Chapter 3 Objectives

1. Describe receptors and ligand.
Receptors are cell-associated proteins located at the surface that bind to ligand. The binding of a receptor and ligand induce changes in the receptor, which act to transmitted the ligand-binding signal into the interior of the cell and alter cellular functions such as proliferation, cell death, cell reproduction.

2. Explain the signal transduction pathway and their elements.
Signal transduction pathway is the route by which ligand-receptor interaction is translated into biochemical change inside the cell. This process is initiated by the binding interaction of complementary ligand and receptor during sufficient time and strength that bring a biochemical change in the receptor. The upstream components consist of elements closest to the receptor. The downstream components are closest to the effector molecule.

3. Describe Immuno-receptor Tyrosine Activation Motif (ITAM) and list some of the molecules associated with B- and T- cell antigen receptors.
The ITAM is a pair of long cytoplasmic tail that is found on signaling proteins within the immune system. It contains tyrosine that is phosphorylated after signal transduction of associated receptors. The phosphorylation of ITAM facilitated the initiation of signaling cascade. Other molecules associated with B and T cell antigen receptors are CD19 /CD20 on B cells that bind to complement molecules attached to antigens and CD4 and CD8 on T cells that bind to regions of the antigen MHC molecule and help in signal transduction. C28 on naïve T-cells interact with ligands CD80 and CD86 for the activation of T-cell.

4. Describe lipid rafts and explain how the relation with B and T cell antigen receptors.
Lipid rafts are specialized regions of lymphocyte membrane. They are ordered, detergent-insoluble, cholesterol- and sphingolipid-rich membrane regions. B-cells signaling cascade is initiated by the phosphorylation of receptor molecules Igα and Igβ produce by raft associated tyrosine kinase Lyn. TCR signaling cascade is initiated by the tyrosine kinase Lck.

5. Explain the activation of Src-family kinases in tyrosine phosphorylation.
SCR-family kinase is important in the early steps of activation of T and B cells. Src-family kinases are inactive configuration by the binding of phosphorylated tyrosine with SH2 domain. On cell activation tyrosine phosphatase removes the inhibitor and Src family kinase partially unfolds. Src-kinase is fully activated when it self phosphorylates on a second activating tyrosine residue.

6. Describe adapter proteins. List the common domains of adapter proteins.
Adapter proteins bid to specific motifs or domains on proteins or lipids. They link one to the other and bring substrates within range of enzymes and meditate the redistribution of molecules. Adapter proteins possess multiple surface domains with precise binding specificity. They participate in protein scaffold, which provides structural framework for signaling cascade. Some domains in adapter proteins are the SH3 that binds to clusters of proline residues and the pleckstrin homology domain (PH) that binds to phosphatidyl inositol triphosphate.

7. Define phosphatidyl inositol bis-phosphate
Phosphatidyl inositol bis-phosphate (PIP2) is a component to of the inner face of the plasma membrane and is phosphorylated by phosphatidyl inositol-3-kinase (PI3 kinase) to form phosphatidyl inositol tris-phosphate (PIP3), which serves as a binding site for proteins bearing PH domain.

8. Explain the process that causes an increase in calcium concentration in the cytoplasm.
PIP2 is hydrolyzed by phospholipase C cleaving inositol triphosphate (IP3) from diacylglyerol (DAG) backbone. IP3 is released into the cytoplasm and interact with IP3 receptor that induces the released of stored calcium ions. Calcium ions double the positive charge and size of radius allowing them binding to cellular proteins. The most important calcium biding protein is calmodulin (CaM), which consist of a dumbbell shape protein that binds four calcium ions in its globular subunits, activates different cellular proteins.

9. Explain the PLC pathway.
Tyrosine phosphorylation reduces CD3 receptor in the localization of protein LAT to the membrane. LAT is phosphorylated and PLCγ1 bind to LAT. As a result PLCγ1 is localized to cell membrane then is activated by tyrosine phosphorylation by the receptor Lck and a second tyrosine kinase Itk. PLCγ1 mediates the cleavage of PIP2 to IP3 and DAG, which remains in the membrane and binds and activates an enzyme protein kinase C (PKC).

10. Describe Ras and the Ras pathway.
Ras is a G-protein that binds to GTP making it capable of binding to serine kinase. Ras is able to hydrolyze GTP to GDP and transmit a positive signal to downstream kinase.
Ras pathway stars when B and T cell are activated, then DAG binds to Ras-GRP that then recruits GEF, SOS. SOS binds to Ras and it induces Ras to bind GTP. Ras binds to members of serine kinase enzymes that phosphorylate one another. RasGTP binds to MAPKKK Raf that stimulates its serine activity. Raf activates MAPKK that will phosphorylate substrate Erk. Erk phosphorylates and activates Erk-1 that will activate Fos. Fos and Jun form AP-1 factor that facilitates the transcription of IL-2.

11. Describe NF-kB and the activation pathway.
NF-kB is heterodimeric transcription factor that binds to the inhibitor of NF-kB (IkB) protein. It is important in the control of proteins for the functioning of innate and adaptive immune system. NF-kB mediates the transcription of proinflammatory events. The pathways that activate NF-kB culminate in the destruction of NF-kB, IkB. The pathway begins when DAG recruits PKCθ to the membrane. PKCθ phosphorylates adapter proteins that recruit TRAF6, which is partially activates IKK. The IKK is fully activated when is phosphorylates and ubiquitinated. IkB is phosphorylates by the phosphorylation of IKK, this degrades the IkB. NF-kB is freed and activates the transcription of target genes.

12. Define immunoglobulin domain.
Immunoglobulin domains are three-dimensional structures of immunoglobin and proteins that contains 110 amino acids. They possess βstrands into a pair of β sheets that for a tertiary domain, β sheets contain hydrophobic and hydrophilic amino acids. Immunoglobulin domains are used by Fc receptors, CD2, CD4, CD8 in T cell receptors, TCR and BCR.

13. Describe the structure of antibodies.
Antibodies have two light and two heavy chains. The light chain is bound by heavy chain by s disulfide bond that form heterodimer. Antibodies form a Y shape, and the binding region is formed of amino acids form the heavy and light chain. The base of the Y consists of C-terminal domains of the heavy chain. The antibody consists of three regions joined by a hinge, which is susceptible to proteolytic cleavage by papain. The antibody can be fragmented into Fab region and the Fc region. Fab regions are two identical fragments that have the antigen-binding specificity and can bind to antigen. The Fc region is identical for all antibodies of the same class and can crystallize easy and binds to the Fc receptors on phagocytic cells.

14. Contrast the major classes of antibody light chains.
The N terminal half of the light chain is called variable and the less variable region is called constant. The constant regions are kappa and lambda chains. Lambda region is divided into lambda 1, 2 3 and 4 based on amino acid substitutions. In light chain are region of hypervariability that interact with the binding of antigen called CDRs.

15. List the major classes of antibody heavy chains.
The five classes of antibody heavy chains are mu, delta, gamma, epsilon, and alpha. The heavy chain has a constant region called isotype that determines the class. Antibodies of the mu isotype are IgM, delta is IgD, gamma is IgG, epsilon is IgE, and alpha is IgA. Isotypes can be divided into sub-isotypes such as alpha can be alpha 1 and alpha 2 thus IgA1 ad IgA2.

16. Describe plasmacytomas.
Plasmacytomas are tumor of plasma cells. Plasma cells are the end stage of B cell differentiation and are the cells located in the bone marrow. Plasmacytomas refers to a single clone cell of plasma cell becomes cancerous cell located in the single bone. It secretes large amounts of antibodies into the serum and tissue fluids, only secreting the light chains.

17. Describe the antigenic determinant and name some of the types of antigenic determinant.
Antigenic determinant are region of an antigen that contact with the antigen-combining region on an antibody. This means that antigenic determinant is antibodies that recognize antibodies. A type of antigenic determinant is anti-isotype antibodies that directed to the constant region of one heavy or light chain class, thus it bids only to a single antibody constant region class or subclass. Other type of antigenic determinant is anti-allotype antibodies that immunize an individual of one species with antibodies from a second animal of the same species bearing an allele. Antibodies that are against antigen binding site are called anti-idiotypic antibodies. They recognize antigenic determinant of a particular combining site, it will have characteristics made up of residues from heavy and light chains.