5.3.1 The specific immune system

Antigens Trigger a Specific Immune Response

1. An antigen is a molecule on a pathogen that the immune system recognises as foreign.
2. A lymphocyte with a complementary receptor recognises the antigen and is activated.
3. The activated lymphocyte divides to form many identical cells.

Antibodies Bind Specific Antigens

1. Activated lymphocytes produce antibodies with binding sites complementary to the antigen.
2. Antibodies bind pathogens, neutralise them or mark them for destruction by phagocytes.
3. The first response is slow because the correct lymphocyte must be selected and cloned.
4. Each lymphocyte carries receptors with one binding shape, so only cells complementary to the antigen are selected.
5. Selected lymphocytes divide by mitosis, producing a clone that can generate a large concentration of one specific antibody.
6. Antibody binding can neutralise a pathogen, cause pathogens to clump or mark them for phagocytosis.

Memory Cells Produce a Faster Second Response

1. Some activated lymphocytes become long-lived memory cells after the infection is controlled.
2. If the same antigen enters again, memory cells divide rapidly and produce many antibody-secreting cells.
3. Antibody concentration rises faster and higher, often destroying the pathogen before symptoms develop.
4. The primary response takes time, so symptoms may develop before antibody concentration is high enough to control the pathogen.
5. Memory lymphocytes persist after recovery and undergo rapid clonal expansion on re-exposure, producing a faster, larger secondary response.

The Response Is Antigen-specific

1. Memory cells for one antigen do not protect against an unrelated antigen.
2. A pathogen with changed surface antigens may escape an existing immune response.

5.3.2 Response to immunisation

Vaccination Creates Memory Without Disease

1. A vaccine contains an inactive or harmless form of a pathogen, or antigens from it.
2. The vaccine antigens cannot cause the full disease but are recognised as foreign.
3. An inactive pathogen retains antigens that lymphocytes can recognise but cannot reproduce and cause the full disease.

Lymphocytes Produce Antibodies and Memory Cells

1. Lymphocytes with complementary receptors are activated and divide.
2. Some cells produce specific antibodies, while others remain as memory cells.

Later Exposure Triggers a Rapid Response

1. Memory cells recognise the same antigen when the live pathogen enters later.
2. They divide rapidly and produce a larger concentration of antibodies in less time.
3. The pathogen is destroyed before it causes serious symptoms.
4. On later exposure, memory cells recognise the same antigen and produce antibodies before pathogen numbers become high enough to cause symptoms.

Booster Doses Restore Protection

1. Memory-cell numbers or antibody concentrations can decline over time.
2. A booster exposes the immune system to the antigen again and strengthens the memory response.
3. A booster repeats antigen exposure, increasing memory-cell numbers and restoring protection when immunity has declined.

Immunity Is Produced Actively

1. Vaccination gives active immunity because the person's own lymphocytes produce antibodies and memory cells.
2. This protection can last much longer than receiving ready-made antibodies.

5.3.3 Advantages and disadvantages of immunisation

Immunisation Protects Individuals and Populations

1. Vaccination produces memory cells, so later infection triggers a faster and stronger antibody response.
2. Fewer vaccinated people develop disease, severe complications or long-term damage.
3. Reducing infections also lowers healthcare demand and time lost from school or work.
4. Vaccination reduces an individual's probability of infection and severe disease, but protection is not complete and differs between people.

Herd Immunity Reduces Transmission

1. Herd immunity occurs when enough people are immune that an infected person is unlikely to meet a susceptible host.
2. Transmission chains are interrupted, protecting people who cannot be vaccinated or who do not respond strongly.
3. The proportion needed depends on how easily the disease spreads and how effective the vaccine is.
4. Herd immunity works only when immunity is common enough to reduce the pathogen's reproductive spread through the population.
5. People who cannot receive a vaccine benefit because they are less likely to contact an infected person, not because they personally become immune.

Immunisation Has Limitations

1. Vaccines can cause short-lived pain, swelling or fever, while serious adverse reactions are rare.
2. No vaccine protects every recipient, and immunity may decline so booster doses are needed.
3. Some pathogens change their antigens, reducing protection from an older vaccine.
4. Developing, storing and delivering vaccines costs money, and low uptake prevents herd immunity.
5. A fair evaluation compares the frequency and severity of vaccine side effects with the frequency and severity of the disease.
6. Low uptake, reduced vaccine effectiveness or antigen changes can allow outbreaks despite an immunisation programme.

Reach a Justified Judgement

1. For diseases that cause serious harm and have effective vaccines, the individual and population benefits usually outweigh the small risk of side effects.
2. The judgement may change if effectiveness is low, protection is short-lived or the disease is uncommon and mild.

Use Evidence Carefully

1. Compare infection rates in similar vaccinated and unvaccinated groups while considering age, exposure and health differences.
2. A correlation between vaccination and lower disease incidence supports effectiveness but other variables must be considered.

5.3.4 Antibiotics and bacterial infections

Antibiotics Target Bacterial Processes

1. An antibiotic is a medicine that kills bacteria or stops them reproducing.
2. Different antibiotics inhibit processes such as bacterial cell-wall synthesis, protein synthesis or DNA replication.
3. These targets differ from the host's cell processes, so a suitable dose harms bacteria more than body cells.
4. Other antibiotics bind bacterial ribosomes or inhibit bacterial DNA replication, stopping growth and reproduction.
5. Human cells lack peptidoglycan walls and have different ribosomes, which provides selective toxicity at a therapeutic dose.
6. Penicillin inhibits enzymes that join bacterial cell-wall material, so a growing bacterium cannot resist internal pressure and may burst.

Antibiotics Do Not Treat Viruses

1. Viruses have no cell wall, ribosomes or independent metabolism for an antibiotic to target.
2. They reproduce using host-cell machinery, so antibiotics do not stop viral replication.
3. Painkillers may reduce viral symptoms but do not kill the virus.

Correct Use Slows Resistance

1. Random mutations can make some bacteria resistant to an antibiotic.
2. Treatment kills susceptible bacteria, while resistant bacteria survive, reproduce and pass on resistance alleles.
3. Using antibiotics only when necessary reduces selection pressure, and completing the prescribed course reduces surviving bacteria.
4. Resistance alleles arise by mutation before treatment; the antibiotic selects resistant bacteria rather than causing directed mutation.
5. Resistant survivors reproduce and pass resistance alleles to descendants, increasing the resistant proportion of the population.

Choose Evidence-based Treatment

1. A culture can be tested against antibiotic discs, and a larger zone of inhibition indicates greater bacterial growth inhibition under the test conditions.
2. The chosen antibiotic must also reach the infection site safely inside the patient.

Separate Treatment From Symptom Relief

1. Antibiotics treat the bacterial cause, while painkillers lower pain or fever without removing the pathogen.
2. The immune system still removes dead bacteria and damaged cells.

5.3.5 Aseptic techniques in culturing

Growing microorganisms

1. A culture medium supplies water and nutrients so microorganisms can grow. It may be a liquid broth or nutrient agar in a Petri dish.
2. On solid agar, one microorganism can divide repeatedly to form a visible colony. A spread of bacteria across the agar is called a bacterial lawn.

Aseptic technique

1. Aseptic technique prevents unwanted microorganisms contaminating the culture and reduces the chance that cultured microorganisms escape into the surroundings.
2. An autoclave uses pressurised steam at a high temperature to sterilise culture medium and Petri dishes before use. Sterilisation kills microorganisms and resistant spores.
3. A sterile inoculating loop is used to transfer microorganisms. If a metal loop is used, it is heated in a Bunsen flame until red hot and allowed to cool before touching the culture.
4. The Petri-dish lid is opened only slightly and briefly. After inoculation, it is secured at two or three points so it stays covered but is not sealed completely.

Antimicrobial cultures

1. A paper disc containing an antibiotic, antiseptic or plant extract is placed on a bacterial lawn. The substance diffuses through the agar.
2. Where bacterial growth is killed or inhibited, a clear zone of inhibition forms. A larger zone usually indicates a more effective antimicrobial substance when all control variables are kept constant.

Interpreting the investigation

1. The plate is inverted during incubation so condensation collects on the lid rather than dripping onto the agar and spreading colonies.
2. School cultures are incubated at $25{}^{\circ }\mathrm{C}$ because temperatures closer to $37{}^{\circ }\mathrm{C}$ would favour microorganisms adapted to the human body, including potential pathogens.

5.3.6 Cross-sectional areas of cultures

Measuring circular areas

1. Bacterial colonies and zones of inhibition are often approximately circular, so their cross-sectional area is calculated from the radius.
2. Measure the diameter through the centre of the circle. If the edge is uneven, measure two perpendicular diameters and calculate their mean.
3. Calculate the radius using $r=\frac{d}{2}$, then use $A=\pi r^2$.

Comparing antimicrobial effects

1. When the same microorganism and experimental conditions are used, a larger zone of inhibition provides evidence that the antimicrobial substance was more effective.
2. Area is proportional to the square of the radius. A zone with twice the radius has four times the area, not twice the area.
3. Use the same units throughout. If the radius is measured in millimetres, the area must be recorded in ${\mathrm{mm}}^2$.

Evaluating measurements

1. An irregular zone is a source of measurement uncertainty. Taking two diameters at right angles and using their mean gives a more representative radius.
2. A larger clear area does not by itself prove that a medicine will work better inside a person. Diffusion through agar, concentration and experimental conditions also affect zone size.

5.3.7 Stages of developing new medicines

Discovering medicines

1. Medicine development begins with the discovery of a substance that may prevent or treat disease. Candidates may come from microorganisms, plants or chemical synthesis.
2. Scientists investigate how the candidate acts, then develop a suitable formulation and dose before testing whether it is safe and effective.

Preclinical testing

1. Preclinical testing takes place before a medicine is given to human volunteers.
2. The substance is tested on cells and tissues to examine its biological effect and identify obvious toxicity.
3. It is then tested in living organisms to investigate how the whole body absorbs, distributes, breaks down and removes it, and to check for harmful effects.
4. These tests provide evidence about toxicity, efficacy and a possible dose. A candidate that is ineffective or unacceptably harmful does not progress.

Clinical trials

1. Clinical trials test the medicine in people. Early trials use a small number of healthy volunteers and a very low dose, which is increased carefully to investigate safety and side effects.
2. Later trials use larger groups of patients to test whether the medicine treats the condition and to refine the effective dose.
3. A placebo contains no active medicine. Comparing a treatment group with a placebo group helps show whether improvement is caused by the medicine rather than expectation or natural recovery.
4. In a double-blind trial, neither the participants nor the researchers assessing them know who receives the medicine until the results are analysed. This reduces conscious and unconscious bias.
5. Random allocation and large sample sizes reduce the effect of individual differences and make the groups more comparable.

Review and monitoring

1. Results are checked by independent scientists through peer review. Regulators examine the evidence before deciding whether the medicine can be licensed.
2. After licensing, the medicine continues to be monitored because rare or long-term side effects may only appear when it is used by many people.

5.3.8 Production of monoclonal antibodies

Monoclonal antibodies

1. A monoclonal antibody is one of many identical antibodies made from a single clone of cells, so every antibody binds to the same specific antigen.
2. Their specificity allows a particular molecule or type of cell to be detected, located or targeted.

Producing hybridomas

1. A lymphocyte that makes the desired antibody is selected. It produces the correct antibody but does not divide repeatedly.
2. The lymphocyte is fused with a tumour cell, which divides rapidly, to form a hybridoma.
3. Hybridoma cells combine both useful properties: they divide to form a clone and each cell produces the desired antibody.
4. The clone is cultured, and the identical antibodies are collected and purified.

Pregnancy tests

1. Pregnancy tests detect the hormone hCG in urine using monoclonal antibodies that bind specifically to hCG.
2. Urine carries coloured antibodies along the strip. If hCG is present, it binds to them and the complex is trapped by fixed antibodies at the test line, producing a coloured line.
3. A separate control line traps excess coloured antibodies whether or not hCG is present. It shows that the liquid moved through the strip and that the test worked.

Diagnosis and treatment

1. Monoclonal antibodies can be attached to fluorescent markers or radioactive substances. After binding to a target antigen, the marker reveals the position of cancer cells or a blood clot.
2. For treatment, an antibody can bind to an antigen found mainly on cancer cells. It may block a growth signal or deliver a toxic drug or radioactive substance directly to the target cells.
3. This targeting can damage fewer healthy cells than non-specific drug treatment or radiotherapy, so it may reduce side effects.
4. Limitations include immune reactions, unexpected side effects, high production costs and the possibility that not every target cell carries the antigen.