C2006/F2402 '06 -- Outline for Lecture 22

(c) 2006 Deborah Mowshowitz . Last updated 04/20/2006 04:10 PM.  Handouts: 22A-22C. 22A = Cells involved; clonal selection; 22B = Role of MHC, development of immune response; 22C = Antibody and gene structure/function.

Minor updates made after the Thursday am lecture. Live lecture covered almost all of this.

I. Specific (= Acquired) Immune Response -- Major cells and Features

    A. Specific Immune system has 2 branches

1. Humoral response -- binding and destruction of antigen done by proteins in "humors" = antibodies in blood and secretions (for ex. milk, tears).

2. Cellular or cell-mediated response -- binding and destruction of antigen done by whole cells bearing a TCR. (TCR on cell surface, not soluble antibody, binds to antigen and triggers a response.)

    B. What Cells are involved?  See handout 22A. White blood cells (leukocytes) -- contain no hemoglobin. WBC divided into two main types

1. Phagocytes -- macrophages, dendritic cells, etc. ( See Purves  18.2 (19.2)). Involved in processing antigens so lymphocytes can respond to them, and/or engulfing (& destroying) antigens identified by the immune system.

2. Lymphocytes. Found in lymph nodes and elsewhere. Do actual production of antibodies and/or execution of cellular immune response.

a. Divided into B and T cells.

(1). Both B & T cells come from same line of stem cells in bone marrow.

(2). B cells mature in bone marrow; T cells in thymus

(3). B cells produce & secrete antibodies. Major players in humoral response.

b. There are 2 types of T cells

(1). Helper T's (TH)

(a). These are required for function of both TC's and TH's . (For details see texts.)

(b). Usually have protein called CD4 on their surface. Therefore said to be CD4+

(c). HIV binds to CD4. Therefore CD4 (accidentally) acts as an HIV receptor (there are other co-receptors) -- allows HIV to enter helper T cells. HIV infection --> loss of helper T's --> complete loss of immune function. (See Purves 18.21 & 22).

(2). Cytotoxic T's (CTL or TC )

(a). Responsible for destructive part of cellular immune response.

(b). Usually have protein called CD8 on their surface. Therefore said to be CD8+

(3). T cells have TCR's on their surface -- TCR's are not secreted or released from cell surface.

    C. What are the Important Features to explain?

1. Specificity & Diversity -- each Ab or TCR is directed against one epitope or antigenic determinant (= piece of antigen -- see Purves 18.6 (19.6), and there are many, many different antigens. How can you make so many different Ab's or TCR's, each specific for a particular antigen or piece of it?

2. Memory -- secondary response is faster, larger, better than primary response. In secondary response, make more Ab, Ab is more effective (binds better to Ag because of slight changes in amino acid sequence of Ab), and Ab response lasts longer. (Purves 18.8 (19.8)) How is this done?

3. Tolerance -- can distinguish self/nonself or normal/abnormal -- make Ab only to foreign/abnormal stuff (except in disease states). TCR only directed against infected cells, not normal ones. How does this work?

4. Response is adaptable -- response depends on amount and type of antigen. How do you "know" which antibody (or TCR) to make in response to a particular antigen?

5. How to helper T cells fit in? How do helper T's and cytotoxic T's distinguish their targets?

    D. Major features of 2 branches of specific immune system -- see table below. 

1. Action of B cells to combat infection: Already discussed antibodies as chemical reagents. What are antibodies really needed for physiologically?

B cells release antibody Ab (antibody) binds Ag (antigen -- usually on surface of microbe) trigger destruction of microbes (microbes are engulfed by phagocytes or lysed) often with the help of complement. (See Purves 18.11 (19.12) & table below.)  Allergies are a side effect of this system.

2. Action of  (cytotoxic) T cells

All T cells TCR on surface; TCR's of cytotoxic T's bind to Ag on surface of virus infected eukaryotic cell destroy target cell by triggering apoptosis. Cytotoxic T cells can trigger apoptosis by juxtacrine signaling; alternatively they can use proteins called perforins to make holes in their targets. Then other proteins enter the holes and trigger apoptosis.  Note complement is similar to perforins but works on prokaryotic invaders; perforins work on rogue eukaryotic cells. (See Purves 18.14 (19.15)) This is why grafts fail; foreign cells of graft look like infected (defective?) cells and are destroyed. 

Note: Many texts say perforin lyses cells -- it makes holes in membrane, and then water enters, causing cells to swell and burst. (This is the way complement kills bacteria.) Newer data indicates perforin works to trigger apoptosis.

3. Role of helper T cells -- needed for function of both B and cytotoxic T cells

All T cells TCR on surface; TCR's of helper T's bind to Ag on surface of cells of immune system. (Cells of immune system with Ag on their surface are called APC's or antigen presenting cells.) Interaction helps activate one or both partners -- promotes the immune response. See texts for details.

    E. Table: Summary of Major features of 2 branches of specific immune system

Immune Response Type



Cell involved in Response

B cells

T cells

Protein Made by Cell

Antibody (Ab)

T cell receptor (TCR)*

Location of Protein

In serum, tears, etc. (released by B cell) or on cell surface.

Always on cell surface (attached to T cell)

Protein Recognizes

Free Antigens (Ag) or Ag attached to microbial surfaces

Antigens attached to surfaces of eukaryotic cells #

Aide in killing targets



Usual targets (for killing)

Microbes, soluble proteins

Infected or cancerous cells (for Tc or CTL)

Side Affect


Graft rejection

*T cell receptor is NOT the receptor for T cells -- it is the protein on the T cells that is the receptor for an antigen. It is the receptor of T cells, not the receptor for T cells. (By analogy, antibody attached to B cells is sometimes called "the B cell receptor" or BCR instead of antibody. BCR and TCR both act as receptors for antigen -- they allow antigen to trigger the immune response, as explained below. So they are also referred to as B or T cell receptors for antigen.)

** Complement = a series of proteins found in blood. Activation of complement involves a cascade of activations similar to that involved in blood clotting. Complement binds to antibody-antigen complexes attached to microbes and triggers phagocytosis or lysis of the microbe bearing the complex.

# Antigen must be attached to a euk. cell surface protein called MHC.

II. Clonal Selection -- How do you account for the "important features" listed above?

    A. B cells (See Handout 22A bottom = Purves fig. 18.7 (19.7))

1. Each cell differentiates produces a single type of Ab on surface ("virgin" or "naive" B). Each cell rearranges its DNA during differentiation, so each cell has a unique set of Ab coding genes and makes a unique antibody -- that is, with a unique set of "grabbers."

Note: As B cells mature and specialize, changes in the antibody they make may occur because of alternative splicing and/or additional rearrangements of the DNA. See texts for details. This is why Ab made in secondary response is better at binding Ag.

2. Ab on surface of cell acts as a "trap". Surface antibody (also called BCR or B cell antigen receptor) acts as trap/receptor for Ag.

3. Activation or destruction of B cell is triggered by binding of Ag to surface Ab (BCR)

a. Destruction. If Ag is perceived as "self" cell destroyed or suppressed ( tolerance).

b. Activation. If Ag is perceived as foreign cell divides clonal expansion, further differentiation into

(1). Effector cells -- short lived but secrete lots of Ab destroy or inactivate targets; class of Ab determines fine points. (In earlier lecture we explained how alternative splicing can allow cell to switch from making surface bound Ab to secreted Ab.)

(2). Memory cells -- long lived and more specialized to make Ab; wait for next time (responsible for memory). 

c. Whether antigen is perceived as "self" or "foreign" depends on time of exposure to the antigen (embryonic vs adult) and additional factors. (This turns out to be very complicated, so we are ignoring the "additional factors.")

4. What's the point?

a. Clonal Selection: Each cell makes a little Ab before any Ag present. Each cell makes a different Ab. This antibody stays on the cell surface and acts as BCR = trap for antigen. Ag acts as a trigger -- binding of Ag to "trap" stimulates only those cells that happen to make Ab that binds to that particular trigger. (This is the selection part that accounts for specificity, diversity, and adaptability.)

b. Clonal expansion: The cells triggered by binding of Ag grow and divide   (more) effector cells  & memory cells. Both types of cells make only the antibody that binds to the trigger Ag. (This is the clonal expansion part that accounts for memory & tolerance -- memory when Ag triggers multiplication, and tolerance when Ag triggers destruction or suppression).

5. Why do you need helper T cells? For most antigens, helper T must bind to B cell-Ag complex in order to activate B cell. (Activated cell makes secreted Ab.)

Try Problem 13-4.

    B. T cells -- similar process as with B cells -- DNA rearrangement occurs so one type of protein with unique binding site made per cell -- but there are differences. See texts for details, and handout 22B.

1. DNA rearrangement occurs during development -- therefore one type of protein with unique binding site made per cell.

2. Protein made by T cell is T cell receptor, not Ab. (See Purves fig. 18.13(19.14)). Each T cell makes a unique TCR (also called T cell antigen receptor) due to DNA rearrangements of TCR genes. 

3. T cell receptor always remains on cell surface; never secreted

4. Clonal expansion occurs in response to Ag more T cells -- effector cells & memory cells.

5. Antigen presentation:

a. Antibody will bind to free antigen in solution (or to part of a whole bacterium). TCR will not.

b. TCR only binds to Ag on surface of another (euk.) cell. (See handout 22B).

c. TC vs TH

(1). TC binds to ordinary (euk.) cell with abnormal epitopes on surface   = infected cell; destroys it.

(2). TH binds to immune cell with abnormal epitopes on surface  =  antigen presenting cell (APC). Binding activates the T cell &/or APC. (Promotes the immune response -- details vary depending on type of APC.)

    C. Role of MHC (For pictures see Purves chap. 18 & handout 22D; see also handout 22B, top) -- explains how helper T's and cytotoxic T's distinguish their targets

1. What is it? MHC = very variable surface protein. There are 2 main types, and many  versions of each type.  Each individual has several different genes for each of the two main types of MHC. Each of these genes has  20-40 or even more variants  (alleles). Since there are several genes per person and many different alleles of each gene in the population, there is a lot of variation in the actual MHC  proteins (and DNA) from person to person. These genes, unlike genes for antibodies and TCR's, do not rearrange during development. So there is variation from person to person, but all cells in a single person have the same MHC genes. 

2. Two types of MHC 

a. All nucleated cells have MHC I on their surface.

b. Cells of immune system (phagocytes & B cells) have MHC II on their surface. (Not all T cells have MHC II at all times, & we will assume T cells do not have MHC II.)

3. Ag sticks to MHC -- Small pieces of antigen (epitopes or antigenic determinants) are 'displayed' on the cell surface, stuck to the MHC molecules. (How the pieces get to the cell surface and attached to MHC depends on type of cell; see texts for details.)

4. Role of MHC:  Two types of T's bind to different MHC's (w/ Ag) -- this is how T cells tell immune cells (that have captured Ag) and infected (ordinary) cells apart.

a. Cytotoxic T's (CD8+) bind to euk. cell with Ag + MHC I (said to be "MHC I restricted") on surface -- note target must have MHC I and Ag.

b. Helper T's (CD4+) bind to euk. cell with Ag + MHC II (said to be "MHC II restricted") on surface -- note target must have MHC II and Ag.

c. What binds to what? How does T cell bind to the Ag-MHC complex on surface of euk cell? (See handout 22B.)

(1). TCR binds to variable part of MHC-Ag complex = bind to Ag itself

(2). CD4 or CD8 binds to part of corresponding MHC (I or II).

The point: T cells recognize their targets (in part) by the type of MHC they have -- infected cells have MHC I and immune cells have MHC II.

III. Ab Structure
(See handout 22C or Purves 18.10 (19.11). This topic will probably be abbreviated in lecture, but is included here in detail to make it easier to follow.

    A. V  vs C -- types of Immunoglobulin (Ig).  

1. There are 5 main classes of Antibody -- IgM, IgD, IgG, IgE, and IgA. See table on handout 22C & Purves Table 18.3 (19.2).

2. V & C: Each Ab or Ig is made up of a V section ("variable" region or Vee) & a C section ("constant" region or Cee).

3. Variable region

a. V is specific for Ag. Determines what Ag will be bound = grabbers. 

 b. V is variable due to differences in sequence, not just differences in folding around Ag. 

c. Every Ab or Immunogloblin (Ig) has (at least) 2 grabbers.

d. All grabbers in one Ab are the same.

e. All the antibodies made by one Ab-producing cell have the same V. All the antibodies made by descendents of that cell have very similar V's. (Minor differences are due to somatic mutation; see see advanced texts if you are interested. We will ignore somatic mutation for the rest of this discussion, and assume all the antibodies made by the descendents of one cell have the same variable region.)

4. Constant region 

a. C determines biological effects -- localization of Ab, and what will happen as consequence of binding Ag. (Whether complement will be activated, whether Ab will be found primarily  in blood or secretions, etc.)

b. 5 main types of C regions, therefore 5 main classes of antibody. (For properties of the dif. classes see handout 22C or Purves Table 18.3 (19.2) )

c. The same V's can go with different C's.  (Called "Class Switching")

(1). All the antibodies made by one Ab-producing cell do not necessarily have the same C.

(2).The antibodies made by descendents of a single cell may have different C's. The same variable region can go with different constant regions as B cell clone expands. How is this possible? Need a closer look at Ig structure

    B. H vs L.  See handout 22C or Purves 18.10 (19.11)

1. Every Ig has 2 kinds of chains, L ("light") and H ("heavy"). Light and heavy refer to relative differences in mol. wt. 

2. Basic unit is 2 of each for a total of 4 chains. (For number of basic four-chain units per Ig, see table.)

3. Variable region (grabber) made of parts of each.

4. Each chain has a constant region

a. 2 kinds for L (kappa or lambda) 

b. 5 basic kinds for H (mu, delta, gamma, epsilon or alpha)

c. Hc (constant part of H) determines class (IgM, IgD, IgG, IgE, IgA)

d. Class (determined by Hc) determines location & other aspects of function (see "special properties" in table)

d. Class switching involves the H chains only, not the L chains.

5.   Myelomas & Hybridomas: Ig structure was figured out by studying proteins made by myeloma cells (cancers derived from Ab-producing cells) or hybridomas (hybrids of Ab-producing normal cells and cancer cells). Only way to get large numbers of cells all making the same Ab/Ig.  See texts for significance of hybridomas and monoclonal antibodies.  (Purves 18.12 (19.13))

    C. Classes of Ab and class switching during development of immune response

1. Order of events (see handout 22B, bottom) during immune response

a. First make M, then M + D -- all on surface.

b. Meet Ag primary response: secrete M.

c. Meet Ag a second time secondary response; secretes usually G but can be E or A.

d. All these Ig's combine with same Ag

2. Implications of structure and switching

a. Can make different variable regions -- zillions of them, one for each dif. epitope. So the IgG, for example, in a person is a mixture -- all IgG molecules have the same constant regions but have different variable regions.

b. During differ. stages of immune response, can make Ab with same variable region but different constant region (for H). Can switch class and/or secreted vs. surface. How is this possible?

3. What we already know: How switch from membrane bound to secreted works. Variable part stays same; Hc changes from hydrophobic to hydrophilic by alt. splicing/poly A addition.

4. What we don't know so far: How do you make so many dif. variable regions AND What changes when you switch classes (from IgM to IgG? M to M + D)?  Must be rearrangement of DNA or alternate splicing of RNA. Different solutions at different steps.

IV. Structure of the DNA -- Basis of Class switching and generation of diversity (G.O.D)

    A. Basic idea: genes for H and L are mosaic -- Each "Gene" has several parts. See texts or handout 22C or Purves 18.18 (19.19.)

    B. Switching occurs at DNA and RNA levels. (Switching at DNA level is unique to immune system.)

    C.  How "gene" is divided  -- region coding for each chain has parts for each type of constant region and several parts for variable region.

    D. How DNA is used to make different versions of the same antibody

1. Pre Ag -- rearrange V/D/J region of DNA to make one variable region per naive/virgin B. Alternate splicing allows cell to produce M and D antibodies with same variable region (but different constant region of H chain).  For details see Purves 18-19 (19-20).

2. Post Ag -- Alt splice of RNA and/or further rearrangement of DNA    new mRNA   new version of antibody. Can have either of the following:

a. Rearrangement of DNA gene for H chain with original variable region and a new "constant" region. Make new class of antibody. (See Purves 18.20 (19.21))

b. Alternative splicing mRNA for secreted version of cell surface antibody -- Same H chain except it's missing part that anchors the protein in the plasma membrane. Go from making "BCR" to making secreted antibody.

    C. Summarize G.O.D (generator of diversity) -- how get so many V's?

1. H & L mix and match

2. V parts (V, D, J) mix and match

3. Joins are inexact (when you rearrange the DNA -- when join V to D etc.)

4. Somatic mutation (post Ag) minor changes in V, not C

    D. TCR is similar, except no somatic mutation

    E. Clonal vs. Natural Selection. Note how clonal selection and natural selection compare. In both cases, need to have many variants (diff. antibodies or dif. organisms) to be able to respond to unpredictable environmental challenges. How is this done? In both cases, make many variants and conditions select (promote propagation of) cells making the few suitable Ab (or carrying out a rare, useful function); the rest are wasted. Random generation of variants seems wasteful, but is the biological solution to preparing for change without conscious planning ahead.

V. So how do other cells get differentiated (specialized) to carry out their particular functions?

Cells of the immune system specialize (differentiate) by rearranging their DNA. Cells of the rest of the body specialize in a different way  -- they keep the same DNA but they still make different proteins.  Next two lectures -- how do they do it?