Chapter 18 Somatic Recombination and Hypermutation in the Immune System

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Chapter 18Somatic Recombination and
Hypermutation in the Immune System
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18.1 The Immune System Innate and Adaptive
Immunity

• antigen A molecule that can bind specifically
  to an antigen receptor, such as an antibody.
• B cell A lymphocyte that produces antibodies.
  Development occurs primarily in bone marrow.
• B cells emerging from the marrow undergo further
  differentiation in the bloodstream and peripheral
  lymphoid organs.

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18.1 The Immune System Innate and Adaptive
Immunity

• T cells Lymphocytes of the T (thymic) lineage.
  T cells differentiate in the thymus from stem
  cells of bone marrow origin.
• They are grouped in several functional types
  (subsets) according to their phenotype, mainly
  expression of surface proteins CD4 and CD8.
• Different T cell subsets are involved in
  different cell-mediated immune responses.

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18.1 The Immune System Innate and Adaptive
Immunity

• adaptive (acquired) immunity The response
  mediated by lymphocytes that are activated by
  their specific interaction with antigen.
• The response develops over several days as
  lymphocytes with antigen-specific receptors are
  stimulated to proliferate and become effector
  cells.
• It is responsible for immunological memory.

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18.1 The Immune System Innate and Adaptive
Immunity

• B cell receptor (BCR) The receptor for antigen
  expressed on the surface of B lymphocytes.
• The BCR has the same structure and specificity of
  the antibody that will be produced by the same B
  cell after its activation by antigen.

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18.1 The Immune System Innate and Adaptive
Immunity

• T cell receptor (TCR) The antigen receptor on T
  lymphocytes.
• It is clonally expressed and binds to a complex
  of MHC class I or class II protein and
  antigen-derived peptide.
• Antibody response An immune response that is
  mediated primarily by antibodies. It is defined
  as immunity that can be transferred from one
  organism to another by serum antibody.

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18.1 The Immune System Innate and Adaptive
Immunity

• innate immunity A response triggered by
  receptors whose specificity is predefined for
  certain common motifs found in bacteria and other
  infective agents.
• The receptor that triggers the pathway is
  typically a member of the Toll-like receptor
  (TLR) family, and the pathway resembles the
  pathway triggered by Toll receptors during
  embryonic development.
• The pathway culminates in activation of
  transcription factors that cause genes to be
  expressed whose products inactivate the infective
  agent, typically by permeabilizing its membrane.

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18.2 The Innate Response Utilizes Conserved
Recognition Molecules and Signaling Pathways

• Innate immunity is triggered by pattern
  recognition receptors (PRRs) that recognize
  highly conserved microbe-associated molecular
  patterns (MAMPs) found in bacteria, viruses, and
  other infectious agents.
• PAMPs Pathogen-associated molecular patterns,
  now referred to as MAMPs, are broadly conserved
  microbial components, including bacterial
  flagellin and lipopolysaccharides, that are
  recognized by PRRs, which critically initiate
  innate immune responses.

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18.2 The Innate Response Utilizes Conserved
Recognition Molecules and Signaling Pathways
Figure 18.01 Innate immunity a summary of MAMPs
and PRRs.
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18.2 The Innate Response Utilizes Conserved
Recognition Molecules and Signaling Pathways

• Toll-like receptors (TLRs) are important PRRs
  that directly activate innate immune responses
  and direct the initial stages of adaptive
  responses. TLRs are expressed in dendritic cells
  (DCs), macrophages, neutrophils, B lymphocytes,
  and some T lymphocytes.
• TLR signaling pathways are highly conserved from
  invertebrates to vertebrates and an analogous
  pathway is found in plants.

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18.2 The Innate Response Utilizes Conserved
Recognition Molecules and Signaling Pathways

• Toll/interleukin 1/resistance (TIR) domain The
  key signaling domain unique to the TLR system.
• TIR is located in the cytosolic face of each TLR,
  and also in TLR adaptors.
• Similar to the TLRs, the adaptors are conserved
  across many species.
• These adaptors are MyD88, MyD88-adaptor-like
  (MAL, also known as TIRAP), TIR-domain-containing
  adaptor protein inducing IFN (TRIF also known as
  TICAM1), TRIF-related adaptor molecule (TRAM
  also known as TICAM2), and sterile
  armadillo-motif-containing protein (SARM).

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18.3 Adaptive Immunity

• Helper T (Th) cells produce signals required by B
  cells to enable them to differentiate into
  antibody-producing cells.
• complement A set of 20 proteins that function
  through a cascade of proteolytic actions to lyse
  infected target cells, or to attract macrophages.
• cell-mediated response The immune response that
  is mediated primarily by T lymphocytes, and
  defined based on immunity that cannot be
  transferred from one organism to another by serum
  antibody.

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18.3 Adaptive Immunity
Figure 18.04 Free antibodies bind to antigens to
form antigen-antibody complexes.
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18.3 Adaptive Immunity

• Cytotoxic T cells (CTLs) or killer T cells are
  responsible for the cell-mediated response in
  which fragments of foreign antigens are displayed
  on the surface of a cell.
• These fragments are recognized by the TCR
  expressed on the surface of T cells.

Figure 18.05 Cell-mediated immunity.
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18.3 Adaptive Immunity

• In TCR recognition, the antigen must be presented
  in conjunction with a major histocompatibility
  complex (MHC) molecule.
• autoimmune disease A pathological condition in
  which the immune response is directed to self
  antigen.

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18.4 Clonal Selection Amplifies Lymphocytes That
Respond to a Given Antigen

• clonal selection The theory proposed that each
  lymphocyte expresses a single antigen receptor
  specificity and that only those lymphocytes that
  bind to a given antigen are stimulated to
  proliferate and to function in eliminating that
  antigen.
• Thus, the antigen "selects" the lymphocytes to be
  activated.
• Clonal selection was originally a theory, but it
  is now an established principle in immunology.

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18.4 Clonal Selection Amplifies Lymphocytes That
Respond to a Given Antigen
Figure 18.06 The B cell and T cell repertoires
include BCRs and TCRs with a variety of
specificities.
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18.4 Clonal Selection Amplifies Lymphocytes That
Respond to a Given Antigen

• Each B cell expresses a unique BCR and each T
  cell expresses a unique TCR.
• A broad repertoire of BCRs/antibodies and TCRs
  exists at any time in an organism.
• Antigen binding to a BCR or TCR triggers the
  clonal proliferation of that receptor-bearing B
  or T cell.

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18.4 Clonal Selection Amplifies Lymphocytes That
Respond to a Given Antigen

• hapten A small molecule that can elicit an
  immune response only when conjugated with a
  carrier, such as a large protein.
• Once antibodies have been induced by the
  carrier-conjugated hapten, the hapten will in
  general bind those antibodies.
• epitope The portion of an antigen that is
  recognized by the antigen receptor on
  lymphocytes.
• It is also called the antigenic determinant.

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GENE RECOMBINATION VIDEO
http//www.youtube.com/watch?vAxIMmNByqtM
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18.5 Ig Genes are Assembled from Discrete DNA
Segments in B Lymphocytes

• An antibody (immunoglobulin) consists of a
  tetramer of two identical light (L) chains and
  two identical heavy (H) chains. There are two
  families of L chains (Ig? and Ig?) and a single
  family of IgH chains.
• Each chain has an N-terminal variable (V) region
  and a C-terminal constant (C) region. The V
  region recognizes the antigen and the C region
  mediates the effector response.

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18.5 Ig Genes are Assembled from Discrete DNA
Segments in B Lymphocytes

• V and C regions are separately encoded by V(D)J
  gene segments and C gene segments.
• A gene coding for a whole Ig chain is generated
  by somatic recombination of V(D)J genes
  (variable, diversity, and joining genes in the H
  chain variable and joining genes in the L chain)
  giving rise to V domains, to be expressed
  together with a given C gene (C domain).

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18.6 L Chains Are Assembled by a Single
Recombination Event

• A ? chain is assembled through a single
  recombination event involving a V? gene segment
  and a J?-C? gene segment.
• The V? gene segment has a leader exon, an intron,
  and a V?-coding region. The J?-C? gene segment
  has a short J?-coding exon, an intron, and a
  C?-coding region.

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18.6 L Chains Are Assembled by a Single
Recombination Event
Figure 18.08 The Cl gene segment is preceded by
a J segment, so that Vl-Jl recombination
generates a productive Vl-JlCl.
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18.6 L Chains Are Assembled by a Single
Recombination Event

• A ? chain is assembled by a single recombination
  event involving a V? gene segment and one of five
  J? segments preceding the C? gene.

Figure 18.09 The Ck gene segment is preceded by
multiple J segments in the germ line.
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18.7 H Chains Are Assembled by Two Sequential
Recombination Events

• The units for H chain recombination are a VH
  gene, a D segment, and a JH-CH gene segment.
• The first recombination joins D to JH-CH. The
  second recombination joins VH to DJH-CH to yield
  VH-DJH-CH.
• The CH segment consists of four exons.

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18.7 H Chains Are Assembled by Two Sequential
Recombination Events
Figure 1810 Heavy genes are assembled by
sequential recombination events.
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18.8 Recombination Generates Extensive Diversity

• The human IgH locus can generate in excess of 104
  VHDJH sequences.
• Imprecision of joining and insertion of unencoded
  nucleotides further increases VHDJH diversity to
  106 sequences.
• Recombined VHDJH-CH can be paired with in excess
  of 104 recombined V?J?-C? or V?J?-C? chains.

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18.8 Recombination Generates Extensive Diversity
Figure 18.13 A single gene cluster in humans
contains all the information for the IgH chain.
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18.9 V(D)J DNA Recombination Uses RSS and Occurs
by Deletion or Inversion

• The V(D)J recombination machinery uses consensus
  sequences consisting of a heptamer separated by
  either 12 or 23 base pairs from a nonamer
  (recombination signal sequence, RSS).

Figure 18.14 RSS sequences are present in
inverted orientation at each pair of recombining
sites.
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18.9 V(D)J DNA Recombination Uses RSS and Occurs
by Deletion or Inversion

• Recombination occurs by double-strand DNA breaks
  (DSBs) at the heptamers of two RSSs with
  different spacers 12/23 rule.

Figure 18.15 Breakage and recombination at RSSs
generate VJC sequences.
Adapted from D. B. Roth, Nat. Rev. Immunol. 3
(2003) 656-666.
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18.9 V(D)J DNA Recombination Uses RSS and Occurs
by Deletion or Inversion

• The signal ends of the DNA excised between two
  DSBs are joined to generate a DNA circle or
  signal circle. The coding ends are ligated to
  join VL to JL-CL (L chain), or D to JH-CH and VH
  to DJH-CH (H chain). If the recombining genes lie
  in an inverted rather than direct orientation,
  the intervening DNA is inverted and retained,
  instead of being excised as a circle.

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18.10 Allelic Exclusion Is Triggered by
Productive Rearrangements

• V(D)J gene rearrangement is productive if it
  leads to expression of a protein.
• A productive V(D)J gene rearrangement prevents
  any further rearrangement of the same kind from
  occurring, whereas a nonproductive rearrangement
  does not.
• Allelic exclusion applies separately to L chains
  (only one V?J? or V?J? may be productively
  rearranged) and to VHDJH chains (one H chain is
  productively rearranged).

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18.10 Allelic Exclusion Is Triggered by
Productive Rearrangements
Figure 18.16 A successful rearrangement to
produce an active light or heavy chain suppresses
further rearrangements, resulting in allelic
exclusion.
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18.11 RAG1/RAG2 Catalyze Breakage and Religation
of V(D)J Gene Segments

• The RAG proteins are necessary and sufficient for
  the cleavage reaction.
• RAG1 recognizes the nonamer consensus sequences
  for recombination.
• RAG2 binds to RAG1 and cleaves DNA at the
  heptamer.
• The reaction resembles the topoisomerase-like
  resolution reaction that occurs in transposition.

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18.11 RAG1/RAG2 Catalyze Breakage and Religation
of V(D)J Gene Segments
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18.11 RAG1/RAG2 Catalyze Breakage and Religation
of V(D)J Gene Segments

• The reaction proceeds through a hairpin
  intermediate at the coding end opening of the
  hairpin is responsible for insertion of extra
  bases (P nucleotides) in the recombined gene.
• Terminal deoxynucleotidyl transferase (TdT)
  inserts additional unencoded N nucleotides at the
  V(D)J junctions.
• The DSBs at the coding joints are repaired by the
  same mechanism that has generated the whole V(D)J
  sequence.

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18.11 RAG1/RAG2 Catalyze Breakage and Religation
of V(D)J Gene Segments

• severe combined immunodeficiency (SCID) A
  syndrome that stems from mutations in different
  genes that result in B and/or T cell deficiency.
• X-linked SCID is due to IL-2R ? chain gene
  mutations autosomal recessive SCID can be due to
  RAG1/RAG2 mutations, Artemis gene mutations, Jak3
  gene mutations, ADA gene mutations, IL-7R a-chain
  mutations, CD3 d or e mutations, or CD45 gene
  mutations.

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18.12 B Cell Differentiation Early IgH Chain
Expression Is Modulated by RNA Processing

• All B lymphocytes newly emerging from the bone
  marrow express the membrane-bound monomeric form
  of IgM (Igµm).
• As the B cell matures after exiting the bone
  marrow, it expresses surface IgD at a high
  levels. Such IgD consists of Igdm containing the
  same VHDJH sequence paired with the same
  recombined ? or ? chain as the IgM expressed by
  the same cell.

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18.12 B Cell Differentiation Early IgH Chain
Expression Is Modulated by RNA Processing

• A change in RNA splicing causes µm to be replaced
  by the secreted form (Igµs) after a mature B cell
  is activated and begins differentiation to
  antibody-producing cells in the periphery.

Figure 18.19 The 3 end of each CH gene cluster
controls the use of splicing junctions so that
alternative forms of the heavy gene are
expressed.
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18.13 Class Switching Is Effected by DNA
Recombination (Class Switch DNARecombination,
CSR)

• Igs comprise five classes according to the type
  of CH chain.

Figure 18.20 Immunoglobulin type and functions
are determined by the H chain.
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18.13 Class Switching Is Effected by DNA
Recombination (Class Switch DNARecombination,
CSR)

• Class switching is effected by a recombination
  between S regions that deletes the DNA between
  the upstream CH region gene cluster and the
  downstream CH region gene cluster that is the
  target of recombination.

Figure 18.21 Class switching of CH genes.
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18.13 Class Switching Is Effected by DNA
Recombination (Class Switch DNARecombination,
CSR)

• CSR relies on a molecular machinery that is
  different from that of V(D)J recombination and is
  acting later in B cell differentiation.

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18.14 CSR Involves AID and Elements of the NHEJ
Pathway

• CSR requires activation of intervening promoters
  (IH promoters) that lie upstream of each of the
  two S regions involved in the recombination event
  and germline IH-CH transcription through the
  respective S regions.
• S regions contain highly repetitive 5'-AGCT-3'
  motifs. 5'-AGCT-3' repeats are the main targets
  of the CSR machinery and DSBs.

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18.14 CSR Involves AID and Elements of the NHEJ
Pathway
Figure 18.22 Class switching passes occurs
through sequential and discrete stages.
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18.14 CSR Involves AID and Elements of the NHEJ
Pathway

• activation-induced (cytidine) deaminase (AID)
  An enzyme that removes the amino group from the
  cytidine base in DNA.
• AID mediates the first step (deoxycytidine
  deamination) in the series of events that lead to
  insertion of DSBs within S regions the DSBs
  free ends are then religated through an NHEJ-like
  reaction or A-EJ pathway.

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18.15 Somatic Hypermutation (SHM) Generates
Additional Diversity

• Somatic hypermutation (SHM) introduces somatic
  mutations in the antigen-binding V(D)J sequence.
• Such mutations occur mostly as substitutions of
  individual bases.

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18.15 Somatic Hypermutation (SHM) Generates
Additional Diversity

• In the IgH chain locus, SHM depends on the iEµ
  and 3'E? that enhance VHDJH-CH transcription.
• In the Ig? chain locus, SHM depends on iE? and
  3'E? that enhance V?J?-C? transcription.
• The ? locus transcription depends on the weaker
  ?2-4 and ?3-1 enhancers.

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18.16 SHM Is Mediated by AID, Ung, Elements of
the Mismatch DNA Repair (MMR) Machinery, and
Translesion DNA Synthesis (TLS) Polymerases

• SHM uses some of the same critical elements of
  CSR.
• Like CSR, SHM requires AID.
• Ung intervention influences the pattern of
  somatic mutations.
• Elements of the MMR pathway and of TLS
  polymerases are involved in SHM and CSR.

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18.16 SHM Is Mediated by AID, Ung, Elements of
the Mismatch DNA Repair (MMR) Machinery, and
Translesion DNA Synthesis (TLS) Polymerases
Figure 18.25 Deamination of C by AID gives rise
to a UG mispair.
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18.17 Chromatin Modification in V(D)J
Recombination, CSR, and SHM

• Chromatin modification in V(D)J recombination,
  CSR, and SHM are induced by the same stimuli that
  drive these processes.
• Transcription factors and transcription target
  histone posttranslation modifications.
• Histone modifications are read and transduced by
  chromatin-interacting factors.

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18.18 Expressed Igs in Avians Are Assembled from
Pseudogenes

• An Ig gene in chickens is generated by copying a
  sequence from one of 25 pseudogenes into the
  recombined (acceptor) V gene gene conversion.

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18.18 Expressed Igs in Avians Are Assembled from
Pseudogenes

• The enzymatic machinery of gene conversion
  depends on AID and enzymes involved in homologous
  recombination.
• Ablation of certain DNA homologous recombination
  genes transforms gene conversion into SHM.

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18.19 B Cell Differentiation in the Bone Marrow
and the Periphery Generation ofMemory B Cells
Enables a Prompt and Strong Secondary Response

• Mature B cells that emerge from the bone marrow
  and are recruited in the primary response express
  a BCR with only a moderate affinity for antigen.
• Toward the end of the primary response, B cells
  expressing BCRs with a higher affinity for
  antigen are selected and later revert back to a
  resting state to become memory B cells.
• Re-exposure to the same antigen triggers a
  secondary response through rapid activation and
  clonal expansion of memory B cells.

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18.19 B Cell Differentiation in the Bone Marrow
and the Periphery Generation ofMemory B Cells
Enables a Prompt and Strong Secondary Response
Figure 18.29 B cell differentiation is
responsible for acquired immunity.
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18.20 The T Cell Receptor forAntigen (TCR) Is
Related to the BCR

• T cells use a mechanism of V(D)J recombination
  similar to that of B cells to express either of
  two types of TCR.
• TCRaß is found on more than 95 and TCR?d on less
  than 5 of T lymphocytes in the adult.

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18.20 The T Cell Receptor forAntigen (TCR) Is
Related to the BCR

• The organization of the TCRa locus resembles that
  of the Ig? locus the TCRß resembles the IgH
  locus, the TCR?, the Ig? locus.

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18.21 The TCR Functions in Conjunction with the
MHC

• The TCR recognizes a short peptide set in the
  groove of an MHC molecule on the surface of an
  antigen-presenting cell (APC).

Figure 18.35 The two chains of the T cell
receptor associate with the polypeptides of the
CD3 complex.
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18.21 The TCR Functions in Conjunction with the
MHC

• The recombination process to generate functional
  TCR chains is intrinsic to the development of T
  cells.
• The TCR is associated with the CD3 complex that
  is involved in transducing TCR signals from the
  cell surface to the nucleus.

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18.22 The Major Histocompatibility Complex (MHC)
Locus Comprises a Cohort of Genes Involved in
Immune Recognition

• The MHC locus codes for Class I, Class II, and
  Class III molecules.

Figure 18.37 The MHC region extends for gt2 Mb.
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18.22 The Major Histocompatibility Complex (MHC)
Locus Comprises a Cohort of Genes Involved in
Immune Recognition

• Class I proteins are the transplantation antigens
  distinguishing self from nonself.
• Class II proteins are involved in interactions of
  T cells with APCs.

Figure 18.36 Class I and class II MHC have a
related structure.
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18.22 The Major Histocompatibility Locus
Comprises a Cohort of Genes Involved in Immune
Recognition

• MHC class I molecules are heterodimers consisting
  of a variant a chain and the invariant ß2
  microglobulin.
• MHC class II molecules are heterodimers
  consisting of an a chain and a ß chain.