BMS 545 Immunology Lecture Notes PDF

WELCOME! BMS 545 IMMUNOLOGY OCTOBER 18, 2024   No more true “homework” until Module 4  Office hours back to normal!  Tues 4-5 pm virtual  Thurs 4-5 pm in-person  I will actually be following the textbook...

WELCOME! BMS 545 IMMUNOLOGY OCTOBER 18, 2024   No more true “homework” until Module 4  Office hours back to normal!  Tues 4-5 pm virtual  Thurs 4-5 pm in-person  I will actually be following the textbook order of the B ANNOUNCEMENTS cell chapters  Chapter 4 is Antibody Development  Chapter 6 is B Cell Development  Chapter 9 is B Cell & Antibody Mediated Immunity  We’ll be going through those in order and probably doing antibodies and BCRs this week, then B cell development & activation next week, then B cell effector function (aka B Cell & Antibody Mediated Immunity) after ANTIBODIES! (IN CASE YOU WANTED TO WATCH IT BY YOURSELVES, LINK IN NOTES)  OBJECTIVES  Describe the structure (in detail) of immunoglobulin  Identify heavy & light chains (the names of each), constant regions, variable regions, epitope binding site, disulfide bond, & describe their purpose/significance  Identify the five types of immunoglobulins based on their structure, function, role, appearance, or a combination of the above  Compare & contrast the five types of immunoglobulins  Define the immunoglobulin fragments and their functions  What’s the difference between CDRs from BCRs and TCRs?  Describe the two types of multivalent antigen  List the various ways epitopes can bind & provide examples  Review definitions from PPT Chapter Opener Figure 4.1 Plasma cells secrete antibody of the same antigen specificity as that of the antigen receptor of their B- cell precursor  A mature B cell expresses membrane-bound immunoglobulin (Ig) of a single antigen specificity  When a foreign antigen first binds to this Ig, the B cell is stimulated to proliferate  Its progeny differentiate into plasma cells that secrete antibody of same specificity as membrane-bound Ig  The structural basis of antibody diversity 4-1 Antibodies are composed of polypeptides with variable and constant regions Remember, a B Cell Receptor is a surface bound immunoglobulin, an antibody is a soluble form of that BCR/immunoglobulin!!!!! Figure 4.2 The immunoglobulin G (IgG) molecule  Each IgG molecule consists of two identical heavy chains (green) & two identical light chains (yellow)  Carbohydrate (turquoise) is attached to heavy chains  Variable (V) & constant (C) regions in the IgG molecule  Amino-terminal regions (red) of heavy & light chains are variable in sequence from one IgG molecule to another  Remaining regions are constant in sequence (blue)  In IgG, a flexible hinge region is located between two arms & stem of the Y *carbohydrate is omitted for simplicity Figure 4.3 The Y-shaped immunoglobulin molecule can be dissected using a protease  By using a protease to cleave the hinge of each heavy chain (scissors) & a reducing agent to break the disulfide bonds that connect the two hinges, the IgG molecule is dissected into 3 pieces: 2 Fab fragments & 1 Fc fragment  Fragment with Antigen Binding (Fab)- a proteolytic fragment of IgG that consists of the light chain & amino terminal half of the heavy chain held together by a disulfide bond between the chains  Fc fragment- a proteolytic fragment of an antibody that consists of the carboxy-terminal halves of the two heavy chains disulfide bonded to each other by the residual hinge region  Called Fc because it was the fragment that was most readily crystallized in early studies of IgG antibody structure  In an intact antibody, the part corresponding to the Fc fragment is called the Fc region. Figure 4.4 The flexible hinge of the IgG molecule allows it to bind with both arms to many different arrangements of antigens on the surfaces of pathogens Figure 4.5 The structures of the human immunoglobulin classes  *Differences in length of heavy-chain C regions, locations of disulfide bonds linking the chains, & presence of a hinge region in IgG, IgA, & IgD, but NOT in IgM & IgE  The isotypes also differ in distribution of N-linked carbohydrate groups (turquoise)  Heavy-chain isotype in each antibody is indicated by a Greek letter (where we get their names)  All these immunoglobulins occur as monomers in their membrane-bound form  In their soluble, secreted form, IgD, IgE, & IgG are monomers  IgA forms monomers & dimers, & IgM forms pentamers Yes, you DO need to know this for the exam Figure 4.6 IgG is built from 12 similarly shaped immunoglobulin domains  Immunoglobulin chains are folded into compact & stable protein domains  Polypeptide backbones of the heavy chains (yellow and purple) & the light chains (both red) are shown as ribbons. Each Fab & Fc fragment is made up of four immunoglobulin domains that produce a similarly shaped globular structure  The structural basis of antibody diversity 4-3 The antigen-binding site of an antibody is formed from the hypervariable regions (HV or HVR) of the heavy- and light-chain V domains CDR = HVR!!!! Figure 4.8 The hypervariable regions of antibody V domains lie in discrete loops at one end of the domain structure  Top: variability plot for the 110 positions within the amino acid sequence of a light-chain V domain  (Light chain) Variability- ratio of # of different amino acids found at a position to the frequency of most common amino acid at that position  Maximum value possible for the variability is 400 (square of 20 aka # of different amino acids found in antibodies). Minimum value is 1  Three hypervariable regions (HV1, HV2, & HV3) can be seen (red) flanked by four framework regions (FR1, FR2, FR3, & FR4) (yellow)  Center panel: correspondence of hypervariable regions to 3 loops at end of V domain farthest from C region  The location of hypervariable regions in heavy-chain V domain is similar (not shown)  Hypervariable loops contribute much of antigen specificity of antigen-binding site  One antigen-binding site is located at tip of each arm of antibody molecule  Bottom: location of light-chain V region in Fab part of IgG molecule  REMEMBER CDR?  Complementarity-determining regions (CDR) loops (numbered 1-3 for each chain)- short region of high diversity in amino acid sequence within the variable region of immunoglobulins & TCR chains  There are 3 CDRs (CDR1, CDR2, CDR3) in each variable region, which collectively contribute to the antigen-binding site & determine antigenic specificity  Most variable parts of the variable domains  AKA “Hypervariable regions (HV)”  What’s the difference between CDRs from BCRs and TCRs?  Elements of the Immune System and Their Roles in Defense 1-7 Immunoglobulins (Ig) & T-cell receptors (TCRs) are the antigen receptors of adaptive immunity Comparison of the B-cell receptor (BCR), antibody, & T-cell receptor  The structural basis of antibody diversity 4-4 Antigen-binding sites vary in shape and physical properties Figure 4.9 Two kinds of multivalent antigen (Part 1)  Many soluble protein antigens have several different epitopes, but each is represented only once on the surface of the protein  This allows 4 IgG molecules with different specificities all bind to protein antigen using a single Fab arm Figure 4.9 Two kinds of multivalent antigen (Part 2)  On pathogen surfaces there are numerous copies of the same epitope  This allows many IgG molecules with identical antigenic specificity to bind to multivalent antigen with both Fab arms Figure 4.10 Epitopes can bind to pockets, grooves, extended surfaces, or knobs in antigen-binding sites  Shown are schematic representations of antibodies (blue) binding to 4 different types of epitope (red)  First: a small compact epitope binding to a pocket in the antigen-binding site  Second: an epitope consisting of a relatively unfolded part of a polypeptide chain binding to a shallow groove  Third: an epitope with an extended surface binding to a similarly sized but complementary surface in the antibody  Fourth: the epitope is a pocket in the antigen into which the antigen-binding site of the antibody intrudes. ***Only one Fab arm of each antibody is shown*** Figure 4.11 Linear and discontinuous epitopes  A linear epitope of a protein antigen is formed from contiguous amino acids  A discontinuous epitope is formed from amino acids from different parts of the polypeptide that are brought together when the chain folds.  ALSO A SCIENTIST  Shiv Pillai, MD, PhD  Director- Harvard Immunology PhD program  The Pillai lab has made fundamental discoveries about immune cells called B lymphocytes & the discovery of novel treatments for B cell leukemias & autoimmune diseases  Also studies how immune cells can “go rogue” in autoimmune diseases like systemic sclerosis & IgG4-related disease, in patients with genetic disorders of the immune system, and in COVID-19 and other severe viral infections