Steps in the Immune Response


Learning Objectives

After successfully completing this unit, the student will be able to:

> B lymphocytes

> Cytotoxic T cells

> Helper T cells

> Suppressor T cells


Part I - The Innate Immune Response

I. Cells of the Immune Response

InnateImmuneCells.png Innate immune cells can be grouped according to when they first become involved in an immune response.

Tissue macrophages and immune dendritic cells exist as sentinels in the peripheral tissues, keeping surveillance for invading pathogens. The macrophage is the key initial player in an innate response, functioning both to eliminate the pathogen and to recruit other innate inflammatory cells.

Neutrophils are attracted to the site of infection by chemokines, macrophage-secreted chemotactic factors that bind to and stimulate specific chemokine receptors on the surface of immune cells. In response to stimulation of their chemokine receptors, circulating neutrophils travel up the chemokine gradient, moving by extravasation. Neutrophils are the main cells seen early in a response to pathogens, and they are the principal cells that engulf and destroy invading micro-organisms. Neutrophils are short lived cells, and they do not re-enter the circulation. The pus that is associated with some types of bacterial infections is largely composed of dead and dying neutrophils.

Circulating monocytes are also attracted to the site of infection by chemokines. As monocytes move into tissues they rapidly differentiate into macrophages and, thus, add to the innate defenses.

II. Pathogen Recognition

Innate immune cells, unlike adaptive immune cells, do not show strict specificity in their recognition of pathogenic microbes. Instead, cells of the inmate immune system recognize and respond to broad classes of invading microbes.

Recognition is initiated when specific pattern recognition receptors, including the well-defined Toll-like receptors (TLRs) on the surface and within the cytoplasm of macrophages, neutrophils and dendritic cells, are triggered by microbe-specific motifs known as pathogen-associated molecular patterns (PAMPs). PAMPs are, in effect, repeating units of danger signals which are common components of specific groups of pathogens.

TLRs are a member of a family of evolutionarily conserved receptors, Toll receptors that were first described in the fruit fly (Drosophila) where it was observed that deficiency of a specific Toll receptor prevented the activity of Drosophila-derived anti-fungal peptides that were required to eliminate fungal infections.


Image source: Cell, Vol. 86, 973 983, September 20, 1996


Different Toll family members were eventually recognized for their involvement in activating anti-bacterial and anti-viral responses. Some of the well characterized human TLRs include,



Although not all the details are known, it appears that the specific combination of pattern recognition receptors triggered on innate immune cells by an invading microbe will determine:

III. Acute Inflammation

Inflammation is an innate immune process that is crucial in combating infection. It is induced by protein cytokines and chemokines that are secreted by innate immune cells which have been activated following binding of microbial components to their pattern recognition receptors (e.g. TLRs).

The hallmarks of an inflammatory response are redness, heat, swelling, and pain. Each of these features reflects a change in local blood vessels.



Source: CDC/ Dr. Heinz F. Eichenwald

Events at Sites of Inflammation

  1. Vasodilation of the microcirculation results in increased blood flow to the infected area. It is responsible for the heat and redness that occurs at sites of inflammation. Increases in local heat can inhibit some pathogens.
  2. Increased permeability of capillaries promotes the movement of fluid and plasma proteins into the interstitium (space between tissue cells), and results in local swelling or edema. Pain is the result of both swelling, which stimulates free nerve endings, and certain plasma proteins. These initial inflammatory events occur within seconds to minutes of infection.
  3. Chemotaxis as neutrophils, monocytes and, sometimes, other white blood cells follow a chemokine gradient and move (extravasate) from small vessels into the infected tissue. One of the key functions of inflammation is to bring effector molecules and cells to the site of infection.
  4. Destruction of pathogens in the tissues occurs by phagocytosis

 Source: ?

Leukocyte Extravasation and Chemotaxis (0:52)

IV. Phagocytosis

IllyaIllich.png Macrophages and neutrophils are phagocytes that engulf and destroy invading microbes and fragments of microbes.The Russian microbiologist, Ilya Mechnikov was the first to observe phagocytosis and to theorize that this process was used by white blood cells to engulf and destroy pathogenic bacteria. In 1908, he received the Nobel Prize in Medicine for his discovery.

Macrophages and neutrophils identify pathogens by means of pattern recognition receptors, such as the TLRs, that recognize repeating patterns of molecules that are unique to microbial pathogens. This recognition triggers the phagocyte to envelope the pathogen in extensions of its plasma membrane and to engulf it internally within large cytoplasmic, membrane-bound vesicles known asphagosomes.

Most microbes are destroyed within the phagosome by mechanisms that include acidification of phagosomal contents or fusion of the phagosome with a lysosome to form a phagolysosome that contains enzymes and other molecules that can breakdown the microbe.


Follow this link to see a video animation explaining phagocytosis.



The video below provides an actual demonstration of phagocytosis.



Part II - The Adaptive Immune Response 

I. Cells of the Adaptive Immune Response

AdaptiveImmuneCells.png If the innate immune response is unsuccessful in eliminating an invading pathogen, a more versatile and specific adaptive immune response is initiated. During this response, resting, naïve T and B cells in the lymph node become stimulated by antigen to proliferate and differentiate into both effector and memory T cells and B cells. Effector cells function immediately to rid the body of the infecting pathogen. In contrast, memory cells do not take part in the ongoing fight against a primary (i.e. first) infection. Rather, they form the basis of immune memory as they remain circulating after the infection is cleared, ready to respond immediately should an attempt at a secondary, re-infection take place. 

Adaptive immunity commences when an immature dendritic cell ingests pathogen within the infected peripheral tissue. The dendritic cell then migrates to the draining lymph node where they present antigenic pathogen peptide in a manner that stimulates resting naïve T cells to proliferate and differentiate into effector and memory CD4+ T helper (Th) cells and CD8+ cytotoxic T cells (a.k.a. cytotoxic T lymphocytes, CTLs). Some effector CD4+Th cells provide, in turn, the help required for antigen-activated B cells to differentiate into antibody producing plasma cells.

The video below is an animation that summarizes the function of dendritic cells in activating T and B cells in lymph nodes. 



Activated effector CD4+ Th cells, CD8+ CTLs, and antibody molecules leave the lymph node and enter the circulation to be transported to the site of infection within peripheral tissues. Antibodies serve to both trigger a system of proteins, the compliment system, to directly lyse bacteria and other microbes, and to flag microbes in such a way that they are more readily targeted by macrophages for phagocytosis.

One of the primary effector functions of CD4+ Th cells in the periphery is to activate macrophages to become more efficient at destroying phagocytized microbes. CD8+ cytotoxic T cells function to kill cells infected with pathogens.


A more recently recognized subset of effector CD4 cells are the CD4+ regulatory T cells (Treg cells). Mounting evidence indicates that Tregs play an important role in inhibiting autoimmune responses

II. Antigens and Epitopes


Antigens are macromolecules are macromolecules such as proteins and polysaccharides (sugars) that are recognized as foreign by the adaptive immune system. T cells, B cells, and antibodies do not recognize entire antigen molecules. Rather, they recognize a small portion of the molecule known as an epitope. A large antigen may have multiple epitopes, each of which is recognized by the surface receptor on a specific clone of T cells or B cells, or by a specific antibody molecule.

Image source: Immunobiology, 5th edition Janeway et al


This hyperlink is to a short video animation that provides an explanation of antigenic determinants (epitopes). 

III. T Cell Receptors, B Cell Receptors, and Antibodies

The antigen receptor on a T cell is called a T cell receptor (TCR) and that on a B cell is called a B-cell receptor (BCR). Each receptor contains an antigen binding site that recognizes a specific antigen epitope and binds to it in a lock-and-key manner.


Image source: Immunobiology, 5th edition Janeway et al

Antibodies produced by a mature plasma B cell recognize the same specific antigen epitope as the BCR on the cell's surface. This is because the BCR on the plasma cell is actually a surface membrane bound form of the antibody that is made by that cell. Antibodies are also known as immunoglobulins and gamma-globulins. They are typically Y-shaped molecules formed from paired heavy and light polypeptide chains. The arms of antibody molecules end in a variable region that, similar to the TCR and BCR, combines with a specific antigen epitope in a lock-and-key manner.

There are five major classes, or isotypes, of antibodies which are defined by the structure of the constant (non-variable) region of their heavy chain, a.k.a. the Fc (Fragment constant) region. The five classes are:

IgG is the most abundant antibody in humans. Each antibody class performs a unique effector function.



Source for both: Immunobiology, 5th edition Janeway et al.


IV. Naïve T Cell and B Cell Activation (Lymphocyte Activation) 

The Generation of an Adaptive Immune Response

Binding of a pathogen-derived antigen epitope to the TCR or BCR on, respectively, a naïve T cell or naïve B cell results in activation of the receptor by stimulating the phosphorylation of tyrosine amino acids within receptor regions known as immunoreceptor tyrosine-based activation motifs (ITAMS). This, in turn, initiates a series of intracellular signaling events that eventually reach the nucleus and stimulate the transcription of genes whose protein products result in the induction of cell proliferation and differentiation. Thus, the end result of activation of a naïve T cell or naïve B cell by a pathogen-derived antigen epitope is: 

  1. Proliferation to produce a clone of cells that have a TCR or BCR with the same antigen specificity (i.e. recognizing the same pathogen-derived epitope) as the original naïve T or B cell.
  2. Differentiation of the naïve T cell or B cell into either an effector or memory, T or B cell.

In a very general way, the immune system recognizes two broad classes of invading pathogens:those that remain extracellular and those that enter cells and reside, for at least part of their lifecycle, intracellularly.

Examples of extracellular pathogens & diseases they cause:

Examples of intracellular pathogens & diseases they cause:

The major response of the adaptive immune system to these two types of pathogens differs and a very broad sense:

Realize, however, that humoral and cell mediated immunity (i.e. responding B cells and T cells, respectively) work in concert to eliminate an infecting pathogen. For example, while antibodies generated by a B cell-mediated response are key in eliminating free, circulating viruses, T cell-mediated immunity is key for destroying a virus once it is within a cell.


Antigen Recognition

The manner in which naïve T cells and naïve B cells are stimulated differs, in part due to differences between the pathogens they encounter (intracellular versus extracellular, respectively). Antibodies bind directly to antigen epitopes on the surface of a pathogen. Structurally, the B cell antigen receptor (BCR) is composed of a transmembrane immunoglobulin molecule containing the same variable region as the antibody it produces. Thus, both the secreted antibody and the BCR of a plasma B cell will bind the same antigen epitope on a pathogen. 

In contrast, binding of the T cell receptor (TCR) to an antigen epitope requires the following series of steps:

  1. The dendritic cell must break down the engulfed pathogen or portion of pathogen into peptide fragments, some of which containing a specific antigen epitope. This is known as antigen processing.
  2. The peptide fragment containing the antigen epitope must next bind to a major histocompatibility complex (MHC).
  3. The antigen epitope:MHC molecule complex is then transported to the surface of the dendritic cell where it can be recognized by a T cell. This process is known as antigen presentation.
  4. Lastly, TCR, in combination with either a CD4 or CD8 surface molecule, then binds the epitope:MHC complex. This binding will elicit a series of intracellular signaling events with the resting naïve T cell that will cause it to proliferation and differentiate into a clone of effector T cells.


Image Source: Immunobiology, 5th edition Janeway et al.

There are two major groups or classes of MHC molecules: MHC class I molecules and MHC class II molecules. In humans, MHC molecules are referred to as human leukocyte antigens (HLA), or simply histocompatibility antigens. Human HLA molecules are products of human major histocompatibility complex (MHC gene locus). There is a great deal of variability between individuals as to the specific collection of HLA antigens that exist on the surface of their cells. T cells are said to be MHC restricted because they will only recognize antigenic peptide (epitope) in the context of a self MHC molecule. 

 Idea.pngTransplantation and HLA Molecules


The HLA antigens are called histocompatibility antigens as they are the surface molecules that determine whether a donor's cells or tissues will be rejected by a transplant patient recipient. If the HLA difference is too great between, for example, a kidney donor and the recipient of that kidney, the recipient's immune system will recognize the kidney graft as foreign and mount an immune response against it that will result in graft rejection. In the case where the donor graft consists of bone marrow, it is possible for the immune cells in the donor bone marrow to recognize recipient tissue as foreign. This condition can lead to graft versus host disease and failure of the bone marrow transplant. HLA typing, or tissue typing, is done to find the closest HLA match between an organ or bone marrow donor and a recipient so as to minimize the possibility of graft rejection and graft versus host disease.

More on HLA typing for bone marrow transplantation

V. T Cell and B Cell Effector Functions

There are two main types of T cells: CD4 positive (CD4+) helper T cells (Th cells) and CD8 positive (CD8+) cytotoxic T cells (CTLs). Aside from differences in effector functions, these two types of differentiated effector cells recognize antigen in slightly different ways. CD4+ Th cells recognize antigenic peptide bound to an MHC class II molecule, and they are said to be class II MHC restricted. In contrast, CD8+ cytotoxic T cells recognize antigen bound to an MHC class I molecule and they are, thus, class I MHC restricted.

CD4+ T helper (Th) cells

While naïve T cells can only be stimulated by antigen presented by a dendritic cell, differentiated effector T cells can also be stimulated by antigen presented by additional types of antigen presenting cells (APC), including macrophages and B cells. Once stimulated, effector T helper cells will provide help and activate adjacent macrophages and/or B cells. They do this by means of both 1) Th cell-secreted cytokines that bind to cytokine receptors on the surface of these cells, and 2) Th cell surface molecules that bind macrophage and B cell surface receptors. Binding of specific macrophage and B cell receptors activates signaling pathways within these cells which stimulate various cellular immune functions. For example, binding of the Th cell cytokine, interferon-gamma (IFN-g) to the IFN-g receptor on the surface of a macrophage stimulates intracellular signaling events that result in enhanced killing of phagocytized bacteria. Binding of the Th cytokines interleukin-4 (IL-4), IL-5 and IL-6 to B cells stimulates the proliferation of those cells and their differentiation into antibody-secreting plasma cells.



Image Source: Immunobiology, 5th edition Janeway et al.

B Cells and Plasma Cells

Antibodies that are produced by differentiated plasma B cells can act in multiple ways to incapacitate and destroy invading microbes. Antibodies can bind and neutralize the effects of toxins produced by pathogenic microbes in a process known as antibody neutralization. Pathogens with antibodies bound to their surface are easily recognized by macrophages which target them for phagocytosis and destruction. This process is called opsonization. Lastly, antibody coated pathogens can activate a system of proteins known as complement proteins that can act either directly to kill the pathogen, or indirectly to promote its ingestion and destruction by macrophages. This is known as complement activation. 


Image Source: Immunobiology, 5th edition Janeway et al.


Video on Opsonization and Phagocytosis of Bacteria



Idea.png Antigenic Drift, Antigenic Shift, and Influenza Virus


Pathogen antigenic epitopes can change, either due to mutation or genomic reassortment, so that they are either poorly recognized or no longer recognized by a previously epitope-specific T cell or B cell antigen receptor, or antibody. The process of change in antigenic epitopes through accumulated mutations is known as antigenic drift. It is this process that is responsible for seasonal influenza epidemics as individuals infected by or vaccinated against influenza one year only have partial immunity to the mutated virus which appears the next year. Specifically, influenza virus undergoes mutation at such a rapid rate that from one year to the next its antigen epitopes are only partially recognized by antibodies generated the year previously, through either natural infection or vaccination. It is the reason why yearly vaccination against influenza is required to maintain an adequate level of protective immunity to the virus. In contrast, antigenic shift is the process whereby reassortment of segments of the genomes of two viruses takes place (e.g. human flu and bird flu). Antigenic shift results in a dramatic change in viral surface epitopes, leaving individuals completely non-immune to the new virus. It is this process that can result in influenza pandemics that can potentially be quite virulent


The following videos explain the process of antigenic drift and antigenic shift.


CD8+ Cytotoxic T Cells (CTLs)

The role of cytotoxic T cells during an immune response is to directly attack and destroy cells infected with an intracellular pathogen, such as a virus. To perform this function, CTLs employ two main proteins,granzymes and perforin that are stored in cytoplasmic vacuoles within the resting CTL. When a CTL encounters an infected cell that is displaying on its surface MHC-bound antigenic peptide, it is stimulated to release perforin into the intracellular space between the CTL and the target cell. Perforin acts to form holes or pores in the surface membrane of the target cell which not only cause direct injury, but also provide a means for granzymes to enter the cell. Granzymes induce target cells to undergo apoptosis (a.k.a. programmed cell death, cell suicide). By killing infected cells, CTLs prevent pathogen replication and new pathogen release.


Cytotoxic T Cells.png

Cytotoxic T Cells2.png

Source: Immunobiology, 5th edition Janeway et al


Source: Human Biology by Sylvia Mader, McGraw Hill Publishers


CTL Killing of Virus Infected Cells

See also:



VI. Immune Memory 

A very important characteristic of the adaptive immune response is that when naïve T cells and B cells are stimulated during a primary immune response, they not only differentiate into effector T and B cells that will respond immediately to eliminate an invading pathogen, but also into memory T and B cells that will remain after the pathogen has been eliminated. Memory cells will continue to circulate in an individual, often long after the original (primary) infection took place. Subsequently, should the same pathogen make a second attempt to infect an individual, the pathogen-specific circulating memory T cells and memory B cells will mount a secondary immune response that is much more rapid and intense than the primary response and, thus, better able to prevent or terminate the infection. Immune memory is the basis for the success of vaccinations in this way is, in fact, the basis for the use of vaccines. Essentially, a vaccine is given to an individual to induce their immune system to mount a primary immune response against a specific pathogen. Subsequently, when that pathogen attempts to infect the individual, immune memory will result in a rapid and robust secondary immune response that hopefully will prevent infection from ever taking place.


 Idea.pngGauging the Timing of an Infection


The initial antibody produced by a plasma cell during a primary immune response is of the IgM isotype.

With time, isotype switching occurs and the plasma cell will produce antibodies of different isotypes, such as IgG or IgE.


Interestingly, if infection reoccurs, and a secondary immune response takes place, IgG is produced immediately by plasma cells, and little or no IgM production occurs. For this reason, antibody isotypes can sometimes be used to gauge the timing of an infection (acute versus convalescent stage), and to determine if it is a first time infection or re-infection.