Exam 2 Flashcards
Of the billions of B cells circulating, what is special about the receptor specificity?
Each is different
How is diversity in antigen binding site generated before activation/during B cell development? (3)
Somatic recombination
Random association of heavy and light chains
Junctional diversity
How is diversity in antigen binding site generated after B cell activation?
Somatic hypermutation
How do variable segments differ?
In amino acid sequences that encode HVR1 and HVR2
Where is HVR3 formed?
From diversity at the junction between V (variable region) and J (joining region) or V, J, and D (diversity region)
Where are diversity segments found?
Only in heavy chain
What do constant segments determine?
Isotype of heavy chains
What is the antibody V region formed from?
Somatic recombination
What does somatic recombination do?
Brings together a single V, J, and D gene segment
Is rearrangement necessary in the antibody C region?
No, it is ready to be transcribed
Does the C region contribute to the diversity in the antigen binding site?
No
What is somatic recombination initiated by?
Recombination signal sequences
What are the 2 types of recombination signal sequences (RSS)?
Sequences with a 12bp spacer
Sequences with a 23bp spacer
What is the 12/23 rule?
12bp RSS can only associate with a 23bp RSS
What does the 12/23 rule ensure?
That segments are joined in the correct order
What is the V(D)J recombinase complex composed of? (2)
RAG-1 and RAG-2 (lymphocyte specific components)
Ubiquitous DNA repair proteins
What is the sequence of events for the formation of a coding joint by V(D)J recombinase complex? (4)
- RAG complex aligns recombination signal sequences
- RAG complex cleaves DNA
- Broken end joined by non-homologous end joining
- Results in a coding joint and a single joint
What is RAG?
Recombination activating gene
What is junctional diversity?
Diversity at the coding joint
What is the sequence of events for junctional diversity? (5)
DNA cleavage by RAG complex leaves hairpin ends
Hairpins cleaved in a random location, generates P nucleotides
TdT randomly adds N nucleotides
Opposite strands pair
Gaps filled by DNA synthesis and ligation
What are P nucleotides?
Palindromic nucleotides
What are N nucleotides?
Non-template nucleotides
What happens after re-arrangement of the variable region?
The transcript is transcribed to mRNA
For a heavy chain, where does transcription proceed through? What does it terminate before?
Cμ and Cδ
Cγ
What do naive B cells express? Where? By what?
IgM and IgD on the surface by alternative splicing
What is the first antibody secreted from naive B cells?
IgM
How often is IgD secreted?
Rarely
How many light chains and heavy chains are there?
295 light chains
5520 heavy chains
Because heavy and light chains associate randomly, how man possible combinations are there?
About 1.6 million
How are gene segments chosen?
Randomly during somatic recombination
Upon B-cell activation, what are immunoglobulin molecules produced as?
Soluble antibodies
What is produced by alternative splicing?
Membrane-bound and secreted immunoglobulin molecules
What produces high affinity antibodies?
Somatic hypermutation
What is required to produce antibodies of a different class?
Isotype/class switching
What does somatic hypermutation do?
Introduces random point mutations in the variable region after B-cell activation
What does somatic hypermutation result in?
Affinity maturation
What happens to antibody affinity for antigen over time?
It increases
What does somatic hypermutation require?
AID (activation induced cytidine deaminase)
What is AID made in?
Activated B cells
What does AID do?
Converts Cytosine to Uracil
What happens to U with AID in somatic hypermutation?
It is removed and replaced with another base
If there is a poor affinity what happens to B cells? (2)
Cannot compete for antigen
Does not receive survival signal so apoptosis occurs
If there is a strong affinity what happens to B cells? (2)
Successfully competes for antigen and receives survival signals
Undergoes more rounds of somatic hypermutation and becomes a plasma cell
Which B cells continue to proliferate and differentiate?
B-cells with the highest affinity receptors
What is class switching regulate by?
Cytokines
What does class switching do?
Increases function diversity, but not antigen specificity
What is the sequence of events for isotype/class switching? (4)
- Transcription induced upstream of switch region
- AID converts Cs in desired switch regions to Us
- Us removed leaving a DNA nick in switch regions
- Recombination at switch regions brings desired V region next to new C region
What removes uracil?
Uracil DNA glycosylase
What excises an abasic nucleotide?
APE-1
What is AID responsible for?
Somatic hypermutation and class switching
What happens in variable regions with AID? What does that lead to?
Uracil is removed
Somatic hypermutation
What happens in switch regions with AID? What does that lead to?
Nucleotides removed DNA nick and class switching
Where do somatic hypermutation and isotope switching take place?
In the germinal center
Chapter 4 part 2 study guide
Chapter 4 part 2 study guide
What are the 2 broad groups of T cells?
CD4 T cells
CD8 T cells
How do T cells carry out their functions?
Through direct cell-cell contact
What are CD8 T cells known as?
Cytotoxic T cells
What do cytotoxic T cells do?
Kill infected cells
What are the 2 broad groups of CD4 T cells?
Helper T cells
Regulatory T cells
What do helper T cells do?
Help the function of the cells
What do regulatory T cells do?
Down regulate the immune response
Anti-inflammatory
How is the type of T cell a CD4 cell turns into determined?
By the cytokines in the area which is determined by the pathogen
What is the structure of a T-cell receptor (TCR)?
One α chain
One β chain
What does each chain of the TCR have?
A variable and constant region
What can the α chain compare to?
Light chain
What can the β chain compare to?
Heavy chain
How many antigen binding sites are on TCRs?
One
What is the antigen binding site on TCRs formed from?
V regions of α and β chains
How many hypervariable regions are the on TCRs?
6: 3 per chain
What does the TCRα chain contain?
V and J segments and a constant region
What is the variable region of the TCRα chain formed through?
Somatic recombination
What is the TCRβ chain composed of?
V, D, and J gene segments and constant regions
What is the variable region of the TCRβ chain formed through?
Somatic recombination
What is diversity in TCRs generated by? (3)
Somatic recombination
Junctional diversity
Random combination of chains
What are the two types of receptors on T cells?
α:β
γ:δ
Are the functions of α:β receptors and γ:δ receptors the same or different?
Different
How much of the total T cell population do the α:β T cells account for?
95%
What are α:β T cells the T cells of?
The adaptive immune system
What do TCRs recognize?
Peptide antigens bound to MHC molecules
What are antigens degraded by?
Conventional dendritic cells
What is MHC?
Major histocompatibility complex
What does MHC do?
Present antigen on the surface of the cells
What does MHC class I present?
Antigens from intracellular pathogens
What does MHC class I activate?
Cytotoxic T cells
What does MHC class II present?
Antigens from extracellular pathogens
What does MHC class II activate?
Helper T cells
What is CD4 expressed on?
Helper T cells and regulatory T cells
What does CD4 bind?
MHC II
What is CD8 expressed on?
Cytotoxic T cells
What does CD8 bind?
MHC I
What is the structure of MHC class I molecules?
Variant α chain
Invariant β2-microglobulin
What is the structure of MHC class II molecules?
Variant α chain
Variant β chain
What are MHC molecules not composed of?
Gene segments
Where are intracellular pathogens present?
Cytoplasm
Where are intracellular pathogen peptides delivered?
To the ER
What are intracellular pathogen peptides in the ER bound by?
MHC class I
How many residues long are intracellular pathogen peptides?
8-10
What are extracellular pathogens brought into the cell in?
Endosomes
What are extracellular pathogens peptide breakdown products loaded onto? Where?
MHC class II In the vesicular system
How many residues long are extracellular pathogen peptides?
13-25
What are extracellular antigens presented on?
MHC class I molecules
What does cross presentation allow?
Dendritic cells to activate cytotoxic T cells (CD8 T cells) even though the dendritic cell is not infected
In cross presentation, what are extracellular derived peptides presented on?
MHC class I molecules
What do most cell types express? Why?
MHC class I Most can be infected with a virus
What types of cells express MHC class II?
Antigen presenting cells
Dendritic cells, macrophages, B-cells
What are MHC molecules are also referred to as?
Human leukocyte antigens
What chromosome is the major histocompatibility complex located on/
6
What are the 3 MHC class I molecules on chromosome 6 that are involved in antigen presentation?
A, B, and C
What are the 3 MHC class II molecules on chromosome 6 that are involved in antigen presentation?
DP, DQ, and DR
How many molecules of MHC class I and MHC class II does each person have?
6 MHC class I 6 MHC class II (3 of each type form the mother and 3 from father)
What are MHC molecules encoded by?
Conventional genes that do not rearrange
In terms of alleles, how can MHC genes be classified?
Polymorphic
Are most individuals homozygous or heterozygous for the highly polymorphic MHC genes?
Heterozygous
What are the different ways MHC molecules can appear in the human population? (3)
Polymorphism (multiple alleles)
Multiple genes
Polymorphism and multiple genes
Since most individuals are heterozygous for highly polymorphic isotypes of MHC molecules, what does it allow for?
A greater number of peptides to be presented during an infection
Since most individuals are heterozygous for highly polymorphic isotypes of MHC molecules, what does it reduce?
Probability that population will succumb to a particular pathogen
What does MHC polymorphism arise in?
Sequences that bind peptide and T-cell receptor
What do MHC molecules have?
Promiscuous binding specificity
What determines the antigens that bind to an MHC?
Anchor residues
At anchor residues, what do peptides that bind a particular MHC molecule have?
The same amino acids
What is the peptide binding motif?
Combination of anchor residues that bind an MHC isoform
What is the T cells receptor specific for?
Peptide and MHC allele
What MHC allele is the T cell receptor specific for?
HLA-A*0201
What peptide is the T cell receptor specific for?
Peptide X
What will most T cells be restricted to?
Recognizing antigen only when self bound to a “self” MHC molecule
Chapter 5 study guide
Chapter 5 study guide
What happens in the bone marrow?
Production of function B-cell receptor
What kind of tolerance is in the bone marrow?
Central tolerance
What is tolerance of B cells?
Removing self-reactive B cells
What happens in the periphery and secondary lymphoid tissues?
B-cell maturation
B-cell activation
What are the stages of B cell development from common lymphoid progenitor to immature B cell? (8)
Common lymphoid progenitor Pro B-cell Rearrangement of heavy chain Large pre B-cell Cell divisions Small pre B-cell Rearrangement of light chain Immature B-cell
How many copies of the heavy gene are there in an individual?
2 copies–one maternal and one paternal
What takes place first in both heavy genes?
DhJh joining
What takes place on one chromosome at a time during B cell development?
Vh-DhJh rearrangement
What does each heavy chain V region have a 1/3 chance of?
Productive rearrangement
What can alter the reading frame in productive rearrangement?
Random addition of P and N nucleotides at junctions
What percentage of B-cells are signaled to die by apoptosis?
50%
What percentage of B-cells are signaled to survive and become pre B-cells?
50%
What does rearrangement one chromosome at a time ensure?
Only 1 type of heavy chain is expressed by the B-cell
What are rearranged heavy chains tested for?
Ability to form a pre B-cell receptor (checkpoint 1)
If the heavy chain on the first allele is non-functional, what happens to the V region on the second allele?
It completes rearrangemtn
If both heavy chains are non-functional, what happens to the cell?
It undergoes apoptosis
What is allelic exclusion?
A cell expresses only one allele of a gene pair
What does allelic exclusion ensure?
That each B cell make only one receptor
If the first heavy chain allele produces a function pre B-cell receptor, what happens to the second heavy chain?
It is not produced
Is heavy chain or light change rearrangement more efficient? Why?
Light chain
Several attempts can be made instead of one attempt on each heavy chain gene
Which chain arrangements are tried first on each chromosome in light chain rearrangement?
κ chain
What is tried if there are no productive κ chain rearrangements?
λ chain rearrangements
What are rearranged light chains tested for?
Ability to form a functional B-cell receptor (second check point)
If the B-cell receptor is function in light chain rearrangement, what happens?
Light chain gene rearrangement ceases
What do many immature B cells have an affinity for?
Self-antigens
What can B cells not leave the bone marrow with?
Receptors that have a high affinity for self antigens
What are 2 things that self-reactive B cells can do?
Try somatic recombination again using different gene segments
Die by apoptosis
What is receptor editing?
Self-reactive B cells are allowed to continue rearranging the light chain
Why are B-cells eliminated?
If they cannot produce a receptor that does not self-react
What are the stages of B cell development from immature B cell to effector B cell? (9)
Immature B cell Negative selection Self tolerant immature B cell (IgM receptor) Alternative splicing of heavy chain mRNA Self tolerant immature B cell (IgM and IgD receptors) Maturation in secondary lymphoid tissue Mature naive B cell Activation by antigen Activated B cell
What are mature naive B cells contracted to secondary lymphoid tissues by?
Chemokines
What are chemises produced by?
Stromal cells and dendritic cells
What are mature naive B cells attracted to primary lymphoid follicles by?
Chemokines secreted by follicular dendritic cells
Where do B cells complete maturation?
Primary lymphoid follicle
What do B cells receive when the interact with follicular dendritic cells?
Pro-survival cytokines
What does continued B cell survival require?
Regular recirculation through primary lymphoid follicles
What happens to B cells if they don’t gain access to primary follicles?
They die by apoptosis
What is peripheral tolerance?
Tolerance of self-antigens induced outside a primary lymphoid tissue
What do self-reactive immature B cells do in the periphery?
Die by apoptosis
Become anergic
Is their receptor editing outside the bone marrow?
No
What are B cells activated by?
An encounter with an antigen
What do some B cells do? (2)
Differentiate immediately to plasma cells and secrete IgM Move to the germinal center and undergo somatic hypermutation and class switching
What do some B cells in the germinal center do?
Become memory B cells
What percentage do B1 cells account for of all B cells?
Approximately 5%
What do B1 cells arise from?
A different precursor that B2 cells (what we have been discussing)
What can B1 cells do in the periphery?
Self-renew
What does self-renew mean?
Not continuously produced by bone marrow
What do B1 cells produce?
A quick supply of antibodies against common carbohydrate antigens in bacteria
What are B1 cells referred to as?
Thymus independent B cells
What could B1 cells be considered?
More of an innate-like immune cells
When are B1 cells first produced? B2?
Fetus
After birth
How many N-regions in VDJ regions do B1 cells have? B2?
Few
Extensive
What is the B1 V region repertoire? B2?
Restricted
Diverse
What is the primary location of B1 cells? B2?
Peritoneal and pleural cavities
Secondary lymphoid organs
What is the model of renewal for B1 cells? B2?
Self renewing
Replaced from bone marrow
What is the level of spontaneous production of immunoglobulin for B1 cells? B2?
High
Low
What are the isotypes secreted in B1 cells and which one is greater? B2?
IgM much greater than IgG
IgG greater than IgM
Is there a requirement for T cell help for B1 cells? B2?
No
Yes
What is the level of somatic hypermutation in B1 cells? B2?
Low-none
High
Is there memory development in B1 cells? B2?
Little or none
Yes
Chapter 6 study guide
Chapter 6 study guide
Where do T cell precursors originate?
Bone maroow
What do T cell precursors mature into T cells?
Thymus
What kind of selection is in the thymus?
Positive and negative selection
What happens to the production of T cells in the thymus with age?
It decreases
What are the stages of T cell development from common lymphoid progenitor to α:β or γ:δ T cells? (8)
Common lymphoid progenitor
Uncommitted double negative thymocytes CD8- and CD4- (committed γ:δ T cells)
Rearrangement of γ δ β chains
Uncommitted double negative thymocytes pre T cell CD8- and CD4-
Cell divisions
Uncommitted double negative thymocytes CD8+ and CD4+(committed γ:δ T cells)
Rearrangement of γ δ α chains
Committed α:β thymocyte
How do the rearrangement of γ δ and β chains commence?
Simultaneously one chromosome at a a time for each gene
If γ and δ rearrange first, what happens to the cell?
It becomes a committed γ:δ T cell
If the β chain rearranges first, what happens to the cell?
It ceases rearrangements
How many times can each β chain attempt productive rearrangement?
2
What does each constant segment of a β chain have?
Its own associated D and J segments
How many attempts are there to produce a functional β chain since their is a D and J segment?
4
What are rearranged β chains tested for?
Ability to form a pre T cell receptor (checkpoint 1)
If the β chain on the first allele is non-functional, what happens to the β chain on the second allele?
It complete rearrangement
How many attempts can be made with α chain rearrangement?
Several
What does α chain rearrangement do?
Eliminates the δ chain gene segments
Is a functional α:β receptor or a γ:δ receptor more likely?
α:β receptor
What are rearranged α chains tested for?
Ability to form a T cell receptor
If a T cell receptor is formed, what happens?
Further rearrangements cease (checkpoint 2)
What are the stages of T cell development from committed α:β thymocyte to effector T cell? (9)
Committed α:β thymocytes Positive selection Restricted single positive thymocytes Negative selection Restricted single positive, tolerant, naive T cells Leave thymus Restricted single positive, tolerant, naive T cells Activation Effector T cell
What are T cells positively selected for?
The ability to bind a self MHC molecule
What are self peptides presented on?
MHC class I and II by cortical epithelial cells
What do T cells that bind self MHC signaled to do?
Survive
What do T cells that do not bind self MHC signaled to do?
Continue with receptor editing
What do unsuccessful T cells undergo?
Apoptosis
What does positive selection determine?
Which co-receptor is expressed, CD8 or CD4
If the self peptide binds to MHC class I, what does it become?
CD8 T cell
If the self peptide binds to MHC class II, what does it become?
CD4 T cell
Since a T cell receptor is specific for MHC alleles, what does it mean for hematopoietic stem cell transplants?
There must be a match between donor and recipient MHC alleles
What are T cell that bind too strongly to self peptide:self MHC complex induced to undergo?
Apoptosis
What participates in the negative selection of T cells? (3)
Dendritic cells
Macrophages
Specialized medulla thyme epithelial cells
In regulatory T cells, what happens with peripheral tolerance?
Tolerance to self antigens continues to develop
What do T cells that recognize self antigen in the absence of inflammation become?
Anergic
What do regulatory T cells recognize? What does it do?
Self antigen bound to self MHC
Suppress naive T cells that recognize an antigen presented by the same dendritic cell
Chapter 7 study guide
Chapter 7 study guide
Which cells undergo somatic recombination and junctional diversity to produce the receptor?
B cell and T cells
Which cells undergo hypermutation?
B cells
Which cells undergo class switching?
B cells
Which cell receptors recognize surface antigens? What about degraded peptides?
B cell receptors
T cell receptors
Which cell receptors recognize antigen presented on MHC molecules?
T cell receptors
Which cell undergo positive selection?
T cells
Which cells undergo negative selection?
B cells and T cells
Which selection, positive or negative, are central tolerance and peripheral tolerance a part of?
Negative selection
