Title: InkBiology / Pathogens, disease and immunity
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Antigen-presenting cell.
Back: A cell displaying antigens from a pathogen it has destroyed on its own cell-surface membrane.

Front: DEFINE
Define: Antigenic variation.
Back: Change in the antigens on a pathogen's surface, so that memory cells and antibodies produced against the previous form are no longer complementary to it.

Front: DEFINE
Define: Plasma cell.
Back: A differentiated B cell that secretes large quantities of a single antibody into blood and lymph. Most survive only a few days; a minority settle in the bone marrow and secrete for years.

Front: DEFINE
Define: Antigen.
Back: A molecule, usually a protein or glycoprotein on a cell surface, that the immune system can recognise as self or non-self and that can trigger an immune response.

Front: DEFINE
Define: Herd immunity.
Back: The protection of unvaccinated individuals that results when a large enough proportion of a population is immune for transmission not to be sustained.

Front: DEFINE
Define: Clonal selection.
Back: The binding of an antigen to the one lymphocyte whose receptor is complementary to it, activating that cell and no others.

Front: SPOT THE ERROR
Say what is wrong with this claim:
White blood cells fight infection by recognising the germ and producing the right antibody for it.
Back: The first cell to arrive recognises nothing in particular. A phagocyte engulfs anything carrying surface molecules it does not read as yours. Recognition of a particular pathogen comes days later, and it comes because that phagocyte displayed the antigens.

Front: DEFINE
Define: Phagosome.
Back: The vesicle formed when a phagocyte's cell-surface membrane closes around an engulfed pathogen.

Front: DEFINE
Define: Clonal expansion.
Back: The repeated division by mitosis of the selected lymphocyte, producing a large clone of genetically identical cells.

Front: DEFINE
Define: Pathogen.
Back: An organism that causes disease in its host.

Front: CHECK YOURSELF
A vaccine against a bacterium is given to a child, who develops a mild fever for a day and no other symptoms. Eighteen months later the child is exposed to the live bacterium and does not become ill at all. Explain what happened on each occasion, in terms of the cells involved.
Back: The vaccine contained antigens from the bacterium. Phagocytes engulfed them and presented the antigens on their cell-surface membranes, and a T-helper cell with a complementary receptor was selected and divided by mitosis.
B cells whose surface antibody was complementary to the same antigen took it in and presented it, were stimulated by activated T-helper cells, and underwent clonal expansion. The clone differentiated into plasma cells, which secreted antibody over the following days, and memory cells, which remained. This was a primary response: slow, small and, because there was no live pathogen reproducing, symptom-free apart from the fever produced by the response itself.
Eighteen months later the memory cells were still circulating. On exposure, the same antigen bound to memory B cells that were already present in large numbers and already selected, so they divided rapidly into plasma cells. Antibody appeared within two or three days rather than eight, at a much higher concentration.
The bacteria were agglutinated and marked for phagocytosis before they had reproduced enough to cause symptoms. The child was never ill because the response was faster than the infection, not because the bacteria never entered.

Front: DEFINE
Define: Memory cell.
Back: A long-lived cell produced by clonal expansion that does not secrete antibody, but divides rapidly into plasma cells if the same antigen is met again.

Front: DEFINE
Define: Constant region.
Back: The part of an antibody that is the same in all antibodies of a class, and that binds to receptors on phagocytes.

Front: DEFINE
Define: Lymphocyte.
Back: A white blood cell carrying receptors of a single shape, produced in bone marrow; T cells mature in the thymus and B cells in the bone marrow.

Front: DEFINE
Define: Antigen.
Back: A molecule, usually a surface protein or glycoprotein, that is recognised as self or non-self and can trigger an immune response.

Front: DEFINE
Define: Variable region.
Back: The part of an antibody whose amino acid sequence differs between antibodies, forming the antigen-binding site.

Front: CHECK YOURSELF
A person recovering from a severe bacterial infection is given an injection of antibodies taken from a donor who has recovered from the same infection. They improve within a day. Six months later they are infected again and become seriously ill. Explain both outcomes, and state what should have been done differently if long-term protection was the aim.
Back: The injection gave artificial passive immunity. Ready-made antibodies with binding sites complementary to the bacterium's antigens were already present in the blood, so agglutination, neutralisation of toxins and marking for phagocytosis began at once, with no lag for clonal selection or expansion. That is why the improvement was so fast.
No memory cells were produced. The patient's own B cells were not selected and did not undergo clonal expansion, because the donor's antibodies bound the antigens and cleared them before the patient's response had developed. The injected antibodies are proteins and were broken down over the following weeks, leaving nothing behind.
Six months later there were therefore no memory cells specific to that antigen. The second infection provoked a primary response, taking around eight days to detectable antibody and at a low concentration, so the bacteria reproduced freely in the meantime and the patient became seriously ill.
For long-term protection they should have been vaccinated as well as given the antibodies: passive immunity for immediate control, and antigen to provoke an active response and leave memory cells. That is exactly the combined treatment used after a possible rabies exposure.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Memory cells are the ones that make antibody quickly the second time you meet a pathogen.
Back: Memory cells secrete nothing while they circulate, which is how they last for decades. On re-exposure they divide rapidly into plasma cells, and it is the plasma cells that secrete antibody. The speed comes from starting with thousands of the right cells.

Front: DEFINE
Define: Antigen-antibody complex.
Back: The structure formed when an antigen binds to the complementary binding site of an antibody.

Front: DEFINE
Define: Antibody.
Back: A protein with a quaternary structure of four polypeptide chains, produced by plasma cells, with variable regions forming two binding sites complementary to one antigen.

Front: CHECK YOURSELF
A long-term smoker has destroyed much of the ciliated epithelium lining her airways, and she also takes a drug that greatly reduces the secretion of stomach acid. She suffers repeated chest infections, and a sample of her sputum is found to contain very large numbers of dead neutrophils. Explain how each of the two changes makes infection more likely, and explain what the neutrophils show about the defences that are still working.
Back: Losing the cilia breaks a physical defence in the middle. Goblet cells are still secreting mucus, and that mucus still traps bacteria and virus particles as it always did, so the trapping half of the barrier is intact. What has gone is the removal. Cilia normally beat the mucus upwards to the throat, where it is swallowed; with the ciliated epithelium damaged, the mucus and everything caught in it stays in the airways, warm and undisturbed, which is a good place for bacteria to reproduce. A defence that traps without clearing has become somewhere for pathogens to accumulate.
Reducing stomach acid breaks a chemical defence at the other end of the same chain. Acid normally holds the gut contents near pH 2, which denatures the enzymes and other proteins of most swallowed bacteria and kills them. Raise that pH and swallowed pathogens survive, including the ones in whatever mucus she does still clear from her lungs, which are swallowed rather than coughed out. Both defences are non-specific: they act on any pathogen at all, and they act at the same speed every time, so neither is improved by how often she has been infected before.
The dead neutrophils show that phagocytosis is running hard. Neutrophils are the short-lived phagocytes that arrive first, drawn to the infected tissue by chemotaxis along a gradient of chemicals from the bacteria and the damaged cells. Receptors on the neutrophil attach to antigens on the bacterial surface, the membrane folds round the bacterium to enclose it in a phagosome, lysosomes fuse with the phagosome and empty hydrolytic enzymes into it, and the bacterium is hydrolysed. Neutrophils die in the process in very large numbers, which is what pus and that sputum sample are.
So the phagocytes are doing the work the barriers are no longer doing, and they are doing it without needing to know what the pathogen is. They are also doing the one thing that leads anywhere: macrophages at the site present the bacterial antigens on their own cell-surface membranes, which is the only route by which a specific response, meaning clonal selection, antibody and memory cells, can begin at all. A question that asks how a non-specific response leads to a specific one is asking about that stage and no other.

Front: DEFINE
Define: Non-self.
Back: Antigens not present on the organism's own cells: pathogens, transplanted tissue, cancerous cells with altered surface proteins, and toxins.

Front: DEFINE
Define: Phagocytosis.
Back: The engulfing and hydrolysis of a pathogen or other foreign material by a phagocyte, forming a phagosome that fuses with a lysosome.

Front: DEFINE
Define: Lysosome.
Back: An organelle containing hydrolytic enzymes, including lysozymes, kept separate from the cytoplasm.

Front: DEFINE
Define: Self.
Back: Antigens present on an organism's own cells, which its lymphocytes do not respond to.

Front: DEFINE
Define: Vaccine.
Back: A preparation containing antigens from a pathogen, given to produce a primary immune response and memory cells without causing the disease.

Front: DEFINE
Define: Non-specific defence.
Back: A defence that acts against any pathogen, without recognising which one it is, and acts at the same speed every time.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Antibodies kill pathogens.
Back: An antibody has two binding sites and no enzymic activity: it cannot lyse, digest or poison anything. It binds, which agglutinates pathogens, blocks the parts that would attach to your cells, and marks them for a phagocyte. The destruction happens inside the phagocyte.