1. Immunology
Innate Immune Protection
1. What are the features of and differences between innate immunity and adaptive
immunity?1
2. What times following exposure to a pathogen do (i) the innate immune system
and (ii) the adaptive immune system, take to respond?2
3. Which 3 areas of the body contain the main physical/anatomical barriers to
‘external’ pathogens, and give an example of how the structure and function of
these barriers prevents the entry or growth of pathogens? 3
4. What is the complement system?4
5. What are cytokines?5
6. What are the 3 pathways leading to the production of C3 convertase enzyme
(required for the production of C3 complement protein)?6
7. What is a protein-associated molecular pattern (PAMP)?7
8. Pattern recognition receptors are the means by which the innate immune system
tells the difference between host and pathogen cells, what are the three types of
PRR and where are they located?8
1 Innate immune system is the ʻfirst line of defenceʼ it responds to pathogens in a non-specific way and
includes NK cells, complement cells, phagocytes and epithelial barriers. The Adaptive immune system
recognizes specific pathogens and initiates processes to eliminate these pathogens, then remembers them
through T cell receptors or ʻmemory cellsʼ. Includes antibodies, B and T lymphocytes.
2 Innate immunity 0-4 hours, acquired immunity >96 hours
3 Skin (dry, difficult for pathogens to grow or penetrate), respiratory system (tight junctions prevent bacteria
from getting through epithelium, mucus production and cilia), GI tract (same as respiratory system +
peristalsis, HCL and gastrin secretion).
4 Part of the innate immune system which complements antibodies in the adaptive immune system. Consists
of a series of liver-synthesised proteins (proteases) which operate via cascade (production of one induces
the next). These circulate in the blood and cleave to larger proteins triggering them to release cytokines.
5 Cytokines are signaling molecules which signal immune cells to release T-cells and macrophages
6 1. Classical: antibody complex, MB lectin: Mannose on pathogen, Alternative: Pathogen
7 Molecules associated with groups of pathogens which are recognised automatically by ʻToll like receptorsʼ
in the innate immune system. This is how the innate immune system tells the difference between host cells
and pathogens. PAMPs are also essential for the survival of the pathogen.
8 Collectin - serum (blood plasma) these are soluble PRRs, Toll like receptors - found on membrane (like a
toll-gate), Nod like receptors - cytoplasm

2. 9. What are the two parts of a collectin and what are their separate functions?9
10.Which Toll-like receptors recognize the following pathogens: Flagellin,
Unmethylated CpG DNA, LPS (Gram-negative), dsRNA, Peptidoglycan &
Lipoproteins10?
11.There are 2 types of NOD like receptors in cell cytoplasm (NOD 1 & NOD 2),
which pathogen associated molecules do they detect? 11
12. What are monocytes and what is their function in immune response?12
13.What are macrophages and what do they do and how long do they last?13
14.What are neutrophils and what do they do and how long do they last?14
15. What happens during phagocytosis? (there are roughly 8 stages) 15
16.Describe the killing mechanism of macrophages and neutrophils via reactive
oxygen intermediaries? (mainly neutrophils)16
9Coll (collagen) like region interacts with the effector part of the immune system, Lectin region binds to sugar
molecules on the surface of pathogen.
10Flagellin = TLR 9, Unmethylated CpG DNA =TLR 5, dsRNA = TLR 3, Peptidoglycan & Lipoproteins = TLR
1,2 &6, LPS (Gram-negative) = TLR 4
11 NOD 1 = gamma glutamyl diaminopimelic acid, NOD 2 = muramyl dipeptide
12
Monocytes are a type of white blood cell which move to sites of infection/inflammation and divide into
macrophages and dendritic cells to elicit immune response. Lifespan is 2-8 days.
13Macrophages are what monocytes divide into when they reach an inflamed area. These cells are
phagocytes which engulf and digest cellular debris (dead matter) and pathogens. They last about 6-16 days
and can ingest over 100 bacteria before they eventually die due to their own digestive compounds.
14Neutrophils are the most abundant type of white blood cell. They are the ʻfirst respondersʼ to a site of
inflammation and travel in the blood in their active form. They are phagocytes but respond quicker than
macrophages. Last about 5 days (short lived) and are only found in blood.
15 Chemotaxis (organisms directing movement by swimming towards highest concentration of food
molecules, receptors or away from poison) and adherence of microbe to phagocyte, ingestion of microbe,
formation of a phagosome (a vesicle formed around a particle absorbed by phagocytosis), fusion of the
phagosome with a lysosome (an organelle which contains enzymes to break down waste materials) to form
a phagolysosome (a phagosome containing digestive enzymes), digestion of microbe and discharge of
waste materials.
16Following phagocytosis, there is an increase in O2 uptake by the cells, oxygen is reduced by NADPH
oxidase to form hydroxyl radicals and hypochlorite. This causes DNA damage and alterations in bacterial
membranes.

3. 17.Describe the killing mechanism of macrophages and neutrophils via reactive
nitrogen intermediaries (mainly macrophages)?17
18.What are the receptors bound by cytokines to induce inflammation and fever?18
19.What are the receptors bound by cytokines to induce macrophage activation?19
20.What are the receptors bound by cytokines to induce CD4 T Cell differentiation?
20
21.What are chemokines?21
22.What are interferons?22
23.What is the function of dendritic cells? 23
Antibody, Lymphocytes and the Generation of Diversity
1. What is a lymphocyte? 24
2. What are the main two types of cells of the adaptive immune system? 25
3. Where is a T cell’s receptor located on it?26
4. What are the two types of T cell and how do they differ?27
17 The reaction forming L-citruline from L-arginine generated NO radicals, catalyzed by the enzyme ʻinducible
nitric oxide synthaseʼ which is induced by cytokines and bacterial components. NO free radicals cause DNA
damage.
18 IL-1 (interleukin 1) and IL-6 (interleukin 6)
19 TNF (alpha) (tumour necrosis factor)
20 IL-12
21Class of cytokines with chemoattractant properties which promote inflammation by making cells adhere to
the surface of blood vessels and migrate to infected tissue (chemotaxis).
22 Produced in response to virally infected cells, includes natural killer cells.
23Dendritic cells process antigen material and present it to other cells of the immune system (antigen
presenting cells)
24Lymphocyte is the name for the whole group of white blood cells which includes T cells, B cells and NK
cells
25 B cells and T cells
26 On the cell surface
27Cytotoxic T cells kill other pathogens and Helper T Cells release cytokines, responsible for for B cell
antibody class switching, activating cytotoxic T cells and maximising phagocytosis.

4. 5. How to B cells change when their surface receptor recognizes a whole antigen
(without the need for it to be fragmented and presented)?28
6. What are the four main ways that antibodies (a.k.a. B cell receptors in soluble
form, immunoglobulins) attack viruses and toxins? 29
7. What is the basic structure of an antibody and how does this relate to binding?30
8. What is a heterodimer and what types of immune cells can be described as these?
31
9. What is gene rearrangement?32
10. Whereabouts in the body does the gene rearrangement happen for (i) B cells and
(ii) T cells?33
11. What is the process of hypermutation and which lymphocytes undergo this
process? 34
12.What is the process of affinity maturation? 35
13. What is class switching? 36
28Cell differentiates into plasma cells that secretes the receptors as antibodies. Antibody is just a word for a
soluble (unattached) B cell receptor.
29Blocks interaction with other cells, promotes phagocytosis and killing activity by other cells, activates the
complement cascade, agglutinates (clumps together) particles.
30All antibodies contain a variable region with two binding sites, and a constant Fc region which determines
the single species of the antibody. The two regions are connected by a hinge region.
31 A heterodimer is a molecule formed by two distinctly different macromolecules. In the case of antibodies
this means it has two bonding sites which consist of one light chain and one heavy chain each. In the case of
T cell receptors consist of one copy each of two different chains. Forming either an alpha-beta or a gamma-
delta T cell receptor. Contrast to antibodies, T cell receptors only have one binding site.
32A process carried out to establish an antibody. Where one whole gene is made by combining different
segments of genes (V regions, D regions, J regions) by Recombination activating genes (RAG)
33B cells in the bone marrow and T cells in the thymus (a specialised immune organ which “educates” T
lymphocytes
34 Further mutation of a B cell which has an antibody attached to it to match it further to the pathogen.
35Picking the best fit out of multiple mutated Ig genes. So as the B cells mature, those with lower pathogen
affinity are weeded out
36Varying of the gene which codes for antigen specificity and so changing the ʻvariable regionʼ of the
antibody

5. 14.What are the four main antibody types and their shapes?37
15.What is IgM and what is its characteristic functional property? 38
16.How many binding sites does an IgM pentameter have?39
17.What is the main function of IgG?40
18.Which immunoglobulin type is associated with mucosal secretion? 41
19.Which immunoglobulin type is associated with parasitic infection and mast cells? 42
20.What enzyme is used both for affinity maturation and class switching?43
21.Whereabouts within the B cell do affinity maturation and class switching occur?44
T Cells, Effector Junctions and the Generation of the MHC
1. What are the main functions of T cells?45
2. What are MHC molecules46
3. What is the RAG enzyme responsible for?47
4. Where do T and B cells originate from in the body?48
37 IgG1 and IgE = ʻY shapedʼ, IgA (dimer) and IgM (pentameter)
38
IgM is the default immunogobulin that B cells start with in development, the Fc region enables the
molecules to form pentameters which is useful in forming immune complexes.
39 Five immunoglobulin branches with 2 binding sites each so 10 in total
40Secreted into the blood after class switching and collate pathogens so that phagocytes can recognize
them, pathogens coated in IgG become targets for NK cells. (antibody dependent cellular cytotoxicity)
41 IgA
42 IgE
43 Activation Induced Cytidine Deaminase (AID)
44 The Germinal Centre
45T cells recognize bound antigen-complexes called MHCs. MHCs (Major Histocompatability Complexes)
are
46MHC stands for major histocompatability complex, it is a specific molecule to which degraded antigens
(epitopes) bind to
47 Rearranging gene segments to create functional receptors (gene rearrangement)
48 Lymphoid progenitor in the bone marrow

6. 5. Regarding gene variation on alpha-beta T cell receptors, what are the 5 names for
the variable chain segments?49
6. What is needed for a cell bound antigen to bind with a T cell receptor?50
7. What are the main similarities and differences between MHC I and MHC II
molecules? 51
8. What are the three basic structural features of antigen presenting cells?52
9. Where do MHC II primarily draw the peptide molecules they present from? 53
10. Whereabouts on the human chromosome are MHCs 1 and 2 located?54
11. In terms of polymorphism in MHCs, where (structurally) do most variations
occur within the molecule? 55
12. What are the two main subtypes of T cell and what do these mean?56
13. What step(s) other ‘signal 1’ must occur before a T cell and APC can bind and
start adaptive immune response? 57
14. Explain the difference between ‘step 1’ and ‘step 2’ of T cell activation?
49 On both chains there are ʻvariableʼ and ʻjunctionʼ chains
50T cells do not bind to antigens on their own, they must have an antigen presented to them after having
been partially degraded into peptide ʻepitopesʼ
51Both are transmembrane proteins which contain a peptide binding groove with a central role in activating
A/B T cell receptors, MHC 1 associates with beta 2 microglobulin whereas MHC 2 is found on all nucleated
cells. MHC 1 present an example of the proteins being synthesised on the inside of the cell.
52 Two alpha helixes either side of an antigenic peptide, all of this sits on top of a beta pleated sheet
53In contrast to MHC 1, MHC II present peptides from exogenous (outside the cell) antigens as opposed to
endogenous (inside the cell) antigens.
54 Chromosome 6, the most highly polymorphic of all the human chromosome regions.
55
In the beta pleated sheet beneath the peptide binding groove (diversity where it is relevant for the
molecule), governs binding to varied ʻepitomesʼ.
56CD8+ and CD 4+ They refer to different types of co-receptor on the T cell. In terms of function CD8 cells
are killers and CD4 are helper. CD8+ T cells preferentially bind antigen-(endogenous) peptide complexes
presented by MHC 1 molecules. Their role is to detect and kill virus producing cells based on their MHC 1
molecules. By contrast CD4 T cells prefer (exogenous) antigen peptide complexes presented by MHC 2.
57 As well as the CD8+ or CD4+ co-receptor (step 1), you also need co-stimulatory molecules which are
expressed in low levels on the surface of antigen presenting cells and bind to another set of molecules which
are also present in low levels on the surface of the T cell. T cell is only activate when the right kind of co-
stimulatory molecules are present on the surface of the corresponding APC.

7. 15. When T cells are activated, they differentiate into various kinds of T cell which
are told apart by they kind of ‘cytokines’ (immune messengers) they produce.
What are the four main changes cytokines signal in the immune response? 58
16. What are perforins, granzymes and granulysin?59
17. What are the two main types of CD4+ (T-Helper) cells and what are their
functions?60
18.What are regulatory type T cells responsible for?61
19.What defines a T cell?
20.How is a T cell receptor generated?
21.Describe the mechanism(s) by which T cells & T cell receptors can generate vast
diversity
22. What are the different types of MHC molecule and why are they important?
23.How do killer cells work differently to Th1 and Th2 cells function to mount an
adaptive response?
Immune Tolerance and Immune Recognition
1. What are the 6 main players in the immune system (3 immune, 3 adaptive)?62
58 1. Activation and polarisation of immune response (immune cells) 2. Decrease in viral replication (virus
infected cells) and increase in apoptosis in virus infected cells 3. Increase in blood vessel permeability
(endothelial cells) 4. Increase in body temperature (hypothalamus)
59All are proteins within the T cellʼs lysosomes, these are secreted onto molecules (APCs) which have
activated them. Perforin = forms a pore in target membrane, Granzymes = activate apoptosis once in the
cytoplasym of the target cell, Granulysin = induces apoptosis
60
T-helper 1 cells act on intracellular pathogens and are responsible for the activation/function of
macrophages, T-helper 2 cells act on extracellular pathogens and are responsible for the activation and
maturation of B cells, they are vital in causing class switching in B cells. They both produce distinct cytokines
61Regulatory t cells suppress inflammation (including suppression of T cells and APCs), they are thus very
important for preventing autoimmune disease. Their targets of actions include supressing antibody or
cytokine function, function of NK and NKT cells etc.
62Adaptive: T Helper cells (CD4, TReg), T Killer cells (CD8), B cells (antigen presenters and antibody
producers), Innate: dendritic cells (antigen presenters), Macrophages (killer cells, antigen presenters) and
Neutrophils

8. 2. What is responsible for controlling the balance between autoimmunity and
immunodeficiency, this is what T cells get their name from?63
3. What happens to thymocytes in the thymus? 64
4. What is the first stage of ‘testing’ in the ‘thymic education’ of T cells? 65
5. What happens to the thymocyte after this stage in terms of MHC binding66
6. What is negative selection and where does it take place?67
7. What are all three stages of thymic education in order?68
8. What causes newly released T cells in circulation to become activated?69
9. What is T cell anergy? 70
10. What is the mechanism of regulatory T cells?71
11.What are the two types of regulatory T-cells? 72
63 Thymus
64Thermocytes go into the thymus and come out as fully mature CD4+ (helper) or CD8+ (killer) cells. The T
cell receptors have been rearranged and cells will express CD4 OR CD8 specifically. They are tested to
ensure receptors are ʻsafeʼ and will not kill host cells.
65 Whether alpha and beta chains can bind without cell death to create a functional T cell receptor.
66Despite possessing both CD4 and CD8, the thymocyte will have a preference for MHC 1 or 2. Once this
has been established, the thymocyte will shed either CD4 or CD8 co-receptors and ʻspecializeʼ
67 Negative selection takes place in thymic medullary epithelial cells or T-mecs, a range of ʻselfʼ antigens are
presented on the cell surface. The fit of the T cell is tested against self antigens, if the fit is induced too
strongly the T cell is then killed off because releasing it would be dangerous (it is an auto-reactive t cell).
681/ Is it a functional TCR, 2/ Does it interact with self MHCs at all? 3/ Does it have too high an affinity for
self antigens.
69They have to come into contact with an antigen which they have not seen before (i.e. not in the thymus),
generally something which has a foreign source.
70 When a T cell remains in circulation but is unresponsive to future stimulation. Signal 2 as well as signal 1
is required to activate cells. If signal 1 is detected the cell becomes anergic. It is a key mechanism of
maintaining tolerance to proteins not expressed in the thymus.
71 Stop proliferation or cytokine production of CD4/CD8 cells, reduce co-stimulation or alter cytokine produc.
72nTreg - naturally occuring regulatory cells, produced in thymus and respond to self antigens. aTreg -
developed in periphery (outside thymus), constant low level exposure to antigen.

9. 12. Toll-like receptors are found on the surface of interdigitating dendritic cells/
Langerhans cells, what do they recognize?73
13. What is the process within dentritic cells which causes the cross-over between
the innate immune system and the adaptive immune system?74
14. How do dendritic cells which have interacted with pathogens cause
inflammation?75
15. What is the ‘third signal’ in T cell activation (other than the co-stimulators and
co-receptors)?76
16. What type of T-cells are produced when there antigen presenting cells prime
naive T cells in the absence of any inflammation?
17. What type of T cells are primed by antigen presenting cells in the case of asthma
or allergy? 77
18. What causes T cells to migrate into inflamed tissue from blood vessels? 78
19. What kind of cells are stored in immunological memory and where are they
stored? 79
Spread of Infection/Control/Resistance
1. How many people globally are living with HIV?80
73Toll like receptors recognize Pathogen Associated Molecular Patterns (PAMPS) attached to foreign
pathogens. These are unique to whole classes of microbes and are a product of bacterial metabolism.
74 Dendritic cells recognize PAMPS on pathogens, pathogens are engulfed by dendritic cells, put into
lysosomes within the cell, proteins from the pathogen are then expressed as MHC molecules on the surface
of the dendritic cell. These MHCs are then picked up by T cells in the adaptive immune system.
75The dendritic cells release cytokines whilst in lymph nodes which up-regulate adhesion molecules (which
make cells stick to blood vessels), so T cells migrate into lymph node and become trapped within lymph for
2-5 days.
76APC secretes cytokines which affect the T cell dependent on which pattern recognition receptors have
been activated by dendritic cells. Controls information on which type of cell the CD4 cell should become.
77 T Helper 2 cells (CD4)
78 Cytokines cause infected area to have more porous capillary epithelium and adhesive factors make cells
stick to edges of blood vessels. If the pathogen they are specific to is not in the area, T cells then return via
afferent lymphatic. If the MHC is present, the T cell binds to it.
79CD4 and CD8 T cells, B cells, plasma cells. The cells are stored in bone marrow, lymph nodes and spleen.
They are called ʻmemoryʼ rather than ʻnaiveʼ cells and exist in 10x-100x frequency (for particular pathogen) if
you have been exposed to that particular pathogen.
80 34 million

10. 2. How many new cases of TB are there per year and what % morbidity does the
disease have?81
3. How many acute cases of malaria are there per year? 82
4. What are the main ‘routes of transmission’?83
5. List the 4 steps an infection travels from ‘reservoir’ to ‘cross infection’84
6. What are the characteristics of gram positive bacteria?85
7. What are the characteristics of gram negative bacteria? 86
8. What are the characteristics of viruses? 87
9. Give some examples of airborne transmitted infections88
10. What is a zoonosis and give a few examples?89
11. Explain the resistance mechanism ‘conjugation’90
12. Explain the resistance mechanism ‘transformation’91
13. Explain the resistance mechanism ‘transduction’92
81 8.8 million new per year, 80% morbididty
82 Around 300 million
83
Ingestion, inhalation, inoculation (bite, needle injury, sexual intercourse), contamination of environment,
mother to baby
84 Reservoir --> route of transmission --> portal of entry --> colonisation or infection --> cross infection
85Resist drying and thus colonize the dry environment of normal skin, produce toxins, spores, slime
capsules.
86 Prefer a moist environment and so colonize the gut and some abnormal skin
87 Differing heat stability, some may be enveloped and therefore resistant to heat and detergent, may be
transmitted in the ʻprodromeʼ the period before the person feels ill, may be carried without symptoms.
88 TB, measles, mumps, colds, flu (incl. most viruses), legionnaires disease
89 An infection which is transmitted between species, e.g. salmolnella, tapeworms, bird flu
90 Conjugation - bacterial plasmid DNA spread between two organisms (usually of the same species)
91 Transformation - when a bacterium takes up DNA from the environment (e.g. from a dead organism)
92 Transduction - when DNA is spread by bacteriophages (viruses that infect bacteria)

11. 14. Where do resistance genes come from?93
What Happens When the Immune System Goes Wrong?
1. What are the three main categories of immune disease?94
2. Which immunoglobulin mediates allergy? 95
3. What is atopy?96
4. How would anaphylaxis be treated in hospital? 97
5. What happens in Graves’ thyroiditis? 98
6. What mechanism causes some autoimmune diseases to be organ specific and
others non-organ specific? 99
7. In what ways can diabetes melitus be characterised as autoimmune and how does
its mechanism differ from that of Grave’s thyroiditis?
8. Which cell is attacked by HIV?100
9. What cells and molecules are involved in allergic/type 1 hypersensitivity response?
101
93 From the antibiotic organisms themselves, they donʼt just arise from mutation
94 Hypersensitivity, autoimmunity, immunodificiency
95 IgE
96An inherited tendency to make type 1 hypersensitivity responses (wheal and flare), degradation of mast
cells and outflow of inflammatory mediators
97Desensitization (giving the same antigen over and over again, suppresses allergic response), monoclonal
antibody given to negate IgE (not first line treatment).
98Autoimmune disease where anti-thyroid antibodies are produced so thyroid gets inflamed, inflammation
behind the eyes which pushes eyes forwards and damages sight
99In organ specific conditions only B cell is destroyed by a specific antigen, In systemic autoimmune disease
there are multiple antigens (non-specific)
100 CD4 cells, so people with HIV become immunodeficient without treatment.
101 In type 1 hypersensitivity an antigen is presented to CD4+ cells which stimulates production of IgE
antibodies specific to the antigen. (only IgE are produced in type 1 response). IgE antibodies cause mast
cells to release histamine, leukotrienes and prostaglandins

12. 10.What is the difference between a primary and secondary immune deficiency?102
11.How do immune based therapies monoclonal antibodies and cytokines work?103
102Primary = part of the bodyʼs immune system is missing or does not function properly (i.e. from birth),
Secondary = where part of the immune system is missing or does not function but this has a clearly
identifiable cause i.e. disease, drug treatment, environmental toxins.
103Monoclonal antibodies are antibodies that are highly specific to a certain cell or pathogen and destroy
only these cells. Cytokines are immune messengers which can stimulate a particular immune response
e.g.elevated white blood cell count. Both can be given as drugs to stimulate a specific response.