BLD434 Section 2 Flashcards
Immunology
Immunoglobulin (Ig) - BCR vs. Ab
protein/gene secreted by plasma cells to create a unique antigen receptor on each naive B cell.
BCR when presented on the B cell membrane
Antibody (Ab) when secreted as an effector protein
CDR
Complementarity Determining Regions
- The exposed amino acid loops at the end of the V Ig-like domain of a heavy chain
Hypervariable region
(same as CDR) the part that is complementary to the Ag-binding site with the target Ag.
This is what changes during somatic hypermutation.
RSS
(Recombination Signaling Sequence)
Heptamer + Nonamer + spacer (12 or 23 nucleotides)
During somatic recombination – Controls where RAG cuts and joins the dsDNA of the light and heavy chains
TdT
Terminal deoxynucleotidyl transferase
- Enzyme that randomly adds N nucleotides to increase diversity during junctional diversity
RAG
Recombination Activating Gene
Two RAG-1 enzymes bind on heptamer and nonamer to pull gene segments together between the V and J. RAG-2 cuts as the border of RSS so V and J can be joined together.
Combinatorial diversity
(Pt. 1 of somatic recombination)
Creates different combinations of different gene segments to increase diversity (L-V-(D)-J-C)
Junctional diversity
(Pt. of somatic recombination)
TdT puts random P and N nucleotides in between the gene segments to create a unique Ag-binding domain (increases diversity in the a.a. seq of the light and heavy chain CDR3s)
Occurs in B & T cells
P nucleotides
short Palindromic sequences formed by cleavage of hairpins that form at the blunt end cut sites
N nucleotides
Non-templated nucleotides stuffed in coding joints.
Somatic Recombination
(Combinatorial Diversity + Junctional Diversity)
Recombine genes within a cell to create its unique antigen receptor to increase diversity of the lymphocyte pool
- changes the variable regions
- initiated by RSS
- enzymes = RAG complex, TdT
- Occurs in B & T cells - if failed, neither will be produced
Effector function of B lymphocytes
Antibody production and secretion
Why are Ig-like domains commonly found in immune system proteins?
Because they are very stable in the harsh conditions of infection sites (pH, salt, proteases)
B-sheet antiparallel - very stable
Gene segments for light chain vs heavy chain
Light = L-V-J-C
Heavy = L-V-D-J-C
2 Types of light chains
Kappa and Lambda
Functions of VL, VH, CL, and CH protein domains
VL and VH: form CDR and allow for diversity and specificity
CL and CH: structural support for Ab - don’t change
What 2 C gene segments are closest to the variable gene segments in the Ig heavy chain locus
C-mu and C-delta are closest to the variable gene segments, so it is convenient for the naive B cells to transcribe here so IgM and IgD can be expressed on their cell surface.
What proteins compose a complete BCR?
2 light chains, 2 heavy chains, Ig-alpha and Ig-beta (signaling molecules)
Ig-alpha an Ig-beta
Signaling molecules that transduce signal that Ag has been bound by BCR, leading to change and cell differentiation
Affinity
The strength of binding between a Ag-binding site and its target epitope on an antigen.
Avidity
Added up affinity
Ex: IgM has 2 Ag-bs per Ab (pentamer)
Somatic Hypermutation
Single nucleotide DNA point mutations (sub) in the Ig hypervariable regions to improve BCR binding affinity for Ag.
- initiated by AID
- high rate of mutation
Only occurs in B cells
Clonal selection
The B cells that bind to Ag better will be selected for in the population while those that don’t will be lost from the population.
Affinity maturation
An improvement in the responding (affinity) B cell pool – achieved by somatic hypermutation then clonal selection
Only occurs in B cells
Surface vs secreted immunoglobulins
Surface (BCR) - have hydrophobic a.a. which embed well into the plasma membrane
Secreted (Ab) - have hydrophilic a.a. which are stable in solution
AID
Activation-induced cytidine deaminase
- initiates somatic hypermutation and isotype switching
What factors control which isotype of Ab the B cell will produce?
Cytokines secreted by CD4 Helper T cells
Isotype switching
Change function of Ab by
- changes the BCR constant heavy chain
- initiated by switch sequences
- enzymes = AID, UNG, APE1
- if failed, can only make IgM
Only occurs in B cells
BCR structure
2 heavy chains, 2 light chains
2 Ag binding domains
12 Ig-like domains minimum
Associated with Ig-a and Ig-B signaling molecules
TCR structure
Single TCR-a (VJ) and single TCR-b (VDJ)
1 Ag binding domain
4 Ig-like domains minimum
CD3 complex
CD4 or CD8 co-receptors
What antigen is recognized by TCR aB?
peptide fragments presented on MHC I and MHC II
What antigen is recognized by TCR gamma delta?
Lipids - through direct binding
Proteins that compose TCR-aB?
Va, VB, Ca, CB
CD3 complex
CD4 or CD8 co-receptors
Proteins that compose TCR gamma delta?
Vgamma, Vdelta, Cgamma, Cdelta
CD3 complex and two zeta chains
Gene segments used to create Va and VB
Va: V and J
VB: V, D, J
Features and functions of gamma delta T cells
- rare (alternate TCR heterodimer)
- mostly in epithelial cells/CT
- involved in homeostasis
- must signal through CD3 complex and zeta chains
- recognize lipids
Endogenous
intracellular proteins produced within cell cytosol
MHC I carries peptide fragments from endogenous proteins
Exogenous
extracellular proteins picked up by pinocytosis (DC), endocytosis (BCR), and phagocytosis (macrophage + DC)
B2-microglobulin
The soluble light chain of MHC I that provides structural support and is required for MHC I expression
Calnexin
Chaperone protein that keeps the heavy chain of MHC folded (stabilized until B2m binds)
Calreticulin
Chaperone protein that keeps the heavy chain of MHC I folded properly until peptide binds (replaces calnexin once peptide binds)
TAP
(Transporter associated with Antigen Processing)
Heterodimeric protein that transports peptides produced in the cytosol, so they can be loaded in MHC I.
proteasome –> ER.
ERp57 enzyme
- Associates the MHC I heavy chain with TAP
- Facilitates peptide loading into MHC I
Tapasin
- Associates the MHC I heavy chain with TAP
- Facilitates peptide loading into MHC I (assembly)
Proteasome
Protein complex that degrades ubiquitinated proteins into peptide fragments
Invariant chain
Covers the peptide binding groove so MHC II doesn’t get loaded with peptides in the ER.
Shuttles MHC II into outgoing endosomes, so it’s released from the ER w/o peptide
CLIP
(Class II-associated invariant-chain peptide)
24-residue fragment that
fills and blocks binding of peptides to MHC II in vesicles
HLA-DM
Human Leukocyte Antigen Complex that is contained within the endosome.
Releases CLIP, so peptides can bind to MHC II
MHC I
- CD8 (cytotoxic) co-receptor
- Present on all nucleated cells
- Presents endogenous (mostly viral) peptides (capable of the other during cross pres.)
- Pita pocket (small) peptide-binding groove
- Calnexin, B2m, calreticulin, TAP, tapasin, ERp57
- HLA –> A,B,C
MHC II
- CD4 (helper) co-receptor
- Present on surfaces of APCs (B cell, macrophage, DC)
- Presents exogenous peptides
- Hot dog (large) peptide-binding groove
- Invariant chain, CLIP, HLA-DM
- HLA –> D (DP, DQ, DR (2,3,4))
How do the APCs obtain antigens & what type of antigens?
B lymphocytes: endocytosis (receptor-mediated) – soluble, viral?
Macrophages: phagocytosis – bacteria, yeast, etc.
Dendritic cells: pinocytosis & phagocytosis (can activate naive T cells) – viral
Cross presentation
MHC I can present exogenous antigens to activate CD8 T cells to respond to viral infections.
DCs take anitgen from apoptotic debris outside cell and process them and put them into MHC I, activating CD8+ in secondary lymphoid tissues (to go kill virus-infected cells in the body)
HLA
Human Leukocyte Antigens
Genes in MHC that help code for proteins to differentiate between self and non-self
Polygeny
Several genes are expressed to perform the same function in a cell
Polymorphism
Having multiple forms - HLA gene sequences (alleles) vary from person to person
Relative numbers of alleles that exist for each HLA gene in the human population
Monomorphic: DR-alpha
Oligomorphic (1-10): E, F, G, DM, DO, B2
Polymorphic (hundreds): DP, DQ
Highly polymorphic (thousands): A, B, C, DRB1, DRB3-5
How are HLA haplotypes inherited?
Each person inherits a complete haplotype from each parent and expresses all alleles form each parent.
Ex: heterozygote expresses 2 haplotypes
How many MHC I and MHC II isoforms can compose an individual’s haplotype?
Minimum = 3 MHC I, 3 MHC II
Maximum = 6 MHC I, 8 MHC II
Most people = 6 MHC I, 6 MHC II
How can interferons modify the level of MHC on cells?
Type I interferons (alpha & beta) enhance antigen expression of MHC I during viral infections
- uses immunoproteasome
Type II interferons (gamma) enhance antigen expression of MHC II heavy and invariant chains
- induced by CIITA (MHC II transcription factor)
Immunoproteasome
- Generates peptides that can fit MHC I molecules.
- Has LMP 2 and LMP 7 which increase nonamer production, TAP, B2m, and expression og MHC I heavy chain
CIITA
Class II Trans Activator Protein
- Transcription factor for MHC II to increase its expression
HLA-E function
- expressed on all nucleated cells
- binds peptide fragments of MHC I leader peptides and presents them to inhibitory receptors on NK cells
- prevent NK cells from attacking self
HLA-G function
- restricted to fetal cells that lack HLA-A,B,C
- provides a NK cell ligand
- Prevents NK cells from attacking self
Anchor residues
A.A. residues on the floor/wall of peptide-binding groove of MHC I & II
- The points where antigen peptides bind (anchor) to the MHC
