Lecture 14 & 15 (Linking V & VI)

Question 1

What are ways in which exogenous peptides can be presented on MHC class I and vice versa? (exceptions to the rules)

Answer 1

1) Cross-presentation
2) Presentation of cytosolic peptides by MHC Class II Molecules
3) Allorecognition

Question 2

What is cross-presentation by dendritic cells (DCs)?

Answer 2

Cross-presentation by DCs involves the redirection of exogenous antigens into the endogenous presentation pathway, allowing them to be presented on MHC Class I molecules.

Question 3

Which cells are capable of cross-presentation?

Answer 3

Dendritic cells (DCs) are the only antigen-presenting cells (APCs) known to exhibit cross-presentation.

Question 4

Give an example of cross-presentation by DCs.

Answer 4

When dendritic cells (DCs) phagocytose virally infected cells, they process the viral antigens and present them on MHC class I molecules, activating CD8⁺ T cells. Normally, exogenous antigens are presented on MHC class II to CD4⁺ T cells, but cross-presentation allows DCs to bypass this rule and stimulate a CD8⁺ response against viruses that they themselves are not infected by.

Question 5

What is the redirection mechanism of cross-presentation?

Answer 5

The actual redirection mechanism of exogenous antigens into the endogenous pathway is unclear, but it requires a “license” from activated CD4+ T cells.

Question 6

What does it mean for a dendritic cell to be “licensed”?

Answer 6

A dendritic cell becomes “licensed” when it presents foreign antigen to a CD4+ T cell, which then provides cytokine and ligand signals, enabling the DC to redirect exogenous antigens into the endogenous pathway.

Question 7

Why do dendritic cells need to be licensed to perform cross-presentation?

Answer 7

Activated CD4+ T cells provide the necessary signals (cytokines and ligands) to license dendritic cells, allowing them to present exogenous antigens on MHC Class I molecules and prime CD8+ T cell responses.

Question 8

How are cytosolic peptides presented on MHC Class II molecules?

Answer 8

Cytosolic peptides can be presented on MHC Class II molecules through a process called autophagy, where the cell digests its own organelles and proteins in lysosomes.

Question 9

What is an autophagosome?

Answer 9

An autophagosome is a specialized vesicle that contains cytoplasmic content and fuses with lysosomes to degrade the contents.

Question 10

What are the steps involved in autophagy for MHC Class II presentation?

Answer 10

1) Parts of the cytoplasm are taken into autophagosomes.
2) Proteins in the autophagosomes are degraded.
3) The process links up to the exogenous pathway, allowing presentation on MHC Class II molecules.

Question 11

Give an example of when autophagy is involved in MHC Class II presentation.

Answer 11

Some pathogens have adapted to resist intracellular killing, requiring macrophages to be stimulated by cytokines to kill these pathogens. These pathogens may also prevent presentation on MHC Class I, and autophagy helps present peptides on MHC Class II.

Question 12

What does MHC restriction mean in T cell responses?

Answer 12

MHC restriction means a T cell can only recognize a specific peptide when it is bound to a specific self MHC molecule.

Question 13

Can you give an example of MHC restriction?

Answer 13

Strain A animals only respond to antigens presented by strain A APCs but not by strain B APCs, due to MHC restriction.

Question 14

What is allorecognition?

Answer 14

Allorecognition is the recognition of non-self MHC molecules (allo-MHC) by some T cells in the body. 1-10% of all T cells can react to allo-MHC.

Question 15

Why is allorecognition important in transplantation?

Answer 15

Allorecognition is the main mechanism of rejection of transplanted organs between genetically different individuals of the same species.

Question 16

What are the two types of allorecognition?

Answer 16

(1) Direct allorecognition: Recipient T cells recognize donor MHC molecules on the surface of donor cells.

(2) Indirect allorecognition: Recipient T cells recognize processed donor peptides presented by the recipient’s own APCs via self-MHC.

Question 17

What is a gene?

Answer 17

A gene is a segment of a chromosome that controls a specific characteristic and encodes for a protein.

Question 18

What is an allele?

Answer 18

An allele is a specific form of a gene.

Question 19

What is a locus?

Answer 19

A locus is the specific chromosomal location of a gene.

Question 20

What genes code for MHC molecules?

Answer 20

MHC molecules are coded by human leukocyte antigen (HLA) genes.

Question 21

Where are MHC genes located?

Answer 21

MHC genes are located in a cluster on chromosome 6 in humans.

Question 22

What are the two main classes of MHC genes?

Answer 22

1) MHC Class I genes: HLA-A, HLA-B, HLA-C

2) MHC Class II genes: HLA-DR, HLA-DQ, HLA-DP, HLA-DM, HLA-DOA, HLA-DOB

Question 23

What is polymorphism?

Answer 23

Polymorphism refers to the existence of multiple variations (forms) or alleles for each gene.

Question 24

How many alleles are there for many MHC genes?

Answer 24

Many MHC genes have more than 100 different alleles.

Question 25

How are MHC alleles identified?

Answer 25

Alleles are identified by a number after the locus, e.g., HLA-A2, HLA-DR3.

Question 26

What is a haplotype?

Answer 26

A haplotype is a particular combination of MHC alleles found on a single chromosome. Each individual inherits one haplotype from each parent.

Question 27

How are MHC alleles expressed?

Answer 27

MHC alleles are codominantly expressed, meaning both maternal and paternal MHC genes are expressed in offspring cells.

Question 28

What makes transplantation difficult?

Answer 28

MHC polymorphism makes transplantation difficult because humans are heterozygous at each locus, leading to diverse MHC expression.

Question 29

What is polygeny?

Answer 29

Polygeny refers to having many copies of related genes, with each individual inheriting 3 MHC-I alleles from each parent (6 alleles total: one for HLA-A, HLA-B, and HLA-C per chromosome).

Question 30

Where are differences found in the peptide binding groove of MHC molecules?

Answer 30

Differences are clustered at amino acid locations within the groove sites, allowing for the presentation of different varieties of peptides.

Question 31

Why are changes outside of the peptide binding groove problematic?

Answer 31

If areas outside the groove are altered too much, it can affect the structure, conformation, and folding of the MHC molecule.

Question 32

Can a given MHC molecule bind to multiple peptides?

Answer 32

Yes, a given MHC molecule can bind numerous different peptides, and some peptides can bind to different MHC molecules.

Question 33

What are the main MHC Class I genes?

Answer 33

The main MHC Class I genes are HLA-A, HLA-B, and HLA-C.

Question 34

What are the main MHC Class II genes?

Answer 34

The main MHC Class II genes are HLA-DR, HLA-DQ, HLA-DP, HLA-DM, HLA-DOA, and HLA-DOB.

Question 35

What is the significance of polymorphism in MHC genes?

Answer 35

Polymorphism refers to the presence of multiple allelic variants of each MHC gene in the population, contributing to the diversity in peptide presentation.

Question 36

How does allorecognition relate to MHC polymorphism?

Answer 36

Allorecognition is the ability of some T cells to recognize non-self MHC. The diversity from MHC polymorphism contributes to transplant challenges.

Question 37

What is the characteristic of receptors with intrinsic kinase activity?

Answer 37

Receptors with intrinsic kinase activity have their own kinase activity and initiate signaling by dimerization and transphosphorylation.

Question 38

How does signaling occur in receptors with intrinsic kinase activity?

Answer 38

Signaling is initiated by the dimerization of the receptor and the transphosphorylation of the receptor itself.

Question 39

What is a key feature of extrinsic receptors?

Answer 39

Extrinsic receptors do not have intrinsic kinase activity but initiate signaling through the recruitment of kinases and dimerization, followed by transphosphorylation.

Question 40

How does signaling occur in extrinsic receptors?

Answer 40

Signaling is initiated by the recruitment of kinases to the receptor, followed by dimerization and transphosphorylation.

Question 41

What determines molecular interactions between proteins?

Answer 41

Molecular interactions are determined by domains in their structure that have selective binding properties, such as the SH2 domain.

Question 42

What does the SH2 domain recognize?

Answer 42

The SH2 domain recognizes phosphorylated tyrosine (phosphotyrosines) on other proteins and is found in many proteins.

Question 43

What are phosphotyrosines?

Answer 43

Phosphotyrosines are phosphorylated tyrosine residues that serve as binding sites for a number of protein-interaction domains.

Question 44

What is the role of adaptor proteins in molecular interactions?

Answer 44

Adaptor proteins help form multimolecular complexes by interacting with other proteins, playing a crucial role in signaling pathways.

Question 45

What are key post-translational modifications involved in signaling?

Answer 45

Phosphorylation and ubiquitination are key modifications that play important roles in protein function and signaling.

Question 46

What is the role of kinases in signaling?

Answer 46

Kinases are proteins that phosphorylate other proteins, typically activating or regulating signaling pathways.

Question 47

What do phosphatases do?

Answer 47

Phosphatases are proteins that dephosphorylate other proteins, often turning off signaling pathways.

Question 48

What is the fate of ubiquitinated proteins?

Answer 48

Ubiquitinated proteins are targeted for degradation by the proteasome or lysosome.

Question 49

How do phosphorylation and ubiquitination affect signaling?

Answer 49

Both phosphorylation and ubiquitination can function to activate or inhibit signaling, depending on the context.

Question 50

Why is it important for signaling to be turned off?

Answer 50

Signaling must be turned off as well as turned on to prevent continuous activation, ensuring appropriate cellular responses.

Question 51

What are the three signals required for optimal T-cell activation?

Answer 51

(1) Signal 1: pMHC:TCR engagement with coreceptor binding. (2) Signal 2: Contact with costimulatory ligands. (3) Signal 3: Cytokines directing T-cell differentiation into distinct effector cell types.

Question 52

What components are involved in TCR binding and signaling initiation?

Answer 52

The TCR complex consists of: - TCR - ITAM domains (Immunoreceptor tyrosine-based activation motifs) - CD3 - Zeta (ζ) chains

Question 53

What happens when pMHC:TCR binding occurs with coreceptor binding?

Answer 53

When pMHC:TCR binding occurs and the coreceptor binds MHC: Lck (Lymphocyte-specific protein tyrosine kinase) is recruited. Lck phosphorylates the ITAMs, initiating more signaling. Zap-70 is recruited to the ITAMs and is phosphorylated by Lck.

Question 54

What role does Zap-70 play in TCR signaling?

Answer 54

Zap-70 binds to phosphorylated ITAMs, is phosphorylated by Lck, and activates many downstream signaling molecules, leading to transcriptional changes.

Question 55

What is the main takeaway from Signal 1 in TCR signaling?

Answer 55

Signal 1 results in intracellular signaling: - Lck is recruited and phosphorylates ITAMs. - Zap-70 is recruited and binds to phosphorylated ITAMs, initiating signaling cascades. - This leads to the transcription of many genes

Question 56

What is the role of costimulation in T-cell activation?

Answer 56

Costimulation is required for T-cell activation, survival, and proliferation. Without it, T-cells may become unresponsive (anergic).

Question 57

What are the key costimulatory ligands and receptors involved in T-cell activation?

Answer 57

1) Ligands on APCs: CD80 (B7.1) CD86 (B7.2) 2) Receptor on T cells: CD28 (Positive costimulatory receptor)

Question 58

What are the negative costimulatory receptors?

Answer 58

- CTLA-4 - PD-1 (These receptors help turn activation off.)

Question 59

What happens when CD28 binds to B7 molecules (CD80/CD86)?

Answer 59

1) Binding to B7 molecules (CD80/86) triggers phosphorylation of CD28. 2) This activates a kinase, which leads to the recruitment of another kinase. 3) Additional signaling follows, facilitating T-cell activation.

Question 60

What is clonal anergy and how does it occur?

Answer 60

- Clonal anergy occurs when T-cells become nonresponsive due to a lack of costimulation. - This is important for regulation and to decrease the risk of autoreactive T-cells. - Anergic T-cells can no longer respond to future stimulation.