Section 5: Antibody- Structure and Diversity

Question 1

Antibody

Answer 1

-the primary function of an antibody is to recognize and bind antigen, and target that antigen to other components of the immune system

Question 2

What does an antibody consist of?

Answer 2

4 polypeptide chains
-2 identical H chains (50kDa)
-2 identical L chains (25kDa)
-each region possesses a region of high sequence diversity (variable region, v) and more conserved sequences (constant region, c)

Question 3

How was the structure of an antibody found?

Answer 3

-the structure was found by using various enzymes to cleave different portions of the molecule
-treatment with PAPAIN yields cuts above disulfide bond
-one fragment would crystalize but not bind antigen (Fc) fragment crystallization portion
-Fc is the variable part and Fab is the constant
-two fragments that could bind antigen; fragment antigen-binding portion (Fab)

Question 4

Treatment with Pepsin yields what in the antibody structure?

Answer 4

-cuts below disulfide bond
-one partial Fc portion
- one fragment that consisted of two cross-linked Fab regions F(ab’)2
-allows cross-linking Fab regions, probably useful for making reagents or assay or neutralizing treatment

Question 5

hinge region

Answer 5

-found in an antibody structure that allows for flexibility in binding antigens
-allows two Fab arms to adopt many different orientations

Question 6

Isotypes

Answer 6

-classes of immunoglobulins defined by the differences in heavy chain C regions
1. IgG
2. IgM
3. IgD
4. IgA
5. IgE
*with their heavy chains denoted γ, μ, δ, α, ε

Question 7

What are the names of the two isotopes of the light chain?

Answer 7

• Kappa (κ) and lambda (λ) with no functional differences found

Question 8

Immunoglobulin domains

Answer 8

-what each antibody is made up of
- light chains: have one variable domain (VL) and one constant (CL)
-the heavy chains: have one variable (VH) and 3 constant (CH 1,2,3)

Question 9

hypervariable regions (HV)

Answer 9

-the variations in the amino acid sequence of the V regions that determine antigen specificity are concentrated here (red) which are flanked by framework regions (yellow)
-3 HV regions are found in each V domain
-the yellow loop is constant and red is the variable region

Question 10

complementary determining regions (CDRs)

Answer 10

-what hypervariable loops are often called

Question 11

Antigen binding

Answer 11

-the most effective antibodies against a pathogen bind to surface molecules
-carbohydrates and proteins (glycoproteins, polysaccharides, glycolipids, peptidoglycan)
-antibodies can bind a large array of chemical structures however these are more commonly implicated in allergic or autoimmune reactions
-limiting factor to what cannot have an antibody developed is the size

Question 12

antigenic determinant (epitope)

Answer 12

-the part of the antigen to which the antibody binds is called
-important to how well the antibody can neutralize or opsonize

Question 13

systemic lupus erythematosus

Answer 13

-antibodies directed towards DNA are characteristic of this autoimmune disease

Question 14

linear epitope

Answer 14

is formed from contiguous amino acids
-bind continuous amino acids in a row

Question 15

discontinuous epitopes

Answer 15

-is formed from amino acids from different parts of the polypeptide brought together by chain folding
-bind to the structure, not the sequential amino acid
-structure can determine how well an antibody works
-pathogens can hide some epitopes in the 3D structure

Question 16

affinities

Answer 16

-because of small differences in shape and chemical properties of the binding site, certain antibodies will bind with different strengths to antigens
-this property makes them useful reagents in detecting and quantifying a particular antigen
-Historically you could immunize an animal and harvest
its antisera, containing Ab to a specific antigen

Question 17

monoclonal antibodies

Answer 17

-the modern method is to isolate a B-cell from the immunized animal and immortalize it by fusion with a tumor cell forming hybridoma cell lines that produce this
-there is one clone, one type of antibody, has a specificity that we can measure and a known affinity

Question 18

monoclonal antibody steps

Answer 18

-using monoclonal antibodies to specific surface markers on cells then we add fluorescent dyes to them, to tell us more information going on

Question 19

antibody diversity

Answer 19

-it is estimated that there are 10^8 Ab specificities that exist in each individual
-if each Ab were produced by a single gene, this would result in about 410^11 nucleotides needed to encode these genes
-there are 2.8510^9 nucleotides in the human genome, so that is not how Ab diversity is achieved

Question 20

somatically recombined

Answer 20

-this is how Ab is encoded in a series of genes to achieve a high level of diversity
-chain variable regions are encoded by 2 or 3 gene segments
-heavy chain (3), V (variable), Diversity (D), and (J) joining
-light chain (2) has Variable (V) and Joining (J)

Question 21

somatic recombination

Answer 21

-V region gene sequences are constructed from gene segments by the process called…
-somatic recombination of V, D, and J segments produces a functional heavy chain gene
-the various C (constant) gene segments that remain
-in the germ line organization of the human immunoglobulin heavy, the lambda chain has about 30 while kapa has up to 35

Question 22

recombination signal sequences (RSS)

Answer 22

-each V, D, and J gene segment is flanked by these sequences
- 9-bp purple
- 7-bp orange
-these RSS are arranged in pairs that are separated by 12- and 23- bp spacers (white)
- the -12 and -23 bp change is the twisting of the DNA to be between the major and minor grooves

Question 23

recombination activating genes (RAG-1 & -2)

Answer 23

-gene segments are joined together by this protein which recognizes the RSS
-to ensure alignment of the gene segments RAG-1 and 2 bring together specific 12 and 23 bp spacers (12/23 rule)
-not a eukaryotic gene does not have introns and exons

Question 24

RNA processing

Answer 24

-gives rise to different isotypes and different secreted or membrane-bound forms of antibodies
-determines the types of isotopes we produce and where the antibody will localize to (secreted or transmembrane)

Question 25

somatic hypermutation

Answer 25

-a cellular mechanism by which the immune system adapts to the new foreign element that confronts it
-mutation in the V region of Ab
-all controlled by T cells and cytokines

Question 26

affinity maturation

Answer 26

-a mutation in the V region of Ab increases the affinity of secreted Ab to Ag
-the B-cells that possess Ab with higher affinity for Ag are encouraged to live while others are programmed to die by helper T cells
-overtime affinity can increase with the reoccurrence of infections and produce better antibodies with higher affinities

Question 27

activation-induced cytidine deaminase (AID)

Answer 27

-is an enzyme that is expressed by only proliferating B cells and converts cytosine to uracil
-isotype switching and somatic hypermutation are dependent upon this
-turned on from T helper cells and cytokines
-targets class switching areas

Question 28

Class switch (isotype switch)

Answer 28

-during an immune response, IgM is produced first by B cells
-helper T cells guide the B-cell to class switch using cytokines
-which excises the U gene segment and combines the VDJ with a new class heavy chain (usually IgG)
-though the class (isotype) of the Ab has changed the antigen binding properties stay the same

Question 29

When do somatic hypermutation and isotype switching occur

Answer 29

-only occurs in B-cells that are activated before they differentiate in to plasma cells

Question 30

Immunoglobulin M (IgM)

Answer 30

• 5-10% of serum Ab (pentameric form)
• B-cell receptor surface (monomeric form)
• First Ab produced in immune response
• Largest of Ab (macroglobulin) note: macroglobulinemia
• does not cross the placenta, the J chain allows for secretion

Question 31

Immunoglobulin M (IgM) Functions

Answer 31

-the best antibody at agglutination (bridging together particles) and precipitation ( bringing together soluble antigens)
- Fixes complement through the classical pathway
-neutralization
-opsonization

Question 32

Immunoglobulin G (IgG)

Answer 32

• 80% of serum antibodies are IgG
• has 4 subclasses (IgG1>IgG2>IgG3>IgG4)
  -high diffusion coefficient, can cross the placenta
  -long half-life

Question 33

Immunoglobulin G (IgG) Functions

Answer 33

-opsonization
-complement activation
-neutralization
-clearance by agglutination and precipitation
-help trigger secondary immune response

Question 34

Immunoglobulin A (IgA)

Answer 34

-second most common antibody in serum (monomeric form)
-primary antibody in secretions (dimeric forms)
-2 subclasses (IgA1-serum) and (IgA2-secreted)
-cannot cross placenta, though it is in breast milk (90% of Ab)

Question 35

Immunoglobulin A (IgA) Functions

Answer 35

-prevents the entrance of pathogens by cross-linking epitopes forming aggregates that are removed by ciliated cells on mucosal surfaces
- also block adhesion molecules of bacteria, viruses, and toxins
- opsonization (neutrophils-Fca)
- can activate alternative complement pathways in some cases
- ** big role in protecting mucosal surfaces*)

Question 36

Immunoglobulin E (IgE)

Answer 36

-0.02% of antibody serum (monomeric)
-rare but extremely reactive in allergy response : immediate type hypersensitivity
- does not cross placenta

Question 37

Immunoglobulin E (IgE) Functions

Answer 37

-Fc portion binds to mast cells, basophiles, eosinophils, and Langerhans cells (DC of skin) with very high affinity
- binding of IgE in these cells cause: degranulation releasing histamine, heparin, and chemotactic factors
-important to the immune response, IgE has a protective role against pathogens (parasites) that have penetrated the IgA and mucosa
-does not bind complement, opsonize, or neutralize

Question 38

Immunoglobulin D (IgD)

Answer 38

• <1% of serum antibody
• B-cell surface receptor (monomeric)
  -does not cross placenta

Question 39

Immunoglobulin D (IgD) Functions

Answer 39

-Does not bind complement, opsonizes, or neutralize
-main function is as B-cell receptor for antigen recognition and activation of B-cell