Immuno. Test 3

adaptive vs innate immunity

innate

Fixed repertoire of pattern recognition receptors

Germline (egg/sperm encoded at birth) → no recombination

Limited diversity (100s)

Specificity → recognize invariant structures

adaptive

Variable repertoire of pattern recognition receptors

TCRs, BCRs, Abs [Ig]

somatic

Unlimited diversity (10¹² - 10¹⁴)

Specificity → unique structures

Evolution of antibody/tcell receptors

evolutionarily immerged at IR event

maturation of t and b cells

b cell matures in bone marrow, the t cells finish maturing in the thymus

they are now mature, but naive (have not encountered an antigen)

sentinel cells

Immature dendritic cells, macrophages, mast cells: recognize infection or antigen and induce inflammation, activation of lymphocytes

they send a message to the lymph node (cytokines), this triggers the APCs

APC

Antigen-presenting cells

• Specialized to capture, concentrate, and display antigens for recognition by lymphocytes

– Dendritic cells; macrophages, B cells; follicular dendritic cells

– Different APCs serve different roles in adaptive immune responses

now the naive B/T cells are effector cells (effector cells can have different functions

Lymphocytes

Mediators of adaptive immune responses; only cells with specific receptors for antigens

effector cells

Function to eliminate microbes; include lymphocytes, granulocytes (neutrophils, eosinophils), macrophages

– Activated lymphocytes capable of performing the functions required to eliminate microbes (‘effector functions”)

– Effector T lymphocytes: cytokine secretion (helper cells), killing of infected cells (CTLs)

– B lymphocytes: antibody-secreting cells (e.g. plasma cells)

local infection to triggering adaptive immunity

pathogens trigger local infection, activate innate immunity → dendritic cells take the pathogen to the lymph node to stimulate adaptive immunity → makes effector cells and now they can travel to the area of infection

b cells

MAKE Abs (antibodies)

B cell Receptor (BCR)

Can have secreted isotypes

IgM and IgD IgG, IgA, IgE (Antibodies)

B-cell isotypes refers to the different classes of antibodies (immunoglobulins) that a B cell can produce, determined by the constant region of the antibody’s heavy chain.

One receptor specificity per cell

t cells

Make cytokines

T cell Receptor (TCR)

alpha-beta and gamma-delta cannot signal

never secreted

One receptor specificity per cell

BCR

Ig → immunoglobulin

isotypes = part of the antibody is the same, part is different

Antigen receptors (B cell)

dictate specificity

antibody

made of 2 different proteins, the light chain and the heavy chain (longer/bigger one)

connected with at least 3 covalent bonds (Sistine)

have an antigen binding region (variable region) and a constant region

TCR

have an alpha and beta chain , heterodimer

have an antigen binding region (variable region) and a constant region

Memory lymphocytes

Long-lived, functionally silent cells; mount rapid responses to antigen

challenge (recall, or secondary, responses)

after an infection is gone some stay, these are the memory cells

Abs have different functions but …

all functions rely on binding to specific antigens and binding to receptors

trigger cells to…

neutralize and inhibit, respitory burst phagocytosis…. ect.

how to antibodies bind to antigens

intermolecular forces

London Dispersion Forces, Dipole-Dipole Forces, Hydrogen Bonding, Ion-Dipole Forces

antibody y shape

Characteristic Y shape: intra and inter molecular disulfide bounds. 2 separate genes make a single antibody

bivalent antibody

An antibody that has two distinct sites to bind with antigens

antigen

something recognized by an antibody or bcr

The BCR and the secreted antibody have the same antigen specificity, but differ in structure: the BCR is membrane-bound, while the antibody is secreted.

epitope

An epitope is the specific part of a foreign substance (antigen) that the immune system recognizes and binds to

bivalency…

increases avidity (sum of all affinities (likelihood to bind)) (sum of all binding interactions on an antigen) and receptor cross linking (process where two or more cell-surface receptors are brought together and bound by a multivalent molecule)

linear and discontinuous epitope

when binding to a protein antigen…

linear recognizes all the structures in a row, discontinuous does not

antigen hypervariable vs constant regions

hypervariable region

where diversity occurs

constant regions

Ig G,M,D,A,E → types of constant regions

mini genes

antibodies

small repetitions, look to be exons but are not

light chains have two segments (kappa and gamma) and heavy chains have one

4 different types -

variable (V) - heavy and light have around 30-45

diversity (D) - only found for heavy

joining (J) - both 4-6

contestant (C) - both 1-9

V(D)J

How is diversity in antigen binding and isotype generated from single genes (humans only have 200,000)

From three segments about 1012 independent specificities

when you multiply/add up all the different combinations from kappa/gamma light chains and h chains there is 2.1×10⁶

plus junctional diversity there is 3×10⁷

^{multiply together and now we have a lot of diversity!}

how do we connect minigenes

VDJ recombination

we want to do this so that when the protein is encoded the reading frame is maintained

to do this we will use DNA breaks and mutations

RAG (1+2) protein complex recognizes sequences on 3’ and 5’ of a J and V → causes a conformational change that signals RAG to make a double stranded break (cleave DNA)

now we have two ends that need to be sealed → the KU protein complex recognizes this and recruits the DNA protein dependent kinase that phosphorylates ARTEMIS

ku makes a hairpin to protect coding joints?

ARTEMIS recruits the enzyme TdT → TdT transfers nucleotides to the ends and adds random non-gene-encoded nucleotides

the DNA is then stuck together by ligase

how B cells change their antibody types (isotypes) during maturation

Initial Expression: IgM and IgD

• Mechanism: Naïve B cells express both IgM and IgD on their surface simultaneously.

• Not a Genomic Modification: This co-expression happens at the RNA level via alternative splicing

Class Switch Recombination

To produce other antibody classes (IgG, IgA, or IgE), B cells must physically alter their DNA through a process called Class Switch Recombination (CSR). This permanent genomic modification changes the Fc region (constant region) of the antibody while keeping the antigen-binding site the same

• The enzyme AID is expressed/upregulated when B cells become activated.

• Function: AID converts cytosine (C) bases to uracil (U) bases in single-stranded DNA

• specifically targets switch regions

• Uracil-DNA Glycosylase Removes the uracil base created by AID.

• AP Endonuclease Cleaves the sugar-phosphate backbone

• Error-Prone DNA Polymerases fills in dna gaps

• When nicks occur close to each other they form a double-strand break.

repaired by dna polymerase and AP endonuclease and uracil DNA glycoslyase

cytokines dictate what class to switch to

The broken ends are joined together, positioning the variable region directly adjacent to a new constant region.