies don’t live for long periods of time.

Active Artificial Immunity Passive Artificial Immunity

1. When you become immune after receiving a When you become immune after being injected
vaccine which contains small, harmless amounts with antibodies which are formed in one individual,
of antigen/disease. extracted, and injected into another individual.
2. The vaccine is injected into the body. Body This is not long term as the infected persons body
responds to the vaccine with a normal immune will not be able to produce the antibodies to fight
response, leaving behind memory cells for future. off the infection in the future.
Inducing immunity:
 Immunization: protecting humans from infection by giving them passive/active artificial immunity.
o Vaccination: the procedure by which you immunise people to produce immunity.
Vaccines give you immunity without you getting the disease. They contain: attenuated viruses
(weakened, harmless viruses), killed bacteria (e.g. whooping cough vaccine contains
whooping cough bacteria that have been killed), a toxin that has been altered into harmless
form, or an antigen-bearing fragment of the pathogen.
 Antibiotics: chemicals/drugs used in humans/animals which inhibit the growth of microorganisms /
are used to treat bacterial infections. Antibiotics are classified as follows:
o Bacteriostatic – these antibiotics completely inhibit/prevent the growth and reproduction of
bacteria and are sufficient for most common infections.
o Bactericidal – these antibiotics destroy the pathogens/bacteria present. Used for more
serious infections or when the immune system is supressed e.g. during a transplant, AIDS.
Antibiotics kill bacteria by selective toxicity i.e. they interfere with or inhibit bacterial metabolism or
function that are crucial for growth and life of the cell, with min. damage to the host. They disrupt
bacterial cell growth and division:
- Inhibit bacterial cell wall synthesis (inhibit enzymes that are needed to make chemical bonds in
bacteria cell walls, preventing the bacteria from growing properly, leading to cell death).
- Disruption of cell membrane (causes changes in permeability that lead to cell lysis (bursting).
- Inhibit nuclei acid synthesis, replication, and transcription (prevent cell division and/or
synthesis of enzymes).
- Inhibit protein synthesis (inhibit enzyme and protein production by binding to bacterial
ribosomes. If the cell can’t make proteins then it will not work effectively).
- Inhibit specific enzymes found in bacterial cells. Bacterial cells are different to mammalian
cells (eukaryotic, don’t have cell walls, have different enzymes and different ribosomes) so
antibiotics can be designed to only target bacterial cells. Viruses don’t have enzymes or
ribosomes, so antibiotics don’t affect them.
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 Broad spectrum antibiotics – kill a wide range of pathogens.
Narrow spectrum antibiotics – kill a limited range of pathogens.
Antibiotics do not work against all pathogens (e.g. HIV) hence research is on-going.

The effectiveness of antibiotics depends on:

- Concentration of the drug in infected area of the body; how quickly it gets to the infected area.
- pH; if it is too high or too low, the antibiotic could die.
- Susceptibility of pathogens – if the pathogen is sensitive it will be killed by a standard dose, if it
is moderately sensitive it will be killed by an increased dose, if it is resistant it will not be killed
by the antibiotic.
Creating drug resistant bacteria:
New medicines are constantly being developed, and pathogens keep evolving through natural
selection to develop resistance to these medicines. Antibiotics only work if the pathogen has the
correct receptor for the drug to bind to.
Mutations: during pathogen reproduction, a mutation could occur which may help the pathogen
develop resistance to an antibiotic (e.g. by changing its receptors). Selection pressure of the
antibiotic and natural selection will result in the resistant pathogens surviving, reproducing and
passing on their viral DNA. Resistant pathogens will become more common while sensitive ones
will die.
Overuse or underuse of antibiotics:
- People using their antibiotics for a limited time results in some pathogens remaining in the
body. The immune system may not be able to cope with these pathogens, so they have a high
chance of mutating and developing resistance, ultimately spreading to other people by
infected patients who assume they have been cured.
- To prevent the creation of ‘superbugs’ (pathogens resistant to multiple antibiotics), antibiotics
should only be used sparingly and as a last resort when completely necessary. This limits the
selection pressure and allows the antibiotics to stay effective.

Hospital Acquired Infections:

‘Superbugs’ are commonly found in hospitals and care homes where antibiotics are used more
frequently. People are more likely to become infected with these resistant pathogens in hospital due
to them already being ill (have weakened immune systems). Hospital acquired infections can be
transmitted through:

Preventing and controlling the spread of infection:

Some HAI’s are antibiotic resistant (e.g. MSRA - Methicillin Resistant Staphylococcus Aureus) which
makes them difficult to treat because antibiotics don’t get rid of the infection, leading to serious health
problems. Codes of practice for doctors and nurses include:
- Doctors shouldn’t prescribe antibiotics for a minor bacterial or viral infection.
- Doctors shouldn’t prescribe antibiotics to prevent an infection.
- Doctors should use a narrow spectrum antibiotic (when the strain has been identified).
- Doctors should rotate the use of different antibiotics.
- Patients should take all of the antibiotics that they are prescribed so the infection fully clears.
- Hygiene - hands of medical staff and visitors should be washed using the correct technique with
hand wash or an alcohol based hand gel. Clothing such as ties and long sleeved shirts should not
be worn as they can carry pathogens and spread them. Hospital wards, toilets etc. should be
thoroughly cleaned as well.
- Isolation of patients – patients who are infected with pathogens need to be isolated ASAP and
need to be given high hygiene rooms with infection control nursing so infections are contained and
not spread (e.g. by coughing/sneezing).
- Screening – Patients should be screened before being admitted into a hospital so that if they are
infected, they can be isolated immediately.
- Equipment and surfaces must be correctly disinfected after use.

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 HIV and TB
Over millions of years vertebrates have evolved better immune systems, but pathogens have also
evolved mechanisms to evade immune systems of hosts (evolutionary race). Two examples are:
Human Immunodeficiency Virus (HIV)
HIV is a virus that infects and kills immune system cells.
It reduces the number of immune system cells in the
body, reducing the chance of being detected.
HIV has a high level of mutation in the genes that code
for antigen proteins. This mutation changes the structure
of the antigen forming an antigenic variation.
HIV disrupts antigen presentation in an infected cell,
preventing immune system cells from recognising and
killing it.
HIV leads to Acquired Immunodeficiency Syndrome
(AIDS), a condition where the immune system
deteriorates and eventually fails. HIV positive people are
classed as having AIDs when symptoms of a failing
immune system appear.
AIDs sufferers develop disease and infection that
wouldn’t normally cause serious problems in healthy
people (opportunistic infections).
It usually takes 8-10 years for HIV to develop into AIDs.
 Stages of HIV/AIDS:
1. Acute phase: acute phase of infection occurs during
the first few weeks.
 3-12 weeks after infection HIV antibodies are
present in the blood; the person is HIV positive.
 Some people feel fine and have no symptoms,
others may experience symptoms such as fever,
sweats, headache, sore throat, swollen lymph
nodes.
 There is a rapid replication of the virus and loss of
helper T cells.
 After a few weeks, infected T helper cells are
recognised by T killer cells which start to destroy
them thus greatly reducing rate of virus replication,
but not totally eliminating it.
2. Chronic phase: prolonged ‘latent’ phase in which the
virus continues to reproduce rapidly, but numbers are
kept in check by the immune system. There may be no
symptoms during this stage, but there may be an
increasing tendency to suffer colds or other infections
which are slow to go away. Dormant diseases like TB
can reactivate. This stage will last longer (many years)
in healthy individuals with strong immune systems.
3. Disease phase: the increased number of viruses (viral
load) and decreasing number of T helper cells
indicates the onset of AIDS. Immune system is left
vulnerable to other diseases (opportunistic infections:
TB, pneumonia). major symptoms such as severe
weight loss, dementia, cancer, TB etc. occur and
eventually lead to death.
Symptoms of HIV/AIDS:
 Fever
 Diarrhoea
 Weight loss
 Dementia
 Secondary/opportunistic
infections
 Tumours (Kaposi’s sarcoma)
Tuberculosis (TB)
TB is caused by the spread of the bacterium
mycobacterium tuberculosis through droplets of mucus
and saliva (coughing, sneezing, talking, etc) which when
inhaled infect phagocytes in the lungs. They can remain
airborne for hours in a poorly ventilated room, and can
survive on bedclothes and in the room.
 Most people don’t develop TB straight away, their immune
system seals infected phagocytes in tubercles in the
lungs. Bacteria becomes dormant and the person shows
no symptoms.
 When bacteria reactivates it overcomes the immune
system, causing TB. Infection and reactivation is likely to
occur when people who have a weakened immune
system, poor diet, poor health, or live in overcrowded,
unhygienic living conditions.
 The length of time between infection and the development
varies from person; weeks to years.
 Stages of TB:
1. Primary infection: occurs mainly in children, can last
several months, no obvious symptoms.
 In a healthy immune system, an inflammatory
response occurs. Macrophages engulf bacteria
(phagocytosis) forming granuloma (masses of
tissue). These granuloma in the lungs are anaerobic
masses of tissue consisting of dead bacteria and
macrophages and are called tubercules.
 After 3-8 weeks, the immune system has control
over the infection; infected region of the lungs heals.
 TB bacteria remain dormant, or survive and
reproduce slowly, inside the macrophages. They
produce substances that prevent the lysosome
fusing with the phagocytic vacuole; the bacteria isn’t
broken down and so multiply undetected.
 The bacteria have thick, waxy cell walls that protect
from being digested by the digestive enzymes in the
tubercules. They also target immune system cells to
reduce antibody production and attack by killer T
cells.
2. Active TB: occurs if the immune system cannot contain
the disease, or if the disease is reactivated. If the
persons immune system weakens (e.g. HIV/AIDS), the
bacteria may overcome the immune system and
reproduce rapidly; by natural selection the best TB
have reproduced and infect the lungs causing fever,
weakness, lung tissue damage, coughing up blood.
Without treatment, the lungs breakdown and the alveoli
become inefficient air spaces.
Symptoms of TB:
 Inflammation of infected area in lungs (primary
infection).
 Coughing (may cough blood), damaged lung tissue.
 Shortness of breath.
 Loss of appetite and weight loss.
 Fever and extreme fatigue.
 Suppressed immune system, susceptible to
opportunistic infection.
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Treatment and control:
HIV/AIDS is currently incurable and relies on bodily fluids
(sperm, mucus, blood) to survive. It is very fragile and will
not survive in open air.
The HIV virus mutates very rapidly hence it is hard to
make vaccines that destroy it. It is also difficult for the
body to react to it as its antigens are always changing.
When the body has made antibodies for HIV, a mutation
has already occurred resulting in different antigens being
present on the surface of HIV, so the antibody is useless.
There are various ways to prevent spread of infection:
 Use protection during sexual intercourse; infection is
spread through bodily fluids.
 Provide public education programmes on the subject.
 Do not share needles; infection is spread through
bodily fluids.
 Immediate use of antiretrovirals (reduce production of
more viruses) if you think you may be infected.
HIV can also be spread from mother to fetus – in the
placenta or during breast feeding in the milk.
Treatment and control:
TB is diagnosed by skin and blood tests, chest X-rays,
and identifying bacteria from spit/phlegm cultures.
Chest x-rays that show an opaque area suggests there
may be a TB infection present (sometimes confused with
a chest infection).
Treatment of active TB involves a cocktail of different
antibiotics (bactericidal or bacteriostatic) so that even if
one doesn’t work (i.e. bacteria is resistant), the others will
work and kill the bacteria.
This is followed by 4-7 months of taking 2 antibiotics; most
people are free of TB after approximately 9 months.
TB bacteria can also spread to infect other parts of the
body. Common sites include lymph nodes (glandular TB),
bones, and the central nervous system.
In glandular TB (more common in Asians) the lymph
glands swell in the neck and armpits.
Caucasians are more likely to get pulmonary TB.

Types of antiretrovirals:
 Reverse transcriptase inhibitor: prevents viral RNA
from making DNA for integration into hosts genome.
 Protease inhibitor: inhibit the proteases that catalyse
the cutting of larger proteins into smaller polypeptides
for use in the construction of new viruses.
 Integrase inhibitor.
 Fusion inhibitor.

Why is a mixture of antibiotics used for treatment?

 HIV has many different strains caused by their rapid
rate of mutation and rapid rate of reproduction.
 This means that some will be resistant to certain
antibiotics.
 If only one antibiotic is used, some will be resistant
and will survive.
 A mixture of antibiotics increases the likelihood of
killing all the strains of HIV so it is completely
eradicated from the body.

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How does HIV cause AIDS?
1. gp120 receptors (glycoproteins located on HIV viruses) attach to CD4 receptors on T helper cell
membranes allowing the virus envelope to fuse with and invade the T helper cell.
2. Once inside the host T helper cell, the virus uses reverse transcriptase (enzyme) to reverse
normal transcription and manufacture DNA from the viral RNA template.
3. The virus then inserts viral DNA into the T helper c ells DNA using integrase (enzyme). Once HIV
genome is integrated into the host cells genome it uses the hosts protein synthesis mechanism to
produce new viral proteins.
4. The new viral proteins together with glycoproteins and nuclear material assemble into HIV viruses.
5. The new viruses bud out of the T cell, taking some of the host cell surface membrane with as their
envelope, killing the T helper cell as they leave.
HIV infected T helper cells will also be destroyed by T killer cells. Thus as the number of viruses
increases, the number of host T helper cells decreases causing macrophages, B cells, and T killer
cells to not be successfully activated, and therefore not function properly. The infected person’s
immune system becomes, so opportunistic infections occur.

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Protein Synthesis
Transcription
1. RNA polymerase (an enzyme) attaches to the
DNA double helix at the beginning of a gene.
2. The H bonds between the two strands breaks.
The strands separate and the DNA uncoils.
3. One of the strands is used as a template to
make an mRNA copy. This DNA template
strand is also called the antisense strand.
4. The RNA polymerase lines up free RNA
nucleotides alongside the template strand.
Complementary base pairing takes place
leaving mRNA as a reverse copy.
5. Once RNA nucleotides have paired up with their
complementary bases on the DNA strand they
join together forming an mRNA molecule.
6. The RNA polymerase moves along the DNA,
separating the strands and assembling the
mRNA strands.
7. The H bonds between the uncoiled strands of
the DNA re-form once the RNA polymerase has
passed by and the strands coil back into a
double helix.
8. When the RNA polymerase reaches a stop
codon, it stops making mRNA and detaches
from the DNA.
9. mRNA moves out of the nucleus via nuclear
pores and attaches to a ribosomes in the
cytoplasm.
Translation
1. Amino acids are joined together at the ribosomes
to make a polypeptide chain, following the
sequence of codons carried by the mRNA.
2. The mRNA attaches itself to a ribosome while
transfer RNA (tRNA) carries amino acids to the
ribosomes.
3. A tRNA molecule with an anticodon that is
complementary to the first codon on the mRNA
attaches itself to the mRNA.
4. A second tRNA molecule attaches itself to the
next codon in the same way.
5. Amino acids attach to the tRNA molecule by
peptide bonds. The first tRNA molecule moves
away, leaving an amino acid behind.
6. A third tRNA molecule binds to the next codon on
the mRNA. Its amino acids binds to the first two
and the second tRNA molecule moves away.
7. This process continues, producing a polypeptide
chain, until it reaches a stop codon on the mRNA.
8. The polypeptide chain moves away from the
ribosome and translation is complete.
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DNA is found in the cell nucleus, and is made up of two strands of
polynucleotides (have a sugar (deoxyribose), a phosphate and a
base) held together in a double helix by H bonds.

DNA contains genes (sections of DNA which are found in

chromosomes) or instructions which code for proteins; they contain
the instruction to make them. Proteins are made from amino acids,
and different proteins have a different number and order of amino
acids which is decided by the order of bases within the gene. Three
bases together it is called a Triplet (codes on DNA) or a Codon
(codes on mRNA).
There are four possible bases: Adenine, Thymine, Cytosine, and
Guanine. These bases form complementary base pairs: A pairs with
T, G pairs with C.

Different codons code for different amino acids; this is the genetic code. In the genetic code each
triplet is read in a sequence, separating it from the triplet before and after it; the code is non-
overlapping as no base of one triplet contributes to part of the next triplet. There is a possible 20
amino acids from 64 possible codons; some amino acids have several codons coding for them.

DNA is copied into RNA (a single polynucleotide strand that contains a sugar (ribose) and uracil
(which replaces thymine)) for protein synthesis. The organelle needed for protein synthesis is found in
the cytoplasm (outside of the nucleus. DNA is too large to move out of the nucleus, so sections are
copied into RNA during transcription. RNA leaves the nucleus and joins onto a ribosome in the
cytoplasm where it is synthesised into a protein (translation).

Genes contain sections that don’t code for

amino acids called introns (non-coding
regions of DNA).
Genes also contain sections that do code for
amino acids called exons (coding regions of
DNA). Introns are separated by exons.
During transcription both introns and exons
are copied, but the introns are removed by a
process called splicing which takes place in
the nucleus as a post transcriptional
modification. The exons can then be joined
together in different orders to form different
mRNA (template) strands during translation of
proteins. In this way, one mRNA gives rise to
more than one protein by post transcriptional
modifications.

mRNA
Carries the genetic code from DNA in the nucleus
to the cytoplasm where it is used to make proteins
during translation.
mRNA is modified before it is translated.
tRNA
Carries the amino acids that are used to make
proteins to the ribosomes.
It has an amino acid binding site at one end and a
sequence of three bases at other end (anticodon).

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