March 19th (Exam 3) Flashcards by Benton Schaefer

What are the two classes of T-cell receptors?

Explain their fundamental difference before we dive into the small details.

T-cells that express the alpha:beta TCR are called alpha:beta T cells

T cells that express the gamma:sigma TCR are called gamma:sigma T cells

They are both heterodimers.

Gamma chain is like that of the alpha chain (analogous to the light chain in Ig)

Delta chain is like that of the beta chain (analogous to the heavy chain in Ig)

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Where can we find the delta chain gene locus?

The gamma chain gene locus?

The delta chain gene locus can be found between the V and J segments of the alpha chain locus on chromosome 14.

The gamma chain gene locus is found on chromosome 7 distinct from the beta chain locus.

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How are the chains that make up gamma:sigma T-cells different from the chains that make up alpha:beta T-cells?

(Location, Gene Segments, Recombination Abilities)

The gamma chain locus (most similar to alpha chain ) exists on chromosome 7 instead of on chromosome 14 like the alpha chain locus. More, the delta chain locus (most similar to the beta chain) exists on chromosome 14 within the alpha chain locus instead of being on chromosome 7 like the beta chain locus
The delta chain locus and gamma chain locus both contain less V segments - making them 5 times less genetically diverse
The delta chain can incorporate two D segments to allow for more variability (more combinations of segments possible + more N nucleotides can be put in) effectively making up for the lack of diversity by less V segments.

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Explain why it would be impossible for a single T-cell to express both alpha:beta TCRs and gamma:delta

It is just physically impossible, because for the alpha chain to rearrange, it must join its V and J segments and therefore cut out the entirety of the sigma chain locus.

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How are gamma:sigma T cells different than alpha:beta T cells?

(Recognition Mechanism, Location, Conservation among Fauna)

gamma:sigma T cells don’t require a MHC complex for recognition
gamma:sigma T cells are found in the tissue more than in circulation (similar to NK cells and other innate lymphocytes)
The functions and purposes of gamma:sigma T cells have not been conserved through evolution.

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What does SCID stand for?

What is it and what causes it?

Severe Combined Immunodeficiency Disease - this is a genetic defect that is caused by the absence of RAG proteins.

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Ask yourself, what are the only types of cells that can be affected by SCID?

Lymphocytes (B and T cells)

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What will happen to an infant if they have SCID?

What may save them?

They will die from common infections unless they receive a bone marrow transplant.

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What do T cell receptors recognize again?

Short peptides bound to MHC complexes right?

How big is a short peptide?

8-25 amino acids long

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How are peptides produced?

What do we call the process of peptide production in human cells?

They are produced by degradation of the pathogen and its proteins.

Antigen processing.

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What does MHC stand for?

What are they?

Major Histocompatibility Complex

They are glycoproteins that bind and transport peptide antigens to the cell surface.

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When an MHC presents peptide antigen to a TCR what do we call this?

Antigen Presentation.

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What is actually recognized by the TCR?

The combination of the MHC and the peptide antigen.

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What can all virally-infected cells do?

How does this differ to that of healthy cells?

Present antigen

Healthy cells present self proteins/peptides

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What name is given to cells that specialize in presenting antigen?

What are the three we have learned about?

Professional Antigen Presenting Cells

DCs (t cell activation)
Macrophages
B - cells (b cells activation)

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Explain MHC Class I

What type of pathogen-derived peptides do they bind?

How are the proteins in which these peptides are derived degraded?

Where does the MHC Class I bind to the peptide?

What type of T cells recognize MHC Class I bound to peptide?

These are peptides that are derived from intracellular pathogens (viruses and some bacteria)
They are degraded in the cytosol (liquid portion)
The MHC Class I will bind to the peptide within the ER
MHC Class I is recognized by Cytotoxic/ CD8 T cells

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Explain MHC Class II

What type of pathogen-derived peptides do they bind?

How are the proteins in which these peptides are derived degraded?

Where does the MHC Class II bind the peptide?

What type of T cells recognize MHC Class II bound to a peptide?

They bind peptides that come from extracellular pathogen proteins.
They need to be degraded by means of endocytosis and lysosomes via vesicles.
The MHC Class II must travel to endosomal vesicles to bind the peptides
CD4/T-Helper T cells

What do we term CD4 and CD8?

What do they do?

These are called T-cell co-receptors.

They cooperate with the T-cell receptor in the recognition of complexes of peptide antigen and MHC molecules.

Describe the binding of T-cell co-receptors to MHC molecules.

They bind to a site that is topologically separate from the site that is bound by the TCR.

Describe the structure of CD4 and define the functions of CD4 T cells that it impacts.

It is a single polypeptide that contains 4 extracellular immunoglobulin-like domains.

It functions to:

Activate macrophages
Improve phagocytic ability
Improve secretion of cytokines and chemokines
Impact B-cell differentiation

Describe the structure of CD8 and the function of CD8 T cells that it impacts.

It is a heterodimer of two polypeptide chains that each contain only one Ig-like domain extracellularly.

The function it imparts (or impacts) is to kill cells that are infected with an intracellular pathogen.

Describe the overall structure of a MHC Class I molecule.

It consists of one transmembrane chain (heavy or alpha) that is non-covalently linked to a small protein called the Beta-2 microglobulin

Now describe the heavy chain of a MHC Class I molecule.

How is the peptide binding site formed?

What are the Ig-like domains and what do they do?

The heavy chain consists of three extracellular domains (alpha 1, alpha 2 and alpha 3)

The peptide binding site is formed by the folding of the alpha 1 and alpha 2 domains of the heavy chain.

The Ig-like domains are the alpha 3 and Beta-2 microglobulin domains and they function to support the peptide binding site

Describe the structure of a MHC Class II molecule.

Define the overall structure.

Define how the peptide binding site is formed.

Define the Ig-like domains that facilitate support of the peptide binding site.

Unlike the MHC Class I molecules the MHC Class II molecules consist of two transmembrane chains (one being alpha and the other being beta)

The peptide binding site is formed by the folding of the peptide binding domains of each chain (alpha 1 and beta 1)

The support for the peptide binding domain is formed by folding of the Ig-like domains of each chain (alpha 2 and beta 2)

What do the Ig-like domains of MHC Class I and MHC Class II molecules respectively grant us?

They allow specific binding to co-receptors of the T-cells.

What are the Ig-like domains of MHC Class I molecules and what co-receptors do they interact with? Describe their structures simply as well.

The Ig-like domains are the alpha 3 domain of the single transmembrane chain along with the small protein Beta-2 microglobulin. Because it is MHC Class I, it will interact with CD8 co-receptor on cytotoxic T cells via their Ig-like domains alpha and beta.

What are the Ig-like domains of MHC Class II molecules and what co-receptors do they interact with? Describe their structures simply as well.

The Ig-like domains are the alpha 2 of one transmembrane chain and the beta 2 of the other transmembrane chain. Because its MHC Class II, it will interact with CD4 co-receptor on T-helper cells via their Ig-like domains D1, D2, D3, D4.

Better explain the peptide binding site in terms of how it binds to peptide. What type of binding holds the peptide?

It is a deep groove that is present on the surface of MHC molecules. Help tightly by non-covalent bonds.

What do we call the idea that MHC molecules can bind thousands of different peptides?

Promiscuous specificity.

What is the difference in the lengths of peptides that MHC Class I and MHC Class II can bind?

MHC Class I binds peptides (8-10) AAs MHC Class II binds peptides (13-25) AAs

What are the two cellular compartments in which the two MHC Classes function distinctly?

1. Cytosol and Nucleus connected via pores - sealed off from outside 2. Vesicular Transport System - ER Golgi, Lysosomes, Endosomes - can contact the outside of the cell.

What is a proteasome? What do the different Beta subunits do?

This is a barrel shaped protein that exists within the cytosol that degrades proteins. The different Beta subunits have varied protease activity, meaning they work in combination to fully degrade proteins.

What is an immunoproteasome? What does IFN gamma have to do with this? Why is this important?

This is a modified proteasome that is initiated after infection. Interferon gamma (released by NK cells during the innate immune response) induces the production of alternative subunits that have different protease activity. Creation of an immunoproteasome with different proteolytic subunits is important, because it prioritizes creation of peptides that are likely to bind to MHC Class I molecules within the ER. This is accomplished by those subunits having activity that cleaves right after hydrophobic residues and less activity cleaving after acidic residues. *Remember that MHC Class I molecules need hydrophobic and basic peptides to bind effectively*

How do peptides newly degraded by the immunoproteasome move from the cytosol to the ER where they meet their friends?

They are helped out by a complex of two structurally similar heterodimers that exist on the membrane of the ER called Transport Associated with antigen Processing (TAP)

How does TAP know which peptides to move?

It preferentially transports peptides that have the characteristics that allow them to bind to MHC I molecules (hydrophobic/basic at the Carboxyl terminus)

What is the fate of most peptides that are transported by TAP?

They don't end up binding to MHC Class I and just end up getting transported back.

What are the different parts of a MHC Class I molecule? Where are they synthesised? Where are they formed?

You have a heavy chain that has three domains alpha 1,2,3 + another protein called Beta-microglobulin. They are synthesised in the cytosol and then transported to ER They are formed and complete folding is accomplished only when the peptide binds.

What happens to the partially folded MHC Class I molecules in the ER? What is the name of the chaperon that protects them and retains their shape until their subunits have folded properly?

They associate with a chaperon on the membrane of the ER to keep the partially folded heavy chain intact. Calnexin

Describe the entire process starting from when Calnexin is released from the MHC Class I complex to a complete MHC Class 1 bound to peptide on the way to the membrane.

Once the folding of heavy chain is complete and it has bound to the Beta-microglobulin the calnexin is released. Then the heterodimer of the heavy chain with microglobulin is incorporated to the Peptide Loading Complex. Only when the peptide loading complex is formed can a peptide that is transported via the TAP can it bind to MHC Class I. The MHC Class I then disassociates from the Peptide loading complex.

What are the different parts of the peptide loading complex?

1. Tapasin (connected to TAP and ) 2. ERp57 does not touch MHC 3. Calreticulin 4. TAP 5. B-microglobulin 6. Alpha heavy chain Class I

What are the three components of peptide editing? Make sure to include all enzymes/proteins that are used.

1. Interaction with tapasin puts the peptide binding site in a more open conformation that makes it more selective for tight binding - only when there is good tight binding can the MHC I molecule break away from the Peptide Loading Complex 2. Sometimes if the peptide fits really well into the peptide binding site but it is too long to fit snug, an enzyme called Endoplasmic Reticulum Amino Peptidase will cleave off AAs from the amino terminal end until it fits 3. Sometimes even after these mechanisms, a peptide is still loosely bound and falls off in the vesicular transport. The calreticulin that is still present in the membrane that is transporting it can stabilize the heavy chains and the MHC Class I molecule can be recycled to try again.