immunology exam 2

What is clonal expansion?

Increases number of antigen-specific lymphocytes from naive lymphocytes.

How are antigen-specific clones activated?

By antigens.

How many possible immunoglobulin sequences can the adaptive immune system generate?

~10^16.

How many different antigens can the adaptive immune system target?

10^7.

What is the purpose of random assortment during B cell development?

To generate many single B cells with randomly assorted B cell receptor sequences.

What happens when infection occurs?

Cells with receptors that can bind to antigens from the pathogen are selected and activated.

What happens to the selected cells?

They undergo clonal expansion and produce antibodies.

Does infection induce the formation of a B cell receptor that binds to an antigen in the microbe?

No, B cells with such receptors pre-exist and are activated.

What are B cells doing in the body?

Circulating throughout the body, looking for something to bind to.

What happens when an existing B cell successfully binds to a pathogen?

That B cell is selected and replicates into many cells.

What happens to B cells prior to selection?

They are only membrane-bound.

What happens to B cells after binding?

They differentiate into plasma cells that can secrete antibodies.

What is an antigen?

Any molecule that can be bound by an antibody, B cell receptor, or T cell receptor.

What can B cell receptors/antibodies bind to?

Any type of macromolecule antigen.

What can T cell receptors bind to?

Protein-based antigens.

What is an epitope?

The specific piece of the antigen that is directly bound.

Can one antigen have more than one epitope?

Yes.

What is a linear epitope?

Antigens that are linear in nature and when bound.

What is a discontinuous epitope?

Antigens that are only close together when bound and folded.

What is an immunoglobulin?

Either BCR or antibody, same genetic loci.

What is a B cell receptor (BCR)?

Membrane-bound immunoglobulin.

What is an antibody?

Secreted immunoglobulin.

What is a heavy chain?

Part of immunoglobulins, there are 2 heavy chains.

What is a light chain?

Part of immunoglobulins, there are 2 light chains (κ and λ).

What is the variable region?

Top portion of immunoglobulins, binds antigens.

Are the 2 variable regions identical?

Yes, the 2 variable regions are identical.

What are complementarity-determining regions (CDRs)?

They are in the variable domains and are important for conferring antigen binding specificity.

What is the constant region?

Bottom portion of immunoglobulins, recognized by other immune cells or molecules.

What is the function of membrane-bound BCR?

Signals to B cell.

What is the function of secreted antibody?

Can be recognized by other immune cells through Fc receptors.

What are isotypes?

Different classes of immunoglobulins (IgG, IgM, IgA, IgD, IgE).

What is affinity?

Describes the strength of interaction between an antibody and an antigen.

What are Fc receptors?

Innate immune cells bind antibodies through Fc receptors.

What is the function of Fc receptors?

Used to move antibodies across cells (transcytosis) and recognized by other immune cells.

What is neutralization?

Coating microbe surface with antibodies to block them from reaching cells.

What is opsonization?

Coating microbe surface to enhance phagocytosis by binding to phagocyte Fc receptors.

What is complement activation?

Binding of antibodies to multivalent antigen; can lead to opsonization.

What is antibody-dependent cell-mediated cytotoxicity (ADCC)?

Antibody coated cell binds to Fc receptor on NK cell to kill microbe.

What is somatic recombination?

Process used at Ig and TCR loci for generating antibody diversity.

What is V(D)J recombination?

Process of DNA recombination that occurs at heavy and light chain loci.

How does somatic recombination occur in heavy chain?

1 V segment, 1 D segment, 1 J segment are randomly chosen and DNA recombination occurs.

How does somatic recombination occur in light chain?

1 V segment, 1 J segment are randomly chosen and DNA recombination occurs.

What is the role of the enhancer in V(D)J recombination?

Brings enhancer closer to leader peptide for transcription.

What are the rules of V(D)J recombination?

Recombination occurs between gene segments at the same locus on the same chromosome.

Give an example of a segment that cannot recombine with another segment.

A V segment from K light chain locus cannot recombine with a J segment from the y light chain locus.

What is the order of recombination for the heavy chain locus?

D to J, V to DJ.

What do recombination signal sequences (RSSs) do?

They dictate which segments can recombine and in which direction.

What is the pairing requirement for 12bp and 23bp RSSs?

12bp RSSs can only pair with 23bp RSSs (and vice versa).

What is the purpose of RSSs?

To ensure that V segments don't recombine with other V segments, same for J-J and D-D.

What is the role of RSSs in V-J recombination?

To prevent random recombination and ensure signal-specific recombination.

What are the two different types of RSSs based on spacer length?

12 bp and 23 bp.

What determines the orientation of RSSs?

Conserved heptamer and nonamer sequences.

What is the function of RAG1/2 recombinase?

It is involved in the recombination process.

What is the pairing requirement for RSSs in the RAG recombinase complex?

Only allows for 12-23 RSS pairing.

What is meant by combinatorial pairing of light and heavy chains?

The process of combining different light and heavy chain segments during recombination.

What are the steps of V(D)J recombination?

1. RAG complex binds to one RSS

2. Recruits other RSS

3. Endonuclease function nicks one strand of DNA on each RSS

4. Hairpin formation and removal (or inversion) of intervening DNA

5. Hairpin opened by nicking

6. P nucleotide addition

7. N nucleotide addition by TdT

8. Pairing and nucleotide excision

9. DNA synthesis to fill in gaps and ligation

What is junctional diversity?

Recombination process itself introduces extra diversity

Estimated to increase diversity by a factor of 3x107

What is the function of RAG1/2 recombinase?

RAG1/2 binds RSS

Synapsis of RAG complexes

Cleavage of RSS

What are recombination signal sequences (RSSs)?

Specific DNA sequences recognized by RAG1/2 recombinase

What happens during the nicking of DNA?

RAG1/2 performs a single-stranded nick at the exact 5' border of the heptameric RSSs bordering both the V and the J segments

What is hairpin formation?

The hydroxyl group that was liberated by the nick at the 3' end of the coding strand attacks the corresponding phosphate group on the noncoding strands of both the V and the J segments to yield a covalently sealed hairpin coding end and a blunt signal end

What is signal end joining?

Signal end joining ligates the ends of the two RSS heptameric sequences that were originally in contact with the V and J coding sequences

What is the coding end?

The covalently sealed hairpin coding end

What is the signal end?

The blunt signal end

What happens during hairpin resolution?

Nicking to open hairpin occurs randomly in different places

This can leave an overhang out nucleotides that need to be filled in

What are P (palindrome) nucleotides?

Nucleotides that fill in and resolve the overhang

Creates a palindrome

What are N (non-templated) nucleotides?

Can be added by TdT

Adds up to 20 random nucleotides

Primarily in heavy chains only

What is the function of terminal deoxynucleotidyl transferase (TdT)?

Adds N nucleotides

What is the process of pairing and nucleotide excision?

Some nucleotides may need to be removed (excised) to allow pairing

What are nucleotides added for?

To fill in gaps

What are non-productive rearrangements?

Rearrangements that do not result in a functional protein

What happens 2/3rds of the time during the addition of junctional diversity?

The resulting coding sequence will have a frameshift

What are frameshift mutations?

Changes in the reading frame of a sequence due to insertions or deletions

What happens if the number of nucleotides added/removed during an insertion/deletion is not divisible by 3?

It will result in a frameshift

What do frameshift mutations almost always lead to?

A premature STOP codon

What happens when a frameshift mutation occurs in the constant region?

It creates an incomplete polypeptide chain and cannot be a part of an Ig

What does a frameshift mutation in the constant region do to translation?

It completely alters or prevents translation of the constant region

What is somatic hypermutation?

A process that improves affinity and occurs after B cell activation

When does somatic hypermutation occur?

After antigen encounter and when the Ig has some affinity

What is the purpose of somatic hypermutation?

To increase affinity

Where does somatic hypermutation occur?

Specifically in variable regions

What type of mutations occur in somatic hypermutation?

Single nucleotide substitutions

What does AID convert C to?

U on one strand

What do general DNA repair pathways repair?

Any base

Where does somatic hypermutation occur randomly?

In variable regions