Immunity

What are some physical barriers to protect from against pathogens

• skin

• mucous membrane

• mucus

• cluttered epithelial cells (tranchea)

• lysozomes (tear, saliva, mucus secretions), which destroys cell wall of cellls

• acidic environment of stomach

Describe neutrophils

• phagocyte

• circulate in the blood

• attracted by signals infected tissues and then engulf and destroy the infecting pathogens.

Describe macrophages

• large phagocytic cells

• some migrate throughout the body, whereas others reside permanently in organs and tissues where they are likely to encounter pathogens.

Describe mast cells

• non phagocyte

• found in connective tissues

• release histamine (inflammatory molecule) to cause dilation of capillaries

Describe dendritic cells

• phagocyte

• mainly populate tissues, such as skin, that contact the environment.

• stimulate adaptive immunity against pathogens they encounter and engulf

Describe eosinophil

• phagocyte

• often found beneath mucosal surfaces

• have low phagocytic activity but are important in defending against multicellular invaders, such as parasitic worms, by discharging destructive enzymes

What are natural killer cells

• non phagocyte

• found in connective tissues

• release histamine (inflammatory molecule) to cause dilation of capillaries

How do phagocytes defect bacteria and what happens after recognition

• phagocytic cells detect fungal or bacterial components using several types of receptors, known as Toll-like receptors (TLR), these receptors recognize and bind to a variety of microbial products

• after detecting invading pathogens, a phagocytic cell engulfs them, trapping them in a phagocytic vesicle

• vesicle then fuses with a lysosome and hydrolytic enzymes in the lysosome degrade the components of the pathogens

What are anitmicrobial proteins

• in mammals, pathogen recognition triggers the production and release of a variety of antimicrobial proteins that attack pathogens or impede their reproduction

• 2 examples of such proteins include interferons and complement proteins

What are interferons

• cytokines are small proteins that aid cell-to-cell communication in immune responses and stimulate the movement of cells towards sites of inflammation and infection

• interferons are a subset of cytokines that provide innate defense by interfering with viral infections

• virus-infected body cells secrete interferons, which induce nearby uninfected cells to express antiviral genes that code for antiviral proteins

• antiviral proteins inhibit viral reproduction which limits the cell-to-cell spread of viruses in the body, helping to control viral infections such as influenza infection

What is a complement system

• infection-fighting complement system consists of 30 complement proteins in blood plasma

• proteins are made continuously in the liver and are circulated in an inactive state

• inactive complement proteins can be activated by substances on the surface of microbes.

• once activated, various different complement proteins assemble into the bacterial membrane to form the membrane attack complex (MAC), which creates a pore on bacterial membrane

• water and salts diffuse into the bacteria via the membrane attack complex, leading to their lysis

• additionally, complement proteins attached to bacteria also promote the recognition of bacteria by phagocytes, hence facilitates phagocytosis of the bacteria

Describe the complement system

• redness, pain and swelling that alert you to a splinter under your skin are the result of a local inflammatory response, the changes brought about by signaling molecules released upon injury or infection.

• histamine, produced by mast cells, is a signaling molecule that triggers the dilation of blood vessels and increase its permeability to antimicrobial proteins and phagocytes near the site of injury

• at the same time, macrophages at the site of injury secrete cytokines which also dilate blood vessels and increase blood flow to the site

• signals attract neutrophils which engulf and digest pathogens and cell debris at the site

• inflammatory response is enhanced by the activated complement proteins

• complement proteins stimulate further release of histamine that promotes more phagocytes to enter the site and increases the rate of phagocytosis of the pathogens.

• outcome is the accumulation of pus – fluid filled with white blood cells, dead pathogens and cell debris

What is acquired immunity

• adaptive immune system has evolved to provide a more versatile means of defence which,

• in addition, provides increased protection against subsequent reinfection with the same pathogen

• adaptive immunity relies on T cells and B cells, which are types of white blood cells called lymphocytes

• substance that elicits a response from a B cell or T cell is called an antigen

• antigens are usually foreign and are typically large molecules, either proteins or polysaccharides

• antigens protrude from the surface of foreign cells or viruses

• antigens, such as toxins secreted by bacteria, are released into the extracellular fluid.

• B cell or T cell has specific lymphocyte cell surface protein called antigen receptor

• specific antigen receptor (on B cell or T cell) is complementary in shape and hence binds to specific antigen

• antigen receptor is also specific enough to bind to just one part of a molecule from a particular pathogen e.g. bacteria or virus.

• small, accessible portion of an antigen that binds to an antigen receptor is called an epitope, or antigenic determinant

• example is a group of amino acids in a particular protein

• single antigen usually has several different epitopes, each binding to a specific antigen receptor via complementary shape

• antigen receptors produced by a single B cell or T cell are identical, hence, these antigen receptors will bind to the same epitope

• each B cell or T cell thus displays specificity for a particular epitope, enabling it to respond to any pathogen that produces molecules containing that same epitope

State the structure of B

• each B cell antigen receptor is a Y-shaped molecule with four polypeptide chains:

• 2 identical heavy chains and 2 identical light chains. Disulfide bridges link the chains together

• transmembrane region near one end of each heavy chain anchors the receptor in the cell’s plasma membrane

• a short tail region at the end of the heavy chain extends into the cytoplasm

• light and heavy chains each have a constant (C) region, where amino acid sequences vary little among the receptors on different B cells, C region includes the cytoplasmic tail and transmembrane region of the heavy chain and all of the disulfide bridges

• within the two tips of the Y shape, the light and heavy chains each has a variable (V) region, where amino acid sequence varies extensively from one B cell to another

• parts of a heavy-chain V region and a light-chain V region form the binding site for an antigen.

• each B cell antigen receptor has two identical antigen-binding sites complementary in shape to specific epitope

• binding of a B cell antigen receptor to an antigen is an early step in B cell activation, leading eventually to the formation of plasma cells that secrete a soluble form of the receptor known as antibody, or immunoglobulin

State the structure of antibody

• antibodies have the same Y-shaped organization as B cell antigen receptors, except that

• antibodies are in a soluble and secreted form rather than membrane bound.

• secreted antibody has a hydrophilic C-terminus at the heavy chains whereas the

• membrane-bound B cell antigen receptor has a transmembrane hydrophobic C-terminus at the heavy chains

Describe the structure of antibody

• IgG is the major antibody class in the blood

• each IgG is made up of four polypeptide chain: two heavy chains and two light chains linked via disulfide bonds.

• each heavy chain and light chain comprise a variable (V) region

• V regions make up the antigen-binding site

• antibody has two identical antigen-binding sites, each has a complementary shape that binds to a specific epitope.

• V region of different antibodies has different amino acid sequences that lead to different tertiary structure, this gives rise to the diversity of antigen binding sites where each binds

• specifically to a different epitope of an antigen.

• light and heavy chains each has a constant (C) region, where amino acid sequences vary little among the receptors on different B cells

• constant region at the C-terminus tail region (also known as Fc region) of some subclasses of IgG can bind to specific receptors (Fc receptors) on macrophages and neutrophils to facilitate phagocytosis, This process is known as opsonisation.

• two heavy chains each has a hinge region which gives flexibility to the structure. This improves the efficiency in which the antibody can bind with antigens.

Antigen recognition of T cells

• T cell, the antigen receptor consists of two different polypeptide chains, an α-chain and a β chain, linked by a disulfide bridge

• near the base of the T cell receptor is a transmembrane region that anchors the molecule in the cell’s plasma membrane.

• outer tip of the molecule, the variable (V) regions of α and β chains together form a single antigen-binding site remainder of the molecule is made up of the constant (C) regions.

• T cell antigen receptor comprises two different polypeptides – α-chain and β-chain while the B cell receptors bind to epitopes of intact antigens circulating in body fluids, T cell receptors bind only to fragments of antigens that are displayed, or presented, on the surface of host cells

• host protein that displays the antigen fragment on the cell surface is called the major histocompatibility complex (MHC) molecule

• 2 main classes of MHC proteins

• class I MHC protein presents foreign peptides to cytotoxic T cells

• class II MHC protein presents foreign peptides to helper T cells

• recognition of protein antigens by T cells begins when a pathogen or part of a pathogen either infects or is phagocytosed by a host cell

• inside the host cell, enzymes in the cell cleave the antigen into smaller peptides.

• each peptide, called an antigen fragment, then binds to an MHC molecule inside the cell.

• movement of the MHC molecule and bound antigen fragment to the cell surface results in antigen presentation, the display of the antigen fragment in an exposed peptide-binding site of the MHC protein

• if cell displaying antigen fragment encounters a T cell with the right specificity, the antigen receptor on the T cell will bind to both the antigen fragment and the MHC molecule

• interaction of an MHC molecule, an antigen fragment, and an antigen receptor is necessary for a T cell to participate in an adaptive immune response

How does cytotoxic T cell help infected body cell

1. viral-infected cells contain viral proteins in the cytosol

2. viral protein is degraded in the proteasome into small antigenic fragments.

3. antigenic fragments are transported into lumen RER via a protein transporter.

4. loading of antigenic fragment onto class I MHC

5. vesicle that contains the antigen-loaded class I MHC buds off from the RER to the Golgi apparatus

6. class I MHC is then transported to the cell surface where it presents the viral antigen to cytotoxic T cells

How does helper T cell help antigen presenting cell

1. antigen taken in by the APC (e.g. macrophages) via endocytosis.

2. fusion of endosome with primary lysosome.

3. hydrolytic enzymes in the lysosome degrades antigen into smaller peptides.

4. class II MHC synthesized in the RER and modified in the Golgi apparatus

5. class II MHC packaged into Golgi vesicle.

6. fusion of endosome and Golgi vesicle allows loading of antigenic peptide onto class II MHC

7. class II MHC is then transported to the cell surface where it presents the antigenic peptide to helper T cells

What is class switching

• class switching is a mechanism to produce the rest of the classes of antibodies after IgM

• IgM is the first class of antibody produced upon exposure to an antigen, followed by IgG, during a primary immune response

• biological function of these 5 (lgG, IgA, Ig D IgE, IgM) different classes is determined by the Fc portion of the antibody

• like somatic recombination, class switching is irreversible as it involves the removal of DNA of the heavy chain constant region.

• since VDJ recombination has already taken place, no further VDJ recombination occurs

• class switching changes the heavy chain constant region but retains its specificity for the antigen.

What is somatic hyper-mutation in B cells

• B cell recognizes an antigen, it is stimulated to divide (proliferate).

• during proliferation, the B cell receptor gene locus undergoes an extremely high rate of somatic mutation that is at least 105 -106 fold greater than the normal rate of mutation across the genome.

• such mutations occur in the rearranged V(D)J segments of the light and heavy chain locus, generating B cell receptor of varying affinity to that specific antigen (Fig. 3.13).

• variation is mainly generated via single base substitutions.

• B cells with deleterious (lethal) mutation undergo apoptosis.

• B cells with increased affinity for that specific antigen undergo proliferation and class switching. Each class-specific B cell then differentiates into memory B cells and plasma cells (secrete antibodies)

• somatic hyper-mutation allows for the selection of B cells that express immunoglobulin receptors that possess an enhanced affinity to bind to a specific foreign antige

Describe genetic structure of B cells

• somatic recombination occurs during the development of a B cell in the bone marrow before antigenic stimulation.

• heavy chain gene is made up of 4 segments: a variable (V) segment, a diversity (D) segment, a joining (J) segment, and a constant (C) segment.

• light chain gene is made up of 3 segments: a variable (V) segment, a joining (J) segment, and a constant (C) segment.

• VDJ segments of H chain gene and VJ segment of L chain gene together encode the variable region of the Ig protein, while the C segment of H chain gene and L chain gene encodes the constant region of the Ig protein.

Describe genetic structure of B cells

Somatic recombination requires the enzyme recombinase to select and recombine the gene

segments coding for the variable region on the Ig (Fig. 3.13a and 3.13b). This gives rise to a great

diversity (~2.6 X 106) of different Ig, each specific for a particular antigen.

• The kappa light chain gene locus for example, contains a single C segment, 40 different V

segments, and 5 different J segments. These alternative copies of the V and J segments are

arranged within the gene in a series (Fig. 3.13b). A functional gene is built from one copy of each

type of segment, thus, the pieces can be combined in 200 different ways (40V x 5J x 1C).

• Recombinase acts randomly, linking any one of the 40 V gene segments to any one of the 5 J

gene segments (heavy chain genes undergo a similar recombination).

• In any given cell, however, only one allele of a light-chain gene (either  or ) and one allele

of a heavy-chain gene undergo recombination.

• The recombination is permanent and is passed on to the daughter cells when the lymphocyte

divides.

• Since the gene segments are randomly selected and recombined, some B cells produce

receptors specific for epitopes on the organism’s own self antigen. If these self-reactive B cells

were not eliminated or inactivated, the immune system could not distinguish self from non-self

antigen and would attack body proteins, cells, and tissues. These self-reactive B cells with

receptors specific for the body’s own molecules are destroyed by apoptosis

What is somatic recombination in B cells

• somatic recombination requires the enzyme recombinase to select and recombine the gene segments coding for the variable region on the Ig

• this gives rise to a great diversity (~2.6 X 106) of different Ig, each specific for a particular antigen.

• kappa light chain gene locus for example, contains a single C segment, 40 different V segments, and 5 different J segments. These alternative copies of the V and J segments are arranged within the gene in a series

• functional gene is built from one copy of each type of segment, thus, the pieces can be combined in 200 different ways (40V x 5J x 1C).

• recombinase acts randomly, linking any one of the 40 V gene segments to any one of the 5 J gene segments (heavy chain genes undergo a similar recombination).

• any given cell, however, only one allele of a light-chain gene (either  or ) and one allele of a heavy-chain gene undergo recombination.

• recombination is permanent and is passed on to the daughter cells when the lymphocyte divides

• since the gene segments are randomly selected and recombined, some B cells produce

• receptors specific for epitopes on the organism’s own self antigen. If these self-reactive B cells were not eliminated or inactivated, the immune system could not distinguish self from non-self antigen and would attack body proteins, cells, and tissues.

self-reactive B cells with receptors specific for the body’s own molecules are destroyed by apoptosis.

When a B cell recognizes an antigen, it is stimulated to divide (proliferate).

During proliferation, the B cell receptor gene locus undergoes an extremely high rate of somatic mutation that is at least 105-106 fold greater than the normal rate of mutation across the genome.

Such mutations occur in the rearranged V(D)J segments of the light and heavy chain locus, generating B cell receptor of varying affinity to that specific antigen (Fig. 3.13).

• Variation is mainly generated via single base substitutions.

• B cells with deleterious (lethal) mutation undergo apoptosis.

• B cells with increased affinity for that specific antigen undergo proliferation and class

switching. Each class-specific B cell then differentiates into memory B cells and plasma cells

(secrete antibodies). (Fig. 3.14)

• This somatic hyper-mutation allows for the selection of B cells that express immunoglobulin

receptors that possess an enhanced affinity to bind to a specific foreign antigen.