Topic 6: Immunity, Infection and Forensics — Edexcel A-Level Biology A (Salters-Nuffield)

Determining time of death uses several independent indicators, each with limits. Decomposition progresses through autolysis and putrefaction; extent of decomposition gives a broad estimate, faster in warm, moist, oxygen-rich conditions. Succession on a body follows a predictable sequence of insects and other organisms, so the stage reached indicates elapsed time. Forensic entomology uses the life cycle of blowflies: eggs, larvae (maggots), pupae and adults, with accumulated temperature (degree days) refining the estimate. Body temperature falls after death until it reaches ambient, so cooling curves help early on, but ambient temperature, body size and clothing affect the rate. Muscle contraction begins with rigor mortis: ATP is lost, actin and myosin lock, then enzymes break the complex down, so the degree of contraction indicates time since death. Combining indicators reduces error.

Micro-organisms decompose organic matter by secreting enzymes that break down proteins, carbohydrates and lipids into small soluble molecules, which they absorb for respiration. This releases carbon dioxide, water and mineral ions. Saprobionts, mainly bacteria and fungi, carry out this external digestion; fungi extend hyphae into dead material. The carbon locked in dead organisms returns to the atmosphere as carbon dioxide, available for photosynthesis, so decomposition is a key part of the carbon cycle. Aerobic conditions give faster, complete decomposition; waterlogged or acidic conditions slow it and can produce methane. Recycling keeps carbon available for living organisms and prevents indefinite accumulation of dead organic matter.

DNA profiling compares variable repeat sequences between individuals. A sample's DNA is extracted, amplified by PCR, cut with restriction enzymes and separated by gel electrophoresis; the band pattern is the profile. In forensics, a crime-scene profile is compared with a suspect's profile: a match supports identification, while a mismatch excludes. In paternity testing, a child's bands must all derive from the two parents, so a candidate parent lacking shared bands is excluded. In plants and animals, profiles reveal genetic relationships, for example confirming pedigree or identifying endangered species. Because repeat numbers vary, profiles are statistically compared, not treated as absolute proof.

PCR makes many copies of a DNA sequence in vitro. A reaction mixture contains the DNA template, primers complementary to the flanking sequences, free nucleotides, a thermostable DNA polymerase such as Taq polymerase, and buffer with cofactors. The mixture is cycled through three temperatures. Around 95 °C denatures the double helix, separating the strands. Around 55 °C lets primers anneal to complementary sequences on each strand. Around 72 °C lets polymerase extend primers by adding nucleotides 5′ to 3′, synthesising new strands. Each cycle doubles the target, so amplification is exponential; after n cycles the target is amplified approximately 2ⁿ-fold. PCR is used to amplify DNA for profiling, diagnosis and sequencing.

Bacteria are prokaryotic cells with a cell wall, cell membrane, cytoplasm, ribosomes, and a circular DNA molecule not enclosed in a nucleus. Some bacteria also have plasmids, flagella, or capsules. Viruses are acellular and much smaller; they consist of a nucleic acid core (DNA or RNA) surrounded by a protein capsid, and some have an outer envelope derived from host cell membranes. Viruses lack cellular structures such as ribosomes, cytoplasm, and cell membrane, and they cannot reproduce independently. Comparing them highlights that bacteria are living cells capable of independent metabolism and reproduction, whereas viruses are obligate intracellular parasites that require a host to replicate. This distinction is fundamental to understanding infection and immunity.

TB is caused by the bacterium Mycobacterium tuberculosis, spread by airborne droplets when an infected person coughs or sneezes. Inhaled bacteria reach the alveoli, where they are engulfed by phagocytes but resist digestion; a primary infection may cause few symptoms while bacteria persist. Reactivation damages lung tissue, producing a persistent cough, weight loss, fever and, if untreated, death. HIV is a retrovirus with RNA and reverse transcriptase. It binds CD4 receptors on helper T cells, fuses, and reverse transcriptase makes DNA from viral RNA; this DNA integrates into the host genome. New virions bud from the cell, destroying helper T cells. Falling helper T cell numbers impair immune responses, so opportunistic infections cause symptoms and, eventually, death.

Non-specific responses act against any pathogen without recognising a specific antigen. Inflammation follows tissue damage: histamine released by mast cells dilates arterioles and increases capillary permeability, so more blood, phagocytes and plasma proteins reach the site, causing redness, heat, swelling and pain. Lysozyme, an enzyme in tears, saliva and nasal secretions, hydrolyses peptidoglycan in bacterial cell walls, causing lysis. Interferon is released by virus-infected cells and binds receptors on uninfected cells, switching on antiviral proteins that inhibit viral replication. In phagocytosis, a phagocyte engulfs a pathogen in a vesicle; lysosomes fuse and release enzymes that digest it.

Antigens are molecules, often proteins or glycoproteins on a pathogen’s surface, that are recognised as non-self and trigger an immune response. Antibodies are Y-shaped glycoproteins produced by plasma cells; each has variable regions that bind a specific antigen epitope, forming an antigen–antibody complex. This binding can neutralise pathogens, agglutinate them or mark them for destruction. Macrophages act as phagocytes: they engulf pathogens and present processed antigen fragments on their surface as antigen-presenting cells (APCs). APCs then activate T helper cells, which in turn stimulate B cells to divide into plasma cells and memory cells. Plasma cells are specialised B effector cells that secrete large quantities of antibody. Thus antigens initiate the response, antibodies mediate specific defence, and macrophages, APCs and plasma cells link recognition to elimination.

B cells and T cells are both lymphocytes with specific receptors, but they have distinct roles. B effector cells (including plasma cells) produce antibodies that bind antigens, leading to neutralisation, agglutination or opsonisation. B memory cells persist after infection and enable a rapid, stronger secondary antibody response. T helper cells release cytokines that activate B cells, T killer cells and macrophages. T killer cells destroy infected or abnormal cells by recognising antigen presented on MHC molecules and inducing apoptosis. T memory cells provide long-term cell-mediated immunity and rapidly expand upon re-exposure. Thus B cells primarily mediate humoral immunity through antibodies, while T cells mediate cell-mediated immunity and regulate the response.

A gene is a DNA sequence that is transcribed to produce pre-mRNA, which is then processed into mature mRNA. Post-transcriptional changes to mRNA allow one gene to produce multiple proteins. These changes include alternative splicing, where different combinations of exons are joined and introns removed, producing different mRNA variants from the same pre-mRNA. Alternative polyadenylation can produce mRNAs with different 3′ ends, affecting stability or localisation. RNA editing can alter nucleotides, changing codons. These mRNA variants are translated into proteins with different amino acid sequences. For example, the human calcitonin gene produces calcitonin in thyroid C cells and calcitonin gene-related peptide (CGRP) in neurones via alternative splicing and polyadenylation. Thus, one gene can give rise to more than one protein through post-transcriptional changes to mRNA.

Pathogens enter the body via major routes: the respiratory tract through inhalation of droplets or particles; the gastrointestinal tract through ingestion of contaminated food or water; the skin through breaks such as cuts, bites or burns; the genitourinary tract through sexual contact or catheterisation; and the conjunctiva of the eye. The body has barriers that protect against infection. The skin is a physical barrier with keratinised cells and sebum, and its acidic pH inhibits microbial growth. Stomach acid (hydrochloric acid) kills many ingested pathogens. Gut flora and skin flora compete with pathogens for nutrients and space and can produce antimicrobial substances. These barriers form the first line of defence and are non-specific. If barriers are breached, pathogens may enter and cause infection.

Immunity arises when the adaptive immune system retains memory of a specific antigen, so a later exposure triggers a faster, larger antibody response. Classify any example using two questions. First, is the antigen encountered naturally, such as infection or transfer across the placenta, or artificially, as in vaccination or injected antibodies? Second, is the protection active, where the person's own lymphocytes produce antibodies and memory cells, or passive, where ready-made antibodies are supplied and no memory forms? Natural active immunity follows infection; artificial active immunity follows vaccination; natural passive immunity follows placental transfer of maternal IgG; artificial passive immunity follows antivenom injection. Active immunity is slow to develop but long-lasting; passive is immediate but temporary.

The evolutionary race is reciprocal selection: host immune defences reduce pathogen reproduction, so pathogen variants that evade those defences survive and reproduce, and the host population then shifts towards recognising the new variants. Pathogen evasion mechanisms provide evidence because each one is an adaptation that counters a specific host defence. Examples include antigenic variation, as in influenza, where surface antigens change so memory cells no longer bind; antigenic drift and shift in influenza; HIV mutating its surface proteins and destroying helper T cells; and malaria parasites changing surface antigens across life-cycle stages. Other mechanisms include hiding inside host cells, blocking phagocytosis with a capsule, and suppressing or destroying immune cells. Each evasion mechanism is inherited and raises fitness, so it spreads through the pathogen population.

Antibiotics differ in how they act on bacteria. A bactericidal antibiotic kills bacteria directly, so the number of viable cells falls; a bacteriostatic antibiotic stops bacteria growing and dividing, so numbers stay roughly constant while the drug is present. Bactericidal drugs often disrupt the cell wall or cell membrane, causing lysis; bacteriostatic drugs often inhibit protein synthesis or DNA replication, halting metabolism. For example, penicillin is bactericidal because it prevents peptidoglycan cross-linking, so the cell bursts by osmosis. Tetracycline is bacteriostatic because it blocks ribosome function. The distinction is not absolute: a bacteriostatic drug can become bactericidal at higher concentration, and host defences help clear static infections. Both types reduce the active infection, but only bactericidal action directly lowers viable counts.

Hospital acquired infections (HAIs) arise from contributory causes such as pathogen transmission via hands, equipment and air, vulnerable patients with weakened immunity, invasive procedures, and overuse or misuse of antibiotics selecting resistant bacteria like MRSA and Clostridioides difficile. Understanding these causes has driven codes of practice: antibiotic stewardship (prescribe only when needed, narrow spectrum, complete course) reduces selection pressure; hospital practice includes hand hygiene, isolation, sterilisation, PPE, environmental cleaning and surveillance. These measures interrupt transmission and limit resistance, protecting patients and staff.

Gel electrophoresis separates DNA fragments by length. DNA is negatively charged due to its phosphate groups, so when placed in an electric field it migrates towards the positive electrode. Shorter fragments move faster and further through the agarose gel matrix, while longer fragments are retarded. To perform the technique, DNA samples are digested with restriction enzymes, loaded into wells in an agarose gel submerged in buffer, and a voltage is applied. After a set time, the gel is stained with a DNA-binding dye and viewed under UV light, revealing bands. The pattern of bands allows comparison of fragment lengths, which is useful in forensic analysis and genetic fingerprinting. The method relies on the constant charge-to-mass ratio of DNA fragments, meaning separation is primarily by size.

This core practical uses a lawn of bacteria on an agar plate to test several antibiotics. A sterile swab spreads a known bacterial culture evenly over the agar to create a lawn. Antibiotic discs are placed on the surface with sterile forceps, spaced apart and pressed gently. The plate is incubated upside down at a suitable temperature, often around 25 °C to 30 °C for school work, so condensation does not drip onto the lawn. After incubation, clear zones around discs show where bacterial growth has been inhibited. The full diameter of each zone, including the disc, is measured in millimetres with a ruler. A larger zone indicates greater sensitivity of the bacterium to that antibiotic, but zone size also depends on the antibiotic concentration and how readily it diffuses through the agar.