The Structure and Function of Antibodies

Question 1

What is an antibody?

Answer 1

The secreted form of the B cell’s B cell receptor

Question 2

What mediates recognition of an antigen?

Answer 2

The recognition of antigen is mediated by the two antigen binding sites of the variable regions.

Question 3

What determines the antibody’s biological role in the immune response?

Answer 3

The constant region of the heavy chain

Question 4

How many polypeptide chains do all immunoglobulin molecules consist of?

Answer 4

Four polypeptide chains: two identical heavy (H) chains and two identical light (L) chains, held together by disulfide bonds.

Question 5

How many types of L and H chains are there?

Answer 5

There are two types of L chains and five types of H chain.

The chains have Greek letter names.

Question 6

What are the two types of L chain?

Answer 6

kappa (κ) chain and lambda (λ) chain

Question 7

What are the five types of H chain?

Answer 7

the gamma (γ), mu (μ), delta (δ), epsilon (ε), and alpha (α) chains

Question 8

What does the type of H chain define?

Answer 8

The type of H chain defines the immunoglobulin class or isotype.

The immunoglobulin may have a κ chain or λ chain L chain, but never both.

For example, both γ2λ2 and γ2κ2 antibodies are IgG antibodies because they have the same γ heavy chain even though they have different light chains.

Question 9

What regions do all antibodies have?

Answer 9

Variable

Hypervariable

Constant

Question 10

How many identical H and L chains does a single antibody molecule have?

Answer 10

A single antibody molecule has two identical H and two identical L chains.

Thus, a single antibody molecule has two identical antigen-binding sites.

Another way of saying this is that antibodies are bivalent.

Question 11

What are the variable regions of antibodies?

Answer 11

The N-terminal portions of both the H and L chains are different for different antibodies and are therefore referred to as variable (V) regions

Question 12

What are the hypervariable regions of the immunoglobulins?

Answer 12

Within the variable regions of the immunoglobulins, there are three short stretches of amino acids that vary the most from one antibody to another.

These are called the hypervariable (HV) regions.

The H and L chain V regions (VH and VL) combine to form the antigen-binding region of the antibody.

The hypervariable regions (HVH and HVL) contribute significantly to the antigen-binding site and are the part of the antibody that contacts the antigen.

Question 13

The rest of the H and L chains are the constant (C) region.

Within a given species of mammals, the amino acid sequences of the constant regions are identical for all antibodies of that particular isotype.

Compare the C region of the H chain and L chain.

Answer 13

Each H chain (μ, δ, γ ε, α) has a different amino acid sequence in its C region. These determine the function of the antibody (how it helps eliminate the antigen). Different isotypes of antibodies have different roles in the immune system.

The C regions of the L chains (κ and λ) have different amino acid sequences but this doesn’t influence the function of the antibodies.

Question 14

Describe the significance of the difference in the amino acid sequences of the C regions of the heavy chains between species.

Answer 14

It can cause problems in a clinical setting when a human patient needs to be transfused with antibody from a non-human species.

Immunologists can also exploit these differences to generate reagents for detecting and quantifying antibody.

For example, it is possible to generate an antibody in a goat that recognizes the heavy chain C region of the human antibody (because, in a goat, the human C region is recognized as a foreign protein).

These antibodies are called “goat anti-human Ig” antibodies because it is a goat antibody that recognizes the constant region of a human antibody.

Question 15

What is the complementarity determining region?

Answer 15

Hypervariable regions are also called “complementarity determining region” or CDR.

Question 16

What is the framework of an immunoglobulin?

Answer 16

The variable regions are sometimes called “framework” - while there is some variability in the amino acid sequences of different antibodies, there is also some conserved features.

These conserved features are important in the overall folding of the protein.

Question 17

What part of the antibody makes contact with the antigen?

Answer 17

The hypervariable region shows extreme amino acid sequence variability - this is the part of the antibody that makes contact with the antigen.

In the three-dimensional structure, the hypervariable regions would be at the “tips” of the antibody.

Question 18

What determines the specificity of the antibody?

Answer 18

The antigen-binding site is a three-dimensional pocket.

The side chains of the amino acids that make up the H and L chain hypervariable regions determine the shape of the antigen-binding site.

The shape of the antigen-binding site determines the specificity of the antibody (i.e., which epitopes it will bind).

Question 19

What is an epitope?

Answer 19

A single antibody molecule binds to only to a small portion of the antigen molecule called the epitope or antigenic determinant.

An epitope has a unique three-dimensional structure.

The antigen-binding site of the antibody has a shape that is complementary to that of the epitope.

The epitope on the antigen fits into the antibody’s antigen-binding site in the same way a key fits into a lock.

Question 20

How many epitopes does a single antigen have?

Answer 20

A single antigen can have many epitopes.

For a protein antigen, an epitope may be only 4–5 amino acids long (the average protein is 200–1000 amino acids long).

There may be many copies of the same epitope, different epitopes, or both.

Epitopes on the surface of the antigen are accessible to the antibody.

Therefore, many antibodies, each with different specificities, can bind to their particular epitope on one antigen particle.

Different antibodies have antigen-binding sites with different shapes, and will therefore bind epitopes with different three-dimensional structures.

Question 21

It is possible for two different antigens to have an epitope in common.

True or false?

Answer 21

True

Question 22

What is the chemical nature of an epitope?

Answer 22

The chemical nature of an epitope can be carbohydrate, lipid, amino acids, nucleic acid etc.

Question 23

What is required for strong binding between the antibody and the epitope?

Answer 23

The antibody will only bind epitopes with a complementary shape (remember the lock and key analogy).

Close contact between the surface of epitope and surface of antigen-binding site is required.

A poor fit would suggest there is weak binding or no binding.

Close contact allows the formation of hydrogen bonds as well as ionic and hydrophobic interactions between the epitope and the antigen-binding site.

Question 24

How many epitopes will a single antibody bind?

Answer 24

Only one or a few similarly shaped epitopes.

Question 25

What are the main types of secreted antibodies?

Answer 25

IgM, IgG, and IgA ## Footnote *People with allergies also make lots of IgE.*

Question 26

Where is IgD found?

Answer 26

IgD does not seem to be secreted; it is only found on the cell surface of naïve B cells.

Question 27

Why can antibodies of different isotypes recognize the same antigen?

Answer 27

Antibodies of different isotypes (also known as classes) can recognize the same antigen because they have the same V region (only their CH regions are different).

Question 28

What is secreted IgM?

Answer 28

Secreted IgM is a pentamer consisting of 5 IgM monomers that are joined to each other by disulfide bonds. Two of the IgM monomers are connected by a polypeptide called a J chain or Joining chain.

Question 29

Describe the role of secreted IgM.

Answer 29

The antigen-binding sites of IgM antibodies often have low binding affinity. However, pentameric IgM has high avidity (= total binding strength) because it has 10 binding sites instead of 2. The more binding sites present, the greater the total binding strength. The amino acid sequence in the μ chain constant region binds very effectively to complement proteins. Bacteria that are coated with IgM will be killed when the complement is activated. IgM can also neutralize pathogen.

Question 30

Where is IgG found?

Answer 30

In the blood

Question 31

IgG is found in the blood and can incapacitate pathogens by neutralizing. It also helps to kill bacteria. Describe 2 ways it can do this.

Answer 31

1. Complement proteins kill bacteria coated with IgG. An amino acid sequence in the γ chain constant region binds very effectively to complement proteins. 2. Phagocytes ingest bacteria coated with IgG antibodies more readily than bacteria without IgG. An amino acid sequence in the γ chain constant region facilitates the binding of IgG to specific receptors on phagocytic cells. ## Footnote *IgG antibodies from the mother can also cross the placenta and provide protection for the fetus.*

Question 32

What is the main immunoglobulnin class in bodily secretions? What is its purpose?

Answer 32

IgA is the main immunoglobulin class in bodily secretions (tears, saliva, mucus, mother’s milk, etc.). Its purpose is to bind to and neutralize pathogens. In other words, it prevents the attachment of the pathogens to host surfaces.

Question 33

Is IgA a monomer or a dimer?

Answer 33

In serum, IgA is a monomer; but IgA in bodily secretions (e.g., saliva) is a dimer. A J chain joins two monomer IgA units (the same joining chain found in the IgM pentamer). The dimeric IgA in bodily secretions is also associated with another polypeptide called the secretory chain. The secretory chain helps IgA cross layers of epithelial cells and get to the appropriate body sites (e.g., the lumen of the gut).

Question 34

Is IgE 'available' in serum to neutralize pathogens? Why or why not?

Answer 34

IgE is secreted into the serum, but almost all of it binds immediately to mast cells and basophils. Therefore, IgE is not “available” in the serum to neutralize pathogens.

Question 35

Which class of antibody can bind to the FcεRI receptor of mast cells and basophils?

Answer 35

An amino acid sequence in the ε chain constant region of IgE binds to a receptor (FcεRI) on these cells.

Question 36

Which antibody is responsible for triggering allergic reactions? Why?

Answer 36

IgE When the IgE on the mast cell or basophil binds an antigen, the cell degranulates and releases large amounts of histamine. Histamine causes the main symptoms of allergic responses.

Question 37

What is the main class of immunoglobulin induced in response to infection by parasites such as intestinal worms?

Answer 37

IgE. Worms are too big to be killed by phagocytosis. Instead, mast cell degranulation results in diarrhea and vomiting which helps to expel the worms.

Question 38

Describe the different isotypes (classes) of secreted immunoglobulin.

Answer 38

The B cell receptor is formed by the membrane bound version of monomeric form. IgA and IgM are polymers connected by the J chain. IgA as an additional protein called the secretory piece which is used to translocate it across epithelial layers and into mucosal secretions. IgD is not thought to be secreted.

Question 39

What is immunoglobulin class switching?

Answer 39

One of the important aspects of an antibody response. In class switching, the VH region the same, but the B cell uses a different CH region. The L chain remains the same. Thus, the class and function of Ig is different, but the antigen specificity remains the same.

Question 40

What are the first antibodies produced in an immune response?

Answer 40

The first antibodies produced in an immune response are always IgM.

Question 41

How may B cells be induced to switch to a different class (isotype)?

Answer 41

Activated T helper cells may then induce some of the B cells to switch to a different class (isotype) of Ig by providing them with specific cytokines.

Question 42

What is an important method for tailoring the adaptive response to best match the antibody to the pathogen?

Answer 42

Class switching. The VH region (represent by X) remains the same - it is simply placed next to a different CH gene segment. In this diagram, the B cell switches from matching the IgM form of the BCR to the IgG form of the BCR.

Question 43

Which antibody class is very effective at neutralizing viruses in mucosal secretions such as the Influenza virus?

Answer 43

IgA

Question 44

Which antibody class is very good at opsonization of bacteria in the blood?

Answer 44

IgG

Question 45

Why is immunoglobulin class switching uni-directional?

Answer 45

Immunoglobulin class switching involves cutting out DNA (splicing certain gene segments). B cells may undergo class switching on more than one occasion, but the mechanism of switching is uni-directional (a B cell can’t be switched back to the original Ig type after splicing because the DNA is lost). Some of the B cells that have undergone immunoglobulin class switching may differentiate into plasma cells and secrete the new class of Ig, whereas other cells may become long-lived memory B cells. *This is another reason that the secondary responses are stronger than the primary response: the type of antibody generated has been better tailored to the particular antigen, right from the start.*

Question 46

What are the three functions of secreted antibodies?

Answer 46

Neutralization Opsonization Complement activation

Question 47

What is antibody neutralization?

Answer 47

Antibodies prevent viruses and toxins from binding to and entering cells (neutralization).

Question 48

What is antibody opsonization?

Answer 48

Antibodies coat virus and bacteria, and improve the efficiency of phagocytosis by neutrophils and macrophages (opsonization).

Question 49

What is antibody complement activation?

Answer 49

Antibodies allow more types of bacteria to be killed by complement proteins (complement activation).

Question 50

Describe complement activation by antibodies.

Answer 50

Although complement proteins are regarded as part of innate immunity, they do work with IgM and IgG antibodies generated during an adaptive immune response. * After IgM or IgG has bound to the surface of a pathogen, the early complement proteins are recruited, resulting in the formation of a C3 convertase. * The C3 convertase cleaves C3 into C3a and C3b. * The binding of C3b to the pathogen surface recruits additional proteins to form the C5 convertase, which cleaves C5 into C5a and C5b. * C5b is also deposited on the pathogen surface and initiates the assembly of late proteins to form the membrane attack complex (MAC).

Question 51

What are the five isotypes or classes or antibody?

Answer 51

IgM, IgD, IgG, IgE, and IgA.

Question 52

What determines the antigen-binding specificity of the antibody, and what determines its class?

Answer 52

The VH and VL combine to determine antigen-binding specificity of the antibody, and the CH determines the isotype (or class) and function of the antibody.

Question 53

Which region of the antibody is species-specific?

Answer 53

The CH region is species-specific.

Question 54

How are the polypeptide chains of immunoglobulins connected?

Answer 54

Igs (both mIgs and sIgs) are composed of 4 polypeptide chains (2H and 2L) that are connected by disulfide bonds.

Question 55

Define: antigen.

Answer 55

**anything that is recognized by a BCR or a TCR**

Question 56

The V regions of the heavy and light chains of BCR and antibodies are involved in antigen recognition. True or false?

Answer 56

True.

Question 57

On antigenic stimulation, the plasma cells revert to B lymphocytes which secrete antibodies for humoral immunity. True or false?

Answer 57

False

Question 58

The main difference between membrane-bound immunoglobulin (mIgs) and secreted antibodies (sIgs) is amino acid sequences at the amino-terminus of the H and L chains. True or false?

Answer 58

False

Question 59

Antibodies are insoluble proteins. True or false.

Answer 59

False.

Question 60

An antibody consists of one copy of the heavy chain and one copy of the light chain, whereas the B cell receptor consists of two copies of each chain. True or false

Answer 60

False

Question 61

The hypervariable regions within the variable region (V region) is what actually makes contact with the antigen. True or false?

Answer 61

True

Question 62

When a B cell class switches, it can change the type of heavy chain it makes, but the V regions of the heavy and light chain remain the same. True or false?

Answer 62

True

Question 63

IgG is secreted as a monomeric immunoglobulin. True or false?

Answer 63

True.

Question 64

IgA is secreted as a dimeric immunoglobulin into the mucosal secretions. True or false?

Answer 64

True

Question 65

IgA is effective at activating complement. True or false?

Answer 65

False

Question 66

IgM and IgG are good at activating the complement proteins. True or false?

Answer 66

True

Question 67

A secreted antibody molecule (e.g., IgG) has two antigen binding sites. True or false?

Answer 67

True

Question 68

IgM and IgG can both act as opsonins. True or false?

Answer 68

False

Question 69

IgM, IgG and IgA can all act to neutralize pathogens. True or false?

Answer 69

True

Question 70

Once a B cell has class switch to IgA, it can go back to make IgM if it turns out that would be the best class of antibody to make. True or false?

Answer 70

False

Question 71

IgE is an antibody that causes allergic reactions to non-harmful antigens, but it is an important immune defense against parasitic worm infections. True or false?

Answer 71

True.

Question 72

The antibody binds to a specific region on the antigen called an epitope. True or false?

Answer 72

True

Question 73

A large antigen can have many different epitopes. True or false?

Answer 73

True

Question 74

An antibody may bind to a linear epitope or a conformational epitope. True or false?

Answer 74

True

Question 75

IgM #1 is from a human - recognizes rabies virus IgM #2 is from a human - recognizes measles virus How are these antibodies the same? How are they different?

Answer 75

The amino acid sequence of the variable regions of IgM #1 and IgM #2 will be different: – reasonable since these antibodies recognize different antigens. The differences will be mostly in the hypervariable region. The amino acid sequence of the constant regions will be identical: – even if they are from different people. Importance: You can transfuse antibodies from one person to another

Question 76

IgM #1 is from a human - recognizes rabies virus. IgM #3 is from a dog - recognizes rabies virus. How are these antibodies the same? How are they different?

Answer 76

The amino acid sequence of the variable regions of IgM #1 and IgM #3 will probably be different (just because rabies is a large virus - unlikely that they will bind to same part of the virus). The amino acid sequence of the constant regions will also be different - there is a species difference - the constant regions of the heavy chains from different species are immunogenic (i.e., they will trigger an immune response). In other words, antibodies from another species can be ‘antigens,’ and *antibodies against antibodies* are made.

Question 77

What plays are a large role in antigen binding?

Answer 77

The antigen binding site is a three dimensional pocket made by the combination of the VH and VL regions. Side chains of the amino acids in the pocket play an important role in antigen binding (size, charge of R group). Covalent bonds require energy and will not contribute to the interactions between the antibody and the antigen.

Question 78

Give an overview of positive selection, negative selection (as per Dr. Kion's announcement)

Answer 78

**Positive selection** – for T cells only – key point is that it selects for T cells that can dock/bind onto MHC. Occurs before negative selection. **Negative selection** – B and T cells – removes cells that are self-reactive. **Both happen in the primary lymphoid organs (bone marrow for B, thymus for T).** In the primary organs, the TCR would bind to MHC + peptide – in positive selection the interaction of the TCR with the MHC has to be adequate for the T cell to get a signal that says, well done – your TCR can interact with MHC! In negative selection of T cells, different cells are involved (and their marking criteria change). In negative selection, strong interactions are bad!