Chapter 24- Acquired immune system

Question 1

Antigen (Ag) presentation

Answer 1

Antigens are acquired by cells through infection, phagocytosis, or endocytosis. They are processed in lysosomes (in immune cells like phagocytes) or by the proteasome. Peptide fragments of antigens are presented with major histocompatibility complex (MHC) molecules on the cell surface to T cells. The presentation activates T cells and therefore acquired immunity begins.

Question 2

MHC molecules

Answer 2

Helps to present antigens. There are 2 types- MHC 1 and MHC 2. The molecules contain loop regions connected by disulfide bonds. These domains are also found in antibodies, so MHCs are considered to be the same family as immunoglobulins. Both have a polymorphic binding site for the antigen that will be presented- this means that the binding sites are capable of accommodating many different antigens

Question 3

MHC 1

Answer 3

MHC 1 presents the antigens of intracellular pathogens of all cells. Every cell in the body possesses MHC class 1 since all cells can be infected by these pathogens.

Question 4

MHC 2

Answer 4

Presents the antigens of extracellular pathogens and pathogens phagocytosed by antigen presenting cells (APCs). Viruses are not included in these antigens because they are obligate intracellular pathogens. Only bacterial and parasitic/fungal antigens are included

Question 5

MHC 1 vs MHC 2

Answer 5

MHC 1 and MHC 2 are different types of heterodimers. MHC 1 has a large alpha chain and a beta-2-microglobulin that are associated with each other. MHC 2 has a large alpha chain and a large beta chain that comes together

Question 6

MHC 1 mechanism

Answer 6

1. MHC 1, once it is translocated, enters the lumen of the ER. It is in a partially unfolded state and is associated with a membrane-bound protein called calnexin that keeps it from misfolding.
2. MHC 1 is fully assembled in the ER lumen
3. The partially folded alpha chain binds beta-2 microglobulin
4. Partly folded MHC1 binds chaperones and a transporter associated with antigen processing (TAP)- a pore for antigens to get into the ER lumen and bind to MHC
5. Elsewhere in the cell, cytosolic proteins are degraded by the proteasome. TAP delivers the peptides to the ER so they can bind to MHC
6. Peptide binds MHC1, promotes full folding
7. The peptide is delivered to the surface of the cell by exocytosis- the biosynthetic secretory pathway

Question 7

MHC 2 mechanism (4)

Answer 7

1. The antigen is taken up from the extracellular space into intracellular vesicles
2. In early endosomes of neutral pH, endosomal proteases are inactive
3. Acidification of vesicles activates proteases to degrade the antigen into peptide fragments
4. Vesicles containing peptides fuse with vesicles containing MHC class 2 molecules

Question 8

T cell receptors (TCRs)

Answer 8

Recognize the antigens presented by MHC molecules. The TCR alpha and beta extracellular domains are variable. These domains form the binding site of the receptor, and they are part of the receptor that recognize the presented antigens. The receptor is also polymorphic because it can recognize many different antigens. CD3 chains are located around the alpha and beta chains and are invariant, they play a role in transducing the signal within the T cell following antigen recognition

Question 9

CD4 and CD8 coreceptors

Answer 9

These proteins recognize the MHC along with the T cell receptor. CD8 T cells are cytotoxic and CD4 T cells are helper T cells. CD8 and CD4 only bind to the invariant portion of the MHC, they do not recognize the peptide fragment. TCR is what binds to the presented antigen peptide

Question 10

TCR signaling (5)

Answer 10

1. Clustering of TCR and its coreceptors recruits and activates Lck (a cytoplasmic kinase).
2. Lck initiates the phosphorylation of CD3 tyrosine residues and starts the phosphorylation cascade
3. Zeta chains are the parts of CD3 that extend deepest into the cytoplasm. The phosphorylated tyrosines on zeta chains act as docking sites for signaling protein ZAP70
4. Lck then phosphorylates ZAP70
5. ZAP70 leads to phosphoinositol and MAPK pathways and eventually leads to the activation of the T cell

Question 11

B7 and CD28

Answer 11

B7 is located on antigen presenting cells and CD28 is located on T cells. They are both co-receptors and allow for TCR costimulation- they are necessary to activate T cell receptors. The signal sent inward into the T cell tells it to become activated, causes the cell to proliferate, and the cell differentiates

Question 12

Immunological synapse

Answer 12

Formed following T cell activation- it prolongs or enhances signaling. At the center, the T cell is interacting with the presented antigen, and adhesion molecules can be observed as we move outward- ICAMs on antigen presenting cells that interact with integrins on the T cells. These molecules basically lock the interaction in place.

Question 13

Proliferation of T cells

Answer 13

Dendritic cells are professional antigen presenting cells and are often one of the first APCs that T cells come into contact with. A T cell receptor recognizes and binds to an MHC 2 on the dendritic cell. The dendritic cell can produce cytokine IL-2 and send it to the T cell. This causes the proliferation of T cells

Question 14

Differentiation of T cells

Answer 14

A T cell receptor recognizes and binds to an MHC 2 on the dendritic cell. The dendritic cell can send specific cytokines to the T cell- there are different cytokines for different types of T cells. This leads to a differentiated and activated T cell

Question 15

CD8 T cells

Answer 15

Cytotoxic, recognize antigens presented by MHC 1

Question 16

CD4 T cells

Answer 16

Helper T cells, they recognize antigens presented by MHC 2. There are multiple subdivisions, including TH1 and TH2

Question 17

T cell activation

Answer 17

Both TC & TH cells originate as naïve. They must be activated by a APC to become an effector T cell- can be any APC, but most often dendritic cells

Question 18

Activation of cytotoxic T cells

Answer 18

Activated by IL-12 and IL-18 so it can become cytotoxic. These cells directly kill infected cells following Ag recognition. Recognizes MHC I:Ag and forms a clustered immunological synapse (focused attack). There are 2 strategies that can be used in a cytotoxic attack.

Question 19

Cytotoxic strategy 1 (5)

Answer 19

1. The cytotoxic T cell secretes a protein called perforin, which forms pores in the membrane of the target (infected) cell
2. The T cell secretes an enzyme called Granzyme B. It enters the infected cell through the perforin pores
3. Granzyme B cleaves the BH3 only protein Bid, making tBid, which is now an activated protein
4. This promotes apoptosis- promotes Bak/Bax to form pores in the outer mitochondrial membrane
5. This results in the release of cytochrome C, which leads to the activation of intrinsic apoptosis

Question 20

BH3-only proteins

Answer 20

These proteins are pro-apoptotic- they are produced or activated in response to an apoptotic stimulus. Then, BH3 proteins bind to or inhibit Bcl-2 proteins. This allows pores to form

Question 21

Cytotoxic strategy 2 (4)

Answer 21

1. Cytotoxic T cells have Fas ligand in their membranes, which the target infected cells have Fas receptors in their membranes. Fas ligand on the T cell interacts with the Fas receptor
2. In the cytoplasmic domain of the Fas receptor, we have a death domain that helps it to associate with FADD (which also has a death effector domain).
3. This helps procaspase 8 to join. When inactive caspase 8 molecules are in close proximity to each other, they can cleave and activate each other
4. Activated caspase 8 leads to extrinsic apoptosis

Question 22

Intrinsic pathway of apoptosis

Answer 22

Stimulated from the inside of the cell and is stress or injury induced. It involves release of cytochrome C from the mitochondria to the cytoplasm. Intrinsic and extrinsic pathways may also be occurring at the same time

Question 23

Extrinsic pathway of apoptosis

Answer 23

Stimulated from the outside of the cell. Depends on receptor-ligand interactions at the cell membrane. TNF cytokines can also initiate apoptosis when they bind to their receptors

Question 24

Specificity of cytotoxic T cells

Answer 24

In a situation like epithelial tissue where the cells are next to each other, a cytotoxic T cell can recognize an infected cell specifically. The T cell will only target that cell and will program it for cell death. The neighboring healthy cells are not killed

Question 25

Cytotoxic T cells when widespread infection occurs

Answer 25

The cytotoxic T cell recognizes and binds the virus infected cell. It programs the target cell for death, inducing DNA fragmentation. The T cell then moves to a new target cell in the tissue, and causes that cell to die by apoptosis. It causes the infected cells to die one after the other

Question 26

Activation of helper T cells

Answer 26

Naïve helper T cells are activated via Ag-presentation by dendritic cells. There are 2 main types of effectors- TH1 and TH2, although there are other cell types. Both TH effector cells express CD40 ligand

Question 27

TH1 cells

Answer 27

Primarily stimulate cell-mediated (phagocytic) immunity. Activate macrophages with cytokine IFN-g (interferon gamma)

Question 28

TH2 cells

Answer 28

Primarily stimulate Ab-mediated immunity. Induce Ab class switch in B cells, activate B cells through secretion of cytokines IL-4 and IL-5

Question 29

TFH

Answer 29

Located in B cell follicles in lymph nodes, stimulate antibody mediated immunity. They mediate selection & survival of B cells and are responsible for B cell activation

Question 30

TH3

Answer 30

Promotes mucosal immunity & production of IgA

Question 31

TH17

Answer 31

Pro-inflammatory cells, promote mucosal immunity

Question 32

TH9

Answer 32

Promotes responses against parasitic worms, plays a role in allergic responses

Question 32

TH1 cell activation mechanism (5)

Answer 32

1. A dendritic cell presents an antigen using MHC class 2.
2. The T cell comes along and recognizes the presented antigen using its T-cell receptor (TCR)
3. The dendritic cell secretes the cytokine IL-12, which allows the T cell to differentiate into an activated TH1 cell
4. Additionally, if a macrophage presents an antigen, the TH1 cell can secrete IFN-g
5. This activates macrophages and other immune cells to allow for cell-mediated immunity

Question 33

Antibodies (Abs) structure

Answer 33

Also called immunoglobulins-proteins with a Y shaped structure, contain circular domains joined by disulfide bonds (a structural motif shared by MHC molecules). There are 4 independently folded protein chains that make up antibodies- 2 heavy chains and 2 light chains. They are all brought together in quaternary structure. The bulk of the antibody, up to the tips of the Y, are called the constant region because the amino acid sequence stays relatively constant. The variable regions are located at the tips of the Y

Question 34

CDR

Answer 34

Complementary determining regions, also called hypervariable regions. The pieces of the hypervariable region (the heavy and light chain) come together to form the antigen binding site. Proper tertiary structure is necessary to bring the binding site together

Question 35

Importance of antibodies (4)

Answer 35

1. Specificity- very specific binding molecules to one antigen
2. Neutralization of pathogens
3. Opsonization
4. Lytic effects- classical pathway

Question 36

Antibody opsonization

Answer 36

Antibodies coat the surface of the pathogen. Phagocytic cells have Fc receptors that recognize the Fc portions of the antibodies. This helps to increase phagocytosis

Question 37

C1q recruitment

Answer 37

Antibodies can bind to antigens on the pathogen surface and recruit the complement. Through the classical pathway, the first complement component would be C1q. This could lead to formation of the MAC and destruction of the pathogen

Question 38

Antibody (Ig) classes

Answer 38

There are 5 classes- IgG, IgD, IgE, IgA, and IgM

Question 39

Structure of each antibody class

Answer 39

IgG, IgD, IgE, and serum IgA have the classic Y structure. IgM is a pentameric antibody, 5 of the Y shapes are brought together through a J chain. IgMs have a low binding affinity, but they have 10 antigen binding sites. Secretory IgA (present on mucosal surfaces) is a dimer that is partially brought together by a J chain. It is stabilized by a protein called the secretory component

Question 40

Functions of IgM antibodies (5)

Answer 40

1. BCR (monomer) the antibody is stuck in the B cell membrane to serve as a B cell receptor in
2. When secreted as a pentamer, it is important for early immune responses
3. Neutralization (+),
4. Good at complement (C1q) recruitment (+++) through the classical pathway
5. Opsonization

Question 41

Functions of IgG antibodies

Answer 41

Switch to IgG later in the immune response- this is the most powerful class of antibody. Subclasses: IgG1, IgG2, IgG3, IgG4. Good at neutralization (++), C1q recruitment (+++), opsonization (+++), and ADCC (++)

Question 42

Functions of IgA antibodies

Answer 42

Neutralization (++), most important for mucosal immunity (+++)

Question 43

Functions of IgD antibodies

Answer 43

Can also be a B cell receptor, no other known functions

Question 44

Functions of IgE antibodies

Answer 44

Important for allergic responses, mast cell degranulation (+++)

Question 45

How are B cells so specific? (2)

Answer 45

1. V(D)J recombination
2. Somatic hypermutation

Question 46

V(D)J recombination

Answer 46

Generates the primary antibody repertoire- these are all of the antibodies you are pre-loaded with prior to getting an infection. This process occurs during the development of B cells in the bone marrow. Each type of Ab chain (κ & λ L-chains, H-chains) is encoded by separate locus on separate chromosomes. Each locus has large number of V gene segments. The chains can come together in different combinations through site-specific recombination. Site-specific recombination produces different combinations of V, D, & J segments, which results in the different specificities of the antibody

Question 47

Light chain variable regions

Answer 47

Encoded by DNA seq from long V gene segment & a short joining (J) gene segment

Question 48

Heavy chain variable regions

Answer 48

Encoded by DNA seq from long V gene segment, short J gene segment and diversity (D) gene segment

Question 49

κ light chain locus

Answer 49

Any of the 40 V gene segments may join to any of the 5 J segments. Encodes 200 different κ-chain V regions

Question 50

Heavy chain locus

Answer 50

Any of the 40 V gene segments may join to any of the 25 D & 6 J gene segments. Encodes 6000 different heavy chain V regions

Question 51

How many different V regions can humans produce?

Answer 51

Humans can produce 320 different VL regions (200 κ and 120 λ) and 6000 different VH regions. Could be combined to make 1.9 X 10^6 different Ag-binding sites, each with specificities for different antigens. Remember, this process occurs before encountering any infection

Question 52

V(D)J recombination of the light chain

Answer 52

This process occurs during B cell development. DNA rearrangement results in different combinations of DNA, which is transcribed into pre-RNA. The pre-RNA is spliced so V3 and J3 are joined with the constant region, forming mature RNA

Question 53

Turning off VDJ recombination

Answer 53

After recombination and the antibodies are expressed, the VDJ recombination is turned off by turning off Rag genes. After the antibodies are made, the genes are no longer needed because the cell will only be making antibodies for a specific antigen

Question 54

What happens during an immune response?

Answer 54

Th2 cells activate B cells. This activation of B cells leads to somatic hypermutation

Question 55

Somatic hypermutation

Answer 55

Following T cells stimulating B cells during infection, antibodies undergo mutations. Occurs long after coding regions have been assembled. There is 1 mutation per V region coding sequence per generation, which is 10^6 X greater than spontaneous mutation rate in other genes- mutation rate speeds up

Question 56

Results of somatic hypermutation

Answer 56

Very few mutations will result in increased affinity for Ag. Ag will stimulate preferentially those few B cells that do make Abs w/ increased affinity. Clones of these altered B cells will preferentially survive & proliferate (if a better antibody is generated), and most other B cells die by apoptosis. Result- Abs become of increasingly higher affinity as immune response progresses

Question 57

Activation-induced deaminase (AID)

Answer 57

During the activation of the B cell, the enzyme AID is activated. It deaminates cytosine to make uracil in variable region gene segments. This produces a mismatch in the double helix that leads to mutations. The mutation could be fixed by regular DNA repair mechanisms, or the base could be replaced with another complementary base pair

Question 58

B cell receptor (BCR) mechanism

Answer 58

This receptor is a form of IgM that is stuck in the membrane of a naive B cell. The BCR can bind to antigens. Once this happens, it provides signals that activate the B cell, and it starts secreting pentameric IgM. This step is beginning the antibody response. Then, the antigen is taken up into the B cell by receptor mediated endocytosis

Question 59

TH2 cell activation

Answer 59

Once an antigen is taken up into the B cell by receptor mediated endocytosis, it is processed and presented on the B cell surface to a TH2 cell. This will activate the TH2 cell.

Question 60

Full immune response (5 steps)

Answer 60

1. A naive T cell recognizes an antigen presented by a dendritic cell with MHC class 2
2. The dendritic cell begins to secrete cytokines like IL-4, which differentiates the T cell into an activated TH2 cell
3. Elsewhere, naive B cells have recognized antigens. Once they recognize the antigen and endocytose it, it leads to secretion of pentameric IgM- the antibody response starts
4. The endocytosed antigen is processed and presented on the surface of the B cell to an activated TH2 cell
5. The activated TH2 cell secretes IL-4, IL-5, and IL-13, which stimulates activation induced deaminase and antibody class switch in the B cell- this is antibody mediated immunity, the B cells are activated

Question 61

Plasma cells

Answer 61

B cells that are highly specialized for making large quantities of Ab w/ 1 specificity- these antibodies are monoclonal- only recognize one antigen. During an infection, a group of plasma cells will each secrete antibodies of a different specificity to have a polyclonal response. The antibody class switch is typically from IgM to IgG but it varies depending on the infection.

Question 62

2 types of activated (effector) B cells

Answer 62

1. Plasma cells
2. Memory B cells

Question 63

Memory B cells

Answer 63

Long-lived B cells that activate rapidly upon a secondary encounter with an antigen. They can directly activate T cells via Ag presentation. The antibody response will therefore be much faster since there is no need for the antigen presenting dendritic cell middleman. This is immunological memory- the basis for immunizations and immunity

Question 64

Immunological memory

Answer 64

We start with naive B cells that have their first exposure to an antigen. The exposure to the antigen results in the development of plasma cells and memory B cells. With the second exposure to the antigen, even more plasma cells and memory B cells are produced. This is the basis of boosters- they increase the pool of B cells

Question 65

Kinetics of the immune response

Answer 65

A normal immune response has an initial peak of IgM antibody secretion. Later, there is a class switch and IgG antibodies are produced. With a second exposure, the IgM peak is much smaller. It is then quickly overtaken by a large IgG peak. This is why vaccinated people may have inapparent infections, because the immune response is so fast they will not develop symptoms