Flashcards in Immuno 6 Deck (48)
What chromosome are the genes for MHC encoded on?
T or F. B cells can recognize particulate or soluble antigens, and the composition of those antigens can be protein, carbohydrate, lipid, nucleic acid...almost anything.
T. In contrast, T cells only recognize peptides in the context of MHC class I or MHC class II molecules. The MHC molecule binds to a protein fragment and “presents” it to the T cell.
Describe the composition of a MHC class I molecule.
MHC class I molecules are heterodimers that are composed of a single MHC encoded protein chain, the alpha chain, and a protein known as beta-2-microglobulin that is not encoded within the MHC complex. The alpha chain has three domains (alpha 1, 2, and 3). The alpha 1 and alpha 2 domains fold in a way that creates a peptide binding cleft (they each have an extended alpha helical region.). The bottom of the cleft is formed by a series of alternating beta-sheet secondary structure. The alpha 3 domain is an immunoglobulin-like domain that has a transmembrane region that anchors the chain into the cell membrane.
Describe the composition of a MHC class II molecule.
MHC class II molecules are heterodimers that are composed of an alpha and a beta chain. Both of these chains are encoded by the MHC locus. Both of these chains have two domains. The alpha 1 and beta 1 domains come together to form the peptide binding cleft. The alpha 2 and beta 2 domains are both immunoglobulin-like domains that have transmembrane regions that anchor the chains into host cell membranes.
The organization of MHC class II molecules is very similar to that of MHC class I molecules. The alpha 1 and beta 1 domains each have an extended alpha helical structure that forms one side of the peptide binding groove, and the “floor” of the peptide binding groove is composed of alternating beta sheet.
T or F. The most important function of MHC molecules is to bind to peptides and present them to T cells. How do they do this?
T. Immunocompetent individuals have a tremendous repertoire of T cells that recognize more than 10^18 different peptide determinants with high specificity. Therefore, MHC molecules must be able to present a large number of different peptides to T cells. They can do this because they bind to peptides in a promiscuous fashion. They do not bind to peptides with the same type of specificity that we have discussed for B cell receptors and will soon discuss for T cell receptors.
In contrast to antibodies or T cell receptors (that bind to a highly specific antigenic determinant), each MHC molecule can bind to many different peptides.
In contrast to antibodies or T cell receptors (that bind to a highly specific antigenic determinant), each MHC molecule can bind to many different peptides. MHC class I and II molecules do have slightly different peptide-binding characteristics
What kinds of peptides will MHC class I molecules bind?
The peptide binding groove of MHC class I molecules is closed on the ends. Their binding groove will only accommodate peptides that are between 8 and 10 amino acids in length. In fact, peptide binding in the groove is stabilized by contacts with the aminoterminal and carboxyterminal ends of the peptide with invariant sites near the ends of the binding groove.
How do MHC class I molecules bind to peptides in a promiscuous fashion?
**Ex. only** They all must be eight amino acids long, but the sequences of all three can be very different. The only similarity requirement between these peptides are at residues 5 and 8. At position 8, each peptide has a leucine residue. At position 5, each peptide has an amino acid that has a large hydrophobic side chain that has a ring structure (i.e. phenylalanine, tyrosine, etc.). Positions 5 and 8 are referred to as anchor residues. Any 8-10 residue peptide that has amino acids with a large hydrophobic side chain with a ring structure at position 5 and a leucine at position 8 will likely be able to bind to this MHC class I molecule.
There are many different isoforms of MHC class I molecules that are expressed within the human population, each of which has different peptide binding characteristics, mostly based on their requirements for the positions of anchor residues within those peptides.
What are the two primary differences between MHC class I and MHC class II molecules?
1. The ends of the binding cleft of class II molecules are open, compared to class I molecules that have closed ends. It is sometimes called the “hot dog in a bun model” because the peptides hang over the edges of the binding groove
2. The open-ended binding groove allows for longer peptides to bind to MHC class II molecules. In fact, peptides that bind to class II molecules must be at least 13 amino acids long, and can be up to at least 35 residues long (maybe longer).
How do MHC class II molecules bind to peptides in a promiscuous fashion?
Ex. Here you can see the sequences of three peptides that were extracted from three identical MHC class II molecules. The central 14 amino acid stretch of each has an identical sequence, but they are all of different lengths. What this shows is that MHC class II molecules can bind to peptides of varying lengths that are all too long to fit completely within its binding groove.
(Bottom Panel): Here you see can a set of peptides that were all extracted from identical copies of a different MHC class II molecule isoform. They are all of different lengths, and they all have very different amino acid sequences. The only commonality of these peptides is that they have anchor residues at 4 different positions that allow them to bind tightly within the binding groove of this particular MHC class II molecule.
(Both Panels): Together, these two panels show that the promiscuity of peptide binding to class II molecules is based on a similar feature to that we discussed for MHC class I molecules. Both MHC class I and MHC class II molecules have pockets within their binding grooves that accommodate particularly shaped amino acid side chains. The interactions between the binding grooves and these anchor residues are responsible for the bulk of the affinity between the peptide and the MHC molecule.
One of the key decisions made by the immune system is whether to respond with an immune response that is ideal for clearing an intracellular infection vs. one that is ideal for clearance of an extracellular infection. These two processing and presentation pathways are designed to help the immune system to determine what type of infection is ongoing.
The MHC class I processing and presentation pathway primarily presents antigens that are derived from intracellular pathogens, while the MHC class II processing and presentation pathway primarily presents antigens derived from extracellular pathogens. It is critical that you remember and understand this.
T or F. The MHC class I processing and presentation pathway primarily presents antigens that are derived from extracellular pathogens
F. They are derived from INTRAcellular pathogens
How are antigens brought into a cell?
Some antigens are brought into the cell via endocytic vesicles via phagocytosis, macropinocytosis, endocytosis, etc. This will be important as we discuss the MHC class II processing and presentation pathway.
Notes on cellular components that are important in antigen presenting
The endoplasmic reticulum is a structure that surrounds the nucleus of the cell that is an important part of the secretory pathway of the cell. All proteins that are destined to become membrane proteins or secreted proteins are translated on ribosomes that are associated with the ER and are trafficked through the ER for modifications and trafficking eventually to the cell surface.
The golgi apparatus is an organelle that carries out the next phase of shipping newly produced membrane or secreted proteins to the cell surface. It gives rise to secretory vesicles that deliver these proteins to the cell surface.
Lysosomes are vesicle-like organelles that have acid hydrolases that are used to break down macromolecules and invading pathogens that are endocytosed by a cell.
T or F. One of the processes that occurs all the time in all cells in each person’s body is recycling of old proteins found in the cytosol of the cell.
Proteins that are targeted for destruction are taken up and degraded by a protein complex known as the _______.
proteosome. This complex digests proteins into smaller and smaller peptide pieces, all the way down to single amino acids that can then be used for new protein synthesis.
Some of the digestion products are peptides. Some of these peptides are transported from the cytosol into the lumen of the endoplasmic reticulum by what is known as the ______.
TAP transporter complex.
What is the TAP transporter complex composed of?
This complex is composed of two proteins: TAP-1 and TAP-2. As the TAP transporter moves peptides from the cytosol to the ER lumen it participates in the process of loading these proteins onto newly synthesized MHC class I molecules.
How are MHC class I molecules synthesized?
Because it is a membrane anchored protein, MHC class I (and MHC class II, for that matter) is targeted for transport through the ER and golgi on its way to the cell surface.
1. A class I heavy chain (composed of a1, a2, and a3) is stabilized by calnexin until B2-microglobulin binds
2. Calnexin is released and the heterodimer of class I heavy chain and B2m forms the peptide loading complex with calreticulin, tapasin, TAP, ERp57, and PDI
3. A peptide delivered by TAP binds to the class I heavy chain, forming the mature MHC class I molecule
4. The class I molecules dissociates from the peptide-loading complex, and is exported from the ER to the golgi and ultimately to the surface of the cell
These events that are occurring all of the time in all host cells, whether an infection has occurred on not.
What happens if a peptide is not loaded into the newly synthesized MHC class I binding groove?
MHC class I molecules are unstable if they have not been loaded with a peptide. If a peptide is not loaded into its binding groove fairly rapidly, that MHC class I molecule will begin to degrade and will be recycled. This is evidenced by the fact that people that have an inherited deficiency of one or both of the TAP transporter proteins, and therefore cannot load peptides onto MHC class I molecules, have very few cells that bear MHC class I molecules on their surface.
What happens in regards to MHC class I synthesis when a host cell becomes infected with an intracellular pathogen?
During an infection with an intracellular pathogen, pathogen-derived proteins will be generated during its replicative cycle and will be available for degradation by the proteosome. Pathogen- derived peptides are therefore going to be among the peptides transported to the ER lumen by the TAP transporter and loaded onto newly synthesized MHC class I molecules. Once the MHC class I molecule bearing a pathogen-derived peptide is transported to the surface of the cell, it can now be presented to T cells. If this is an antigen-presenting cell, the peptide will be presented to naïve T cells with the goal of activating a pathogen-specific T cell response .
If the cell is not an antigen presenting cell, an effector T cell with specificity for that peptide can now potentially recognize the cell as infected and effect its destruction.
So, the immune system takes advantage of a normal housekeeping function of all cells for activation of T cell responses and for recognition of infected cells by effector T cells.
One caveat that you should be aware of: the vast majority of the peptides that are loaded onto MHC class I molecules are derived from self proteins. Therefore, it is critical that all self- reactive T cells be removed from the T cell repertoire.
How are MHC class II molecules synthesized?
MHC class II molecules are also shuttled through the ER soon after they are synthesized. The design of the immune system requires that these MHC class II molecules do not get loaded with cytosol-derived peptides as they are trafficked through the ER. Therefore, soon after they are synthesized, MHC class II proteins are associated with a protein known as the **invariant chain**. Part of this protein fits into the peptide binding groove of the MHC class II molecule. This chain remains associated with the class II molecule until it has completed its passage through the ER and Golgi apparatus and it resides in cytosolic vesicles.
Once in the vesicle, the invariant chain is cleaved, leaving only a short peptide (that is know as the CLIP fragment) in the binding groove of the MHC class II molecule, where it prevents other peptides from having access to the binding groove.
If this vesicle fuses with a phagolysosome, which contains materials collected from the extracellular milieu that are being processed, a protein known as HLA-DM interacts with the MHC class II molecule and dislodges the CLIP peptide so that a processed peptide can be loaded into the binding groove of the MHC class II molecule before it is transported to the cell surface for display to naïve T cells.
Only antigen-presenting cells (with one exception) express MHC class II proteins. It is also important for you to remember that the vast majority of all peptides ever loaded onto MHC class II molecules in a persons body are derived from self-proteins. Only during an infection will that be a source of non-self proteins for loading onto MHC class II molecules. Again, it is critical that self-reactive T cells be removed from the repertoire.
MHC class II processing and presentation pathway from start to finish
Extracellular antigens are taken up by phagocytosis/ endocytosis constantly in all antigen presenting cells. These cells are also always producing new MHC class II proteins that are trafficked through the ER and Golgi apparatus. The invariant chain blocks the binding groove of the class II molecule until it completes its journey to a cytoplasmic vesicle. This prevents peptides transported into the ER by the TAP transporter from loading into its binding groove. When the vesicle fuses with a phagolysosome, the CLIP peptide is removed, and a peptide derived from the extracellular milieu is then loaded into the binding groove of the MHC class II molecule. It is now transported to the surface of the cell for display for presentation to naïve T cells.
***These two pathways are not mutually exclusive. Some peptides derived from intracellular infections will be loaded onto MHC class II molecules, and some peptides derived from extracellular pathogens will be loaded onto MHC class I molecules. However, these loading efficiencies will be much lower than for the two pathways that I just described.
Which enucleated cells do not express MHC class I?
erythrocytes. there would be no reason for them too because T cells are not able to kill cells that do not have a nucleus.
All other hematopoietic cells do (i.e T cells, B cells, macrophages, dendritic cells, neutrophils)
What other cells express some MHC class I on their surface?
thymic epithelium, liver hepatocytes, kidney epithelium, neural tissue
Because neuronal cells are not regenerated very well and because their function is so vital to the host, they are designed to be very refractory to immune effector mechanisms. It would not be useful for the immune system to kill infected cells of the brain (for instance) because those cells function may be critical to survival. I suppose the same could be said of the kidneys and liver.
T or F. MHC class II expression is restricted to professional antigen presenting cells (dendritic cells, macrophages, and B cells)
T. because their role is to present peptide antigens to naïve T cells.
MHC class II is also found on _____.
CD4 T cells only recognize peptides bound to MHC class ___ proteins
class II proteins.
CD8 T cells only recognize peptides bound to MHC class ___ proteins.
class I proteins