immunology: parham's the immune system chapter 2- antibodies and b cell diversity

note: i switched from janeway's "immunobiology" to parham's "the immune system" for its conciseness (30 pages per chapter vs. 50 pages)

this chapter introduces b cells and antibodies and the way that they are produced before encountering antigen, and the way that they are modified after encountering antigen. antibodies are y-shaped molecules which are made up of 2 "heavy" chains and 2 "light chains". each of these chains has a constant region, all 4 of which make up the stem of the y, and a variable region, which make up the two arms of the y (one light chain variable region and one heavy chain variable region per arm). the variable region at the arms of the y contain 3 hypervariable regions that are the binding sites for antigen. antibodies are expressed either on the surface of b cells, where they are bound with a hydrophobic anchor at the carboxy terminus of the constant region, or as free floating molecules.

the production of antibodies in naive b cells is designed to make an incredible diversity of structure in the variable regions of the antibody. the more diverse the antibody repertoire is, the more likely it will bind to a antigen, and thus the process of producing variability is introduced in the production of antibodies in several different places: initially during random recombination of gene segments, also in junctional diversity, then through somatic hypermutation.

while genes for other proteins are transcribed from continuous sections of DNA (loci) from which DNA might be spliced out, the DNA for antibody molecules is represented in gene segments, in which there are multiple varied choices for each section of the gene. for example, for each light chain there are two gene segments required to make the variable region; a V segment and a J segment. there are 30 such V segments and 5 J segments to choose from, resulting in 180 possible combinations of the variable region for the light chain. the heavy chain has more possible segments and yet another segment, D, which adds more variability and results in about 10,000 possible configurations. furthermore, the unique combination of light chain plus heavy chain variable regions represent another source for variability.

when the junctions between these gene segments are formed during recombination, further variability is added by enzymes that add palindromic sequences as well as random nucleotides between the gene segments. the antibody can then be produced and expressed on the b cell surface. the first antibodies that are produced are IgG and IgM- classifications of antibodies based on their constant region.

somatic hypermutation occurs after the b cell has encountered antigen- this involves both a proliferation of b cells, and random mutation / nucleotide substitution in the variable region of the antibody. this produces large quantities of b cells with slightly different variable regions, some of which have a higher affinity for the antigen than the original b cell antibody. this b cell is positively selected for in a process called affinity maturation and the higher affinity antibody is produced in greater quantities.

a b cell can receive signals from cytokines to "class switch" its antibodies, which refers to changing the "constant" region of the antibody (the stem of the y). the variable region is the same, which means the antibody still has the same antigen specificity; however the effector actions and role in the body can be different. for example, IgM is the first antibody produced, is relatively inflexible and forms a pentameric ring. IgA is present in epithelial linings and secretions and the lumen of the gut. IgG is the most common antibody present in the blood and acts directly on antigens to neutralize or opsonize for phagocytosis. IgE is specialized to stimulate mast cells during inflammation or infection.

questions
1. what are the five classes of antibodies?
2. what is the most common antibody?
3. the chains in immunoglobulins are linked by...
4. describe the middle portion of an IgG molecule.
5. what are the kappa and lambda isotypes?
6. what are hypervariable regions?
7. how many hypervariable regions are there per variable domain?
8. what is the antigen binding site composed of? what else are they called?
9. what is an antigenic determinant or epitope?
10. what is a multivalent antigen?
11. what is the difference between a linear and discontinuous epitope?
12. what sort of forces does binding of antigen to antibody depend on?

13. where and when in a b cell's development does rearrangment of gene segments for antibody production occur?
14. what are the types of gene segments that encode the variable regions of the light and heavy chains?
15. what are the main differences between the gene segments that code for the variable sections of the antibody?
16. what is somatic recombination?
17. describe the difference between somatic recombination of a light chain vs. a heavy chain.
18. approximately how many different arrangements of gene segments are possible for light vs. heavy chains?
19. what are RSS's?
20. what is the 12/23 rule for RSS's?
21. what is the RAG?
22. what is the difference between the coding joint and the signal joint?
23. what is meant by "junctional diversity"?
24. what is unique about IgM and IgD?
25. what is allelic exclusion?
26. what are Ig-alpha and Ig-beta?

27. what happens to IgM and IgD upon the b cell's encounter with antigen?
28. what is the main difference between membrane bound and secreted immunoglobulins?
29. what is somatic hypermutation?
30. what is the frequency of mutation/nucelotide substitution in somatic hypermutation?
31. what is affinity maturation?

32. what are the characteristics of IgM?
33. what are the characteristics of IgG?
34. what are the characteristics of IgA?
35. what are the characteristics of IgE?

answers
1. IgA, IgD, IgE, IgG, IgM
2. IgG
3. disulfide bonds.
4. it is a relatively flexible "hinge" region that can be cleaved proteolytically.
5. a the class of immunoglobulin based on the light chain classification in the constant region.
6. regions on the exposed tip of variable domains that have a particularly diverse expression of amino acids.
7. 3
8. the combining of the hypervariable region from the variable domains of both the light and heavy chains. also called complementary determining regions (CDR).
9. the part of an antigen that the antibody binds to
10. an antigen that has more than one epitope.
11. linear is when the CDR binds to adjacent amino acids and discontinuous is when the CDR binds to amino acids that have been brought together by the antigen's chain folding.
12. noncovalent bonds such as hydrogen bonding, van der waal's forces, salt bridges, etc

13. in the bone marrow, early in b cell development.
14. for light chain: variable and joining gene segments. for heavy chain: variable, joining, and diversity gene segments.
15. the sequences that encode the first and second hypervariable regions.
16. the joining of gene segments to form the heavy or light chains.
17. for a light chain only one recombination is required; between the V and the J segments. for a heavy chain two recombinations are required: between the J and D, then the J/D to the V segment.
18. about 300 for light and 10,000 for heavy.
19. recombinant signal sequences, the gene sequences that flank the gene segments.
20. an RSS has either a 12 or 23 long base pair spacer in its middle; a 12 RSS can only be combined with a 23 RSS- this allows the different gene segments to be joined correctly to each other, in the right order and sequence.
21. the recombinant activating genes
22. after recombination, the coding joint is the joint between the adjoined gene segments whereas the signal joint is the loop of base pairs that was excised out between the gene segments.
23. junctional diversity is introduced in the "hairpin" that is formed when gene segments are combined by the RAG complex. the hairpin is then spliced and P (palindromic) and N nucleotides (added randomly) are added in, increasing the diversity of gene sequence in the third hypervariable region.
24. these are immunoglobulins that are produced and expressed first and simultaenously by the naive b cell before encountering antigen.
25. every B cell has two copies, or alleles, of the heavy or light chain locus which can be rearranged to produce a particular immunoglobulin. instead of drawing from both alleles, each B cell only uses one.
26. the transmembrane proteins that freshly produced immunoglobulins associate with in the endoplasmic reticulum which form a complex that bind to the b cell membrane surface. the Ig-alpha and beta proteins have longer tails which extend into the cytoplasm which are involved in intracellular signalling during antigen binding.

27. they are expressed in the secreted form instead of the membrane bound form.
28. the membrane bound form has a hydrophobic anchor on the carboxy terminus of the heavy chains, allowing it to stay on the cell membrane.
29. a process that the b cells undergo after encountering antigen where random nucleotide mutations occur in the variable regions of both the light and heavy chains, producing a great diversity of "mutant" immunoglobulin molecules, some of which have an even higher affinity for antigen than the original.
30. one mutation per cell division, more than a million times the normal mutation rate for a gene.
31. the process by which the b cells which bear mutant immunoglobulins produced by hypermutation which have a higher affinity for antigen are selected for and proliferate.

32. IgM is the first antibody produced by the b cells in response to pathogen and is often in the pentameric form, where it has less flexibility but more binding sites for antigen.
33. IgG is the most common antibody found in circulation and tissues. it is smaller than IgM and has a flexible hinge region, allowing the Fab regions to move indepently. it also has more effector actions than IgM, such as opsonization and activating the complement system. it can also pass through the placenta.
34. IgA is the principal antibody secreted by the lymph tissue into the lumen of the gut, as well as other secretions such as tears and sweat. it is often in the dimeric form.
35. IgE is the antibody which is highly specialized to stimulate mast cells during inflammation, causing it to release its histamine and heparine granules.