Exam 2: Chapter 4 Flashcards
What are some properties of IgG?
Transport across placenta, diffusion into extravascular sites
What receptor is IgM missing that makes it unrecognizable to macrophages/neutrophils?
Fc receptor
What fragments are formed when papain cleaves an antibody?
Two fragment antigen binding (Fab) fragments and a fragment crystallizable (Fc) fragment
What does the antigen binding region interact with?
The epitopes on the surface of pathogens
What two joints form during combinational diversity?
A signal joint (lost over time) and a coding joint (codes for protein)
What regions surround the Hypervariable regions?
Frame work regions
What is somatic hypermutation?
Process by which activated B cells will try to increase V domain diversity by mutating the V coding sequences
How is the expression of IgM and IgD regulated?
Alternative splicing
What is a naïve B cell?
A B cell that has rearranged both heavy chains and both light chains
What is the function of the RAG 1 and RAG 2 complex?
To cut the DNA
Where does antibody flexibility come from?
The hinge region
What is a unique property of IgG4?
In circulation, two IgG4 molecules can exchange pieces to form functionally monovalent antibodies that recognize two things
What are the three hypervariable regions called?
Complementarity Determining Regions (CDR) 1, 2, and 3
What are recombination signal sequences?
Conserved recognition sequences that are 7 and 9 bp long, separated by either a 12 or 23 bp spacer
What does the 12/23 rule ensure?
That VJ always join in light chains, and that VDJ always join in heavy chains
What is affinity?
The binding strength of an antibody
What is flow cytometry?
A method that is used to analyze cell populations or sort cells by Fluorescence Activated Cell sorting (FACs)
How are the three hypervariable regions encoded?
Two are encoded by sequence differences in the V segment, and the third is generated by the junction of VJ and VDJ in the light and heavy chains
What two forms of IgA are produced?
Monomers and dimers
How are antibodies produced?
By B lymphocytes that secret them into the plasma of blood and lymph
What is a main function of IgA?
Neutralization
Which antibody is the most abundant in the blood and lymph?
IgG
What is the first antibody made by B cells?
IgM
What type of molecule has the ability to digest antibodies?
Proteases
What does the heavy chain encode?
Both the antigen binding region and the constant region
Is class switching reversible or irreversible?
Irreversible
What are Ig-alpha and Ig-beta?
Co-receptors that allow newly made B cell receptors to transit through the ER and golgi to the cell surface; once on the surface they signal into the cell that the antigen receptor is bound to its antigen
What happens when a naïve B cell recognizes an antigen?
It becomes activated and starts to proliferate and secrete antibodies
What are hybridomas?
Fusion cells formed from activated B cells and myeloma cells
What are linear epitopes?
Epitopes whose structure is formed by adjacent connected components
How does junctional diversity increase the size of the antibody repertoire?
Since the repairing of cleaved chromosomes is sloppy, new DNA sequences can be added to the junction between the segments
What are the two types of light chain?
Kappa and lambda
What are some functions of IgG?
Neutralization, opsonization, activation of complement
How large is the antibody repertoire estimated to be?
10^16 different antibody types
How do light chain variable regions develop?
A single VL segment is combined with a single JL segment
What is the main function of IgM?
To activate complement
What type of forces allow for antigen binding domains to interact with epitopes?
Non-covalent forces, including electrostatic forces, hydrogen bonds, van der Waals forces, hydrophobic interactions
What are some functions of antibodies?
Neutralize toxins and viruses, opsonize pathogens
What domain of the antibody varies?
The antigen-binding sites (variable region)
What is important about hybridomas?
They are immortal cells that can continuously produce antibodies
What enzymes are involved in somatic hypermutation?
Activation induced cytidine deaminase (AID) and Uracil-DNA glycosylase (UDG)
Why does class switching play an important role in the immune response?
Each constant region has distinct effector functions
What are switch regions?
Sequences upstream of the different constant regions that are recognized by class switch machinery, resulting in the removal of intervening sequences and the production of a new isotype
What segments encode the variable region of the light chain?
The variable (V) and joining (J) segments
What does the light chain encode?
Antigen binding regions
What is the 12/23 rule?
A 23 bp RSS spacer will only combine with a 12 bp RSS spacer, and vice versa
What are the medical implications of IgE?
It is important for fighting parasites, but also causes allergies
Which IgG subclasses directly recruit phagocytes?
IgG1 and IgG3
How many Ig domains form a light chain?
2
What is the function of Artemis?
To join chromosome ends
What happens in patients with AID mutations?
They are unable to undergo class switching, which prevents them from forming any antibodies other than IgM (hyper IgM syndrome)
What immunoglobulin changes are reversible and regulated?
Transcription activated with coexpression of IgM and IgD, synthesis changes from membrane Ig to secreted antibody
What are the two poly-Adenylation sites, and what do they each encode?
pAum codes for a membrane protein, while pAus codes for a secreted protein (antibody)
What is allelic exclusion?
The mechanism by which each B cell only rearranges one heavy and one light chain, ensuring it will only recognize a single antigen
What is the function of DNA-PK?
To recognize broken ends of the DNA
How does combinational diversity work?
Heavy and light chain genes contain various gene segments that can be randomly combined to form different functional heavy and light chains
How are class switching and somatic recombination similar?
Both have sequences that are recognized and cut, and the information in between the cuts is removed
What does “humanizing of antibodies” do?
Replaces the heavy and light chains of monoclonal antibodies made in other species with the human version of the chains, in order to prevent human immune systems from recognizing the antibodies as foreign
What are discontinuous epitopes?
Epitopes whose structure is made up of components that are not adjacent, but come together to form an epitope site
What is the process of generating new high affinity antibodies called?
Affinity maturation
What are monoclonal antibodies?
Large antibody quantities that are all the same and come from a single activated B cell
How is IgM secreted?
As a pentamer
Where are the mutations of somatic hypermutation concentrated?
In the hypervariable regions (CDRs)
What is IgE?
A specialized antibody that functions in conjunction with mast cells
What holds the two halves of an antibody together?
Disulfide bonds
How many different antigen receptors can each B cell make?
1
What happens when a B cell recognizes an antigen?
A signal is propagated by the antigen receptor that stimulates the differentiation and maturation of the B cell into a plasma cell, which secretes antibodies
What proteins catalyze the somatic recombination reaction?
Recombinase Activating Genes 1 and 2 (RAG1 and 2), and the non-homologous end joining (NHEJ) proteins DNA Ligase IV, DNA-PK, Artemis, and Ku
What is isotype switching/class switching?
Process by which antibodies switch their constant regions in order to tailor their response to a pathogen and improve effector functions
What is the main function of IgD?
To bind to basophils in the respiratory tract
How many polypeptide chains is each antibody made up of?
4 - 2 heavy chains and 2 light chains
What polypeptide chains are antibodies made up of?
Heavy chains and light chains
What is the entire collection of antibodies made by a person called?
Antibody repertoire
Why must antibodies be incredibly stable?
The environments in which they work are hostile, and could potentially destabilize their structure
How do the four subclasses of IgG differ?
They have variations in the length and bonding of their hinge regions
How are class switching and somatic hypermutation similar?
Two of the enzymes used in somatic hypermutation (AID and UDG) also function in class switching
Why is there very little IgE in circulation?
It binds very tightly to the IgE receptor on mast cells
What type of epitope can still be recognized after being denatured?
Linear epitopes
What structures correspond to the frame work and hypervariable regions?
The frame work regions are beta sheets, while the hypervariable regions are loops
How many subclasses of IgG exist?
4 (IgG1, IgG2, IgG3, IgG4)
How do antibodies interact with pathogens?
They bind to specific epitopes on the pathogen surface
What provides stability to antibodies?
Repeats of similar sequence motifs that form the Immunoglobulin (Ig) domain
What is somatic recombination?
The combination of gene segments during B cell development that results in the random joining of VJ and VDJ segments
How does junctional diversity occur?
The RAG complex cleaves recombination signal sequences, forming hairpins that are subsequently cleaved by Artemis to form palindromes. Nucleotide bases are added to the 3’ ends of the palindromes by Terminal deoxynucleotide Transferase (TdT), and the strands pair. Unpaired nucleotides are removed by exonuclease, and the gaps are filled in by DNA synthesis and ligation to form the coding joint
What are catalytic antibodies?
Antibodies that can also catalyze chemical reactions
What is the main property of the IgA monomer?
Diffusion into extravascular sites
Which antibody domain interacts with effector cells?
The constant region
How does class switching work?
AID causes a Cytosine to Uracil base switch. UDG then removes the Uracil since it does not match with Guanine, leaving an a-basic space behind. APE then cuts out the non-base, leaving a single stranded gap called a nick. DNA ends up nicked in two switch regions, and these two switch regions come together, forming a loop. The loop is removed, and the two remaining fragments are joined together to form a new protein sequence
What is the function of Ku?
To bind to broken DNA ends and recruit the other NHEJ proteins
What is the purpose of somatic hypermutation?
To generate B cells with higher affinity, which will eventually become memory cells
What immunoglobulin changes are irreversible?
V-region assembly, generation of junctional diversity, assembly of transcriptional controlling elements, somatic hypermutation, and class switching
How do heavy chain variable regions develop?
A single DH segment is combined with a single JH segment; a single VH segment then adds to the DH portion of the DJ complex
Where is the dimer of IgA produced?
In the mucosal tissues
What types of antibodies are expressed on the surface of naïve B cells?
IgM and IgD
What are the two types of diversity generated in B cells?
Combinational diversity and junctional diversity
Which antibody is most abundant in tears, milk, and saliva?
IgA
What are multivalent pathogens?
Pathogens with multiple epitopes, either different or repeating
What fragments are formed when pepsin cleaves an antibody?
A main F(ab)2 fragment and several smaller fragments of the destroyed Fc
What segments encode the variable region of the heavy chain?
The variable (V), diversity (D), and joining (J) segments
What protein holds the dimer of IgA together?
J chain protein
What is the function of DNA Ligase IV?
To seal breaks in the DNA
What is the main property of the IgA dimer?
Transport across epithelium
What are the five antibody isotypes, and what heavy chain constant regions do they have?
IgA - alpha IgD - delta IgM - mu IgG - gamma IgE - epsilon
What molecule cleaves the DNA hairpin?
Artemis
Where are the differences in the variable region of antibodies concentrated?
In the Hypervariable Regions (HVs) of the antibody
