Immunology Ch 4

P nucleotides

'Palindromic' nucleotides added into the junctions between immunoglobulin and T-cell receptor gene segments during the somatic recombinations that generate a rearranged variable-region sequence. They are an inverse repeat (palindrome) of the nucleotide sequence at the end of the adjacent gene segments

Fab (Fragment antigen binding)

A proteolytic fragment of IgG that consists of the light chain and the amino-terminal half of the heavy chain held together by a disulfide bond between the chains. It is called Fab because it is the 'fragment with antigen binding' specificity. In the intact IgG molecule, the parts corresponding to the Fab fragment are often called Fab or Fab arms.

Hypervariable regions (HV)

AKA complementarity-determining region. A short region of high diversity in amino acid sequence within the variable region of immunoglobulin and T-cell receptor chains. There are three CDRs (CDR1, 2, and 3) in each variable region, which collectively contribute to the antigen-binding site and determine the antigenic specificity. This is the most variable part of the variable domain.

Discontinuous (conformational) epitopes

An antigenic structure on a protein that is formed from several separate regions in the primary sequence of a protein brought together by protein folding. Antibodies that bind conformational epitopes bind only to native folded proteins.

agammaglobulinemia

An inability to make antibodies, reflected by abnormally low amounts or absence of antibodies in the blood.

Complement-determining regions

Another name for hypervariable region

Fc region (Fc piece)

Another name for the Fc fragment of an antibody

IgA is involved with:

Antibody invloved with: opsonin complement activation most abundant in mucosal secretions more made in body than any other antibody

IgD is involved with

Antibody invloved with: sensitization for killing by NK cells

IgE is involved with

Antibody involved with: sensitization of mast cells sensitization of basophils least abundant in serum

Monoclonal antibodies

Antibody produced y a single clone of B lymphocytes so that all the antibody molecules are identical in structure and antigen specificity.

Catalytic antibodies

Antibody that binds an antigen, chemically changes it, and then releases it.

Linear epitopes

Antigenic structure in a protein that consists of a linear sequence of amino acids within the protein's primary structure.

Fc receptors

Cell-surface receptor for the Fc portion of immunoglobulin isotypes.

Framework region

Comprises the β strands and loops not involved in antigen binding

heavy chain

Contributes arouns 50 kDa to the overall molecular weight of IgG

Somatic recombination

DNA recombination that occurs between gene segments in the immunoglobulin loci and T-cell receptoir loci in developing B cells and T cells, respectively. It generates a complete exon composed of a V gene segment and a J gene segment (and a D gene segment at the immunoglobulin and T-cell receptor heavy-chain loci) that encodes the variable region of an immunoglobulin or T-cell receptor polypeptide chain.

variable (V) gene segment

DNA sequence in the immunoglobulin or T-cell receptor genes that encodes the first 95 or so amino acids of the V domain. There are multiple different V gene segments in the germline genome. To produce a complete exon encoding a V domain, one V gene segment must be rearranged to join up with a J or a rearranged DJ gene segment

Acrtivation-induced cytidine deaminase (AID)

Enzyme that deaminated DNA at cytosine residues, converting them to uracil. The activity of this enzyme and the consequenct repair of the damaged DNA are the basis of fomatic hypermutation and isotype switching in activated B cells.

Terminal deoxynucleotidyl transferase (TdT)

Enzyme that inserts non-templated nucleotides (N nucleotides) into the junctions between gene segments during the rearrangement of the T-cell receptor and immunoglobulin genes.

Antiserum

Fluid component of clotted blood from an immune individual that contains antibodies against a given antigen. Contains a heterogeneous collection of antibodies that bind the antigen.

Fc (fragment crystallizable)

Fragment of an antibody that consists of the carboxy-terminal halves of the two heavy chains disulfide-bonded to each other by residual hinge region. It is produced by proteolytic cleavage of antibody. It is called Fc for 'fragment crystallizable'. In an intact antibody the part corresponding to the Fc fragment is called Fc, Fc region, or Fc piece.

Opsonins

Generaly name for antibodies and complement proteins that coat pathogens, thereby facilitating their phagocytosis by neutrophils or macrophages carrying receptors for the opsonin

Hyper-IgM syndrome (immunodeficiency)

Genetically determined immunodeficiency disease in which B cells cannot switch their immunoglobulin heavy-chain isotype, and so make unusually high amount of IgM and no other isotypes. It leads to abnormally susceptibility to infections with pyogenic bacteria, particularly in the sinuses, ears, and lungs. It can be due to several different underlying mutations.

Multivalent

Having more than one binding site for the same or different ligands

Neutralizing antibodies

High-affinity IgA and IgG antibodies that bind to pathogens and prevent their growth or entry into cells.

Hybridoma

Hybrid cell lines that make monoclonal antibodies of defined specificity. They are formed by fusing a specific antibody-producing B lymphocyte with a myeloma cell that grows in tissue culture and does not make any immunoglobulin chains of its own.

Which of the IgG subclasses is most efficient at activating complement? Why?

IgG3 is most efficient at complement activation. The hinge region of IgG3 is the longest of all the IgG subclasses. Its length and flexibility make the IgG3 Fc region more accessible for binding C1 compared with the other IgG subclasses

Which of the IgG subclasses is least efficient? Why?

IgG4 fails to activate complement because its Fc region binds C1 poorly.

Which of the IgG subclasses would you think was in principle most desirable for use as a therapeutic monoclonal antibody, and why? Are there any disadvantages to using this subclass and how might they be overcome?

IgG4 would be considered the most desirable in principle because it lacks the ability to activate complement, and so will not trigger complement-mediated inflammation, which could cause damage to the patient. However, the monoclonal IgG4 will swap immunoglobulin chains with the patient's IgG4 at high frequency, thus becoming functionally monovalent, comprising its ability to bind as strongly to antigen as the other, stable IgG subclasses. One solution would be to alter the CH3 region of IgG4 genetically in such a way that it cannot swap heavy:light chain units with other IgG4 antibodies but retains the inability to activate complement.

Allelic exclusion

In reference to B-cell development, the fact that each mature B cell expresses only one of the two immunoglobulin heavy-chain or light-chain alleles. For each locus, half of the cells in the B-cell population express the maternal allele, and the remaining cells express the paternal allele.

Hypervariable region

Located within a V domain and varies greatly between different antibodies

Naive B cells

Mature B cell that has left the bone marrow but has not yet encountered its specific antigen

Affinities

Measure of the strength with which one molecule binds to another at a single binding site

Affinity

Measure of the strength with which one molecule binds to another at a single binding site.

Chimeric monoclonal antibodies

Monoclonal antibody that combines mouse variable regions with human constant regions

Somatic hypermutation

Mutation that occurs at high frequency in the rearranged variable-region DNA segments of immunoglobulin genes in activated B cells, resulting in the production of variant antibodies, some of which have a higher affinity for the antigen.

N nucleotides

Non-templated nucleotides added at the junctions between gene segments of T-cell receptor and immunoglobulin heavy-chain variable-region sequences during somatic recombination. The N nucleotides contribute to the diversity of these molecules. They are not encoded in the gene segments but are inserted at random by the enzyme termical deoxynucleotidyltransferase (TdT).

Lambda

One of the two types of immunoglobulin light chain; the other is κ

Kappa

One of the two types of immunoglobulin light chain; the other is λ

Light chain

Pairs with the amino-terminal part of a heavy chain to form one of the two arms of an antibody

Ig-α/Ig-β

Polypeptide chains associated with the B-cell receptor that transduce signals to the interior of the B cell when the B-cell receptor binds antigen

Intravenous immunoglobulin (IVIG)

Preparation of serum gamma glubulin containing many different antibodies that is used as a treatment to replace antibodies and increase platelets in immunodeficiency and autoimmune diseases.

Constant (C) domains

Protein domain that makes up the constant regions of the immunoglobulin and T-cell receptor polypeptide chains and immunoglobulin light chains contain one constant domain; immunoglobulin heavy chains contain two or three, depending on the isotype.

Immunoglobulin-like domains

Protein domain that resembles the immunoglobulin domain in structure but is present in a variety of other proteins, including MHC class I and II molecules, CD4 and CD8

Immunoglobulin (Ig) domain

Protein structure module consisting of about 100 amino acids that fold into a sandwich of two β sheets held together by a disulfide bond. Immunoglobulin heavy and light chains are made up of a series of immunoglobulin domains. Similar domains are present in numerous other immune system proteins.

Humanize

Refers to the process by which a mouse monoclonal IgG having high affinity and specificity for an antigen of clinical interest is converted into an antibody that resembles a human IgG but retains the specificity and affinity of the mouse antibody. By means of genetic engineering the heavy and light chain CDR loops of a human IgG are replaced by the corresponding CDR loops from the mouse monoclonal antibody. This gives a humanized mouse monoclonal antibody. When administered to a patient the humanized antibody does not provoke a strong anti-IgG response, as it is the case for mouse antibody. Thus patients can be given multiple doses of humanized antibody over extended period of time, with much less risk of adverse side effects such as serum sickness.

Joining (J) gene segments

Relatively short DNS sequence present in multiple different copies at all immunoglobulin and T-cell receptor loci. At gene rearranegemnt, a J and a V gene segment are joined directly in immunoglobulin light-chain genes and T-cell receptor alpha and gamma chain genes, and via a D gene segment in the immunoglobulin heavy-chain gene and T-cell receptor beta and delta genes

Switch sequences or switch regions

Short DNA sequence preceding each heavy-chain constant region gene, at which somatic recombination occurs when B cells switch from producing one immunoglobulin isotype to another.

Diversity (D) gene segments

Short DNA sequence present in multiple versions in immunoglobulin heavy-chain loci and T-cell receptor beta and delta chains loci. In te rearranged functional genes at these loci, a D gene segment connect the V and J gene segments. The D stands for 'diversity', because the D gene segments provide additional diversity in these receptor chains.

Gene segments

Short DNA sequence that occurs in multiple slightly variable copies in the immunoglobulin and T-cell receptor genes, and from which the V-region gene is assembled.

Recombination signal sequences (RSS)

Short stretch of DNA flanking each of the gene segments that are rearranged to generate V-region exons. They are the sites at which somatic recombination occurs.

Flow cytometry

Technique in which individual cells can be counted or identified by their cell-surface molecules after fluorescent labeling.

Plasma cells

Terminally differentiated B lymphocyte that secreted antibody

Constant (C) region

That part of an immunoglobulin or T-cell receptor (or of its constituent polypeptide chains) that is of identical amino acid sequence in molecules of the same isotype but different antigen-binding specificities.

Variable (V) domain

The amino-terminal domain of immunoglobulin and T-cell receptor polypeptide chains. Paried variable domains make up the antigen-binding site.

Isotypes

The class of an immunoglobulin - a distinct heavy-chain constant region encoded by a different constant-region gene. The heavy-chain constant region determines the effector properties of each antibody class.

Immunoglobulin G (IgG)

The class of immunoglobulin having gamma heavy chains. The most abundant class of immunoglobulin in plasma.

Immunoglobulin A (IgA)

The class of immunoglobulin having α heavy chains. Typically present as a dimer in mucosal secretions. Monomeric in the blood.

Immunoglobullin D (IgD)

The class of immunoglobulin having δ heavy chains. It appears as surface immunoglobulin on mature naive B cells but its function is unknown. Transcription of IgD is coordinated with that of IgM.

Immunoglobulin M (IgM)

The class of immunoglobulin having μ heavy chains. The first immunoglobulin to appear on the surface of B cells and the first antibody secreted during an immune response. It is secreted in pentameric form.

12/23 rule

The fact that V(D)J recombination can only occur between gene segments with particular lengths of spacer in the recombination signal sequences, which means that a VH region cannot be joined directly to a JH region without the involvement of DH. Two types of spacers are 12 and 23 nucleotides in length,

Immunoglobulins

The general name for antibodies and B-cell antigen receptors

Affinity maturation

The increase in affinity of the antigen-binding sites of antibodies for antigen that occurs during the course of an adaptive immune response. It is the result of somatic hypermutation of the rearranged immunoglobulin V-gene region and the consequent selection of mutated B cells that make antigen receptors of higher affinity for their antigen.

Coding Joint

The joint between the ends of two rearranged immunoglobulin or T-cell receptor gene segments

Signal joint

The joint present in the circle of DNA that is formed as a byproduct of V(D)J recombination and discarded

Heavy (H) chains

The larger of two types of polypeptide in an immunoglubulin molecule. It consists of one variable domain and a number of constant domains. Immunoglobulin heavy chains come in variety of heavy-chain isotypes, or classes, each of which confers a distinctive effector function on the antibody molecule.

Constant region

The most conserved region of the molecule with limited variation between molecules

Immunoglobulin superfamily

The name given to all the proteins that contain one or more immunoglobulin or immunoglobulin-like domains.

Avidity

The overall strength of binding of an antibody with multiple binding sites to an antigen (also with multiple sites)

V domain

The part of the antibody that binds antigen

Antigenic determinant (epitope)

The portion of an antigenis molecule that is bound by an antibody or gives rise to the MHC-binding peptide that is recognized by a T-cell receptor.

Isotype (class) switching

The process by which a B cell changes the class of immunoglobulin it makes whilt preserving the antigenic soecificity of the immunoglobulin. Involves a somatic recombination process that attaches a different heavy-chain constant-region gene to the existing variable-region exon.

Framework regions

The relatively invariant amino acid sequences within the variable domains of immunoglobulins and T-cell receptors that provide a structural scaffold for the antigen-binding complementarity-determining regions.

V(D)J recombinase

The set of enzymes needed to recombine V, D, and J segments in the rearrangement of immunoglobulin and T-cell receptor genes. Includes RAG-1 and RAG-2 proteins

Antigen-binding site

The site oon the immunoglobulin or T-cell receptor molecule that binds specific antigen

Light (L) chains

The smaller of the two types of polypeptide chains in an immunoglobulin molecule. It consists of one variable and one constant domain, and id disulfide-bonded to a heavy chain in the immunoglobulin molecule. There are two classes: kappa and lambda.

Antibody repertoire

The total number of different specific antibodies that can be made by an individual, estimated at around 10^9

Germline form (configuration)

The unrearranged organization of the immunoglobulin and T-cell receptor genes in the DNA of germ cells and in somatic cells other than T cells and B cells.

Recombination-activation genes

Two genes that are essential for the rearrangement of immunoglobulin and T-cell receptor genes in B cells and T cells, respectively. They encode the proteins RAG-1 and RAG-2, which form a protein complex that catalyzes the recombination process.

When IgG is cleaved with a protease that targets the hinge region, which of the following is generated? a. Two Fab fragments and one Fc fragment b. Two Fc fragments and two Fab fragments c. Fc fragments that bind antigen d. Fab fragments that facilitate antibody effector function e. A membrane-bound form of antibody

a. Two Fab fragments and one Fc fragment

The phenomenon of allelic exclusion ensures that B cells a. Use only one V, D, and J segment during somatic recombination b. Express only one type of heavy chain and one type of light chain c. Do not undergo alternative splicing until cell proliferation commences. d. Do not secrete antibody until antigen is encountered. e. Carry out affinity maturation directed at heavy chains and not light chains f. Derived from B-cell lymphomas are heterogeneous.

b. Express only one type of heavy chain and one type of light chain

Humanized monoclonal antibodies are best described as a. Antibodies made in mice in which the mouse antibody genes have been replaced with human equivalents b. Human antibodies in which the CDR loops have been replaced by mouse-derived CDRs of the desired specificity c. Antibodies made in culture by human hybridomas d. Antibodies containing mouse Fab regions of both the heavy and light chain and human Fc regions e. Antibodies containing human Fab regions of both the heavy and light chain and mouse Fc receptors.

b. Human antibodies in which the CDR loops have been replaced by mouse-derived CDRs of the desired specificity

A protein epitope formed as a result of three-dimensional folding of the protein, and which is destroyed if the protein denatures, is called ______ epitope. a. Linear b. Multivalent c. Conformational d. Complementarity e. Framework

c. Conformational

Which of the following recombinations is not permitted during somatic recombination in the heavy-chain and light-chain immunoglobulin loci? (Select all that apply) a. DH : JH b. V lambda : J lambda c. D kappa : VH d. VH : JH e. VH : DH

c. D kappa : VH d. VH : JH

Which of the following statements regarding the process of differential splicing of primary RNA transcripts encoding immunoglobulins is incorect? a. It does not require rearrangement of genomic DNA sequences. b. It underlies the production of both membrane-bound IgM and IgD in naive B cells. c. It is the mechanism involved in isotype switching. d. It occurs during B-cell differentiation into plasma cells when antibodies are produced in their secreted form. e. It permits the production of different types of protein originating from the same RNA transcript.

c. It is the mechanism involved in isotype switching.

The antigen-binding site of an immunoglobulin is formed from a. The V regions of light chains only b. The C regions of heavy chains only c. Paired V regions of a single heavy chain and a single light chain d. Paired V regions of two light chains e. Paired C regions of two heavy chains

c. Paired V regions of a single heavy chain and a single light chain

IgM is involved with

complement activation

Which of the following statements best explains why the immune system can continue to make antibodies after treatment with the anti-CD20 antibody rituximab? a. New CD20-positive B cells are reconstituted so quickly that antibody concentration during and after treatment is unaffected. b. Rituximab stimulates B-cell proliferation, so far a short while after its administration there is actually an increase in antibody concentration c. Rituximab is a mouse monoclonal antibody and therefore its Fc region is unable to bind to the surface receptors on human NK cells that bind to Fc. d. Plasma cells do not express CD20 on their cell surface, and antibody production by these cells continues unhampered. e. Rituximab stimulates anti-antibody production, leading to its rapid clearance by the body.

d. Plasma cells do not express CD20 on their cell surface, and antibody production by these cells continues unhampered.

Three-week-old Xavier Capelleto was brought to the emergency room with a bright scaly rash that first developed on his legs and then spread to his trunk and face. He also had blisters on his palms and the soles of his feet. Xavier's parents said that he had been experiencing looser bowel movements than expect, a large amount of yellow pus had been accumulating around the swollen eyelids, and he showed signs of oral thrush. Tests revealed that Zavier's lymphocyte count was only 8% of total white blood cells (normal 50%), all immunoglobulins were markedly decreased except for IgE, and no thymic shadow was detected on a chest X-ray. Eosinophilia was also detected. His parents were told that Xavier had an autosomal recessive form of severe combined immunodeficiency (SCID) known as Omenn syndrome, which affects the development of both B cells and T cells. A bone marrow transplant was recommended; however, Xavier died from respiratory failure due to an opportunistic bacterial infection. This history is consistent with a genetic deficiency in a. alpha or beta-defensins b. Activation-induced cytidine deaminase (AID) c. MHC class I d. RAG-1 or RAG-2 e. Toll-like receptors

d. RAG-1 or RAG-2

The numbered events listed below participate in the generation of junctional diversity. Put them in chronological order. a. DNA strands pair, and unpaired nucleotides are removed by exonuclease activity b. P-nucleotides are generated after nicking of one DNA strand c. DNA polymerase fills in gaps, and DNA ligation forms a coding joint. d. The RAG complex cleaves heptamer RSSs, and DNA hairpins are formed. e. Terminal deoxynucleotidyl transferase adds N-nucleotides to the 3' end of the stretch of P-nucleotides.

d. The RAG complex cleaves heptamer RSSs, and DNA hairpins are formed. b. P-nucleotides are generated after nicking of one DNA strand e. Terminal deoxynucleotidyl transferase adds N-nucleotides to the 3' end of the stretch of P-nucleotides. a. DNA strands pair, and unpaired nucleotides are removed by exonuclease activity c. DNA polymerase fills in gaps, and DNA ligation forms a coding joint.

Which of the following does not contribute to generating the diversity of antigen-binding specificities among immunoglobulins? a. Somatic hypermutation b. Random combination of heavy and light chains c. Somatic recombination d. Activation-induced cytidine deaminase (AID) e. Alternative splicing of heavy-chain RNA transcripts

e. Alternative splicing of heavy-chain RNA transcripts

Aliya Agassi, a 3-year-old girl with pneumonia, a temperature of 40.8C, respirations 42 per minute (normal 20), and blood oxygen saturation of 90% (normal is more than 98%), was admitted to the hospital. Her neck and armpit lymph nodes were enlarged, and X-rays confirmed inflammation in the lower lobe of her right lung. Her medical history revealed two previous cases of pneumonia and six middle-ear infections that were treated successfully with antibiotics. A blood culture grew Haemophilus influenzae. Blood testss showed elevated levels of IgM above normal levels of serum IgA and IgG were not detected. Her father had normal levels of IgA, IgG, and IgM. Which of the following is the most likely cause fo her symptoms? a. Acute lymphoblastic leukemia b. IgA deficiency c. X-linked agammaglobulinemia d. Severe combined immunodeficiency e. X-linked hyperIgM syndrome f. AID deficiency g. Myeloma

f. AID deficiency

IgG is involved with

opsonin complement activation transport cross placenta most abundant in serum sensitization of mast cells sensitization for killing by NK cells

Clonal selection

the central principle of adaptive immunity. It is the mechanism by which adaptive immune responses derive only from individual antigen-specific lymphocytes, which are stimulated by the antigen to proliferate and differentiate into antigen-specific effector cells.

Immunoglobulin E (IgE)

the class of immunoglobulin having ε heavy chains. Involved in reactions against internal parasites, particularly helminth worms, and in allergic reactions.

Variable (V) region

the part of an immunoglobulin or T cell receptor, or of its constituent polypeptide chains, that varies in amino acid sequence between isoforms with different antigenic specificities. It is responsible for determining antigen specificity.