Innate immunity

Question 1

Mature T cells are found

Answer 1

Some mature T cells also reside in the bone marrow. Although T cells complete their maturation in the thymus, not the bone marrow, mature CD4+ and CD8+T cells will recirculate back to the bone marrow. Lymph nodes and spleen

Question 2

Pluripotent hematopoietic stem cells are

Answer 2

rare, representing less about 0.05% of cells in the bone marrow.

Question 3

HSCs can be mobilized

Answer 3

from the bone marrow and circulate in the blood, which is now used as a source of stem cells for transplantation.

Question 4

Macrophages will increase

Answer 4

both MHC class I and class II expression after activation; however, TH cells are CD4+ and recognize antigenic peptide bound to MHC class II.

Question 5

T cells develop in … and B cells in…

Answer 5

T cells develop in the thymus; B cells develop in the bone marrow and achieve full maturity in the spleen.

Question 6

Lymphoid follicles are found

Answer 6

in all secondary lymphoid tissues, including that associated with mucosal tissues (MALT)

Question 7

Infection and associated inflammation stimulate

Answer 7

the release of cytokines and chemokines that enhance blood cell development (particularly to the myeloid lineage).

Question 8

FDCs present

Answer 8

soluble antigen on their surfaces to B cells, not T cells.

Question 9

Dendritic cells can arise from

Answer 9

both myeloid and lymphoid precursors

Question 10

B and T lymphocytes have

Answer 10

antigen-specific receptors on their surface, but NK cells, which are also lymphocytes, do not.

Question 11

B cells are generated

Answer 11

outside the bone marrow in birds and ruminants

Question 12

Which cells are myeloid?

Answer 12

Dendritic cells, neutrophils, basophils and macrophages

Question 13

Which cells are lymphoid?

Answer 13

NK cells, T cells, B cells and ILCs

Question 14

Secondary lymphoid organs

Answer 14

Lymph nodes, spleen, and barrier tissues (MALT and skin). All these organs trap antigen and provide sites where lymphocytes can interact with antigen and subsequently undergo clonal expansion.

Question 15

Primary lymphoid organs

Answer 15

Bone marrow and Thymus. These organs function as sites for B-cell and T-cell maturation, respectively.

Question 16

What two characteristics distinguish HSCs from mature blood cells?

Answer 16

HSCs are stem cells, which, unlike mature fully differentiated cells, are (1) multipotent and (2) capable of self-renewal.

Question 17

How does the thymus help us avoid autoimmune responses?

Answer 17

The thymus helps us avoid autoimmune responses by negatively selecting thymocytes expressing T-cell receptors that bind to self-peptide–MHC complexes with high affinity. Thymocytes with new TCRs scan the surfaces of epithelial cells in the cortex and medulla of the thymus; if they bind too tightly to surface MHC molecules presented by these cells they are eliminated (typically but not exclusively by clonal deletion).

Question 18

At what age does the thymus reach its maximal size?

Answer 18

Teenage years (puberty). In humans, the thymus reaches maximal size during puberty (b). During the adult years, the thymus gradually atrophies.

Question 19

What is the role of immunodeficient mice (i.e., mice that are missing one or more immune cell type) in demonstrating the success of HSC enrichment?

Answer 19

Immunodeficient mice are missing one or more immune cell type (either because of genetic mutations or chemotherapy). Injection of stem cells will restore these cell types—an easily measured outcome. As HSCs are successively enriched in a preparation, the total number of cells that must be injected to restore these cell populations decreases.

Question 20

A monocyte

Answer 20

Monocytes are the blood-borne precursors of macrophages. Monocytes have a characteristic kidney bean–shaped nucleus and limited phagocytic and microbial killing capacity compared with macrophages

Question 21

Macrophage

Answer 21

Macrophages are much larger than monocytes and undergo changes in phenotype to increase phagocytosis, antimicrobial mechanisms (oxygen dependent and oxygen independent), and secretion of cytokines and other immune system modulators. Tissue-specific functions are also found in tissue macrophages.

Question 22

What effect would removal of the bursa of Fabricius (bursectomy) have on chickens?

Answer 22

The bursa of Fabricius in birds is the primary site where B lymphocytes develop. Bursectomy would result in a lack of circulating B cells and humoral immunity, and it would probably be fatal.

Question 23

Major cell type presenting antigen to naïve T cells

Answer 23

Dendritic cells

Question 24

Phagocytic cell of the central nervous system

Answer 24

Microglial cells

Question 25

Granulocytic cells important in the body’s defense against parasitic organisms.

Answer 25

Eosinophils

Question 26

Gives rise to red blood cells

Answer 26

Myeloid dendritic cells and HSCs

Question 27

Generally, first cells to arrive at site of inflammation

Answer 27

Neutrophils

Question 28

Supports maintenance of HSCs:

Answer 28

Osteoblasts

Question 29

Gives rise to thymocytes

Answer 29

HSCs

Question 30

Circulating blood cells that differentiate into macrophages in the tissues.

Answer 30

Monocytes

Question 31

An antigen-presenting cell that arises from the same precursor as a T cell but not the same as a macrophage

Answer 31

Lymphoid dendritic cells

Question 32

Cells that are important in sampling antigens of the intestinal lumen

Answer 32

M cells

Question 33

Granulocytic cells that release various pharmacologically active substances

Answer 33

Eosinophils, Mast cells and Neutrophils

Question 34

White blood cells that play an important role in the development of allergies

Answer 34

Eosinophils and mast cells

Question 35

Cells that express antigen-specific receptors

Answer 35

Lymphocytes and NKT cells

Question 36

Cells that share a common progenitor with T and B cells, but do not have antigen-specific receptors

Answer 36

Innate lymphoid cells

Question 37

Under resting conditions, where is NFAT localized in a cell?

Answer 37

Cytoplasm

Question 38

Under activated conditions, where is NFAT localized in a cell?

Answer 38

Nucleus

Question 39

How is NFAT released from its resting condition and permitted to relocalize?

Answer 39

By dephospyrylation with the enzyme calcineurin phosphatase, activated by binding to the calcium-calmodulin complex. Activation of the cell results in an increase in intracytoplasmic calcium ion concentration.

Question 40

Immunosuppressant drugs such as cyclosporin act via inhibition of the calcineurin phosphatase. If NFAT is ubiquitous, how do you think these drugs might act with so few side effects on other signalling processes within the body?

Answer 40

There are many possible answers to this question. For example, there may be multiple forms of NEAT, and so these drugs may just interact with particular forms of the enzyme. Other cells may have alternative pathways that can bypss the need for calcineurin, whereas T cells may not. In fact, cyclosporin bind to the protein immunophilin, which is specifically expressed in activated T cells, and it is the complex of cyclosporin and immunophilin that inhibits activity calcineurin.

Question 41

In the early days of experiments designed to detect the T-cell receptor, several different research groups found that antibodies directed against immunoglobulin proteins appeared to bind to the T-cell receptor. Given what you know about the structure of immunoglobulins and the T-cell receptor, why is this not completely surprising?

Answer 41

Immunoglobulin proteins and the T-cell receptor share a common motif: the immunoglobulin fold, which may be the binding target for these antibodies.

Question 42

Interactions between receptors and ligands at the cell surface

Answer 42

Receptor-ligand binding can activate the receptor and result in phosphorylation and receptor cross-linking.

Question 43

Reduction and alkylation of the antibody molecule.

Answer 43

Reduction enabled the breakage of disulfide bonds between the heavy and light chains and the pairs of heavy chains in the IgG molecule. Alkylation ensured that the bonds between the separated chains would not reform. Scientists could then separate the chains and figure out their molecular weight and how many chains belonged to each molecule

Question 44

Enzymatic digestion of the antibody molecule.

Answer 44

Papain digested the molecule in the hinge region, releasing two antigen-binding fragments (Fabs) and one non–antigen-binding fragment, which spontaneously crystallized (Fc). This told investigators that there were two antigen-binding sites per molecule and suggested that part of the molecule was not variable in sequence (since it was regular enough in structure to crystallize). Pepsin isolated the divalent antigen-binding part of the molecule from the rest.

Question 45

Antibody detection of immunoglobulin fragments

Answer 45

Antibodies were generated that specifically recognized the Fab and Fc fragments. Antibodies to Fab were found to bind to both heavy and light chains, thus indicating that the antigen-binding sites had components of both chains. Antibodies to Fc fragments bound only to the heavy chain

Question 46

What is an ITAM?

Answer 46

An ITAM is an immunoreceptor tyrosine-based activation motif. It is a motif with a particular sequence containing phosphorylatable tyrosines in the cytoplasmic regions of several immunologically important proteins

Question 47

What proteins modify the ITAMs in Igα and Igβ?

Answer 47

Igα and Igβ are part of the signaling complex in B cells and are phosphorylated by the Src-family kinase Lyn, when the B-cell receptor (BCR) moves into the lipid raft regions of the membrane on activation.

Question 48

Define an adapter protein

Answer 48

An adapter protein bears more than one binding site for other proteins and serves to bring other proteins into contact with one another without, itself, having any enzymatic activity.

Question 49

Describe how an interaction between proteins bearing SH2 and phosphorylated tyrosine (pY) groups helps to transduce a signal from the T-cell receptor to downstream signal transduction pathway components.

Answer 49

Activation of the TCR results in activation of Lck, a Src family kinase. Lck phosphorylates the tyrosine residues on the ITAMs of the CD3 complex associated with the TCR. ZAP-70 then binds to the phosphorylated tyrosine (pY) residues via its SH2 regions, and is then itself phosphorylated and activated.

Question 50

IgM has 10 antigen-binding sites per molecule, whereas IgG only has two. Would you expect IgM to be able to bind five times as many antigenic sites on a multivalent antigen as IgG? Why/why not?

Answer 50

I would expect IgM to be able to bind more molecules of antigen than IgG, but perhaps not five times more. Steric hindrance/conformational constraints may prevent all 10 antigen-binding sites of IgM from being able to simultaneously bind to 10 antigenic sites.

Question 51

You and another student are studying a cytokine receptor on a B cell that has a Kd of 10–6M. You know that the cytokine receptor sites on the cell surface must be at least 50% occupied for the B cell to receive a cytokine signal from a helper T cell. Your lab partner measures the cytokine concentration in the blood of the experimental animal and detects a concentration of 10–7M. She tells you that the effect you have been measuring could not possibly result from the cytokine you’re studying. You disagree. Why?

Answer 51

Because you know that, in at least one case, activation of a cell can result in an alteration of the phenotype of the cytokine receptor, resulting in a dramatic increase in its affinity for the cytokine. For example, the IL-2 receptor (IL-2R) exists in two forms: a moderate-affinity form consisting of a βγ dimer and a high-affinity form, synthesized only following cell activation that consists of an αβγ trimer.

Question 52

Activation of Src-family kinases is the first step in several different types of signaling pathways. It therefore makes biological sense that the activity of this family of tyrosine kinases is regulated extremely tightly. Describe how phosphorylation of Src-family kinases can deliver both activating and inhibitory signals to Src kinases.

Answer 52

Src family kinases have two tyrosine sites on which they can be phosphorylated: an inhibitory site and an activating site. In the resting state, the inhibitory site is phosphorylated by the kinase Csk, and the kinase folds up on itself, forming a bond between an internal SH2 group and the inhibitory phosphate, shielding the active site of the enzyme. Cleavage of the phosphate group from the inhibitory tyrosine allows the enzyme to open its structure and reveal the active site. Further activation of the enzyme then occurs when a second tyrosine is phosphorylated and stabilizes the activated state.

Question 53

You have generated a T-cell clone in which the Src-family tyrosine kinase Lck is inactive. You stimulate that clone with its cognate antigenic peptide, presented on the appropriate MHC platform, and test for interleukin-2 secretion as a measure of T-cell activation. Do you expect to see IL-2 secretion or not? Explain.

Answer 53

Since Lck lies at the beginning of the signaling pathway from the T-cell receptor, a T cell with an inactive form of Lck will not be able to undergo activation to secrete IL-2.

Question 54

Name one protein shown to be defective in many cases of X-linked agammaglobulinemia and describe how a reduction in the activity of this protein could lead to immunodeficiency.

Answer 54

The signaling kinase Bruton’s tyrosine kinase (Btk) is defective in 85% of cases of X-linked agammaglobulinemia. It is encoded on the X chromosome, and hence most cases of this disease occur in boys. Phosphorylation by Btk activates PLCγ, which cleaves phosphatidylinositol bisphosphate (PIP2) into inositol trisphosphate (IP3) and diacylglycerol (DAG) following activation of pre-B cells through the pre-B-cell receptor, or of B cells through the immunoglobulin receptor. This leads eventually to activation of the NFAT and MAP kinase transcription factor pathways, culminating in B-cell differentiation and proliferation, which cannot occur in the absence of a functioning Btk protein.

Question 55

The B- and T-cell receptor proteins have remarkably short intracytoplasmic regions of just a few amino acids. How can you reconcile this structural feature with the need to signal the presence of bound antigen to the interior of the cell?

Answer 55

Both the BCR and the TCR are noncovalently associated on their respective cell membranes, with signal transduction complexes that function to transduce the signal initiated by antigen binding to the receptor and into the interior of the cell. In the case of the B-cell receptor, the signal transduction complex is composed of Igα/Igβ. ITAMs on Igα/Igβ are phosphorylated by tyrosine kinases that are brought into close proximity with the B-cell receptor complex on the oligomerization of the receptor and its movement into the lipid raft regions of the membrane, which occur on antigen binding. The phosphorylated tyrosines of Igα/Igβ then serve as docking points for downstream components of the signal transduction pathway. In the case of the TCR, the signal transduction complex is the CD3 set of proteins, which contains six chains and serves a similar function to Igα/Igβ. ΙTAMs on CD3 are phosphorylated by Src family kinases, particularly Lck, and then serve as docking points for downstream components of the TCR signaling pathway. Lck in turn is associated with the TCR coreceptors CD8 and CD4.

Question 56

Describe one way in which the structure of antibodies is superbly adapted to their function. (1)

Answer 56

(a) The antibody is a Y-shaped molecule with the antigen-binding regions located at the two tips of the Y. At the junction of the three sections is a flexible hinge region that allows the two tips to move with respect to one another and hence to bind to antigenic determinants arranged at varying distances from one another on a multivalent antigen.

Question 57

Describe one way in which the structure of antibodies is superbly adapted to their function. (2)

Answer 57

Within the variable region domains of the heavy and light chains, a common β-pleated sheet scaffold includes multiple antiparallel β strands in a conserved conformation. However, at the turns between the β strands, there are varying numbers and sequences of amino acids, corresponding to hypervariable regions in the immunoglobulin variable region sequences. These enable the creation of many different antigen-binding sites.

Question 58

Describe one way in which the structure of antibodies is superbly adapted to their function. (3)

Answer 58

The constant regions of antibody molecules form the bridge between the antigen-binding region and receptors on phagocytic cells that will engulf antigen-antibody complex, or components of the complement system that will bind to the Fc regions of the antibody and aid in the disposal of the antigen. Different constant region structures bind to different Fc receptors and complement components.

Question 59

Your adviser has handed you (a graduate student) a T-cell clone that appears to be constitutively (i.e., always) activated, although at a low level, even in the absence of antigenic stimulation, and he has asked you to figure out why. Your benchmate suggests you start by checking out the sequence of its lck gene, or the status of the Csk activity in the cell. You agree that those are good ideas. What is your reasoning?

Answer 59

Src family kinases such as Lck are located at the beginning of many signal transduction pathways, and their activities are subjected to rigorous control mechanisms. Lck is maintained in an inactive state by being phosphorylated on an inhibitory tyrosine residue. This phosphorylated tyrosine is then bound by an internal SH2 domain that holds Lck in a closed, inert conformation. If the DNA encoding this tyrosine residue has been mutated or eliminated, such that this phosphorylation cannot occur, then there will be a constitutive level of Lck activity. Since the enzyme that phosphorylates this inhibitory tyrosine is Csk, a reduction in Csk activity would have the same effect.

Question 60

Pleiotropy

Answer 60

is the capacity to bring about different end results in different cells

Question 61

Synergy

Answer 61

is the ability of two or more cytokines affecting a cell to bring about a response that is greater than the sum of each of the cytokines.

Question 62

Redundancy

Answer 62

is the property that describes the fact that more than one cytokine can bring about the same effect.

Question 63

Antagonism

Answer 63

is the tendency for two cytokines binding to the same cell to bring about opposite effects, or to reduce/eliminate the response to the other.

Question 64

Cascade induction

Answer 64

is the ability of a cytokine to bind to one cell and to induce that cell to secrete additional cytokines.

Question 65

How might receipt of a cytokine signal result in the alteration of the location of a lymphocyte?

Answer 65

A cytokine may induce the expression on the cell surface of new chemokine receptors and/or new adhesion molecules that would cause the cell to move to a new location and, once present, to be retained there.

Question 66

Describe one mechanism by which type I interferons “interfere” with the production of new viral particles.

Answer 66

When a type I interferon binds to its receptor on a virally infected cell, the interferon signal results in the activation of a ribonuclease that breaks down cytoplasmic RNA. It is particularly effective against double-stranded RNA.

Question 67

Lymphocytes derived from a patient with a severe immunodeficiency disease known to affect only a single protein chain prove unable to respond to the cytokines IL-2, IL-4, IL-7, and IL-15, in addition to several others. Given what you know about the specificity of cytokine receptors, explain how a defect in a single protein chain can prevent the binding of so many different cytokines to their cellular receptors.

Answer 67

The receptors for these cytokines share a common γ chain, which functions as a signal-transducing unit following recognition of each of these cytokines by cytokine-specific α-chain receptor components. The receptors for IL-2 and IL-15, but not the others, also contain a β chain, to form heterotrimeric receptors. The IL-4 and IL-7 receptors are heterodimeric.