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THE IMMUNE SYSTEM, FOURTH EDITION
CHAPTER 5: ANTIGEN RECOGNITION BY T
LYMPHOCYTES
© 2015 Garland Science
5–1 a. b. c. d. e. T cells recognize antigen when the antigen
forms a complex with membrane-bound MHC molecules on another host-derived cell
is internalized by T cells via phagocytosis and subsequently binds to T-cell receptors in
the endoplasmic reticulum
is presented on the surface of a B cell on membrane-bound immunoglobulins
forms a complex with membrane-bound MHC molecules on the T cell
bears epitopes derived from proteins, carbohydrates, and lipids.
5–2 T-cell receptors structurally resemble
a. the Fc portion of immunoglobulins
b. MHC class I molecules
c. secreted antibodies
d. a single Fab of immunoglobulins
e. CD3 ε chains.
5–3 If viewing the three-dimensional structure of a T-cell receptor from the side, with the T-
cell membrane at the bottom and the receptor pointing upwards, which of the following is
inconsistent with experimental data?
a. The highly variable CDR loops are located across the top surface.
b. The membrane-proximal domains consist of Cα and Cβ.
c. The portion that makes physical contact with the ligand comprises Vβ and Cβ, the domains
farthest from the T-cell membrane.
d. The transmembrane regions span the plasma membrane of the T cell.
e. The cytoplasmic tails of the T-cell receptor α and β chains are very short.
5–4 Unlike B cells, T cells do not engage in any of the following processes except
a. alternative splicing to produce a secreted form of the T-cell receptor
b. alternative splicing to produce different isoforms of the T-cell receptor
c. isotype switching
d. somatic hypermutation
e. somatic recombination
5–5 When comparing the T-cell receptor α-chain locus with the immunoglobulin heavy-chain
locus, all of the following are correct except
a. the T-cell receptor α locus differs because it has embedded within its sequence another
locus that encodes a different type of T-cell receptor chain
b. both are encoded on chromosome 14
c. the T-cell receptor α-chain locus does not contain D segments
d. the T-cell receptor α-chain locus contains more V and J regions
1e. f. the T-cell receptor α-chain locus contains more C regions
they both contain exons encoding a leader peptide.
5–6 Unlike the C regions of immunoglobulin heavy-chain loci, the C regions of the T-cell
receptor β-chain loci
a. are functionally similar
b. do not contain D segments
c. are more numerous
d. are encoded on a different chromosome from the variable β-chain gene segments of the
T-cell receptor
e. do not encode a transmembrane region
f. possess non-templated P and N nucleotides.
5–7 a. b. c. d. e. f. Which of the following statements regarding Omenn syndrome is incorrect?
A bright red, scaly rash is due to a chronic inflammatory condition.
Affected individuals are susceptible to infections with opportunistic pathogens.
It is invariably fatal unless the immune system is rendered competent through a bone
marrow transplant.
It is the consequence of complete loss of RAG function.
There is a deficiency of functional B and T cells.
It is associated with missense mutations of RAG genes.
5–8
A. B. Identify which features of the RAG genes have similarity to the transposase gene of
transposons.
have evolved in humans.
Explain how the mechanisms for immunoglobulin and T-cell receptor rearrangement may
5–9 a. b. c. d. e. All of the following statements regarding γ:δ T cells are correct except
they are more abundant in tissue than in the circulation
the δ chain is the counterpart to the β chain in α:β T-cell receptors because it contains V,
D, and J segments in the variable region
they share some properties with NK cells
activation is not always dependent on recognition of a peptide:MHC molecule complex
expression on the cell surface is not dependent on the CD3 complex.
5–10 Match the term in Column A with its complement in Column B.
Column A Column B
___a. T-cell receptor δ-chain gene 1. positioned in the T-cell receptor α-
chain locus between Vα and Jα gene segments
___b. CD3 complex 2. made up of γ, δ and ε components
___c. T-cell receptor β-chain gene 3. located on chromosome 7
___d. CD4 4. counterpart to the T-cell receptor α-
2chain gene
___e. T-cell receptor γ-chain gene 5. four extracellular domains
5–11 During T-cell receptor _____-gene rearrangement, two D segments may be used in the
final rearranged gene sequence, thereby increasing overall variability of this chain.
a. α
b. β
c. γ
d. δ
e. ε.
5–12 commonly referred to as
a. endocytosis
b. promiscuous processing
c. antigen processing
d. antigen presentation
e. peptide loading.
The degradation of pathogen proteins into smaller fragments called peptides is a process
5–13 a. b. d. e. All of the following are primarily associated with CD4 T-cell function except
improve phagocytic mechanisms of tissue macrophages
assist B cells in the production of high-affinity antibodies
c. kill virus-infected cells
facilitate responses of other immune-system cells during infection
assist macrophages in sustaining adaptive immune responses through their secretion of
cytokines and chemokines.
5–14 and recipient.
a. CD3
b. MHC molecules
c. T-cell receptor α chains
d. γ:δ T cells
e. β2-microblobulin.
The primary reason for transplant rejections is due to differences in _____ between donor
5–15 class II molecules.
Explain the importance of promiscuous binding specificity exhibited by MHC class I and
5–16 is not included?
a. nucleus
b. Golgi apparatus
c. endoplasmic reticulum
d. exocytic vesicles
e. lysosomes.
When describing the various components of the vesicular system, which of the following
35–17 a. b. c. d. e. Which of the following is not a characteristic of immunoproteasomes?
They make up about 1% of cellular protein.
They consist of four rings of seven polypeptide subunits that exist in alternative forms.
They are produced in response to IFN-γ produced during innate immune responses.
They produce a higher proportion of peptides containing acidic amino acids at the
carboxy terminus compared with constitutive proteasomes.
They contain 20S proteasome-activation complexes on the caps.
5–18 a. b. c. d. e. Identify which of the following statements is true regarding the transporter associated
with antigen processing (TAP).
TAP is a homodimer composed of two identical subunits.
TAP transports proteasome-derived peptides from the cytosol directly to the lumen of the
Golgi apparatus.
TAP is an ATP-dependent, membrane-bound transporter.
Peptides transported by TAP bind preferentially to MHC class II molecules.
TAP deficiency causes a type of bare lymphocytes syndrome resulting in severely
depleted levels of MHC class II molecules on the surface of antigen-presenting cells.
5–19 a. tapasin
b. calnexin
c. calreticulin
d. ERp57
e. β2-microglobulin.
All of the following are included in the peptide-loading complex except
5–20 Which of the following best describes the function of tapasin?
a. Tapasin is an antagonist of HLA-DM and causes more significant increases in MHC class
I than MHC class II on the cell surface.
b. Tapasin is a lectin that binds to sugar residues on MHC class I molecules, T-cell
receptors, and immunoglobulins and retains them in the ER until their subunits have adopted the
correct conformation.
c. Tapasin is a thiol-reductase that protects the disulfide bonds of MHC class I molecules.
d. Tapasin participates in peptide editing by trimming the amino terminus of peptides to
ensure that the fit between peptide and MHC class II molecules is appropriate.
e. Tapasin is a bridging protein that binds to both TAP and MHC class I molecules and
facilitates the selection of peptides that bind tightly to MHC class I molecules.
5–21 The mechanisms contributing to peptide editing include which of the following? (Select
all that apply.)
a. removal of amino acids from the amino-terminal end by endoplasmic reticulum
aminopeptidase (ERAP)
b. cathepsin S-mediated cleavage of invariant chain
c. the participation of tapasin in finding a ‘good fit’ for class I heterodimers
d. recycling an MHC class I heterodimer if the peptide falls out of its peptide-binding
groove
e. upregulation of HLA-DM by interferon-γ.
45–22 Match the term in Column A with its description or function in Column B.
Column A Column B
___a. cathepsin S 1. a chaperone that directs empty MHC
class I molecules to the inside of the cell
___b. HLA-DM 2. activated by acidification in
phagolysosomes
___c. endoplasmic reticulum aminopeptidase
(ERAP)
3. complex
a thiol-reductase in the peptide-loading
___d. receptor-mediated endocytosis 4. removes class II-associated invariant-
chain peptide (CLIP)
___e. ERp57 5. internalization of
immunoglobulin:antigen complexes by B cells
___f. HLA-G 6. expressed only by extravillous
trophoblasts
___g. HLA-F 7. trims peptides to fit MHC class I
molecules
5–23 Explain how mycobacteria avoid immune recognition by T cells during infection.
5–24 Identify the three functions of the invariant chain.
5–25 Explain specifically how interferon-γ produced during an infection enhances (A) antigen
processing in the MHC class I pathway, and (B) antigen presentation in the MHC class II
pathway.
5–26 Discuss how T-cell receptors differ from immunoglobulins in the way that they recognize
antigen. Use the following terms in your answer: peptides, antigen-presenting cells, MHC
molecules, and antigen-binding sites.
5–27 Pathogens that infect the human body replicate either inside cells (such as viruses) or
extracellularly, in the blood or in the extracellular spaces in tissues.
A. Identify (i) the class of T cells that are stimulated by intracellular pathogens, (ii) their co-
receptor, (iii) the MHC molecule used for recognition of antigen and (iv) the T-cell effector
function.
B. Repeat this for the classes of T cells that are stimulated by extracellular pathogens. For
the purposes of this question, count those pathogens (such as mycobacteria) that can survive and
live inside intracellular vesicles after being taken up by macrophages as extracellular pathogens.
5–28 _______ antigens:
a. carbohydrate
b. lipid
c. protein
In contrast to immunoglobulins, α:β T-cell receptors recognize epitopes present on
5d. carbohydrate and lipid
e. carbohydrate, lipid, and protein.
5–29 (F).
a. b. c. d. e. Indicate whether each of the following statements regarding T cells is true (T) or false
__ T cells and B cells recognize the same types of antigen.
__ T cells and B cells require MHC molecules for the recognition of peptide antigens.
__ T cells require an accessory cell called an antigen-presenting cell, which bears MHC
molecules on its surface.
__ T-cell receptor and immunoglobulin genes are encoded on the MHC.
__ The T-cell receptor has structural similarity to an immunoglobulin Fab fragment.
5–30 Which of the following characteristics is common to both T-cell receptors and
immunoglobulins?
a. Somatic recombination of V, D, and J segments is responsible for the diversity of
antigen-binding sites.
b. Somatic hypermutation changes the affinity of antigen-binding sites and contributes to
further diversification.
c. Class switching enables a change in effector function.
d. The antigen receptor is composed of two identical heavy chains and two identical light
chains.
e. Carbohydrate, lipid, and protein antigens are recognized and stimulate a response.
5–31 the following domains?
a. Vα and Cα
b. Vβ and Cβ
c. Cα and Cβ
d. Vα and Cβ
e. Vα and Vβ.
The antigen-recognition site of T-cell receptors is formed by the association of which of
5–32 The most variable parts of the T-cell receptor are
a. Vα and Cα
b. Vβ and Cβ
c. Cα and Cβ
d. Vα and Cβ
e. Vα and Vβ.
5–33 an intact T-cell receptor?
a. 2
b. 3
c. 4
d. 6
e. 12.
How many complementarity-determining regions contribute to the antigen-binding site in
65–34 IgG possesses _______ binding sites for antigen, and the T-cell receptor possesses
_______ binding sites for antigen:
a. 1; 1
b. 2; 1
c. 1; 2
d. 2; 2
e. 2; 4.
5–35 In terms of V, D, and J segment arrangement, the T-cell receptor α-chain locus resembles
the immunoglobulin _______ locus, whereas the T-cell receptor β-chain locus resembles the
immunoglobulin _______ locus:
a. λ light chain; κ light chain
b. heavy chain; λ light chain
c. κ light chain; heavy chain
d. λ light chain; heavy chain
e. κ light chain; λ light chain.
5–36 In B cells, transport of immunoglobulin to the membrane is dependent on association
with two invariant proteins, Igα and Igβ. Which of the following invariant proteins provide this
function for the T-cell receptor in T cells?
a. CD3γ
b. CD3δ
c. CD3ε
d. ζ
e. All of the above.
5–37 Owing to the location of the δ-chain locus of the T-cell receptor on chromosome 14, if
the _______-chain locus rearranges by somatic recombination, then the δ-chain locus is
_______:
a. α; also rearranged
b. α; deleted
c. α; transcribed
d. β; deleted
e. γ; also rearranged.
5–38 Explain how professional antigen-presenting cells optimize antigen presentation to T
cells despite the relatively limited capacity of any particular MHC molecule to bind different
pathogen-derived peptides.
5–39 a. b. c. d. e. Which of the following is not a characteristic of native antigen recognized by T cells?
peptides ranging between 8 and 25 amino acids in length
not requiring degradation for recognition
amino acid sequences not found in host proteins
primary, and not secondary, structure of protein
binding to major histocompatibility complex molecules on the surface of antigen-
presenting cells.
75–40 a. b. c. d. e. Which of the following statements regarding CD8 T cells is incorrect?
When activated, CD8 T cells in turn activate B cells.
CD8 is also known as the CD8 T-cell co-receptor.
CD8 binds to MHC molecules at a site distinct from that bound by the T-cell receptor.
CD8 T cells kill pathogen-infected cells by inducing apoptosis.
CD8 T cells are MHC class I-restricted.
5–41 Antigen processing involves the breakdown of protein antigens and the subsequent
association of peptide fragments on the surface of antigen-presenting cells with
a. immunoglobulins
b. T-cell receptors
c. complement proteins
d. MHC class I or class II molecules
e. CD4.
5–42 Which of the following statements regarding T-cell receptor recognition of antigen is
correct?
a. α:β T-cell receptors recognize antigen only as a peptide bound to an MHC molecule.
b. αβ T-cell receptors recognize antigens in their native form.
c. α:β T-cell receptors, like B-cell immunoglobulins, can recognize carbohydrate, lipid, and
protein antigens.
d. Antigen processing occurs in extracellular spaces.
e. Like α:β T cells, γ:δ T cells are also restricted to the recognition of antigens presented by
MHC molecules.
5–43 Which of the following describes a ligand for an α:β T-cell receptor?
a. carbohydrate:MHC complex
b. lipid:MHC complex
c. peptide:MHC complex
d. all of the above
e. none of the above.
5–44 MHC class II molecules are made up of two chains called _______, whose function is to
bind peptides and present them to _______ T cells:
a. alpha (α) and beta (β); CD4
b. alpha (α) and beta2-microglobulin (β2m); CD4
c. alpha (α) and beta (β); CD8
d. alpha (α) and beta2-microglobulin β2m); CD8
e. alpha (α) and beta (β); γ:δ T cells.
5–45 The complementarity-determining region (CDR) 1 and CDR2 loops of the T-cell receptor
contact the _______:
a. side chains of amino acids in the middle of the peptide
b. co-receptors CD4 or CD8
c. membrane-proximal domains of the MHC molecule
8d. e. constant regions of antibody molecules
α helices of the MHC molecule.
5–46 The CDR3 loops of the T-cell receptor contact the _______:
a. side chains of amino acids in the middle of the peptide
b. co-receptors CD4 or CD8
c. membrane-proximal domains of the MHC molecule
d. constant regions of antibody molecules
e. α helices of the MHC molecule.
5–47 extracellular domains:
a. α1:β1
b. β1:β2
c. α2:β2
d. α2:α3
e. α1:α2.
The peptide-binding groove of MHC class I molecules is composed of the following
5–48 a. α1
b. β1
c. α2
d. β2
e. α3.
To which domain of MHC class II does CD4 bind?
5–49 a. α1
b. β1
c. α2
d. β2
e. α3.
To which domain of MHC class I does CD8 bind?
5–50 a. b. c. d. MHC molecules have promiscuous binding specificity. This means that
a particular MHC molecule has the potential to bind to different peptides
when MHC molecules bind to peptides, they are degraded
peptides bind with low affinity to MHC molecules
none of the above describes promiscuous binding specificity.
5–51 T-cell receptors interact not only with peptide anchored in the peptide-binding groove of
MHC molecules, but also with
a. anchor residues
b. peptide-binding motif
c. variable amino acid residues on α helices of the MHC molecule
d. β2-microglobulin
e. invariant chain.
95–52 a. b. c. d. Cross-priming of the immune response occurs when _____. (Select all that apply.)
viral antigens are presented by MHC class I molecules on the surface of a cell that is not
actually infected by that particular virus
cytosol-derived peptides enter the endoplasmic reticulum and bind to MHC class II
molecules
phagolysosome-derived peptides bind to MHC class II molecules
peptides of nuclear or cytosolic proteins are presented by MHC class II molecules.
5–53 In reference to the interaction between T-cell receptors and their corresponding ligands,
which of the following statements is correct?
a. The organization of the T-cell receptor antigen-binding site is distinct from the antigen-
binding site of immunoglobulins.
b. The orientation between T-cell receptors and MHC class I molecules is different from
that of MHC class II molecules.
c. The CDR3 loops of the T-cell receptor α and β chains form the periphery of the binding
site making contact with the α helices of the MHC molecule.
d. The most variable part of the T-cell receptor is composed of the CD3 loops of both the α
and β chains.
e. All of the above statements are correct.
5–54 a. b. d. The diversity of MHC class I and II genes is due to _____. (Select all that apply.)
gene rearrangements similar to those observed in T-cell receptor genes
the existence of many similar genes encoding MHC molecules in the genome
c. somatic hypermutation
extensive polymorphism at many of the alleles
e. isotype switching.
5–55 referred to as their
a. haplotype
b. allotype
c. isotype
d. autotype
e. HLA type.
The combination of all HLA class I and class II allotypes that an individual expresses is
5–56 All of the following are oligomorphic except
a. HLA-G α chain
b. HLA-DO β chain
c. HLA-DQ β chain
d. HLA-A α chain
e. HLA-DR α chain.
5–57 All of the following are highly polymorphic except
a. HLA-A α chain
b. HLA-DO α chain
c. HLA-B α chain
10d. HLA-DR β chain
e. HLA-C α chain.
5–58 polymorphism?
a. HLA-A
b. HLA-B
c. HLA-C
d. HLA-DP
e. HLA-DR.
Of the following HLA α-chain loci, which one exhibits the highest degree of
5–59 all that apply.)
a. β2-microglobulin
b. HLA-G α chain
c. TAP-1
d. invariant chain
e. tapasin
f. HLA-DR α chain.
Which of the following are not encoded on chromosome 6 in the HLA complex? (Select
5–60 The _____ refers to the complete set of HLA alleles that a person possesses on a
particular chromosome 6.
a. isoform
b. isotype
c. oligomorph
d. allotype
e. haplotype.
5–61 Peptides that bind to a particular MHC isoform usually have either the same or
chemically similar amino acids at two to three key positions that hold the peptide tightly in the
peptide-binding groove of the MHC molecule. These amino acids are called _____ and the
combination of these key residues is known as its _____.
a. alleles; allotypes
b. anchor residues; peptide-binding motif
c. allotype; haplotypes
d. invariant chains; haplotypes
e. restriction residues; MHC allotype.
5–62 Provide an explanation of why it is believed that MHC class I genes are the evolutionary
ancestors of MHC class II genes.
5–63 Match the term in Column A with its description in Column B.
Column A Column B
___a. MHC restriction 1. mechanism enabling extracellular
antigens to bind to MHC class I molecules
___b. cross-presentation 2. evolutionary maintenance of divergent
11MHC molecule phenotypes
___c. heterozygote advantage 3. recognition of peptide antigen by a
given T-cell receptor when bound to a
particular MHC allotype
___d. balancing selection 4. mechanism used to increase
polymorphisms of HLA class I and class II
alleles involving homologous recombination
between different alleles of the same gene
___e. interallelic conversion 5. presentation of a wider range of
peptides when MHC isotypes inherited from
each parent are different
5–64 Directional selection is best described as
a. all polymorphic alleles preserved in a population
b. T-cell receptor interaction with peptide:MHC complexes directed to a planar interface
c. a mechanism in T cells that is analogous to affinity maturation of immunoglobulins
d. selected alleles increase in frequency in a population
e. selection of most appropriate transplant donor directed at the identification of identical or
similar combinations of HLA alleles compared with the transplant recipient.
5–65 Describe (A) five ways in which T-cell receptors are similar to immunoglobulins, and (B)
five ways in which they are different (other than the way in which they recognize antigen).
5–66 Compare the organization of T-cell receptor α and β genes (the TCRα and TCRβ loci)
with the organization of immunoglobulin heavy-chain and light-chain genes.
5–67 T-cell receptors do not undergo isotype switching. Suggest a possible reason for this.
5–68 a. b. d. e. The role of the CD3 proteins and ζ chain on the surface of the cell is to
transduce signals to the interior of the T cell
bind to antigen associated with MHC molecules
c. bind to MHC molecules
bind to CD4 or CD8 molecules
facilitate antigen processing of antigens that bind to the surface of T cells.
5–69 a. b. c. d. e. Which of the following accurately completes this statement: “The function of _______ T
cells is to make contact with _______ and _______”? (Select all that apply.)
CD8; virus-infected cells; kill virus-infected cells
CD8; B cells; stimulate B cells to differentiate into plasma cells
CD4; macrophages; enhance microbicidal powers of macrophages
CD4; B cells; stimulate B cells to differentiate into plasma cells
All of the above are accurate.
5–70 The immunological consequence of severe combined immunodeficiency disease (SCID)
caused by a genetic defect in either RAG-1 or RAG-2 genes is
12a. b. c. d. e. lack of somatic recombination in T-cell receptor and immunoglobulin gene loci
lack of somatic recombination in T-cell receptor loci
lack of somatic recombination in immunoglobulin loci
lack of somatic hypermutation in T-cell receptor and immunoglobulin loci
lack of somatic hypermutation in T-cell receptor loci.
5–71
A. (i) Describe the structure of an MHC class I molecule, identifying the different
polypeptide chains and domains. (ii) What are the names of the MHC class I molecules produced
by humans? Which part of the molecule is encoded within the MHC region of the genome? (iii)
Which domains or parts of domains participate in the following: antigen binding; binding the T-
cell receptor; and binding the T-cell co-receptor? (iv) Which domains are the most polymorphic?
B. Repeat this for an MHC class II molecule.
5–72 What is meant by the terms (A) antigen processing and (B) antigen presentation? (C)
Why are these processes required before T cells can be activated?
5–73
A. Describe in chronological order the steps of the antigen-processing and antigen-
presentation pathways for intracellular, cytosolic pathogens.
B. (i) What would be the outcome if a mutant MHC class I α chain could not associate with
β2-microglobulin, and (ii) what would happen if the TAP transporter were lacking as a result of
mutation? Explain your answers.
5–74 a. HLA-DM
b. HLA-DO
c. HLA-DP
d. HLA-DQ
e. HLA-DR.
Which of the following removes CLIP from MHC class II molecules?
5–75
A. Describe in chronological order the steps of the antigen-processing and antigen-
presentation pathways for extracellular pathogens.
B. What would be the outcome (i) if invariant chain were defective or missing, or (ii) if
HLA-DM were not expressed?
5–76
A. B. What is the difference between MHC variation due to multigene families and that due to
allelic polymorphism?
How does MHC variation due to multigene families and allelic polymorphism influence
the antigens that a person’s T cells can recognize?
5–77 What evidence supports the proposal that MHC diversity evolved by natural selection
caused by infectious pathogens rather than exclusively by random DNA mutations?
135–78 CD8 T-cell subpopulations are specialized to combat _______ pathogens, whereas CD4
T-cell subpopulations are specialized to combat _______ pathogens:
a. bacterial; viral
b. dead; live
c. extracellular; intracellular
d. intracellular; extracellular
e. virulent; attenuated.
5–79 Which of the following describes the sequence of events involved in processing of
peptides that will be presented as antigen with MHC class I?
a. plasma membrane →TAP1/2 →proteasome →MHC class I →endoplasmic reticulum
b. TAP1/2 →proteasome →MHC class I →endoplasmic reticulum→plasma membrane
c. proteasome →TAP1/2 →MHC class I →endoplasmic reticulum →plasma membrane
d. proteasome →TAP1/2 →endoplasmic reticulum →MHC class I →plasma membrane
e. endoplasmic reticulum →proteasome →MHC class I →TAP1/2 →plasma membrane.
5–80 One type of bare lymphocyte syndrome is caused by a genetic defect in MHC class II
transactivator (CIITA), which results in the inability to synthesize MHC class II and display it on
the cell surface. The consequence of this would be that
a. B cells are unable to develop
b. CD8 T cells cannot function
c. CD4 T cells cannot function
d. intracellular infections cannot be eradicated
e. peptides cannot be loaded onto MHC molecules in the lumen of the endoplasmic
reticulum.
5–81 Which of the following describes the sequence of events involved in the processing of
peptides that will be presented as antigen with MHC class II?
a. protease activity →removal of CLIP from MHC class II →binding of peptide to MHC
class II →endocytosis →plasma membrane
b. endocytosis →protease activity →removal of CLIP from MHC class II →binding of
peptide to MHC class II →plasma membrane
c. removal of CLIP from MHC class II →binding of peptide to MHC class II →protease
activity →endocytosis →plasma membrane
d. binding of peptide to MHC class II →endocytosis →removal of CLIP from MHC class II
→protease activity →plasma membrane
e. plasma membrane →endocytosis →protease activity →removal of CLIP from MHC
class II →binding of peptide to MHC class II.
5–82 a. erythrocyte
b. hepatocyte
c. lymphocyte
d. dendritic cell
e. neutrophil.
Which of the following cell types does not express MHC class I?
145–83 Which of the following cell types is not considered a professional antigen-presenting
cell?
a. macrophage
b. neutrophil
c. B cell
d. dendritic cell
e. all of the above are professional antigen-presenting cells.
5–84 answer may be correct.
Match the answer on the right that best describes the function on the left. More than one
___ a. an intracellular, monomorphic
MHC class I isotype whose function is
unknown
1. HLA-A, HLA-B, HLA-C
__ b. cells
form ligands for receptors on NK
2. HLA-E, HLA-G
__ c. participate in peptide loading of
MHC class II molecules
3. HLA-F
__ d. present antigen to CD4 T cells 4. HLA-DP, HLA-DQ, HLA-DR
__ e. present antigen to CD8 T cells 5. HLA-DM, HLA-DO
5–85 Which of the following HLA-DRB genotypes is not possible in an individual? (X: X
represents diploid genotype.)
a. DRB1: DRB1
b. DRB1, DRB3: DRB1, DRB4
c. DRB1: DRB1, DRB5
d. DRB1, DRB4: DRB1
e. DRB3: DRB1, DRB5.
5–86
A. How many HLA-DR α:β combinations can be made by an individual who is
heterozygous at all HLA-DRβ loci, inherits the DRβ haplotype DRB1 from their mother, the
DRβ haplotype DRB1, DRB4 from their father, and also inherits different allelic forms of DRA
from each parent?
B. Repeat this exercise given the same information except that the maternal DRβ haplotype
is DRB1, DRB3.
5–87 Which of the following is mismatched?
a. peptide-binding motif: combination of anchor residues in a peptide capable of binding a
particular MHC haplotype
b. MHC restriction: specificity of T-cell receptor for a particular peptide:MHC molecule
complex
c. d. e. balancing selection: maintenance of variety of MHC isoforms in a population
directional selection: replacement of older MHC isoforms with newer variants
interallelic conversion: recombination between two different genes in the same family.
155–88 Which is the most likely reason that HIV-infected people with heterozygous HLA loci
have a delayed progression to AIDS compared with patients who are homozygous at one or more
HLA loci?
a. The greater number of HLA alleles provides a wider variety of HLA molecules for
presenting HIV-derived peptides to CD8 T cells even if HIV mutates during the course of
infection.
b. Heterozygotes have more opportunity for interallelic conversion and can therefore
express larger numbers of MHC alleles.
c. Directional selection mechanisms favor heterozygotes and provide selective advantage to
pathogen exposure.
d. As heterozygosity increases, so does the concentration of alloantibodies in the serum,
some of which cross-react with and neutralize HIV.
5–89
A. What is the maximum number of MHC class I and class II molecules that a heterozygous
individual could theoretically express? Explain your answer. (Ignore the possibility of MHC
class II molecules composed of chains from different isotypes.)
B. How does this relatively small number of MHC molecules have the potential to bind the
huge number of antigenic peptides encountered in the environment, and what features of a
peptide determine whether it will be bound by a given MHC molecule?
5–90 (A) Explain the difference between interallelic conversion and gene conversion, and (B)
provide an example for both.
5–91 directional selection?
In the context of MHC isoforms, what is the difference between balancing selection and
5–92
A. What are alloantibodies?
B. How do alloantibodies arise naturally?
C. Why are alloantibodies problematic for transplantation?
ANSWERS
5–1 a
5–2 d
5–3 c
5–4 e
5–5 e
165–6 a
5–7 d
5–8
A. RAG genes do not contain introns, and they function to facilitate the cleavage of double-
stranded DNA.
B. It has been proposed that the evolution of rearranging antigen-receptor genes began with
the insertion of a transposable element into a gene encoding an innate immune receptor. This
gene was not only split into two segments, but also became flanked by repetitive DNA sequences
donated by the transposon. A later chromosomal rearrangement event translocated the
transposase genes to a different chromosome, where they evolved into the ancestral RAG-1 and
RAG-2 genes. The repetitive DNA sequences left behind at the original receptor gene location
evolved into the recombination signal sequences (RSSs), and the segments of the receptor gene
evolved into V and J sequences. Eventually this led to a family of rearranging genes on five
chromosomes encoding the immunoglobulin heavy- and light-chain genes, and the T-cell
receptor α, β, γ, and δ genes.
5–9 e
5–10 a—1; b—2; c—3; d—5; e—4
5–11 d
5–12 c
5–13 c
5–14 b
5–15 Each MHC molecule can bind to a very large number of peptides made up of different
sequences of amino acids. The consequence of this promiscuity is that humans need only encode
a relatively small number of MHC molecules in their genome if they are to bind to the huge
number of pathogen-derived peptides encountered during a lifetime of infections. Because MHC
molecules are coexpressed on the cell surface, this also ensures that an appropriate density of
MHC molecules populates the cell surface to ensure efficient T-cell engagement and subsequent
activation.
5–16 a
5–17 d
5–18 c
5–19 b
175–20 e
5–21 a, c, d
5–22 a—2; b—4; c—7; d—5; e—3; f—6; g—1
5–23 Both the MHC class I and MHC class II pathways are subverted by mycobacteria during
intracellular growth and replication. Although mycobacteria are obligate intracellular pathogens
their proteins do not enter the cytosol, so proteasomes are unable to generate mycobacteria-
derived peptides for the MHC class I pathway. Mycobacteria are also resistant to degradation by
lysosomal enzymes because they inhibit phagolysosome formation. This interferes with the
MHC class II pathway.
5–24
1. Invariant chain protects the peptide-binding groove of MHC class II molecules from
binding to endoplasmic reticulum-derived peptides.
2. Binding of invariant chain to MHC class II molecules stabilizes their conformation so
that they are eventually able to bind peptides.
3. Invariant chain facilitates the transport of MHC class II molecules from the ER to the
MIIC cellular compartment, where they can bind peptides.
5–25
A. Interferon-γ causes a shift from the production of constitutive proteasomes to that of
immunoproteasomes. This is accomplished through increased expression of alternative subunits
(LMP2 and LMP7) that are present in the immunoproteasome. These proteasomes exhibit
modified protease activities favoring the production of peptides (antigen processing) that can
bind to MHC class I molecules. Specifically, cleavage after hydrophobic residues is enhanced
and cleavage after acidic residues is decreased.
B. Interferon-γ increases the expression of HLA-DM but not HLA-DO. This causes a shift
in the balance of these two molecules, resulting in an overall decrease in the antagonist activity
of HLA-DO. If HLA-DM is more abundant, it has the ability to catalyze the release of CLIP
from MHC class II molecules and facilitate the replacement of CLIP with other peptides for
presentation to CD4 T cells (antigen presentation). Another way in which interferon-γ increases
antigen presentation in the MHC class II pathway is by increasing the expression levels of MHC
class II molecules on both professional and non-professional antigen-presenting cells.
5–26 First, T-cell receptors can bind to only one type of antigen, namely protein fragments
called peptides. Immunoglobulins can bind to peptides, intact proteins, carbohydrates, and lipids.
Second, unlike immunoglobulins, T-cell receptors cannot bind to a free antigen directly, but
instead require accessory antigen-presenting cells that present the peptide antigens in association
with cell-surface glycoproteins called MHC class I and class II molecules. Third, T-cell receptors
possess a single antigen-binding site; immunoglobulins have at least two binding sites for
antigen, and more in the case of secreted dimeric IgA (four sites) and secreted pentameric IgM
(ten sites).
5–27
18A. (i) Pathogens that are propagating freely within cells (for example viruses) are eradicated
by the actions of cytotoxic T cells. (ii) Cytotoxic T cells express a glycoprotein called CD8, a T-
cell co-receptor that interacts with (iii) MHC class I on antigen-presenting cells. (iv) Once
activated, cytotoxic T cells kill cells infected with the pathogen, which are displaying pathogen
peptides on MHC class I molecules, and thereby inhibit further replication of the pathogen and
infection of neighboring cells.
B. (i) Pathogens that reproduce in extracellular spaces, for example encapsulated bacteria
such as Streptococcus pneumoniae, are eradicated after the activation of other cell types by
helper T cells, namely the classes TH1 and TH2. (ii) TH1 and TH2 cells express a glycoprotein
called CD4, a T-cell co-receptor that interacts with (iii) MHC class II molecules on antigen-
presenting cells. (iv) TH1 cells activate macrophages that are displaying pathogen peptides
(derived from phagocytosed pathogen) on MHC class II molecules on their surface. This
stimulates increased phagocytosis by the macrophage and destruction of pathogens inside
phagolysosomes. Activated macrophages also secrete inflammatory mediators that have an
important part in eradicating the infection by helping to induce inflammation which recruits
phagocytic cells and effector lymphocytes to the site of infection. TH1 cells also induce switching
of B cells to certain antibody isotypes. TH2 cells activate B cells displaying antigen-derived
peptides on MHC class II molecules, resulting in the differentiation of the B cells into plasma
cells and the production of antibodies that remove the extracellular pathogen or its toxins as a
result of neutralization, opsonization, and complement activation.
5–28 c
5–29 a—F; b—F; c—T; d—F; e—T
5–30 a
5–31 e
5–32 e
5–33 d
5–34 b
5–35 c
5–36 e
5–37 b
5–38 Professional antigen-presenting cells express several different types of MHC molecule on
the cell surface, and each type has the potential to bind to different peptides. In addition, MHC
molecules are highly polymorphic, so that most individuals are heterozygous and encode
different allelic forms at each gene locus. The variety of peptides that can bind to these MHC
molecules is therefore increased.
195–39 b
5–40 a
5–41 d
5–42 a
5–43 c
5–44 a
5–45 e
5–46 a
5–47 e
5–48 d
5–49 e
5–50 a
5–51 c
5–52 a, d
5–53 d
5–54 b, d
5–55 e
5–56 c
5–57 b
5–58 b
5–59 a, d
5–60 e
5–61 b
205–62 MHC class I molecules not only have the role of presenting antigen to T cells, but they
also possess additional functions in the body not associated with MHC class II molecules. For
example, they participate in iron homeostasis, IgG uptake in the gastrointestinal tract, and the
regulation of NK-cell function in innate immunity. In addition, MHC class I and class I-like
genes are not confined to chromosome 6, in contrast with MHC class II genes. Finally,
vertebrates exist (such as Atlantic cod) that have only MHC class I genes in their genome, and
lack MHC class II genes.
5–63 a—3; b—1; c—5; d—2; e—4
5–64 d
5–65
A. Similarities. (1) The T-cell receptor has a similar overall structure to the membrane-
bound Fab fragment of immunoglobulin, containing an antigen-binding site, two variable
domains, and two constant domains. (2) T-cell receptors and immunoglobulins are both
generated through somatic recombination of sets of gene segments. (3) The variable region of the
T-cell receptor contains three complementarity-determining regions (CDRs) encoded by the Vα
domain and three CDRs encoded by the Vβ domain, analogous to the CDRs encoded by the VH
and VL domains. (4) There is huge diversity in the T-cell receptor repertoire and it is generated in
the same way as that in the B-cell repertoire (by combination of different gene segments,
junctional diversity due to P- and N-nucleotides, and combination of two different chains). (5) T-
cell receptors are not expressed at the cell surface by themselves but require association with the
CD3 γ, δ, ε, and ζ chains for stabilization and signal transduction, analogous to the Igα and Igβ
chains required for immunoglobulin cell-surface expression and signal transduction.
B. Differences. (1) A T-cell receptor has one antigen-binding site; an immunoglobulin has at
least two. (2) T-cell receptors are never secreted. (3) T-cell receptors are generated in the
thymus, not the bone marrow. (4) The constant region of the T-cell receptor has no effector
function and it does not switch isotype. (5) T-cell receptors do not undergo somatic
hypermutation.
5–66 The organization of the TCRα locus resembles that of an immunoglobulin light-chain
locus, in that both contain V and J gene segments and no D gene segments. The TCRα locus on
chromosome 14 contains about 80 V gene segments, 61 J gene segments, and 1 C gene. The
immunoglobulin light-chain loci, λ and κ, are encoded on chromosomes 22 and 2, respectively.
The λ locus contains about 30 V gene segments and 4 J gene segments, each paired with a C
gene. The κ locus contains about 35 V gene segments, 5 J segments, and 1 C gene segment. The
arrangement of the κ locus more closely resembles that of the TCRα locus except that there are
more J segments in the T-cell receptor locus.
The organization of the TCRβ locus resembles that of the immunoglobulin heavy-chain
locus; both contain V, D, and J gene segments. The TCRβ locus contains about 52 V gene
segments, 2 D gene segments, 13 J gene segments, and 2 C genes, encoded on chromosome 7.
Each C gene is associated with a set of D and J gene segments. The immunoglobulin heavy-
chain locus on chromosome 14 contains about 40 V segments, 23 D segments, and 6 J segments,
21followed by 9 C genes, each specifying a different immunoglobulin isotype. The heavy-chain C
genes determine the effector function of the antibody.
5–67 T-cell receptors are not made in a secreted form, and their constant regions do not
contribute to T-cell effector function. Other molecules secreted by T cells are used for effector
functions. There is therefore no need for isotype switching in T cells, and the T-cell receptor loci
do not contain numerous alternative C genes.
5–68 a
5–69 a, c, d
5–70 a
5–71
A. (i) The complete MHC class I molecule is a heterodimer made up of one α chain and a
smaller chain called β-microglobulin. The α chain consists of three extracellular domains α1, α2,
and α3—a transmembrane region and a cytoplasmic tail. β2-Microglobulin is a single-domain
protein noncovalently associated with the extracellular portion of the α chain, providing support
and stability. (ii) The polymorphic class I molecules in humans are called HLA-A, HLA-B, and
HLA-C. The α chain is encoded in the MHC region by an MHC class I gene. The gene for β2–
microglobulin is elsewhere in the genome. (iii) The antigen-binding site is formed by the α1 and
α2 domains, the ones farthest from the membrane, which create a peptide-binding groove. The
region of the MHC molecule that binds to the T-cell receptor encompasses the α helices of the α1
and α2 domains that make up the outer surfaces of the peptide-binding groove. The α3 domain
binds to the T-cell co-receptor CD8. (iv) The most polymorphic parts of the α chain are the
regions of the α1 and α2 domains that bind antigen and the T-cell receptor. β2-Microglobulin is
invariant; that is, it is the same in all individuals.
B. (i) MHC class II molecules are heterodimers made up of an α chain and a β chain. The α
chain consists of α1 and α2 extracellular domains, a transmembrane region, and a cytoplasmic
tail. The β chain contains β1 and β2 extracellular domains, a transmembrane region, and a
cytoplasmic tail. (ii) In humans there are three polymorphic MHC class II molecules called
HLA-DP, HLA-DQ, and HLA-DR. Both chains of an MHC class II molecule are encoded by
genes in the MHC region. (iii) Antigen binds in the peptide-binding groove formed by the α1 and
β1 domains. The α helices of the α1 and β1 domains interact with the T-cell receptor. The β2
domain binds to the T-cell co-receptor CD4. (iv) With the exception of HLA-DRα, which is
dimorphic, both the α and β chains of MHC class II molecules are highly polymorphic.
Polymorphism is concentrated around the regions that bind antigen and the T-cell receptor in the
α1 and β1 domains.
5–72
A. Antigen processing is the intracellular breakdown of pathogen-derived proteins into
peptide fragments that are of the appropriate size and specificity required to bind to MHC
molecules.
B. Antigen presentation is the assembly of peptides with MHC molecules and the display of
these complexes on the surface of antigen-presenting cells.
22C. Antigen processing and presentation must occur for T cells to be activated because (1) T-
cell receptors cannot bind to intact protein, only to peptides, and (2) T-cell receptors do not bind
antigen directly, but rather must recognize antigen bound to MHC molecules on the surface of
antigen-presenting cells.
5–73
A. Proteins derived from pathogens located in the cytosol are broken down into small
peptide fragments in proteasomes. The peptides are transported into the lumen of the
endoplasmic reticulum (ER) using the transporter associated with antigen processing (TAP),
which is a heterodimer of TAP-1 and TAP-2 proteins anchored in the ER membrane. Meanwhile,
MHC class I molecules are assembling and folding in the ER with the assistance of other
proteins. Initially, the MHC class I α chain binds calnexin through an asparagine-linked
oligosaccharide on the α1 domain. After folding and forming its disulfide bonds, the α chain
binds to β2-microglobulin, forming the MHC class I heterodimer. At this stage, calnexin is
released and the heterodimer joins the peptide-loading complex composed of tapasin,
calreticulin, and ERp57, which position the heterodimer near TAP, stabilize the peptide-loading
complex, and render the heterodimer in an open conformation until a high-affinity peptide binds
to the heterodimer through a process known as peptide editing. The heterodimer consequently
changes its conformation, is released from the peptide-loading complex, and leaves the ER as a
vesicle. Arrival at the Golgi apparatus induces final glycosylation, and finally the peptide:MHC
class I heterodimer complex is transported in vesicles to the plasma membrane, where it presents
peptide to CD8 T cells.
B. (i) If an MHC class I α chain is unable to bind β2-microglobulin, it will be retained in the
ER and will not be transported to the cell surface. It will remain bound to calnexin and will not
fold into the conformation needed to bind to peptide. Thus, antigens will not be presented using
that particular MHC class I molecule. (ii) If TAP-1 or TAP-2 proteins are mutated and not
expressed, peptides will not be transported into the lumen of the ER. Without peptide, an MHC
class I molecule cannot complete its assembly and will not leave the ER. A rare
immunodeficiency disease called bare lymphocyte syndrome (MHC class I immunodeficiency)
is characterized by a defective TAP protein, causing less than 1% of MHC class I molecules to
be expressed on the cell surface in comparison with normal. Thus, T-cell responses to all
pathogen antigens that would normally be recognized on MHC class I molecules will be
impaired.
5–74 a
5–75
A. Extracellular pathogens are taken up by endocytosis or phagocytosis and degraded by
enzymes into smaller peptide fragments inside acidified intracellular vesicles called
phagolysosomes. MHC class II molecules delivered into the ER and being transported to the cell
surface intersect with the phagolysosomes, where these peptides are encountered and loaded into
the antigen-binding groove. To prevent MHC class II molecules from binding to peptides
prematurely, invariant chain (Ii) binds to the MHC class II antigen-binding site in the ER. Ii is
also involved in transporting MHC class II molecules to the phagolysosomes via the Golgi as
part of the interconnected vesicle system. Ii is removed from MHC class II molecules once the
phagolysosome is reached. Removal is achieved in two steps: (1) proteolysis cleaves Ii into
23smaller fragments, leaving a small peptide called CLIP (class II-associated invariant chain
peptide) in the antigen-binding groove of the MHC class II molecule; and (2) CLIP is then
released by HLA-DM catalysis. Once CLIP is removed, HLA-DM remains associated with the
MHC class II molecule, enabling the now empty peptide-binding groove to sample other
peptides until one binds tightly enough to cause a conformational change that releases HLA-DM.
Finally, the peptide:MHC class II complex is transported to the plasma membrane.
B. (i) Defects in the invariant chain would impair normal MHC class II function because
invariant chain not only protects the peptide-binding groove from binding prematurely to
peptides present in the ER but is also required for transport of MHC class II molecules to the
phagolysosome. (ii) If HLA-DM were not expressed, most MHC class II molecules on the cell
surface would be occupied by CLIP rather than endocytosed material. This would compromise
the presentation of extracellular antigens at the threshold levels required for T-cell activation.
5–76
A. Multigene family refers to the presence of multiple genes for MHC class I and MHC
class II molecules in the genome, encoding a set of structurally similar proteins with similar
functions. MHC polymorphism is the presence of multiple alleles (in some cases several
hundreds) for most of the MHC class I and class II genes in the human population.
B. T cells recognize peptide antigens in the form of peptide:MHC complexes, which they
bind using their T-cell receptors. To bind specifically, the T-cell receptor must fit both the
peptide and the part of the MHC molecule surrounding it in the peptide-binding groove. (i)
Because each individual expresses a number of different MHC molecules from the MHC class I
and class II multigene families, the T-cell receptor repertoire is not restricted to recognizing
peptides that bind to just one MHC molecule (and thus all must have the same peptide-binding
motif). Instead, the T-cell receptor repertoire can recognize peptides with different peptide-
binding motifs during an immune response, increasing the likelihood of antigen recognition and,
hence, T-cell activation. (ii) The polymorphism in MHC molecules is localized to the regions
affecting T-cell receptor and peptide binding. Thus, a T-cell receptor that recognizes a given
peptide bound to variant ‘a’ of a particular MHC molecule is likely not to recognize the same
peptide bound to variant ‘b’ of the same MHC molecule. Polymorphism also means that the
MHC molecules of one person will bind a different set of peptides from those in another person.
Taken together, these outcomes mean that because of MHC polymorphism, each individual
recognizes a somewhat different range of peptide antigens using a different repertoire of T-cell
receptors.
5–77 MHC polymorphisms are non-randomly localized, predominantly to the region of the
molecule that makes contact with peptide and T-cell receptors. Random DNA mutations, in
contrast, would be scattered through the gene, giving rise to amino acid changes throughout
MHC molecules and not just in those areas important for peptide binding and presentation.
5–78 d
5–79 c
5–80 c
245–81 b
5–82 a
5–83 b
5–84 a—3; b—1, 2; c—5; d—4; e—1
5–85 e
5–86 m and p denote maternal and paternal allotypes, respectively.
A. The answer is 6. The possible combinations are as follows:
(1) DRA-m:DRB1-m; (2) DRA-m:DRB1-p; (3) DRA-m:DRB4-p; (4) DRA-p:DRB1-m; (5)
DRA-p:DRB1-p; and (6) DRA-p:DRB4-p.
B. The answer is 8. The possible combinations are as follows:
(1) DRA-m:DRB1-m; (2) DRA-m:DRB3-m; (3) DRA-m:DRB1-p; (4) DRA-m:DRB4-p; (5)
DRA-p:DRB1-m; (6) DRA-p:DRB3-m; (7) DRA-p:DRB1-p; (8) DRA-p:DRB4-p.
5–87 e
5–88 a
5–89
A. There are three MHC class I isotypes in humans (HLA-A, HLA-B, and HLA-C) and they
are expressed from both chromosomes. Assuming that each gene is heterozygous, the maximum
number of different MHC class I α chains that could be expressed is 6. Because β-microglobulin
is invariant, this means that six different MHC class I molecules could be produced. For MHC
class II molecules, assuming complete heterozygosity and the presence of two functional DRB
genes (DRB1 and DRB3, 4, or 5) on both chromosomes, the maximum number of MHC class II
molecules that could be expressed is 16 (Figure A5–89). Therefore, the total number of different
MHC class I and MHC class II molecules that can be expressed is 22.
<<insert Figure A5-89>>
Figure A5–89 The number of HLA molecules that can be expressed in a single individual.
m, maternal chromosome; p, paternal chromosome.
B. MHC molecules have promiscuous binding specificity, which means that one MHC
molecule is able to bind a wide range of peptides with different sequences. For all MHC
molecules, only a few of the amino acids in the antigen peptide are critical for binding to amino
acids in the peptide-binding groove. The critical amino acids in the peptide are called anchor
residues; they are the same or similar in all peptides that bind to a given MHC molecule. The
other amino acid residues in the peptides can be different. The pattern of anchor residues that
binds to a given MHC molecule is called the peptide-binding motif. Hence, a very large number
of discrete peptides can bind to each MHC isoform, the only constraint being the possession of
the correct anchor residues at the appropriate positions in the peptide. MHC class I molecules
25also bind peptides that are typically nine amino acids long, whereas MHC class II molecules bind
longer peptides with a range of lengths.
5–90
A. Interallelic conversion is a recombination between homologous alleles of the same gene.
Gene conversion is a recombination between non-homologous alleles of different genes.
B. An example of interallelic conversion would involve recombination between HLA
B*5101 and HLA B*3501. An example of gene conversion would involve recombination
between HLA B*1501 and HLA Cw*0102.
5–91 Balancing selection maintains a variety of MHC isoforms in a population, whereas
directional selection replaces older isoforms with newer variants.
5–92
A. Alloantibodies are antibodies specific for variant antigens encoded at polymorphic genes
within a species (for example blood group antigens and MHC class I and class II molecules).
B. They arise naturally during pregnancy when the mother’s immune system encounters
fetal cells expressing variant antigens derived from the father but not expressed by the mother.
C. If present, alloantibodies with specificity for transplanted organs will mediate graft
rejection.
26
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