Term
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Definition
| The tagging of pathogens for phagocytosis |
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Term
| Describe the classical pathway of the complement system. |
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Definition
| The C1 complex comprising 1 c1q (hexamer) and 2 c1r in complex with 2 c1s. Binding of more than one c1q (to pathogen or Fc region of antibody) causes a conformational change in (c1r:c1s)2-complex, which activates the autocatalytic activity of c1r. The active form then cleaves c1s to generate an active serine protease. C1s can then cleave C4 into c4a (soluable inflammatory mediator) and c4b. C4b binds to the surface and binds C2, which is then also cleaved by c1s, forming c2a(another serine protease). C4b2a remains covalently attached to the surface where this complex cleaves C3 to c3a (soluable inflammatory mediator) and c3b in large number, which coat the pathogen surface. |
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Term
| Which cell types does Innate like lymphocytes (ILLs) comprise? |
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Definition
| Gamma:delta T-cells, B-1 cells and NK cells. |
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Term
| What are the general features of innate like lymphocytes (ILLs)? |
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Definition
| ILLs are cells that do not need to undergo clonal expansion to respond efficiently to the antigens they recognise. The do express members of the RAG-complex, thus they do undergo Receptor gene rearrangements. Cells include gamme:delta T-cells, B-1 cells and NK cells. |
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Term
| What are the general features of gamma:delta T-cells (location, function, and TCR). |
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Definition
| Although little is known of their function, they seem to protect the epithelial surfaces and blood stream in an innate like manner. The available data suggests that they recognise their antigen (heatshock protein, mycobacterial lipid ligands or phosphorylated ligands) directly, in a MHC-independent manner. Their TCRs are not highly diverse, and they do not need to undergo clonal expansion to be effective. Their name arises because they express a gamme:delta chain TCR in stead of the higly diverse alpha:beta chain TCR of normal TCs. |
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Term
| What are the general features of B-1 cells? (Location, function, and Ig-production) |
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Definition
| B-1 cells are a minor subpopulation of the B-cells and a member of the innate like lymphocytes. They arize in early embryonic development, they use a distinctive and limited set of gene rearrangements to make receptors, they are self-renewing outside of the central lymphoid organs and they are the predominant lymphocyte in peritoneal and pleural cavities. They can make IgM antibody reponses mainly towards polysaccharide antigens, without the assistance of T-cells, hence the ILL-status. No memory. |
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Term
| Draw an antibody and explain the different parts. |
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Definition
| Y-shaped. The stem is and bottom of the arms are constant region. The "hands" of the arms are variable (N-terminal). The medial chains are the heavy chain, while the latteral are light chains. The LCs are either both kappa- or lambda-chains. The variable regions contain the antigen-binding properties - each variable Ig domain contains 3 hypervariable sites for binding (12 in total). The constant region determines the isotype and if the AB is a receptor or soluable (BCRs have hydrophobic C-terminal sequence allowing for membrane anchorage). |
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Term
| What is the difference between a conformational/discontinuous epitope and a liniar/continuous epitope. |
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Definition
A conformational/discontinuous epitope is a binding site, which arises from a conformational change in the target protein, e.g. two alpha-helices of different chains come together in the protein fold, and the binding site comprises aminoacids of both.
If the epitope is composed of a single segment of peptide it is called a liniar/continuous epitope. |
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Term
| Draw a TCR and explain the different regions. |
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Definition
| Two chains (alpha:beta or gamme:delta) linked by a disulphide bond in the stalk region. Each chain contains two Ig domains. The top is variable, while the bottom is constant. Below the constant is a stalk region, then a transmembrane, and finaly a cytoplasmic region. The Ig domains can be associated with carbohydrates. |
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Term
| Draw a MHC class I molecule and a MHC class II molecule. How do they differ in terms of properties of peptides bound. |
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Definition
MHC-1, long alpha-chain (1,2,3) and beta-2 microglobulin. MHC-2, beta-1, beta-2 chain paired with alpha-1, alpha-2 chain. 1's are top.
Both have a cleft between 2 alpha helices, where the peptide is bound. MHC-1s have a small cleft, and the peptide is burried deeper. Binds peptide of 8-10 aa's in length and hydrophobic/basic peptides are preferred.
MHC-2s have a bigger cleft. Peptides bound are min 13 bases in length. |
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Term
| Draw a MHC class I molecule and a MHC class II molecule. How do they differ in terms of properties of peptides bound. |
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Definition
MHC-1, long alpha-chain (1,2,3) and beta-2 microglobulin. MHC-2, beta-1, beta-2 chain paired with alpha-1, alpha-2 chain. 1's are top.
Both have a cleft between 2 alpha helices, where the peptide is bound. MHC-1s have a small cleft, and the peptide is burried deeper. Binds peptide of 8-10 bases in length and hydrophobic/basic peptides are preferred.
MHC-2s have a bigger cleft. Peptides bound are min 13 bases in length. |
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Term
| Draw the two co-receptors associated with their MHC molecules. |
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Definition
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Term
| What is the function of co-receptors. |
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Definition
The co-receptors are necessary for effective TCR:MHC binding. They greatly increase the association, in addition to bringing the kinase Lck, which is bound to both co-receptors, into proximity of the TCR. They also contribute to clustering of TCR complexes, greatly increasing the phosphorylation accessory chains.
CD4 is expressed by naive T-cells destined to be T-helper cells and Tregs and binds with D1 to invariant sites on MHC class 2 molecules between the beta1 and beta2 segments.
CD8s are usually heterodimers of alpha and beta chains, however, alpha-homodimers can also form in absence of beta. CD8 is expressed by naive T-cells destined to become cytotoxic T-cells. CD8 binds MHC class I molecules. |
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Term
| Which cells express which MHC molecules? |
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Definition
MHC class I molecules can be expressed by all cells, but are most abundant on in high risk of viral infections, e.g. cells of epithelia in respiratory, urinary and gastrointestinal tract. Hepatocytes express lower levels, and erythrocytes almost none.
MHC class II molecules are often found on B-cells, macrophages, dendritic calls and other uptaking cells, but never on tissue cells.. |
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Term
| Describe which genetic components that make up both the light chain and heavy chain of an immunoglobulin molecule and draw the genetic loci, schematicly. |
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Definition
The variable region of the light chain (LC) is encoded on 2 seperate gene segments. The VL gene segment and the JL gene segment.
The segments of the lambda LC locus are arranged with ca. 30 V-lambda gene segments ---- space ---- a single J-lambda segment and then 4 constant lamda-LC segments.
30 V-lambda--.....--J-lambda----4x C-lambda
The segments of the kappa LC locus:
40x V-kappa--....--1-5x J-kappa---1x C-kappa.
The variable region of the heavy chains is encoded on 3 gene segments. The VH, the D and the JH gene segments.
The HC locus:
40x Vh--...--1-25x D---1-6x Jh---Cmy-Cdelta |
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Term
| What are the general characteristics of recombination signal sequenses (RSS's). |
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Definition
Consists of a heptamer, a spacer and a nonamer. The sequences of the heptamer and the nonamer are conserved, while only the length of the spacer is conserved, being either 12 or 23 bp in length, consistent with a single or two turns of the DNA helix. This ensures that the heptamer and nonamer are always on the same side of the helix.
The heptamer is always continuous with the either the J, D or V gene segments. D segments differ in having two RSS sequences flanking it, while J and D segments only have one. The purpose of the RSS's is basepairing of the heptamers and nonamers, which is the foundation of the recombination events that lead to formation of the variable region of Igs. In addition to this, the RSS's are what the RAG1/2 complex recognises.
In general RSS's with a 12 bp spacer always pairs with RSS's containing a 23 bp spacer. This is known as the 12/23 rule.
In the lambda LCs, the V segment RSS's all have 23 bp spacer, and the J segments 12.
In the kappa LC, it is the other way arround - V=12, J=23.
For the HC, both V and J RSS's have 23 bp spacer, while the D segment has two flanking RSS's with 12 bp spacers each. This makes sense, as D has to pair with J on one side (first) and V on the other, and the 12/23 rule must be honored. |
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Term
| Explain how e.g. a V and a J segment are recombinered together. |
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Definition
A RAG1/2 heterodimer binds to the RSS of a V and another RAG1/2 binds to the RSS of a J segment. The two heterodimers now allign the RSS12 with the RSS23 forming the RAG-complex, whose endonuclease activity cut DNA strands, leaving a coding (containing the V and J segments) end and a signal end (containing the RSS's). The cut causes the formation of a small hairpin between the plus and minus strand on each of the double stranded DNA ends.
The KU complex recruits and complexes with the DNA protein kinase cs (DNA-PKcs), thereby holding the signal end together, and phosphorylates the nuclease Artemis, which primes the ends for ligation. Finally the DNA ligase IV in cooperation with the DNA repair protein XRCC4 ligates the signal joint.
Simultaniously the coding ends are also kept together by the KU complex, artemis is phosphorylated and makes a single stand nick in the hairpin formed by the RAG-complex. XRCC4 modifies the opened hairpins, while a lymphoid specific enzyme called terminal deoxynucleotidyl transferase (TdT) adds nucleotides at random. Finally the coding joint is ligated by DNA ligase IV.
The result is
--| V | p | n | p |J|---
Where p are palendromic sequences arising from opening of the hairpins by artemis, and n are random nucleotides inserted by TdT. The sequence of the above is not known in detail.
N sequences are most often seen in HC rearrangements, not so much in LC. |
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Term
| Draw the TCR alpha and beta loci in humans. |
|
Definition
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Term
| Do you see P and N sequences after gene rearrangements of the TCR? If yes, where? |
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Definition
| Yes, the alpha chain all contain P and N sequences. |
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Term
| Draw the TCR delta and gamma chain loci. |
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Definition
| See page 159, the delta chain locus is found within the alpha chain locus. |
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Term
| Explain how IgMs and IgDs arise. |
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Definition
| The Cdelta Ig domain is located just 3' to the Cmy Ig domain and both of them are transcribed, however, due to alternative splicing only one of them will make out the isotype-determining constant region of the HC. |
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Term
| Explain how both a transmembrane and a soluable Ig can arise from the same locus. |
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Definition
See the figure on page 165.
The last two exons of the heavy chain constant region determines if the Ig is transmembrane or soluable. These exons encode a hydrophobic peptide that alows for membrane anchorage. If the transcript is polyadenylated downstream of these last two exons, a sequence (SC) encoding a hydrophilic peptide for soluability, is spliced out. If, however, the transcript is polyadenylated between the SC and the next to last exon, the two last exons are not transcribed. |
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Term
| Which Igs can form polymers and how? |
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Definition
| IgM can form pentamers, while IgA can form dimers. In both cases two of the Igs form a disulfide bond to the J chain. In addition the IgA have a disulfide bond between the two, while each IgM monomer is connected by 4 disulfide bonds. See figure page 166. |
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Term
| What is the purpose og Ig polymerisation? |
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Definition
It allows the polymers to be transported across epithelial borders, by virtue of the poly-Ig receptor via the J-chain. This is mostly relevant with IgA-dimers, who are transported into the lumen of intestines to provide protection by netralisation. It can also be relevant for IgM in IgA defficient individuals.
IgMs usually do not bind particularly strongly as they are made early in immune responses, before somatic hypermutaion and affinity maturation. However, bacterial surfaces contain highly repeated structures, which polymerised IgM can bind more avidly, as more binding sites contributes to overall avidity. |
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Term
| A single enzyme is responsible for initiating somatic hypermutaion, gene conversion and class switching of activated B-cells. What is it called? |
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Definition
| Activation induced cytidine deaminase (AID) |
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Term
| What does Activation induced cytidine deaminase (AID) do and what is the consequenses? |
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Definition
It is responsible for initiating somatic hypermutaion, gene conversion and class switching of activated B-cells.
It causes massive amounts of C->U conversions - so many that repair enzymes cannot keep up.
These Uracils are recognised by "Uracil-DNA glycosylase" which removed the base-part of the uracil, leaving an abasic site. These lead to somatic hypermutations.
Abasic endonuclease (APE1) remove the rest of the abasic residue, making a single stranded nick. Lots of these nicks are thought to be a required signal to initiating the process of templated replication with homologous sequences that occur in gene conversion.
Finally, ss nicks in specific regions flanking constant regions are thought to generate the ds-breaks required for class switching. |
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Term
| Explain how, where, when and in which cells somatic hypermutation (SH) takes place. |
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Definition
SH occurs in activated mature B-cells (BC), thus they have a functional BCR, which has recognised its antigen and the BC has migrated to peripheral lymphoid tissues.
The enzyme "activation induced cytidine deaminase" (AID) causes C->U conversions all over the assembled Ig-variable region. This results in many single bp mutations, giving rise to a slightly altered BCR in each B-cell clone. These clones are then subjected to positive and negative selection.
SH does not occur in inactive loci, because AID needs ss DNA as substrate, which only transcribed DNA is. Constant regions are not as affected, and it does not happen at all in TCRs. |
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Term
| Explain how isotype switching occurs. |
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Definition
| Cytokines from T-cells determine to which isotype the switch occurs. What happens is, that the Cmy or Cdelta constant domains are switched out with either Cgamma, Calpha or Cepsilon. Each has its own switch region and non-homologous recombination events between the switch region of the initial subtype and the new then occur. Everything between the two switch regions is deleted. |
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Term
| Which types of pathogens give rise to peptide presentation on MHC class I molecules? |
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Definition
| Pathogens found in the cytosol, e.g. vira. |
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Term
| Which types of pathogens give rise to peptide presentation on MHC class II molecules? |
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Definition
| Pathogens that have been phagocytised, internalised by receptor-mediated uptake or macropinocytosis. |
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Term
| Where are MHC class I molecules assembled? |
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Definition
| In endoplasmatic reticulum. |
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Term
| How are peptides for MHC class I molecules brought into vicinity of the MHCs? |
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Definition
| The peptides are transported into the ER by a heterodimer of "transporters associated with antigen processing" (TAP) 1/2, the TAP-complex, which is ATP-dependent. |
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Term
| Which peptide-features are prefered by the TAP-complex? |
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Definition
| 8-16 aminoacids in length, with hydrophobic or basic residues at the C-terminus. Also the complex has a bias for peptides with proline in the first 3 aa's from the N-terminus. These are the exact features of peptides bound by MHC class I molecules. |
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Term
| From where does peptides of the MHC class I molecules originate? |
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Definition
| They are fragments of broken down proteins, from self or pathogens found in the cytosol. The method of break-down is the ubiquitin-dependent proteasome mediated proteolysis. |
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Term
| How is the immunoproteasome initiated? |
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Definition
| Interferons, such as IFN-gamma, expressed during viral infections, increases expression of TAP1+2 MHC class I molecules in cells infected with cytosolic pathogens. In addition to this, 3 proteases (LMP2, LMP6 and MECL-1), which substitute for their counterparts in the proteasome, are also expressed. The proteasome, having LMP2+7 and MECL-1 as part of it, is referred to as the immunoproteasome. |
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Term
| What is the function of the immunoproteasome? |
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Definition
| To break down cytosolic pathogen proteins (but also self-proteins) to peptides that are preferred by the TAP-complex and MHC class I molecules. This is done by increasing cleavage after hydrophobic residues and decreasing cleavage after acidic. |
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Term
| Explain how IFN-alpha, beta and gamma contribute to optimizing the loading of peptides onto MHC molecules. |
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Definition
All upregulate expression of the TAP-complex, tapasin and the MHC-molecules themselves. They cause expression of the proteases LMP2, LMP7 and MECL-1 (parts of the immunoproteasome [IP]).
IFN-gamma induces formation of the PA28-complex, which increases the rate of peptide release and of the right length by binding to the IP. It also upregulates the "ER aminopeptidase associated with antigen processing" (ERAAP), which trimmes peptides, that are too long for MHC class I-loading. It also increases expression of MHC-IIs, HLA-DM and Ii, but causing the expression of the transcription factor "class II transactivator" CIITA.
So:
TAP-complex, tapasin, MHC-I, LMP2+7, MECL-1, PA28-complex and ERAAP are all upregulated by. |
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Term
| Explain how peptides arizing from pathogen membranes (e.g. glycoproteins of viral envelopes) and secretes proteins can be presented by MHC class I molecules. |
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Definition
| Viral or bacterial membrane- or secreted proteins are translocated to the ER from the cytosol. From there they are again transported out into the cytosol and degraded by the immunoproteasome. This process is known as retrograde translocation. And the phenomenon is not desribed in more detail than this. P. 186-187. |
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Term
| Explain the term cross-presentation. And mention a scenario, where this is important. |
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Definition
Retrograde translocation allows the given MHC-I expressing cell to present peptides of exogeneous origin. An example could be that one epithelial cell is infected with a virus. Particles from this virus is then transported to another cell by the vesicular system. These vesicles then fuse with the ER of the recipient cell, and the viral proteins are then transported by retrograde translocation to the cytosol, still of the recipient cell, and degraded by the immunoproteasome, which then of course breaks down the viral proteins into peptides of 8-10 aa's.
When these peptides are presented to CD8 T-cells, it is called cross-presentation.
A subtype of dendritic cells expressing CD8 are particularly efficient in phagocytosis of exogenous antigens, translocating them into the the ER, back into the cytosol and finally presenting them on MHC-I molecules for CD8 T-cells. This pathway is important in activating CD8 T-cells against vira that do not infect antigen presenting cells. |
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Term
| Explain how MHC class I molecules are assembled. |
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Definition
The alpha-chain and the beta2-microglobulin (B2m) are transported seperately to the ER. the chaperone calnexin binds the alpha-chain and retains it in a partly folded state. When the B2m binds to the a-chain, the a:B2m heterodimer dissociates from calnexin and is bound by the MHC class I loading complex. This complex consists of calreticulin, tapasin, Erp57 and the TAP-complex.
Calreticulin holds the a:B2m, while tapasin brigdes between the TAP-complex and a:B2m. Erp57 probably has a role in breaking and reforming the disulfide bond of the alpha-2 domain of the alpha chain.
In addition to transporting peptides into the ER for MHC-loading, the TAP-complex keeps the a:B2m receptive to peptide loading, and along with tapasin has an peptide editing function, trying out different peptides, until a good fit is found. The binding of a good fitting peptide to the MHC, allows its release from the loading complex and the fully assembled peptide:MHC-I is now ready to be transported to the cellular surface. |
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Term
| Give five examples of how vira can avoid MHC-presentation of virus-derived peptides. |
|
Definition
Some viruses produce immunoevasins.
They can avoid presentation by:
-Blocking the TAP-complex, preventing peptides from entering the ER.
-Blocking the TAP-ATPase activity, also preventing peptide admission.
-Retaining the MHC class I molecules in the ER, preventing access to the surface.
-Preventing the TAP-tapasin interaction, preventing peptide loading.
-Targeting MHC class I molecules for degredation, thus they never reach the surface. |
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Term
| Explain how MHC class II molecules are assembled. |
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Definition
The assembly occurs step wise. Initially MHC-IIs are translocated to ER, where calnexin binds the pre-MHC-II and a small peptide called "invariant chain" (Ii). A complex of 3 Ii's and 3 MHC-IIs is assembled, which cases the release from calnexin. These complexes are then released into the cytosol in vesicles, which fuse with the endosomes. Here the pH sensitive proteases, such as cathepsin S, cleave the Ii step wise. First the part of the Ii that keeps the 3 MHC-IIs in complex is cleaved, leaving the MHC with a membrane bound peptide chain, attached in the cleft. Seccondly the membrane associated peptide chain is cleaved and the MHC is left with only a small peptide called "MHC-II-associated invarient chain peptide" (CLIP) in the cleft.
The MHC-II:CLIP molecules are found in a special compartment of the endosome called "MHC-II compartment" (MIIC). Here a MHC-II-like molecule called HLA-DM catalyzes the release og CLIP and also functions to stabilize the empty MHC-IIs. Peptides arizing from proteins degraded by Cathepsins in the endosome can now be bound by MHC-IIs. HLA-DM also catalyze the release of ill-fitted peptides from the MHC-IIs, thus peptides are continously fitted and released, until a good fit is found. The fully assembled MHC-IIs leave for the surface by vesicular transport.
In thymic epithelial cells (TECs) and B-cells, another MHC-II like molecule, called HLA-DO is also expressed. HLA-DO acts negatively on HLA-DM, inhibiting both the release of CLIP and peptide fittings of MHC-IIs. This inhibitory effect is overcome during inflammatory responses, where IFN-gamma is produced by T- and NK cells, as only HLA-DM is upregulated by IFN-gamma, and the shear numbers of HLA-DM far out-competes the HLA-DOs. Why B-cells and TECs need to regulate their antigen presentation in this way is not known. |
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Term
| Explain how pepides for MHC class II molecules are derived. |
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Definition
| Protein uptaken by dendritic cells, macrophages or B-cells, by phagocytosis, macropinocytosis or receptor mediated uptake or autophagy enter the cell in a vesicle called the endosome. As these progress into the cell pH drops and the endosomes fuse with lysosomes. Contained in these are pH sensitive proteases, such as Cathepsin S and L, so the pH drop results in degredation of the uptaken proteins. Cells who have been stimulatied with IFN-gamma contain "IFN-gamma induced lysosomal thiol reductase" (GILT) in the endosome, which is responsible for the reduction of disulfide bonds as part of the degredation. |
|
|
Term
|
Definition
| The delivery of cytosolic self-proteins and organelles for degredation, leading to presentation of self-peptides on MHC class II molecules. |
|
|
Term
| Draw the HLA-locus and explain. |
|
Definition
There are 3 pairs of class II alpha and beta chain. Their genes are called HLA-DP, DQ and DR. For all of these the beta chain lies upstream of its corresponding alpha chain. The genes encoding TAP1 and 2, LMP2 and 7, and Tapasin (TAPBP), HLA-DO (DOA and DOB), HLA-DM (DMA and DMB) are also found in the locus. Further downstream are the genes encoding three kinds of MHC class I alpha-chains called HLA-B, C and A.
The genes are ordered as follows.
|TAPBP|---|DP-B|DP-A|--|DOA|--|DMA|DMB|--|LMP/TAP|--|DOB|--|DQB|DQA|--|DRB|(DRB2)|DRA|......|HLA-B|-|HLA-C|-----|HLA-A| |
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Term
|
Definition
| A group of specialised MHC class I molecules behaving like MHC class II. They bind glycolipids in their cleft. CD1a, b and c bind foreign lipids, while CD1d and e bind self lipids. They are expressed on dendiric cells, monocytes and some thymocytes and they are not recognised by CD4 nor CD8 cells, but by a specialised group og T-cells with a diverse repetoire of alpha-beta TCRs. |
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Term
| What does SH2 domains recognise? |
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Definition
| Phosphotyrosines, example Grb2 |
|
|
Term
| What does SH3 domains recognise? |
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Definition
| proline rich sequense motifs, example Sos |
|
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Term
| What is the terminal result of activated Ras, Rac, Rho, and Cdc42, respectively? |
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Definition
Ras => proliferation
Rac, Rho and Cdc42 => actin modulation |
|
|
Term
| What is a GEF? Give an example. |
|
Definition
| GTP exchange factor, RasGRP => RasGDP -> RasGTP |
|
|
Term
| What is a GAP? Give an example |
|
Definition
| GTPase activating protein. => RasGTP -> RasGDP |
|
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Term
| How does the the BCR signal, when antigen is bound? |
|
Definition
| Through "Immunoreceptor tyrosin-based activation motifs" (ITAMs) of the invariant accesory proteins Ig-alpha and Ig-beta. These two and the BCR together is called BCR-complex. |
|
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Term
|
Definition
| "Immunoreceptor tyrosin-based activation motifs" |
|
|
Term
| Draw the TCR signaling complex. |
|
Definition
|
|
Term
| How many BCRs or TCRs does CD4 T-cells, CD8 T-cells and B-cells need engadged to be activated? |
|
Definition
CD4s need 10-50
CD8s need 1-3
B-cells need ~20 |
|
|
Term
| Which kinases are responsible for phosphorylating ITAMs of the TCR-complex? |
|
Definition
| Two members og Src family of kinases, Lck and Fyn. Lck is associated with the co-receptors CD4 and CD8, while Fyn is weakly associated with the Zeta-chains of the CD3-complex. |
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Term
| What happens, when a fully functional TCR binds its peptide:MHC-ligand? |
|
Definition
|
|
Term
| NFkB, NFAT and AP1 bind to the promotor, and are all needed for the expression of a certain cytokine. Which? |
|
Definition
|
|
Term
| Which kinases are responsible for phosphorylating ITAMs of the BCR-complex? |
|
Definition
| The Scr family members Fyn, Blk and Lyn. |
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|
Term
| ZAP-70 is not expressed in B-cells, which kinases has its place? |
|
Definition
|
|
Term
| What does the B-cell co-receptor complex consist of? |
|
Definition
| CD19, CD21 (aka CR2) and CD81 |
|
|
Term
| How can the B-cell co-receptor complex contribute to BCR signaling? |
|
Definition
| CD21 (aka CR2) binds C3d or C3dg (both break-down products of the complement C3b), which causes the cytosolic phosphorylation of CD19. This creates a binding site for Fyn, Blk or Lyn, which enhances phosphorylation of ITAMs on the BCR-complex. In addition the PI-3 kinase is recruited, starting an additional pathway of PIP2 -> PIP3, which leads to PKB/Akt activation, inhibition of apoptosis and cell growth. |
|
|
Term
| Which cells express the CD28 ligand, and what is the ligand? |
|
Definition
| Antigen presenting cells express a heterodimer called B7, consisting of B7.1 and B7.2. |
|
|
Term
| Which cells express CD28? |
|
Definition
|
|
Term
| Which receptor binds the co-stimulatory ligand B7, and which cells express the receptor? |
|
Definition
| CD28 binds the heterodimer B7, consisting of B7.1 and B7.2. It is expressed by all naive T-cells. |
|
|
Term
| How does CD28 contribute to T-cell activation. |
|
Definition
| Binding of TCR to peptide:MHC is not enough for activating the B-cell. It must also bind B7, through CD28, which causes cytoplasmic phosophorylation of CD28. This can lead to both Ras activation, causing proliferation, in addition to PKB, activation through recruitment of PI-3K, leading to inhibtion of apoptosis and proliferation. |
|
|
Term
| mention the two pathways to apoptosis. |
|
Definition
Extrinsic pathway, through death receptor
Intrinsic/mitochondrial pathway, through noxious stimuli, like starvation or lack of growth factors. |
|
|
Term
| Which initiator caspase is used in extrinsic pathway and intrinsic/mitochondrial pathway? |
|
Definition
extrinsic: caspase 8
intrinsic: caspase 9 |
|
|
Term
| Which caspases are effector caspases? |
|
Definition
|
|
Term
| Which Bcl-2 family members are pro-apoptotic and how do they work? |
|
Definition
| Bax, Bak and Bok bind to mitochondrial membrane and release cytocrome C. |
|
|
Term
| Which Bcl-2 family members are anti-apoptotic? |
|
Definition
| Bcl-2, Bcl-XL and Bcl-W, they bind to mitch. membrane and inhibit Cyt. C release. |
|
|
Term
| How does cytocrome C release lead to caspase 9? |
|
Definition
| Cytocrome C bind "apoptotic protease activation factor 1" (Apaf-1), which causes oligopolymerisation of Apaf-1. This recruits alot of pro-caspase 9, and enough of these causes self-activation to caspase 9. |
|
|
Term
| How are signaling mediated through Toll like receptors. |
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Definition
| Mediator proteins, such as MyD88, who has Toll-IL-1 (TIR) domains, binds to a TIR domain on the cytoplasmic part of the TLR. |
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Term
| Describe how binding of lipopolysaccharide (LPS) results in IFN-gamma expression and NFkB activation. |
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Definition
LPS bound by TLR-4. TIR domain is bound by TIR domain of MyD88, which bind IRAK, which bind TRAF-6, which phosphorylates the Mapkkk TAK1. This leads to activation of IKK, which releases NFkB from its inhibitor.
LPS bound by TLR-4. TIR domain is bound by TIR domain of TRIFF, which bind IkappaKepsilon and TBK1, who activate IRFs which cause IFN-gamma expression.
TRIFF can also bind TRAF-6, resulting in NFkB release via pathway described above. |
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Term
| Which things are bound by 7TM receptors? |
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Definition
| Bacterial peptides, mediators of inflammation and chemokines. |
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Term
| Describe signaling through 7TM receptors, with trimeric G-proteins. |
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Definition
G-alpha activates adenylate cyclase -> AMP -> cAMP
G-beta:gamma -> PLC -> PIP3 -> IP3 and DAG osv. |
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Term
| Where do B-cells develop? |
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Definition
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Term
| Where do T-cells develop? |
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Definition
| Bone marrow, initially, maturation in thymus |
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Term
| Which cells are responsible for delivering signals for B- and NK cell development? |
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Definition
| Bone marrow stromal cells. |
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Term
| How does bone marrow stromal cells mediate the signals necessary for B-cell development? |
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Definition
| They secret IL-7 and the chemokine CXCL12, which are both necessary for growth and survival, at least in mice. In addition they provide cell:cell contacts. |
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Term
| What are the cellular stages from stem cell to NK cell? |
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Definition
| stem cell -> multipotent progenitor cell -> early lymphocyte progenitor cell -> common lymphocyte progenitor -> pre-NK cell -> NK cell |
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Term
| What are the cellular stages from stem cell to immature B-cell? |
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Definition
| stem cell -> multipotent progenitor cell -> early lymphocyte progenitor cell -> late lymphocyte progenitor -> large Pre B-cell -> small Pre B-cell -> immature B-cell |
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Term
| At which developmental stage does the heavy chain D to J segments rearrange in the B-cell? |
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Definition
| early lymphocyte progenitor |
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Term
| At which developmental stage does the heavy chain V to DJ segments rearrange in the B-cell? |
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Definition
| late lymphocyte progenitor |
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Term
| At Which developmental stage can the first pre-BCR be seen transiently? |
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Definition
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Term
| What is characteristic about the "small pre-B-cell" developmental stage. |
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Definition
This is the stage where the light chain V to J segment rearrange.
The my-chain of the BCR is only observed intracellularly. |
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Term
| What is the checkpoint criterium for entering the small pre-B-cell stage? |
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Definition
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Term
| When in the B-cell development is the terminal deoxynucleotidyl transferase (TdT) expressed. |
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Definition
| At the pro-B-cell stages, when the HC locus is rearranging.Its expression declines during the pre-cell stages, and this is why nearly all D to J and V to DJ joints contain N nucleotides, while only 25% of light chain V to J joints do. |
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Term
| what is the difference beween immature and mature B-cells in terms of AB isotypes expressed. |
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Definition
| Immature B-cells only express IgMs, while mature both express IgMs and IgDs - both arizing from alternative splicing. |
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Term
| What is the function of the pre-BCR? |
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Definition
| To test if the HC rearragements have been succesful, and to deliver survival signals, in case it is. |
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Term
| Describe the structure of the pre-BCR. |
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Definition
| The pre-BCR consist of a functional my-chain and two invariant surrogate chains called lambda5 and VpreB. Lambda5 resembles the constant region of the lambda light chain, while VpreB resembles the variant region. |
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Term
| Two transcription factors are responsible for expression of genes involved in gene rearrangements in B-cells. What are they called and when are they expressed? |
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Definition
From early progenitor B-cell and on.
They are called E2A and EBF. |
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Term
| Which genes are regulated by the transcription factors E2A and EBF? |
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Definition
| RAG-1+2, Pax-5, which is responsible for CD19 and Ig-alpha expression. Also the surrogate chains lambda5 and VpreB. |
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Term
| What does the B-cell go through in the immature stage of development? |
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Definition
The BCR is tested for autoreactivity (still in the bone marrow). low-no reactivity means the cells will get to mature and they are carried via the venous blood the spleen.
If they do react strongly to self-antigen, they undergo another round of rearrangements of the LC (receptor editing) until a non-autoreactive BCR is produced or the LC V and J segments are exhausted, in which case => apoptosis. |
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Term
| Which receptors does the NK T-cells express? |
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Definition
| A TCR of little diversity in addition to the NK1.1 receptor, which is also found on NK cells. |
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Term
| Which cells recognise CD1 molecules? |
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Definition
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Term
| Which cytokine is particularly important in T-cell development? |
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Definition
|
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Term
| Describe the structure of the pre-TCR |
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Definition
| The surrogate alpha-chain pTx pairs with a functional intact Beta-chain. |
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Term
| Where in the thymus does positive and negative selection of T-cells occur? |
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Definition
positive: Cortex
negative: medulla |
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Term
| Where in the T-cell development is ZAP-70 important? |
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Definition
| It promotes the progression from the double-positive thymucyte to single-positive thymucyte. |
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Term
| Fyn is important for the development of a special type of T-cells, which? |
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Definition
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Term
| What is the importance of expression of the gene AIRE in T-cell development, and under influence of what is it expressed? |
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Definition
Expression of AIRE results in expression og ubiquitous proteins and compounds, such as insulin, for presentation to T-cells.
AIRE is expressed under the influence of lymphotoxin (LT) signaling. |
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Term
| Mention an important survival factor for B-cells in follicles of e.g. lymph node. Also mention its receptor. |
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Definition
| B-cell activating factor (BAFF), its receptor on B-cells is BAFF-R. |
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Term
| Mention a way of attracting only mature B-cells to follicles of the peripheral lymphoid tissues. |
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Definition
| Follicular dendritic cells (FDCs) express and secrete the chemokine CXCL13, which can be bound only by mature B-cells, having already bound their antigen, as immature B-cells do not express the receptor CXCR5. |
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Term
| Mention a special surface marker of B-1 cells. |
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Definition
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Term
| What is special about marginal zone B-cells, in terms of surface molecules. |
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Definition
| Less Fc-epsilon-RII (CD23), more CD1 and more CR1+2 |
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Term
| Mention two things that are necessary for T-cell survival in the periphery, and where the get these from. |
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Definition
| IL-7 and self-peptide:self:MHC contact. Both are supplied by dendritic cells of T-zones in lymph nodes. |
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Term
| Which adresins does L-selectin bind, when is it expressed, on which cells, and where are the adresins expressed? |
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Definition
| L-selectin is expressed by all leukocytes and binds to CD34 and GlyCAM-1 expressed by HEVs of lymph nodes. |
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Term
| Describe a the only way dendritic cells can produce IL-12. |
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Definition
| See noter "dendritic cells" lidt over halvvejs i bog 2 |
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Term
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Definition
| Se noter bog to hen mod slutning |
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Term
| Effector t-cells have different surface molecules, binding different adressins. What has changed. |
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Definition
| They stop expressing L-selecting, by LFA-1 and CD2 are upregulated. VLA-4 is expressed, binding VCAM-1 expressed by VECs at SOI. |
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Term
| What are the main cytokines secreted by Th1 cells, and Th2? |
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Definition
Th1: IFN-gamma, and IL-2
Th2: IL-4 and IL-5 |
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Term
| which cytokines promote Th1 differentiation? |
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Definition
| IFN-gamma (from innate cells, NK, macrophages and dendritic cells), and IL-12 (from dendritic cells) |
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Term
| Which cytokine promote Th2 differentiation? |
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Definition
| not much is known but IL-4 and absense of IFN-gamma. |
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Term
| Which cytokine mix promotes Th17 differentiation. |
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Definition
| IL-6, TGFbeta, (IL-23) and absense of IL-4 and IL-5. |
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Term
| What does Th17 cells secrete? |
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Definition
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Term
| What is the main function of Th1, Th2 and Th17 cells? |
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Definition
Th1, stimulate secretion of IgGs promoting opsonisation (cell mediated immunity).
Th2, stimulate secretion of IgMs, As and Es (humoral immunity)
Th17 cause production of chemokines by epithelial or stromal cells for neutrophil recruitment. |
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Term
| mention two distantly acting cytokines and their functions. |
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Definition
| IL-3 and GM-CSF are both secreted by Th1 and Th2 cells and cause production of macrophages and granulocytes from bone marrow. Also dendritic cells from bone marrow progenitors. |
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