# Lecture 19: Adaptive Immunity
## Microbiology
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## Learning Objectives
By the end of this lecture, students will be able to:
1. Distinguish between innate and adaptive immunity in terms of specificity, memory, and timing
2. Describe the development, activation, and effector functions of T lymphocytes (CD4+ and CD8+)
3. Explain antigen processing and presentation via MHC class I and MHC class II pathways
4. Describe the development, activation, and effector functions of B lymphocytes
5. Explain the structure and function of antibodies and the five immunoglobulin classes
6. Distinguish between humoral and cell-mediated immunity and explain when each predominates
7. Describe immunological memory and the basis of primary vs. secondary immune responses
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## Lecture Content
### I. Overview of Adaptive Immunity
Adaptive immunity, also called **acquired** or **specific** immunity, is distinguished from innate immunity by four key features. **Specificity** means that receptors recognize particular antigenic epitopes with extraordinary precision. **Diversity** arises from the enormous repertoire of antigen receptors generated by somatic gene rearrangement. **Memory** enables a faster and stronger secondary response upon re-exposure to the same antigen. **Self/non-self discrimination** is maintained through clonal deletion and anergy, which eliminate or silence self-reactive lymphocytes and establish immunological tolerance.
The adaptive immune system takes **days to weeks** to mount a primary response, but secondary responses occur much more rapidly, within one to three days. Adaptive immunity operates through two complementary arms: **humoral immunity**, mediated by B cells and the antibodies they produce, which targets extracellular pathogens and toxins, and **cell-mediated immunity**, mediated by T cells, which targets intracellular pathogens and abnormal cells.
### II. Antigens and Epitopes
An **antigen** is any molecule that can be recognized by the adaptive immune system. An **immunogen** is an antigen capable of eliciting an immune response; all immunogens are antigens, but not all antigens are immunogens. The **epitope (antigenic determinant)** is the specific portion of an antigen recognized by a lymphocyte receptor or antibody. **B cell epitopes** can be conformational (dependent on three-dimensional shape) or linear, and they are recognized on native molecules. **T cell epitopes** are short linear peptides of 8--25 amino acids that are presented by MHC molecules. A **hapten** is a small molecule that is antigenic but not immunogenic on its own; it must be coupled to a carrier protein to elicit an immune response. Penicillin is a classic example of a hapten.
### III. Antigen Processing and Presentation
#### A. MHC Molecules
The **Major Histocompatibility Complex (MHC)** encodes cell surface glycoproteins that present peptide antigens to T cells. In humans, this is known as the **HLA (Human Leukocyte Antigen)** system, located on chromosome 6.
**MHC class I** molecules (HLA-A, HLA-B, HLA-C) are expressed on **all nucleated cells** and present **endogenous peptides** -- derived from cytoplasmic proteins, whether self or viral -- to **CD8+ T cells**. Their structure consists of an alpha chain with alpha-1, alpha-2, and alpha-3 domains plus beta-2-microglobulin, with the peptide-binding groove formed between the alpha-1 and alpha-2 domains. They present peptides of 8--10 amino acids.
**MHC class II** molecules (HLA-DP, HLA-DQ, HLA-DR) are expressed primarily on **professional antigen-presenting cells (APCs)** -- dendritic cells, macrophages, and B cells -- and present **exogenous peptides** from phagocytosed extracellular pathogens to **CD4+ T cells**. Their structure consists of an alpha chain and a beta chain, with the peptide-binding groove formed between the alpha-1 and beta-1 domains. They present larger peptides of 13--25 amino acids. MHC molecules are **highly polymorphic**, ensuring population-level diversity in antigen presentation.
#### B. MHC Class I Pathway (Cytosolic/Endogenous)
In the MHC class I pathway, cytoplasmic proteins (whether self or viral) are degraded by the **proteasome** into peptide fragments. These peptides are transported into the ER by **TAP (Transporter Associated with antigen Processing)** and loaded onto MHC I molecules with the assistance of tapasin, calreticulin, and ERp57. The peptide-MHC I complex is then transported through the Golgi to the cell surface, where it is recognized by **CD8+ cytotoxic T cells (CTLs)**.
#### C. MHC Class II Pathway (Endosomal/Exogenous)
In the MHC class II pathway, extracellular antigen is internalized by endocytosis or phagocytosis into an APC and degraded in **endosomes and lysosomes** by acidic proteases such as cathepsins. Meanwhile, MHC II molecules are synthesized in the ER with the **invariant chain (Ii/CD74)** blocking the peptide groove. The MHC II-Ii complex is transported to endosomes, where the invariant chain is degraded, leaving the **CLIP** fragment in the groove. **HLA-DM** then catalyzes the exchange of CLIP for the antigenic peptide. The loaded peptide-MHC II complex is transported to the cell surface for recognition by **CD4+ helper T cells**.
#### D. Cross-Presentation
Dendritic cells have the unique ability to load exogenous antigens onto MHC class I molecules, not just MHC class II. This process, called **cross-presentation**, allows activation of CD8+ T cells against pathogens that do not directly infect dendritic cells and is critical for antiviral and antitumor immunity.
A side-by-side comparison of MHC class I and MHC class II antigen processing pathways. Left panel (MHC I pathway): A virus-infected cell with viral proteins in the cytoplasm; proteasome degrades proteins into peptides; TAP transporter shuttles peptides into the ER; peptides loaded onto MHC I molecules; peptide-MHC I complex travels through the Golgi to the cell surface; a CD8+ T cell recognizes the complex via its TCR and CD8 co-receptor. Right panel (MHC II pathway): A dendritic cell phagocytoses a bacterium; bacterium degraded in phagolysosome; MHC II with invariant chain (Ii) travels from ER to the endosome; Ii is cleaved leaving CLIP; HLA-DM exchanges CLIP for bacterial peptide; peptide-MHC II complex reaches the cell surface; a CD4+ T cell recognizes the complex via its TCR and CD4 co-receptor. Labels clearly indicate key molecules at each step.
### IV. T Lymphocytes
#### A. T Cell Development
T cell precursors migrate from the bone marrow to the **thymus** for maturation. **Thymic selection** ensures that only functional, self-tolerant T cells enter the periphery. **Positive selection** occurs in the cortex: T cells that can recognize self-MHC molecules survive, while those that cannot undergo apoptosis, ensuring MHC restriction. **Negative selection** occurs in the medulla: T cells that bind self-MHC/self-peptide complexes too strongly are deleted, preventing autoimmunity through central tolerance. The transcription factor AIRE (autoimmune regulator) drives expression of tissue-specific antigens in the thymus to ensure thorough negative selection. Mature naive T cells -- either CD4+ or CD8+ -- exit the thymus and circulate through secondary lymphoid organs.
#### B. T Cell Activation (Two-Signal Model)
T cell activation requires at least two signals. **Signal 1** is provided when the TCR recognizes a peptide-MHC complex on an APC, establishing specificity. **Signal 2** is the co-stimulatory signal: **B7 (CD80/CD86)** on the APC binds **CD28** on the T cell. Without signal 2, the T cell becomes **anergic** (functionally unresponsive), a mechanism of peripheral tolerance. **Signal 3** consists of cytokines from the APC that direct T cell differentiation into specific functional subsets. Successful activation leads to clonal expansion and differentiation into effector and memory T cells.
#### C. CD4+ Helper T Cell Subsets
CD4+ T cells differentiate into several functional subsets depending on the cytokine environment. **Th1** cells, induced by IL-12 and IFN-gamma, produce IFN-gamma and TNF-alpha. They activate macrophages for killing of intracellular pathogens such as those causing tuberculosis and listeriosis, and they promote cell-mediated immunity. **Th2** cells, induced by IL-4, produce IL-4, IL-5, and IL-13. They help B cells produce IgE, activate eosinophils, and are important for defense against helminths, though they are also involved in allergic responses. **Th17** cells, induced by IL-6, TGF-beta, and IL-23, produce IL-17 and IL-22. They recruit neutrophils and defend against extracellular bacteria and fungi, especially at mucosal surfaces, but are also implicated in autoimmune diseases.
**Tfh (T follicular helper)** cells reside in germinal centers and are essential for B cell activation, class switching, and affinity maturation. They express CXCR5 and produce IL-21. **Treg (regulatory T cells)** express the transcription factor FoxP3 and produce IL-10 and TGF-beta. They suppress excessive immune responses, maintain self-tolerance, and prevent autoimmunity and immunopathology.
#### D. CD8+ Cytotoxic T Lymphocytes (CTLs)
CD8+ CTLs recognize peptide-MHC I complexes on infected or abnormal cells and kill their targets through two principal mechanisms. The **perforin/granzyme pathway** involves perforin forming pores in the target cell membrane, through which granzymes enter and activate caspases, triggering apoptosis. The **Fas/FasL pathway** involves FasL on the CTL binding Fas on the target cell, initiating a caspase cascade that leads to apoptosis. CTLs are critical for defense against viruses, intracellular bacteria, and tumors, and they require CD4+ T cell help for full activation and the formation of durable memory.
### V. B Lymphocytes and Humoral Immunity
#### A. B Cell Development and Activation
B cells develop and mature in the **bone marrow**, where each cell comes to express a unique **B cell receptor (BCR)** -- a membrane-bound immunoglobulin, initially IgM and IgD.
**T-dependent activation** by protein antigens proceeds through a coordinated series of steps. The BCR binds antigen and internalizes it. The antigen is processed and presented on MHC II. A Tfh cell recognizes the peptide-MHC II complex and provides co-stimulation through the CD40L-CD40 interaction along with cytokines. The B cell is activated and undergoes clonal expansion. Within the **germinal center**, somatic hypermutation introduces point mutations in the variable regions of the immunoglobulin genes, and clones with higher-affinity receptors are selected, a process known as **affinity maturation**. Simultaneously, **class switch recombination** (isotype switching) changes the constant region from IgM to IgG, IgA, or IgE. B cells ultimately differentiate into **plasma cells** (dedicated antibody-secreting factories) and **memory B cells** that persist for rapid responses upon re-exposure.
**T-independent activation** occurs with polysaccharides, LPS, and other antigens with repeating epitopes that can cross-link multiple BCRs, activating B cells without T cell help. This response produces mainly IgM with limited class switching and no affinity maturation. It is particularly important for responses to encapsulated bacteria.
#### B. Antibody Structure and Function
**Immunoglobulins (Ig)** are Y-shaped molecules composed of two identical **heavy chains** and two identical **light chains** (kappa or lambda). The **variable regions (V)** at the tips of the Y form the antigen-binding sites (the Fab region), with two binding sites per monomer. The **constant regions (C)** define the isotype or class and determine effector function (the Fc region). A hinge region between Fab and Fc provides flexibility.
**Five classes of immunoglobulins** exist, each with distinct properties. **IgG** is the most abundant antibody in serum (approximately 75%), crosses the placenta to provide passive immunity to the fetus, and mediates opsonization, complement activation via the classical pathway, and ADCC. Four subclasses (IgG1--IgG4) exist. **IgM** is the first antibody produced in a primary response. In serum it circulates as a pentamer with 10 antigen-binding sites, making it an excellent complement activator, but it does not cross the placenta. **IgA** is the predominant antibody in mucosal secretions, where it exists as a dimer (secretory IgA) and protects mucosal surfaces. It is found in saliva, tears, breast milk, and GI secretions. **IgE** has the lowest serum concentration and binds to Fc-epsilon-RI on mast cells and basophils, mediating type I hypersensitivity (allergic reactions) and defense against helminths. **IgD** is co-expressed with IgM on naive B cells and plays a role in B cell activation, but has low serum levels.
#### C. Antibody Effector Functions
Antibodies protect the host through several mechanisms. **Neutralization** involves antibodies binding to toxins, viruses, or bacterial adhesins and blocking their biological activity. **Opsonization** occurs when IgG coats pathogens, enhancing their phagocytosis via Fc receptors on phagocytes. **Complement activation** is triggered when IgM and IgG (especially IgG1 and IgG3) activate the classical pathway via C1q binding. **ADCC** occurs when IgG-coated target cells are recognized by NK cells via Fc-gamma-RIII (CD16), leading to target cell killing. **Mucosal immunity** is provided by secretory IgA, which prevents microbial attachment and entry at mucosal surfaces. **Neonatal immunity** is conferred by maternal IgG crossing the placenta (mediated by FcRn) and IgA in breast milk protecting the infant gut.
A detailed diagram of antibody structure and the five immunoglobulin classes. Panel A: Structural anatomy of an IgG molecule -- two heavy chains and two light chains linked by disulfide bonds; labeled Fab region (variable domains VH and VL forming the antigen-binding site), Fc region (constant domains CH2 and CH3), hinge region. Panel B: Comparison of the five Ig classes arranged left to right -- IgG (monomer, most abundant, crosses placenta), IgM (pentamer with J chain, first produced, best complement activator), IgA (dimer with J chain and secretory component, mucosal defense), IgE (monomer, bound to mast cells, allergy and anti-helminth), IgD (monomer, on naive B cell surface). Each class includes key properties listed beneath. Panel C: Antibody effector functions illustrated -- neutralization (antibody blocking toxin from binding receptor), opsonization (IgG coating bacterium, phagocyte binding via Fc receptor), complement activation (IgM on bacterial surface, C1q binding), ADCC (IgG on target cell, NK cell binding via CD16).
### VI. Primary and Secondary Immune Responses
The **primary response** occurs upon the first encounter with an antigen. After a lag period of 7--14 days, detectable antibody appears, with IgM produced first and followed by IgG as class switching occurs. The primary response generates a lower antibody titer and lower-affinity antibodies, but it also generates memory B and T cells.
The **secondary (anamnestic) response** occurs upon re-exposure to the same antigen. It has a faster onset (1--3 days) and produces antibody at a 10- to 100-fold higher magnitude. The response is predominantly IgG (already class-switched) and of higher affinity due to prior affinity maturation. Memory cells are long-lived, persisting for years to decades. This differential between primary and secondary responses is the immunological basis for **vaccination**.
### VII. Integration of Innate and Adaptive Immunity
Innate immunity provides the **initial defense** and critically shapes the adaptive response. **Dendritic cells** serve as the essential bridge: they detect PAMPs, process antigen, migrate to lymph nodes, and activate naive T cells. The cytokine milieu produced by innate cells determines which T helper subset will differentiate: IL-12 from macrophages and DCs drives Th1 development, IL-4 from basophils drives Th2 development, and IL-6 combined with TGF-beta drives Th17 development.
In return, adaptive effector mechanisms amplify innate killing. Th1-derived IFN-gamma activates macrophages for enhanced microbicidal activity. Antibodies opsonize pathogens for more efficient phagocytosis and activate complement. Feedback regulation through Tregs and anti-inflammatory cytokines (IL-10, TGF-beta) limits immunopathology and ensures that the response is proportionate to the threat.
A flowchart showing the integration of innate and adaptive immunity during a bacterial infection. Timeline across the top: 0-4 hours (innate barriers), 4-96 hours (innate cellular response), 1-2 weeks (adaptive response). Left section: bacteria breach epithelial barrier; tissue-resident macrophages and dendritic cells detect PAMPs via TLRs; macrophages phagocytose bacteria and release cytokines (TNF-alpha, IL-1, IL-6, IL-12); neutrophils are recruited. Center section: dendritic cells carrying antigen migrate through lymphatics to the draining lymph node; present peptide-MHC II to naive CD4+ T cells (signal 1 + signal 2); IL-12 drives Th1 differentiation. Right section: Th1 cells produce IFN-gamma to activate macrophages; Tfh cells help B cells in germinal centers; B cells undergo class switching and affinity maturation; plasma cells secrete IgG antibodies; IgG opsonizes remaining bacteria; memory T and B cells generated. Arrows throughout show cytokine communication between the two arms.