Antibodies 1

B lymphocytes

Antibodies are secreted by what

Antigen

protein that an immune cell can recognize, usually foreign

Epitope (aka antigen determinant)

Particular part of the antigen bound by the antibody

Antibody

specialized protein that directly binds to a specific antigen

Pathogen

organism that can cause disease

Proteins, immunoglobulins (Ig)

what are antibodies?

1. IgG

2. IgD

3. IgE

4. IgA

5. IgM

5 different types of antibodies

isotopes have different structures and specialties

antigen “types”

1. recognize function

2. deffence (effector) function

two major functions of antibodies

Must recognize foreign material (bacteria cell wall, protein, virus, etc.)

Antibodies recognization function":

Must initiate a response to protect against a foreign material

defence antibody function

Domains

fundamental units of tertiary structure and function

functions

A protein that has several domains has several…

multiple polypeptide chains that make up domains:

two heavy chains and two light chains

antibodies are composed of:

one constant and one variable domain

two light chains:

three constant and one variable domains

heavy chains:

Variable domains

domains of antibody chains that make up the antigen binding site which are hypervariable, confers to antigen specificity

two

how many antigen binding sites per antibody?

One certain ligands bind

Proteins are this highly specific:

1. size

2. shape

3. charge

4. hydrophobicity

antibodies are complementary in: [4]

Induced fit

Conformational changes may occur upon ligand binding. This adaptation is called:

1. tighter binding of the ligand

2. high affinity for different ligands

induced fit of antibodies allows for:

complementary groups to interact fully

Conformational changes in the antibody or antigen can lead to tighter binding, by allowing;

NOn-covalent interactions

Antibodies bind to antigen via:

complementarity determining regions (CDR)

Antibodies interact with antigen at :

12 domains

how many domains in IgG have the same domain fold:

Immunoglobulin fold

domain fold in IgG

2 beta sheets with loops connecting the antiparallel beta strands

The Ig domain is sandwich of:

disulphide bonds

link between light and heavy chains, and the two heavy chains together

1. two fragments bound antegen and called Fab

2. thirdfragment called Fc. Fc retains effector functions

What happens after papain digestion

initiates the processors your immune system used to actually take out the invader

Fc retains the effector functions by

1. small molecules (e.g., phosphorylcholine)

2. macromolecules (e.g., protein)

two kinds of antigens

in the cleft of antigen binding region

Small molecules often bind where in antigen-binding

1. electrostatic

2. hydrogen bonds

3. van der waals

4. hydrophobic

Interactions between the antibody and antigen [4]

contact is more extensive, sometimes interacting with all CDRs and 20 or more residues of the antibody. Interaction tends to be larger and flatter

how do large molecules contact with antigen binding site

histamine

detection of allergen causes body to release:

tighter the binding

the more interactions there are and the more complementary the binding surface, the

1. shape at binding site (complementary and concave)

2. Amino acid sidechains to maximize noncovalent interactions

factors determine specificity and affinity of antibody for antigen

dissociation constant, Kd, which is in units of molar concentration

Most common way to quantify the strength of binding between protein and ligand

Tighter the binding

greater the binding affinity

The smaller the Kd, the