L1-3: Immunity, Antibodies (T and B cells) & MHC molecules Flashcards
What are the 2 chains of an antibody called?
The heavy & light chain
Which part of an antibody interacts with the epitope of an antigen?
The paratope (also called the antigen binding site)
Define the Fab and Fc regions of an antibody
Fab (fragment antigen binding) region is where antigens bind to the antibody. Its composed of one C and V domain of each the heavy and light chain
Fc (fragment crystallisable) region is the tail region of an antibody that interacts w cell surface receptors called Fc receptors and some proteins of the complement system
The antigen binding site of an antibody is made up of?
The paired V regions (from heavy & light chains)
The Lamda and Kappa chains form the ______ chain of an antibody?
The light chain
How many hypervariable regions are involved w antigen binding in a single antibody molecule?
3 in the V heavy and V light region (total 6)
Antibodies only recognise peptide antigens. True or false?
False. Antigens (Ag) can be almost any molecule, along w non-biological molecules e.g. chemicals, metal
What are the first and second phase of the immune response called?
The innate phase then the acquired phase
How do T cells recognise antigens
Recognises only peptide fragments of antigens bound to MHC expressed by APC. These are presented in the cleft/ binding groove of MHC class I or class II molecules
TCR is membrane bound receptor. True or false?
True
BCR however is secreted
Describe the structure of TCR
Its a heterodimer with 4 domains composed of an alpha and beta chain.
- Each chain has a variable and constant region &; each contributes 3 CDRs to Ag binding
- The V domains interact w Ag= peptide bound to MHC molecule
- Each domain has a carbohydrate attached
- Each chain has a cytoplasmic tail bound with a disulphide bond and these tails are in the transmembrane region
What is the function of MHC molecules?
To bind peptide fragments derived from pathogens and display them on the cell surface for recognition by the appropriate T cells
What are the differences between MHC I and MHC II molecules?
- For MHC I the antigen binding cleft is formed by the alpha 1& 2 domains, whereas for MHC II its formed by the alpha and beta 1 domains
- MHC I are found on all nucleated body cells, while MHC II are only found on macrophages, dendritic cells and B cells
Which genes are part of MHC I molecules
HLA-B, HLA-C & HLA-A
These molecules are encoded by seperate alpha chain gehes
- A single gene encodes the beta 2 micriglobulin which associates with HLA-A, HLA-B and HLA-C
Which genes are part of MHC I lI molecules
HLA- DR: made of 2 beta and 1 alpha domain
HLA- DQ: made of a alpha and beta domain
HLA- DP: made of an alpha and beta domain
Describe the structure of MHC I molecule
MHC I has 3 alpha domains (top right to bottom right order) and a beta 2 domain and one tail. Is a heterodimer
- alpha 1&2 domains fold to form beta sheet structure known as peptide binding site
- DNA encoding these domains is very polymorphic (many different alleles here)
- alpha 3/ beta 2 microglobulin fold into Ig like domains
Describe the structure of a MHC II molecule
MHC II has 2 beta (left) and 2 alpha (right) domains with 2 tails.
- alpha and beta chains are encoded by separate genes within MHC
- both alpha and beta 2 domains are Ig like
- polymorphic alpha and beta 1 form peptide binding site
What kind of antigens do you MHC class one molecules bind to?
Binds peptide 8-10 AAs to present to TCR
What kind of antigens do you MHC class II molecules bind to?
Binds peptide 13+ AAs to present to TCR
What does HLA stand for?
Human leukocyte antigens
How are V and C regions encoded?
By seperate gene segments that rearrange during lymphocyte differentiation
Describe the difference between the V region in the H chain( TCR beta) & L chain (TCR alpha)
- TCR beta is encoded by 3 gene segments: V, J, D but
- TCR alpha is endoded by 2 gene segments: V & J (vaj)
Gene rearrangement during B cell development forms what?
a functional gene duhhh (via NHEJ)
Outline the process of producing a functional immunoglobulin gene
- Germline DNA sample procured
- Gene segments joined via somatic recombination and DNA is rearranged
- Transcription of primary transcipt RNA
- RNA spliced into mRNA which is then translated to create polypeptide chian
Which chain has greater variability, L or H chains?
- H chains due to 3 segments- (DJ then VD)
- while L chain genes have kappa segments first (VJ) which have lower variability. If kappa rearrangement is unsuccesful then lambda genes rearrange
H, kappa, lambda chains are encoded at different loci. Name them.
14, 2 and 22 respectively
How is DNA rearrangement guided?
By RECOMBINATION SIGNAL SEQUENCES (RSS) which flank the V, D, J regions and use V(D)J recombinase, an enzyme complex
What is the function of RAG (recombination activating gene) 1/2 genes?
They encode lymphoid specific components of the V(D)J recombinase
Name a consequence of mutation in RAG genes
Immunodeficiency
In a single B cell only one allele of either the H or L chain can be expressed? True or false
True. In the L chain either kappa or lambda is expressed, never both! This is so a B cell produces only one Ab specificity
Explain the 5 mechanisms for generation of Ab diversity
- Multiple germline genes: multiple VH, Vkappa and K lambda & also multiple D and J (remember no D for kappa and lambda)
- Combinationatorial diversity: different V, D and J segments recombine to produce difference sequences
- Junctional diversity: includes imprecise joining & N regions (random additions of nts at junctions of VD and DJ y terminal transferase)
- Combinations of H and L chains
- Somatic hypermutation: mutation freq in Ab Vh gene orders higher than normal spontaneous mutation rate. Occurs in germinal centres as B cells recognise Ag and proliferate
Briefly explain somatic hypermutation
AID (activation-induced deaminase) acts on DNA to de-aminase cytosine to uracil.
- Uracil is then recognised by error prone DNA repair pathways leading to mutations
- This process allows B cells to produce antibodies that are better able to bind infections
Ag recognition triggers B cell differentiation. What happens next?
-its unique BCR cells are secreted as an Ab
Name a similarity and difference betwen membrane BCR and the secreted Ab
- They hace the same Ag specificity as original VDJ regions aren’t altered
- The secreted form however has an alternatice C region that lacks a transmembrane region
The constant region of each H chain is encoded by what?
A different C region gene segment (i.e. Cmu, Cgamma, Cepilson and Calpha)
What do the 4 gamma chain gnes correspond to?
The 4 IgG subclasses
Why is IgM the first isotype Ab expressed by each developing B cell?
The Cmu is physically the closest to the V,D&J genes on the H chain locus
Where do gene segments rearrange during T cell development?
In the thymus
Somatic hypermutation occurs in TCR genes. True or false
False, no somatic hypermutation occurs in TCR genes
Name the gene segments and chromosomal loci for TCR and Ig genes
TCR alpha: V, J, C on chromosome 14
TCR beta: V, J, C and D on chromsome 7
What cells express MHC molecules?
- Class I molecules: all nucleated cells
- Class II molecules: particular cells e.g. B cells, macropahges, dendritic cells
Gene rearrangment occurs in MHC molecules. True or false?
False. Genes are co dominiantly expressed genes and located within MHC
Up to how many different MHC molecules can an individual have?
12
MHC molecules are the most polymorphic genes known. True or false?
True. They have many alleles?
What is a use of MHC’s high polymorphism?
It allows the binding of a vast range of peptides that can be presented to T cells
What is a limitation of MHC’s high polymorphism?
It increases risk of many immune-mediated diseases e.g. autoimmune diseases & makees organ donor selection very complex
Which type of peptides are presented by MHC molecules?
- Peptides from protein Ag synthesised in cell cytoplasm (endogenous Ag) are presented by class I MHC
- Peptides derived from exogenous Ag are presented by class II MHC
In both cases, the protein Ag need to be processed into peptides capable of binding
Describe the mechanism of Ag processing and presenting in MHC class I molecules
- Ag synthesised in cytoplasm
- Protein cleaved to peptides by proteasome
- Peptides transported to ER by TAP transporter
- Peptides bind to MHC class I molecules
- MHC I peptide complex is then transported to the cell surfave
Describe the mechanism of Ag processing and presenting in MHC class II molecules
- Ag is endocytosed into intracellular vesicles inside cell
- Proteins claved to peptides by acid proteases in vesicles
- Vesicles fuse with vesicles containing MHC class II molecules
- Peptides bind MHC class II molecukes
- MHC II peptide complex is then transported inside vesicles to cell surface
What is the TAP transporter
It’s a component of a multi-protein assembly & the peptide loading complex, including tapasin and calreticulin
What happens to proteasomes in cells receiving inflammatory cytokine signals?
They are modified to produce altered peptides
How do MHC II molecules prevent binding in the groove?
By binding to the invariant chain in the ER
How do lysosomal enzymes afffect MHC II molecules preventing groove binding?
In endocytic pathways they degrade binding to the invariant chain, leaving CLIP peptide associated with the binding groove
What is the function of the CLIP peptide
To prevent the degradation on the MHC II dimera prior to
antigenic peptides binding, and to prevent autoimmunity. Peptides from Ag displace clip upon binding
What is the purpose of HLA-DM?
It’s required for the loading of peptides into the groove.
Name the 3 main functions of the immune system
- Be able to recognise and repsond to any invading organism
- Not overreact to benign or self
- Be able to direct effector mechanisms against different pathogens
Done via linking innate and adaptive immune respnses
Name features of specific immunity
- High degree of specificity
- Exhibits memory
- Clonally distributed receptors
- Large repertoire (low freq of cells specific for any antigen and response takes time to develop)
Describe B lymphocytes
They are a type of white blood cell. It’s membrane form of Ig binds free anigen, which is secreted when the B cell is activated now known as an antibody
State the genearal process of antibodies
- Bind and encapsulate bacteria
- Activate the complement cascade (opsonisation & classical pathway activation & MAC)
- Activate effector cellls (cells that express FcR receptor (receptor that binds Fc region of anitbody))
Describe the structure of an antibody
- Has 4 polypeptide regions:
- Has Fab (fragment antigen binding) and Fc region
- Composed of a constant and variable domain of each the light and heavy chain (left& right respectively)
- Constant region is responsible for Ab structure and interacting w/ other molecules
What are the 5 anitbody isotopes?
Ig M, A, D, G, E (MADGE)
What determines an isotype?
Heavy chain (c region). Each isotype differs in structure and function
Describe the function of V regions
- V regions are specific for a given Ab
- Have concentrated regions of variability
- Have hypervariable regions (3 in Vh and l each) creating 6 hypervariable loops called COMPLEMENTARY-DETERMIING REGIONS (CDR1-3) which act as Ag binding sites
How are antigens recognised?
By epitopes recognised by Abs. These may either be continuous or conformational (discontinuous)
How do CDRs function in Abs?
CDRs present in an Abs V region determines the specificity and affinity of an Ab for Ag
T lymphocytes have a membrane only form. True or false?
True
How do T cells provide immune function
They recognise peptide fragment of Ag bound to MHC expressed by the APC
Name 2 key differences between B and T cell function
- B cells can bind free Ags, while T cells can only bind processed antigens
- B cells have a membrane and secreted frorm, while T cells only have a membrane form which is presented
