Chapter 8 Definitions and Learning Objectives Define the following terms:Proliferation Differentiation Gene rearrangement Exon RAG TdT Repertoire  heavy chain  light chain  light chain Surrogate light chain Pre-BCR Pre-TCR Tolerance RSS Artemis N nucleotides P nucleotides Junctional diversity Allelic exclusion Thymocyte Thymic epithelial cells AIRE DNA ligase Stem cell Pro-lymphocyte Pre-lymphocyte Immature lymphocyte Mature lymphocyte Selection (+/-) Affinity Neglect Germline Alternative splicing V pre-B λ5 B-1 cell B-2 cell RNA processing Transcription Translation Polypeptide Deletion Inversion CD25 Thymic education Thymocytes BtkLearning Objectives - Important concepts to know At the end of this chapter, you should be able to: 1. Describe B and T lymphocyte development, including: a. the stages and checkpoints of lymphocyte maturation b. the receptors and cell surface molecules (if any) present at each stage of development c. where each of the stages of lymphocyte development are taking place (hint: think central or peripheral development) d. at which time(s) during development the lymphocyte can recognize antigen e. the time(s) at which gene rearrangement is occurring f. the time(s) during development which RAG is functional g. the time(s) during development which TdT is functional h. the time(s) when lymphocyte proliferation occurs i. the cell surface markers that can be used to identify lymphocytes in the various stages of development 2. Explain the difference between an immature lymphocyte and a mature lymphocyte. 3. Explain what it means to be a naive lymphocyte versus an effector lymphocyte. Which cells are considered naive and which are considered effectors? 4. Explain the process of negative and positive selection. a. What is the purpose of this type of selection? b. Where is this occurring? (hint: link positive and negative selection to the various stages of lymphocyte development) c. What is the consequence if a lymphocyte binds to self antigen during selection with high affinity and does not subsequently undergo apoptosis?5. Explain the process of VDJ rearrangement. Some important points to consider are: a. What is the purpose of VDJ rearrangement? b. What do “V”, “D”, and “J” stand for? c. What cells can perform VDJ rearrangement? d. What gene loci are used to make each of the receptors? e. What is the importance of the RSS? f. What is the 12/23 rule? g. What enzymes/molecules are required at the various stages of VDJ gene rearrangement (hint: think about what we need to cut, splice, modify, and join the DNA), and what do they do? h. Which gene loci are used first to make the polypeptides? Which gene segments are rearranged and attached together first? What is the product of gene rearrangement? i. What do we mean by a “productive/functional gene rearrangement”? What happens if there is no productive/functional gene rearrangement? (hint: how many tries to we get?) j. How many polypeptides are produced in each of the cells? What polypeptides are required to be made for B cells and T cells? k. What is the difference between the VDJ gene segment and the C gene segment? l. Compare allelic exclusion and light chain isotype exclusion. i. What is allelic exclusion? ii. What is the consequence of allelic exclusion and what does it mean for antigen recognition? iii. List the cells which follow the rule of allelic exclusion and which do not. m. When does VDJ rearrangement take place (in respect to antigen encounter)? Note: It may be helpful to make a chart comparing each of these characteristics among the different cells that can perform VDJ gene rearrangement.6. Identify the difference between an  T cell and a  T cell. 7. Explain the purpose of forming the pre-BCR and the pre-TCR. What components comprise the pre-BCR and pre-TCR? What are the consequences if this is not formed on the first try? What other options, if any, do we have? What happens if these receptors are formed? 8. List the components and function of the surrogate light chain. 9. Describe junctional diversity. a. What is it? b. Why is it important/beneficial in immunology and for the immune response? c. By what mechanism and enzyme is this provided? 10. Explain the function and importance of Btk to lymphocyte development. What disease is associated with a defect in this enzyme? What is the immunologic consequence of this defect? 11. Describe the process, purpose, and consequence of alternative mRNA splicing. 12. Identify the types of mature B cells discussed and explain their differences including location, function, and derivation. What receptors do each of these cells they have on their cell surface? (this will become very important for our discussion on humoral immunity) 13. Discuss the process of negative and positive selection, including: a. Describe what it means for a T cell to be double negative, double positive, or single positive. b. Describe the function of thymic epithelial cells regarding lymphocyte development. c. Describe the function of AIRE and its importance to T cell development. 14. Rationalize how we know if a T cell will become a CD4+ T cell or a CD8+ T cell. As a side, we will talk about tolerance and receptor editing later in the course, but you may wish to make a note of it here so you can come back to it later.Please look up the following information in your textbook: Please read p. 173: Identify why the cytokine IL-7 is important to B and T cell development. What immunodeficiency can result from a defect in one of the components of the IL-7 receptor? What are epigenetics? How does this relate to lymphocyte development? What are some examples of post-translational modifications? Please read the last two paragraphs (beginning with “The movement of cells...”) p.191: Identify the chemokines and chemokine receptors involved in regulating the movement of T cells through the thymus. What approximate percentage of T cells die by apoptosis during thymic education? Why? Please read the section on “Pre-T Cell Receptor” on p.193 and 194: Identify the 4 things that will occur if a pre-TCR is functional (to be filled out next to image 8-14B in your notes). Please read the section on “γδ T Lymphocytes” on p.197: What is the most common gene rearrangement that is usually made first? What type of cell does this produce? γδ T cells provide defense against microbes at what particular region