4.

The myeloid lineage comprises most of cells of the innate immune system
- common myeloid progenitor, CMP: precursor of macrophages, granulocytes, mast cells,
and dendritic cells, megakaryocytes, red blood cells

- three types of phagocytes: macrophages, granulocytes, dendritic cells

- macrophage: phagocytosis, activation of bactericidal mechanisms, antigen presentation

a. resident in all tissues  arise during embryonic development
b. or bone marrow (minor)  mature from monocytes
c. monocytes  circulate in blood  migrate into tissues  differentiation
d. long lived cells, several functions
i. engulf and kill
ii. dispose of pathogens and infected cells targeted by an adaptive immune
response
iii. monocytes are phagocytic too / but primarily macrophages function first
iv. orchestrate immune responses  induce inflammation  prerequisite to
successful immune response
v. general scavenger cells  clear dead cells and cell debris

- activation of complement triggers inflammation and phagocytosis;

bacterial surfaces  cascade of proteolytic reactions
 coat the microbes with fragments of proteins
 recognized by specific complement receptors of macrophages and
neutrophils
 phagocytosis and destroyed

- granulocytes: polymorphonuclear leukocytes

a. short lived
b. mature in bone marrow
c. during immune response  production increases, migration to infection site

- neutrophil: phagocytosis, activation of bactericidal mechanisms

a. numerous and important cells in innate immune response
b. phagocytosis, degradative enzymes and other antimicrobial substances in granules
c. hereditary deficiencies of neutrophil function  infection

- eosinophil: killing of antibody-coated parasites

- basophil: promotion of allergic responses, augmentation of anti-parasitic immunity
 - mast cell: release of granules containing histamine and active reagents
a. development in bone marrow, migrate as immature precursors, mature in peripheral
tissues (skin, intestines, airway mucosa)
b. granules contain inflammatory mediators  histamine, proteases
c. protect internal surfaces from pathogens & parasitic worms

- allergic inflammation  eosinophils, basophils, mast cells

- dendritic cell: antigen uptake in peripheral sites, antigen presentation

a. phagocytic cells, including several related lineages
b. elaborate membranous processes
c. immature dendritic cells  bloodstream  tissues
d. macropinocytosis  ingest large amount of ECF
e. main role = clearance of microorganisms
f. sensor cells  trigger itself to produce mediators  activate other immune cells
g. role in activating a particular class of lymphocytes  T lymphocytes (adaptive
immune system)
h. both innate and adaptive!

5. Sensor cells express pattern recognition receptors that provide an initial discrimination
between self and nonself
- no infection  only purified antigens with adjuvant(killed bacteria, bacterial extracts) can
activate T cells experimentally
- important sensor cells that detect infection and initiate responses by producing
mediators
a. neutrophiles
b. macrophages
c. dendritic cells
 express invariant innate recognition receptors
(pattern recognition receptors, PRRs)

- PRR recognizes pathogen-associated molecular patterns (PAMPs)

a. part of many microorganisms
b. not of the host body’s cells
 c. mannose-rich oligosaccharides, peptidoglycans, lipopolysaccharides of bacterial cell
wall, unmethylated CpG DNA common to many pathogens
 conserved, targets for recognition

- some PRRs are transmembrane proteins

 toll like receptors (TLRs);
detect PAMPs derived from extracellular bacteria,
or bacteria taken into vesicular pathways by phagocytosis

- some PRRs are cytoplasmic proteins

 NOD like receptors (NLRs)
Sense intracellular bacterial invasion
viral infection
 differences of structures and locations of mRNA and viral RNA
 or between host and microbial DNA

- some receptors expressed by sensor cells  detect cellular damage induced by

pathogens
- Macrophages  many kinds of receptors that recognize different pathogens
a. mannose and glucan receptors, scavenger receptor
 bind cell wall carbohydrates of bacteria, yeast, fungi

b. TLRs / macrophages, dendritic cells, etc.

 heterodimer of TLR-1 and TLR-2
lipopeptides from pathogens / Gram(+)

 TLR-4
liposaccharides from Gram(-)
and lipoteichoic acids from Gram(+)

-
6. Sensor cells induce an inflammatory response by producing mediators such as chemokines
and cytokines
- Macrophages and neutrophils / sensor cells can directly induce effector function
 such as phagocytosis and degradation of encountered bacteria

+ production of inflammatory mediators

 cytokines and chemokines

- cytokine; proteins secreted by Immune cells  affects nearby cells

a. many kinds of cytokines exist
b. produced by different cells

- chemokine;
a. act as chemoattractant; neutrophils and monocytes (bloodstream  tissue)
b. help organize various cells in lymphoid tissues
/ discrete regions where specialized responses can take place

- cytokines and chemokines released by activated macrophages

 recruit cells from the blood into infected tissues
 inflammation, helps to destroy pathogen

- inflammation
a. increases the flow of lymph / adaptive immune response initiation
(infected tissue  microbes or cells bearing antigens  nearby lymphoid tissues)
b. adaptive immunity generation  inflammation also recruits effector components

c. calor, dolor, rubor, tumor / heat, pain, redness, swelling

 effects of cytokines or mediators on the local blood vessels
 dilation and increased permeability of blood vessels
 - cytokines and complement fragments
 endothelial cells  cytokines
 adhesive properties alteration
 circulating leukocytes  sticking to the endothelial cells
 migration to infected site  pain

- macrophages and neutrophils  a.k.a. inflammatory cells

a. influx of neutrophils  monocytes  macrophages  reinforcing and sustaining the
innate immune response  inflammation continues  eosinophils  destruction of
invading microorganisms

- inflammation processes
a. bacteria trigger macrophages to release cytokines and chemokines
b. vasodilation and increased vascular permeability cause redness, head, swelling
c. inflammatory cells migrate into tissue, releasing inflammatory mediators that cause
pain

7. Innate lymphocytes and natural killer cells are effector cells that share similarities with
lymphoid lineages of the adaptive immune system
- common lymphoid progenitor (CLP)  bone marrow /
 antigen specific lymphocytes of the adaptive immune system
 or innate lineages
 - CLP  natural killer (NK) cells
a. lymphocyte like cells with a distinctive granular cytoplasm
 recognize and kill certain tumor cells and cells infected with herpesviruses
b. lack the antigen specific receptors of the adaptive immune stem cells
c. express innate receptors  respond to cellular stress and infections by
viruses
d. release lytic granules that kill some virus infected cells

- CLP  innate lymphoid cells (ILCs)

reside in peripheral tissues such as intestine, where inflammatory responses occur

11. Antigen receptor genes are assembled by somatic gene rearrangements of incomplete
receptor gene segments
- Innate immune systems  inflammatory stimuli (TLR, NOD proteins) detection
 limited number of sensors

- Adaptive immunity  specificities

 seemingly infinite but yet are encoded by a finite number of genes

- Immunoglobulin variable regions are inherited as sets of gene segments

a. each encoding a part of the variable region of one of the immunoglobulin
polypeptide chains
b. B-cell development in bone marrow
  gene segments are irreversibly joined by DNA recombination
 form a stretch of DNA encoding a complete variable region
c. TCR; similar process of gene rearrangement in thymus during development of T cells

 combinational diversity
small amount of genes  diversity of receptors

 junctional diversity
during recombination;
random addition or subtraction at junctions of the gene segments

 amplified by the fact that each receptor has two different variable
chains

12. Lymphocytes activated by antigen give rise to clones of antigen-specific effector cells that
mediate adaptive immunity
- two critical features about lymphocyte development
// that specialize adaptive immunity from innate immunity

a. lymphocyte expresses only one receptor specificity (clonal / mature lymphocyte

differs)
 innate immune system express different patter recognition receptors shared by
many pathogens

b. gene rearrangement process  irreversibly change lymphocyte’s DNA

 progeny inherit the same receptor specificity
 proliferation of individual lymphocytes forms a clone of cells

- lymphocyte receptor repertoire; similar to natural selection

(clonal expansion, secrete clonotypic antibodies)
 clonal selection theory

- clonal selection
a. a single progenitor cell gives rise to a large number of lymphocytes, each with a
 different specificity
b. removal of potentially self-reactive immature lymphocytes by clonal deletion
c. pool of mature naïve lymphocytes
d. proliferation and differentiation of activated specific lymphocytes to form a clone of
effector cells

- postulates of the clonal selection hypothesis

a. each lymphocyte bears a single type of receptor with a unique specificity
b. interaction between foreign molecule and lymphocyte receptor  high affinity 
activation
c. the differentiated effector cells derived from an activated lymphocyte  bear
receptors of identical specificity to those of the parental cell
d. lymphocytes bearing receptors ubiquitous self molecules are deleted at an early
stage of development, absent from the repertoire of mature lymphocytes
13. Lymphocytes with self-reactive receptors are normally eliminated during development or
are functionally inactivated
- might react against an individual’s own self antigens
- twin  common placenta  unresponsive or tolerant
- exposure of foreign tissues during embryonic development // tolerant
 clonal deletion

- receive either too much or too little signal  eliminated during development
 apoptosis, programmed cell death

- anergy; induction of inactive state

14. Lymphocytes mature in bone marrow or the thymus and then congregate in lymphoid
tissues throughout the body
- central or primary lymphoid organs; generation of lymphocytes
 bone marrow, thymus

- peripheral or secondary lymphoid organs; mature naïve lymphocytes, initiation of

adaptive immune response
 lymph nodes = spleen, and the mucosal lymphoid tissues of gut, nasal and respiratory
 tract, urogenital tract, other mucosa

- bone marrow  B and T lymphocytes

- B cells; complete development within bone marrow / bursa of Fabricius
- T cells; migrate to the thymus, complete development there
- after maturation  bloodstream  circulate peripheral lymphoid tissues
15. adaptive immune responses are initiated by antigen and antigen presenting cells in
secondary lymphoid tissues
- T cell;
a. encounters with dendritic cells
b. picked up antigens at sites of infection, migrated to secondary lymphoid organs
c. activation of dendritic cells’ PRR by PAMP  dendritic cells in the tissues engulf the
pathogen and degrade intracellularly
d. also take up extracellular material  virus particles and bacteria, by receptor
independent micropinocytosis
 display of peptide antigens on the MHC molecules of dendritic
cells
 activates the antigen receptors of lymphocytes

- PRRs  dendritic cells to express cell surface proteins called co-stimulatory molecules 
T lymphocyte to proliferate and differentiate
- Dendritic cell == antigen presenting cells (APCs)
 Crucial link between innate and adaptive immune response

- macrophages, B cells can also act as antigen presenting cells

- dendritic cells  specialized in initiating adaptive immune response

- free antigens  stimulate antigen receptors of B cells,

 but most B cells require helper T cells’ help
 optimal antibody responses

- the activation of naïve T lymphocytes  first stage in all adaptive immune response
- innate (neutro, eosin, basophil, monocyte) - dendritic cell -> adaptive (B, T cell)

- initiation of adaptive immune response of dendritic cells and T cells

a. immature dendritic cells reside in peripheral tissues  engulf and degrade,
macropinosome formation (macropinocytosis)
b. dendritic cells migrate via lymphatic vessels to regional lymph nodes
c. mature dendritic cells activate naïve T cells in lymphoid organs such as lymph nodes

16. lymphocytes encounter and respond to antigen in the peripheral lymphoid organs
- antigen - lymphocytes encountering  peripheral lymphoid organs
a. lymph nodes
b. spleen
c. mucosal lymphoid tissues
 mature naïve lymphocytes are continually recirculating
 where pathogen antigens are carried by dendritic cells primarily

- peripheral lymphoid organs

a. specialized to trap antigen bearing dendritic cells
b. composed of aggregations of lymphocytes in nonleukocyte stromal cells’ framework
 basic structural organization, provide survival signals
c. resident macrophages and dendritic cells

- infection
 antigen bearing dendritic cells
 draining lymph nodes, afferent lymphatic vessels
 where activation of antigen specific lymphocytes occurs
 activated lymphocytes  proliferation and differentiation
 effector cells (efferent lymphatic vessel)
 bloodstream  tissues

- naïve lymphocytes that no recognition their antigen also leave through the efferent
lymphatic vessel and returned to the blood, recirculate through lymphoid tissues

- lymph nodes
a. highly organized lymphoid organs at convergence of vessels of lymphatic system
b. collects ECF from tissues and returns it to the blood
c. lymph; ECF produced by filtration from blood
d. peripheral tissues  lymphatic vessels or lymphatics (flow)

- afferent lymphatic vessels

a. drain fluid from the tissues
b. carry pathogens and antigen bearing cells  lymph nodes
c. free antigens diffusion to lymph node, dendritic cells actively migrate to lymph node
by chemokines
d. lymphocytes are attracted chemokines either //
 through blood vessels called high endothelial venules (HEV)
 thicker and rounded appearance
 enter lymph nodes by squeezing through the walls
- B lymphocytes are localized in follicles  outer cortex of lymph node
- T lymphocytes are localized in paracortical areas, T-cell zones, deep cortex

- Lymphocytes (blood  lymph nodes)

 paracortical areas first,
 antigen presenting dendritic cells and macrophage localized there
 free antigen diffusing through the lymph node can be trapped on
dendritic cells and macrophages
 antigen – antigen presenting cells – naïve T cells
 T cell zone juxtaposition <T cell activation eventually>

- B cell activation  required helper T cell’s cooperation

 border of follicle and T-cell zone
 some of B cell follicle include germinal centers
 B cell proliferation and differentiation into plasma cells

- human; spleen; behind the stomach;

no direct connection with the lymphatic system;
collects antigen from the blood,
involved in immune responses to blood borne pathogens
lymphocytes enter and leave spleen

- collection of senescent (old) RBCs  disposal of RBC (red pulp)

- lymphocytes surrounded by arterioles running through spleen (white pulp)

- sheath of lymphocytes around an arteriole
 periarteriolar lymphoid sheath (PALS)
 contains mainly T cells
- intervals  lymphoid follicles
 mainly B cells

- marginal zone; surrounds the follicle; few T cells;

- rich macrophages,
- resident noncirculating B cells
 marginal zone B cells
 produce antibodies that have low affinity to
bacterial capsular polysaccharides rapidly

 blood borne microbes, soluble antigens, antigen:antibody

 complexs are filtered from the blood by macrophages and
immature dendritic cells within the marginal zone
 dendritic cells in marginal zone  migrate to T-cell area 
activate

17. Mucosal surfaces have specialized immune structures that orchestrate responses to
environmental microbial encounters
- mucosal immune system / mucosa-associated lymphoid tissue (MALT)
- gut-associated lymphoid tissues (GALT)
tonsils, adenoids, appendix, Peyer’s patches (M cells – microfold, antigen
collection)
- respiratory tract
 nasal-associated lymphoid tissue (NALT)
 bronchus-associated lymphoid tissue (BALT)

18. Lymphocytes activated by antigen proliferate in the peripheral lymphoid organs,

generating effector cells and immunological memory
- lymphocyte  recognizing specific antigen
 stops migrating, nucleus and cytoplasm increases, new mRNA and
proteins producing  lymphoblast  proliferation
- B  plasma cell
- T  cytotoxic and helper
 effector lymphocytes
- no recirculation usually
- memory cells; persist after antigen has been eliminated
19. Innate immune responses can select from several effector molecules to protect against
different types of pathogens
- NK cells and ILCs // lymphocytes similarities, particularly T cells
- NK - ILC
a. no antigen specific receptors a. same progenitor in bone marrow
b. exhibit cytotoxic capacity of T as NK cells
cells b. no antigen specific receptors
c. cytokines production c. differ in cytokines / similarities
with helper T cells

- cytokines
a. promote immunity to intracellular pathogens; interferon-gamma
 activating phagocytes to more efficiently kill by inducing target
tissues to resist pathogens
 type I immunity
 ILC making IFN-gamma is called ILC1
b. Other ILC subsets produce cytokines favoring effector module  type 2, 3
 Parasitic and extracellular pathogens

- Effector module
Cytotoxicity: NK cells, CD8 T cells (killer T)
 Elimination of infected and stressed cells

[type 1] Intracellular immunity: ILC1, helper T1 cells

 Elimination of intracellular pathogens; activation of macrophages

[type 2] Mucosal and barrier immunity: ILC2, helper T2 cells

 Elimination and expulsion of parasites; recruitment of eosinophils,
basophils, and mast cells

[type 3] Extracellular immunity: ILC3, helper T17 cells

  Elimination of extracellular bacteria and fungi; recruitment and
activation of neutrophils
20. Antibodies protect against extracellular pathogens and their toxic products
- humoral immunity; mediated antibodies

- classes or isotypes  different functions

- three ways participating roles

a. neutralization
bacterial toxin -> neutralization -> ingestion my macrophage (or neutronphil)

b. opsonization
bacteria in extracellular space -> opsonization -> ingestion by macrophage
* bacteria evade phagocytosis / outer coat is not recognized by PRR of phagocytes
 Fc receptor recognize bacteria which is surrounded by antibodies

c. complement activation
bacteria in plasma -> complement activation -> lysis and ingestion
*main role of complement  help phagocytes to engulf bacteria which is not
recognized by itself  phagocytes have complement receptors

21. T cells orchestrate cell-mediated immunity and regulate B-cell responses to most
antigens
- intracellular invader  T lymphocytes
 cell mediated immune response of adaptive immunity

- T lymphocytes
 a. Develop in thymus
b. TCR characterization, expression of certain markers / cell surface protein (co-
receptors)
c. peptide:MHC complex  transported cell surface and displayed to T cells

CD8 – selectively recognize peptides

that is bounded on MHC class I protein  cytotoxic T cells function
(MHC I molecules are expressed on most cells of the body -> important)

- MHC class I algorithms

a. virus infects cell
b. viral proteins synthesized in cytosol
c. peptide fragments of viral proteins bound by MHC class I in ER
d. transported to cell surface
 recognized by MHC I receptor & CD8 of cytotoxic T cells
 caspases (cysteine in active site, cleave proteins at aspartic acid)
 active cytosolic nuclease (host and viral DNA cleavage)

CD4 – selectively recognize peptides

that is bounded on MHC class II protein  helper T cells function

- MHC class II; dendritic cells, macrophage, B cells

 recognize antigens taken up by phagocytosis from the extracellular env.

TH1, TH2, TH17  produce cytokines in patterns similar to the subsets of ILCs
TFH cell  interacts with B cells to regulate antibody production

TH1; mycobacteria(avoid lysosome fusion)  overcome the blockage

Chapter 2. Innate immunity: the first lines of defense

1. Infectious diseases are caused by diverse living agents that replicate in their hosts
- extracellular infection site
a. interstitial spaces ( viruses, bacteria, protozoa, fungi, worms/helminths)
b. blood
c. lymph
 phagocytosis / capsule  complement / antibodies
d. epithelial surfaces
 antimicrobial peptides, antibodies (IgA)

- intracellular infection site ( viruses, protozoa, mycobacteria)

 a. cytoplasmic
 NK, cytotoxic T cells
b. Vesicular
 T cell and NK cell dependent macrophage activation

- damaging ways
a. direct
i. exotoxin  adaptive immune system (maj)
ii. endotoxin  bacterial structure trigger phagocytes to release cytokines
e.g. LPS of Gram(-) bacteria
iii. direct cytopathic effect

b. indirect
i. immune complexes
ii. anti-host antibody
iii. cell-mediated immunity

3. Infectious agents must overcome innate host defenses to establish a focus of infection
- microorganism must first invade the body by binding or crossing epithelium
- evading or overwhelming innate host defenses  infection  replication  disease
occurs

- infection and the response to it

a. pathogens adhere to epithelium
 phagocytes especially in lung

b. local infection penetration of epithelium

 wound healing, antimicrobial proteins and peptides,
phagocytes, complement

c. local infection of tissues

 blood clotting, complement, cytokines, chemokines,
phagocytes, NK cells, activation of macrophages,
dendritic cells migrate to lymph nodes
 initiate adaptive immunity

d. adaptive immunity
  infection cleared by specific antibody,
T cell dependent macrophage activation, cytotoxic T cells
-

4. Epithelial cells and phagocytes produce several kinds of antimicrobial proteins

- Epithelia  more than barrier
- acid pH of stomach and digestive enzymes, bile salts, fatty acids, lysolipids
- lysozyme (made from Paneth cells)
 glycosidase of peptidoglycan
(N-acetylglucosamine, GlcNAc + N-acetylmuramic acid, MurNAc)
+ cross linking peptide bridges
 cleaves beta – 1, 4 linkage / more effective in Gram(+) bacteria

- secretory phospholipase A2 (Paneth cells either)

 enter the cell wall, access and hydrolyze phospholipids in the cell membrane, killing

- antimicrobial peptides
 defensins, cathelicidins, histatins

- defensin
a. many eukaryotic organisms
b. short cationic peptides , three disulfide bonds  stabilize amphipathic structure
c. disrupt the cell membranes of bacteria and fungi, some viruses
d. insertion of the hydrophobic region into the membrane bilayer  pore formation
e. alpha, beta, theta defensins, gram positive, negative, fungi

- inactive propeptides  generation of antimicrobial peptides

defensin alpha  neutrophil’s primary granules
**(cellular proteases remove anionic propiece of propeptide of defensin alpha)
***primary granules of neutrophils similar to lysosomes, contain many agents
  phagosome

- Paneth cell
 produce alpha defensins == cryptdins,
proteases (trypsin) works to make it

- beta defensins
a. lack the long propiece of alpha defensins,
b. presence of microbial products
c. made by epithelia outside the gut, respiratory and urogenital tracts, skin, tounge
d. made by keratinocytes in epidermis
e. type II pneumocytes in lungs are packaged into lamellar bodies

- theta  primates, human  mutated, inactivated

- cathelicidin
a. lack of disulfide bonds
b. made by neutrophils, macrophages,
c. infection by keratinocytes in the skin and epithelial cells in the lungs and intestine
d. propeptides  two linked domains  processed before secretion
e. sotred in secondary granules
f. activated when primary and secondary granules are induced to fuse with
phagosomes
g. neutrophil elastase (in primary granules)

- histatins
a. oral cavity by the parotid, sublingual, submandibular glands
b. short, histidine rich, cationic peptides  pathogenic fungi

- lectins
a. carbohydrate binding proteins
b. C-type lectins  require calcium / for binding activity of their carbohydrate
recognition domain (CRD)
c. RegIIIgamma  Paneth cells // peptidoglycan binding // cleavage by trypsin

d. RegIIIalpha a.k.a. HIP/PAP  heameric pore

e. RegIII family kill gram(+)

5. The complement system recognize features of microbial surfaces and marks them for
destruction by coating them with C3b
- stages of complement action
a. pattern recognition trigger
b. protease cascade amplification / C3 convertase
c. inflammation, phagocytosis, membrane attack

- zymogen, pro-enzymes  enzymatically active only after proteolytic cleavage by another

complement protein

- three pathways
a. lectin
b. classical
c. native
 C3 convertase is generated
 Cleaves C3 to generate large amounts of C3b  opsonin
 and C3a  inflammation

 C5 convertase (C3 convertase + C3b)

 C5a  C3b – CR1 of phagocytes  activate phagocytose
 C5b  late events of complement activation /
 Membrane attack complex, MAC

6. The lectin pathway uses soluble receptors that recognize microbial surfaces to activate the
complement cascade

7. The classical pathway is initiated by activation of the C1 complex and is homologous to

the lectin pathway

9. The alternative pathway is an amplification loop for C3b formation that is accelerated by
properdin in the presence of pathogens

10. Membrane and plasma proteins that regulate the formation and stability of C3
convertases determine the extent of complement activation

13. Ingestion of complement tagged pathogens by phagocytes is mediated by receptors for

the bound complement proteins

14. The small fragments of some complement proteins initiate a local inflammatory response
15. The terminal complement proteins polymerize to form pores in membranes that can kill
certain pathogens

16. Complement control proteins regulate all three pathways of complement activation and
protect the host from their destructive effects

17. Pathogens produce several types of proteins that can inhibit complement activation

Chapter 3. The induced response of innate immunity

1. After entering tissues, many microbes are recognized, ingested, and killed by phagocytes

2. G-protein-coupled receptors on phagocytes link microbe recognition with increased

efficiency of intracellular killing

- Antimicrobial mechanisms of phagocytes

a. Acidification
b. Toxic oxygen derived products
c. Toxic nitrogen oxides
d. Antimicrobial peptides
- macrophage
cathelicidin, macrophage elastase derived peptide
- neutrophil
 Alpha defensins, beta defensin, cathelicidin, azurocidin, BPI, lactoferrin

e. Enzymes; lysozyme, acid hydrolases

f. Competitors; neutrophil – lactoferrin, vitamin B12

- Neutrophil engulf and kill the microbes to which they bind

- Bacterial fMLF peptides activate Rac2  taken up into phagosomes
- Phagosome + primary + secondary granules  Rac2  NADPH oxidase, superoxide

3. Microbial recognition and tissue damage initiate an inflammatory response

- Cytokines produced by macrophages cause dilation of local small blood vessels
- Leukocytes  peripheral site of blood vessel / adhesion
- Extravasate, blood clotting
- monocytes
 Chemokine receptors on leukocytes
 Adhesion molecules
 Migration to tissue, differentiates into inflammatory monocyte
4. Toll-like receptors represent an ancient pathogen-recognition system
- Antifungal responses in Drosophila
- Homologs were found in other animals  toll-like receptors

Plasma membrane
- TLR1:2 dimer  triacyl lipopeptides / binding  dimerization
- TLR2:6 dimer  diacyl lipopeptides
- TLR5  flagellin
- TLR4  LPS / binding  dimerization

Endosome
- TLR3  dsRNA
- TLR7 / 8  ssRNA
- TLR 9  CpG DNA

5. Mammalian Toll-like receptors are activated by many different pathogen-associated

molecular patterns

6. TLR-4 recognized bacterial lipopolysaccharide in association with the host accessory

proteins MD-2 and CD14

7. TLRs activate NFkappaB, AP-1, and IRF transcription factors to induce the expression of
inflammatory cytokines and type I interferons
 - Dimerization TLRs
 IRAK1, 4  E3 ubiquitin ligase TRAF-6 activation
 TRAF-6 polyubiquitination  ubiquitin – TAK1  activation
 TAK1 – polyubiquitin chain – IKKs
 phosphorylates IkappaB which is binding with NFkappaB
 IkappaB degradation, NFkappaB  nucleus  cytokine genes
 Inflammatory and type I interferons

8. The NOD-like receptors are intracellular sensors of bacterial infection and cellular damage
- Polyubiquitination of RIP2
- Rest is same

12. Activation of innate sensors in macrophages and dendritic cells triggers changes in gene
expression that have far-reaching effects on the immune response
- dendritic cells  bacteria – TLR-4 with CD14  MHC molecules providing far away

15. Cytokines and their receptors fall into distinct families of structurally related proteins
- heterodimeric receptors
- heterodimeric receptors with a common chain
- heterodimeric receptors
- TNF receptor family
- Chemokine receptor family – G protein linked

16. Cytokine receptors of the hematopoietin family are associated with the JAK family of
tyrosine kinases, which activate STAT transcription factors

17. Chemokines released by macrophages and dendritic cells recruit effector cells to sites of
infection

18. Cell-adhesion molecules control interactions between leukocytes and endothelial cells
during an inflammatory response
- Selectins; bind carbohydrates; initiate leukocyte endothelial interaction
- Integrins; bind to cell adhesion molecules
- Immunoglobulin superfamily; cell adhesion, ligand for integrins

19. Neutorphils make up the first wave of cells that cross the blood vessel wall to enter an
inflamed tissue
20. TNF-alpha is an important cytokine that triggers local containment of infection but
induces shock when released systemically
Gram (-) bacteria infection
- Local infection  tissue secretion of TNF-alpha by macrophages
 Increased phagocytes, migration of lymphocytes, platelets
- Systemic infection  macrophages, liver and spleen, secret TNF-alpha into bloodstream
 sepsis

21. Cytokines make by macrophages and dendritic cells induce a systemic reaction known as
the acute-phase response

22. Interferons induced by viral infection make several contributions to host defense

23. Several types of innate lymphoid cells provide protection in early infection

24. NK cells are activated by type I interferon and macrophage derived cytokines
Interferon production  NK cell mediated killing  T cell mediated killing

25. NK cells express activating and inhibitory receptors to distinguish between healthy and
infected cells
- NK cell activating ligand – activating receptor
- MHC class I – inhibitory receptor of NK cell  inhibit signals from activating receptors

- Absent MHC class I  no negative signall  activation of activating reeptors

 release granule, induce apoptosis
- TNF family / target (DR5)  caspase  activation  apoptosis

Chapter 4. Antigen recognition by B cell and T cell receptors

1. IgG antibodies consist of four polypeptide chains

- IgG
- 두 개의 heavy chain => disulfide bonds
- Light chian – heavy chain => disulfide bonds
 - 총 4 개, 4 개

3. The domains of an immunoglobulin molecule have similar structures

- consists of beta stands

4. The antibody molecule can readily be cleaved into functionally distinct fragments
- proteolytic cleavage
a. by papain => Fc 와 Fab 의 분리
b. by pepsin => Fab 2 개 붙은 형태(F(ab’)2)와 pFc’의 분리

5. The hinge region of the immunoglobulin molecule allows flexibility in binding to multiple
antigens
- 60 도
- 90 도

6. Localized regions of hypervariable sequence from the antigen binding site

- Hyper variable (HV) region of genes exist
 꺾이는 부분  antigen binding site

7. Antibodies bind antigens via contacts in CDRs that are complementary to the size and
shape of the antigen
- CDR, complementary determining region

8. Antibodies bind to conformational shapes on the surfaces of antigens using a variety of

noncovalent forces
- Electronic forces
- Hydrogen bonds
- Van der waals forces
- Hydrophobic forces
- Cation-pi interaction; cation and electron cloud of nearby aromatic group

10. Some species generate antibodies with alternative structures

- Human IgG
- Camelid IgG: no CH1 and CL, only heavy chain and variable region
- Shark IgNAR: Fc is long, only heavy chain, and Fab has only variable region

11. The TCRalpha:beta heterodimer is very similar to a Fab fragment of immunoglobulin

 - Alpha & beta chain is linked by disulfide bond
- Variable + constant region + stalk segment (where disulfide bond forms)
- Transmembrane region + cytoplasmic tail

13. There are two classes of MHC molecules with distinct subunit compositions but similar
three-dimensional structures

- MHC class II  alpha:beta heterodimer

- MHC class I  alpha 1 ~ 3, alpha1 에 beta2 micro globulin 이 결합됨

15. MHC class I molecules bind short peptides of 8~10 amino acids by both ends

16. The length of the peptides bound by MHC class II molecules is not constrained

17. The crystal structures of several peptide:MHC:T-cell receptor complexes show a similar
orientation of the T-cell receptor over the peptide:MHC complex

18. The CD4 and CD8 cell-surface proteins of T cells directly contact MHC molecules and are
required to make an effective response to antigen
- CD4  D1~D4 일직선 / 1,2 가 MHCII 의 beta 와 붙음
- CD8  alpha & beta units are bind by disulfide bond / alpha 가 alpha2, 3 과 붙음

19. The two classes of MHC molecules are expressed differentially on cells
Chapter 5. The generation of lymphocyte antigen receptors

1. Immunoglobulin genes are rearranged in the progenitors of antibody-producing cells

2. Complete genes that encode a variable region are generated by the somatic recombination
of separate gene segments
- Germline DNA;
recombination  D-J rearrangement recombination
 V-J or V-DJ  transcription
 splicing  translation (no l)

- Light chain; L, V, J, C (CL) => V + J 가 노출

- Heavy chain; L, V, D, J, C (CH1, -, 2, 3) => V + D + J 가 노출

3. Multiple contiguous V gene segments are present at each immunoglobulin locus

- V; variable, D: diversity(only on heavy chain), J: joining(맞닿는 부위), C: constant
- V 사이에 L 존재

4. Rearrangement of V, D, and J gene segments is guided by flanking DNA sequences

- V segments may be in either forward or reverse orientation of transcription
- Forward oriented + J gene  loop  deletion of loop
- Reverse oriented + J gene  coiled configuration  inverted
*** RSS recombination signal sequence 간 인식!
5. The reaction that recombines V, D, and J gene segments involves both lymphocyte-specific
and ubiquitous DNA-modifying enzymes
*** RSS recombination signal sequence 간 인식에 관여
 RAG1:2
 Cleavage of RSSs
 Coding joints + signal joints
 Ku70:Ku80 binds each of DNA ends
 Signal joints  DNA ligase IV:XRCC4 (5’ phosphorylated blunt
ends)
Coding joints  DNA-PK:Artemis opens hairpin
 TdT processes DNA ends
 DNA ligase IV:XRCC4

- RAG1:2
- Nonamer binding domains(RAG1:2 – RAG1:2) + Zn2+ domains

6. The diversity of the immunoglobulin repertoire is generated by four main processed

- Combinational diversity
- Junctional diversity
- Combinational diversity of heavy and light chain
- Somatic hyper mutation

7. The multiple inherited gene segments are used in different combinations

8. Variable addition and subtraction of nucleotides at the junctions between gene segments
contributes to the diversity of the third hypervariable region

- DNA-PK:Artemis  open hairpins, generating palindromic P-nucleotines

- N-nucleotide additions by TdT
- Pairing  unpaired sequences are removed by exonuclease  DNA synthesis
- D – PNP – J <hyper variable region>

9. The T-cell receptor gene segments are arranged in a similar pattern to immunoglobulin
gene segments and are rearranged by the same enzymes
- Alpha chain locus; L & V – J – C
- Beta chain locus; L&V – D- J- C
10. T-cell receptors concentrate diversity in the third hypervariable region

12. Different classes of immunoglobulins are distinguished by the structure of their heavy-
chain constant regions
- M, D G, E, A
- G; prevalent, plasma, crossing placenta
- M; small intestine concentration
- A; mucosa
- E; epithelium bound to mast cells

13. The constant region confers functional specialization on the antibody

- Fc region of isotypes bind receptors by effector cells
- Initiate complement system
- Fc portion  deliver antibodies / active transport

14. IgM and IgD are derived from the same pre-mRNA transcript and are both expressed on
the surface of mature B cells

15. Transmembrane and secreted forms of immunoglobulin are generated from alternative
heavy-chain mRNA transcripts
- Transmembrane; M1 & M1 after C genes
- Secreted; SC right after C

16. IgM and IgA can form polymers by interacting with the J chain
- Dimeric IgA
- Pentameric IgM

Chapter 6. Antigen presentation to lymphocytes

1. Antigen presentation functions both in arming effector T cells and in triggering their
effector functions to attack pathogen infected cells
- Cytosolic pathogens
degraded in cytosol, MHC class I presenting to CD8 T cells  cell death

- intravesicular pathogens
degraded in endocytic vesicles, MHC class II presenting to CD4 T cells  kill

- extracellular pathogens and toxins

degraded endocytic vesicles, MHC class II presenting CD4 T cells  B cells, Ig
 - cross presentation; exogenous pathway of loading MHC I molecules (dendritic cells)
- cross priming; activation of naïve T cells by cross presentation pathway

2. Peptides are generated from ubiquitinated proteins in the cytosol by the proteasome
- 19s + 20s + 19s  proteosome
- Polyubiquitinated proteins
 19s cap  degradation in catalytic core
 releasing to cytosol

3. Peptides from the cytosol are transported by TAP into the endoplasmic reticulum and
further processed before binding to MHC class I molecules
- TAP1, 2
a. transmembrane domain, hydrophobic, ER lumen
b. ATP binding cassette / ABC domain at cytosol

4. Newly synthesized MHC class I molecules are retained in the endoplasmic reticulum until
they bind a peptide
- Peptide fragments generated from proteasome  TAP  ERAAP  MHC class I +
protein

- MHC class I alpha chains + beta macroglobulin (calnexin)

- Making complex contains TAP

5. Dendritic cells use cross-presentation to present exogenous proteins on MHC class I

molecules to prime CD8 T cells

6. Peptide:MHC class II complexes are generated in acidified endocytic vesicles from proteins
obtained through endocytosis, phagocytosis, and autophagy
- Antigen is taken up from the ECF into vesicles
- Early endosomes of neutral pH, proteases are inactive
- Acidification of vesicles  degradation
- Fuse with vesicles containing MHC class II molecules

7. The invariant chain directs newly synthesized MHC class II molecules to acidified
intracellular vesicles
 - Invariant chain  Trimerization domain’s CLIP  groove of MHC class II
 LIP10 – CLIP - li
- Li cleavage  LIP10 cleavage  only CLIP bound to MHC class II
- Blockage function of binding of peptides

- li is cleaved in acidified endosome  peptide binding x yet

- HLA-DM binds to MHC II  releasing CLIP, allow other peptides bind

8. The MHC class II-like molecules HLA-DM and HLA-DO regulate exchange of CLIP for other
peptides

9. Cessation of antigen processing occurs in dendritic cells after their activation through
reduced expression of the MARCH-1 E3 ligase

10. Many proteins involved in antigen processing and presentation are encoded by genes
within the MHC

11. The protein products of MHC class I and class II genes are highly polymorphic
- Polymorphic  several morphology
- Polygeny  multiple genes

12. MHC polymorphism affects antigen recognition by T cells by influencing both peptide
binding and the contacts between T cell receptor and MHC molecule

14. Many T cells respond to superantigens

Chapter 7. Lymphocyte receptor signaling

1. Transmembrane receptors convert extracellular signals into intracellular biochemical events

- Intrinsic kinase domain
ligand binding
 dimerize  activating the kinases / phosphorylate each other  downstream

- kinase is noncovalently associated

ligand binding
 dimerize  activating kinases, phosphorylate each other  downstream

3. Small G proteins act as molecular switches in many different signaling pathways

- GDP – small G proteins (Ras)  inactivate
- GEF (guanine nucleotide exchange factors)  GTP binding  active Ras  GTP
hydrolysis

7. Antigen receptors consist of variable antigen-binding chains associated with invariant

chains that carry out the signaling function of the receptor
- CD3 – TCR – CD3 / ITAMs inside cell
- ZAP70; SH2 domain X2 + kinase domain  binding with ITAM
 CD4 and TCR == MHC class II  ITAM = ZAP70
 Phosphorylation by Lck

- BCR 에서도 Fc 에 Igbeta – Igalpha dimer 의 세포내부 ITAM 으로부터 signaling 진행

19. T-cell receptor signaling induces cytoskeletal reorganization by activating the small
GTPase Cdc42
20. The logic of B-cell receptor signaling is similar to that of T-cell receptor signaling, but
some of the signaling components are specific to B cells
- B7.1 / .2  CD28 // expressed in APCs
- CD28 phosphorylation  PI3K  PIP3
 recruits PDK1, phosphorylation  Akt activation
 recruits Itk, phosphorylation  PLC-gamma
 recruits Vav, Cdc24 activation

21. The cell-surface protein CD28 is a required co-stimulatory signaling receptor for naive T-
cell activation

24. Inhibitory receptors on lymphocytes downregulate immune responses by interfering with

co-stimulatory signaling pathways
- CTLA-4  bind with B7

Chapter 8. The development of B and T lymphocytes

1. Lymphocytes derive from hematopoietic stem cells in the bone marrow

- Stem cell  pro B cell  pre B cell  immature

2. B-cell development begins by rearrangement of the heavy-chain locus

3. The pre-B-cell receptor tests for successful production of a complete heavy chain and
signals for the transition from the pro-B cell to the pre-B cell stage

4. Pre-B-cell receptor signaling inhibits further heavy-chain locus rearrangement and

enforces allelic exclusion

5. Pre-B cells rearrange the light-chain locus and express cell-surface immunoglobulin

6. Immature B cells are tested for autoreactivity before they leave the bone marrow
<bone marrow>
- No self reaction  migration to periphery, mature B cell

- Multivalent self molecule  clonal deletion, receptor editing

 apoptosis, non autoreactive mature B cell

- Soluble self molecule  migrate to periphery  anergic B cell

- Low affinity non cross linking self molecule  periphery  clonally ignorant

- Strong ligation of IgM by self antigen

 B cell development arrest, light chain rearrangement
 If still has self reactive feature  apoptosis

7. Lymphocytes that encounter sufficient quantities of self antigens for the first time in the
periphery are eliminated or inactivated
<spleen>
- Multivalent, soluble  apoptosis
- Low affinity and non crosslinking self moleculr  mature, ignorant
- No self reaction  mature (IgD, IgM)

8. Immature B cells arriving in the spleen turn over rapidly and require cytokines and positive
signals
through the B-cell receptor for maturation and long-term survival

9. B-1 B cells are an innate lymphocyte subset that arises early in development

10. T-cell progenitors originate in the bone marrow, but all the important events in their
development occur in the thymus
 - Thymic stromal cell – notch formation, gene rearrangement
- Self MHC recognition  strong interaction  remove
- Maturated T cells  encounter foreign antigens from dendritic cells in peripheral
lymphoid
- Activated T cells  proliferate, eliminate infection

11. Commitment to the T-cell lineage occurs in the thymus following Notch signaling
- Double negative  double positive (CD4, 8)  single positive

12. T-cell precursors proliferate extensively in the thymus, but most die there

13. Successive stages in the development of thymocytes are marked by changes in cell-
surface molecules

14. Thymocytes at different developmental stages are found in distinct parts of the thymus

16. T cells expressing γ:δ T-cell receptors arise in two distinct phases during development

17. Successful synthesis of a rearranged β chain allows the production of a pre-T-cell

receptor that triggers cell proliferation and blocks further β-chain gene rearrangement

18. T-cell α-chain genes undergo successive rearrangements until positive selection or cell
death intervenes

22. Thymic cortical epithelial cells mediate positive selection of developing thymocytes
- Normal MHC class II  both CD8 and CD4 T cells mature
- MHC II negative mutant  only CD8
- Mutant with MHC II but expressed in thymic  both CD8 and CD4
-

23. T cells that react strongly with ubiquitous self antigens are deleted in the thymus

25. The specificity and/or the strength of signals for negative and positive selection must
differ

26. Self-recognizing regulatory T cells and innate T cells develop in the thymus

27. The final stage of T-cell maturation occurs in the thymic medulla
Chapter 9. The adaptive immune response
1. T and B lymphocytes are found in distinct locations in secondary lymphoid tissues
- dendritic cell with antigen  lymph node
 HEV, high endothelial venule  B cell to B cell zone / T to T zone

3. T and B cells are partitioned into distinct regions of secondary lymphoid tissues by the actions
of chemokines

- stromal cells & HEVs  secrete chemokines CCL21

 dendritic cells have receptor of CCL21
 secretion of CCL19, attracts T cell
 initially attracted B cell either
 B cell  differentiation of follicular dendritic cells
 secrete CXCL13  more B cells

4. Naive T cells migrate through secondary lymphoid tissues, sampling peptide:MHC complexes
on dendritic cells
- dendritic cells, HEV  T cells enter lymph node
a. T cells not activated by antigen  exist
b. Activated by antigen  lose exiting ability, proliferate
 effector cells

5. Lymphocyte entry into lymphoid tissues depends on chemokines and adhesion molecules
- Rolling; selectins
- Activation; chemokines
- Adhesion; integrins
- Diapedesis; chemokines
6. Activation of integrins by chemokines is responsible for the entry of naive T cells into lymph
nodes

7. The exit of T cells from lymph nodes is controlled by a chemotactic lipid

- Proliferation 전; S1PR1 decreases, CD69 increases

- Proliferation 후; 반대  efferent lymphatic  S1P attracts effector T cells to get out

8. T-cell responses are initiated in secondary lymphoid organs by activated dendritic cells
- Dendritic cells / Macrophages
- B cells  microbial toxin

9. Dendritic cells process antigens from a wide array of pathogens

- Conventional dendritic cells

- Plasmacytoid dendritic cells

 IFN alpha, beta / CXCR3 /

10. Microbe-induced TLR signaling in tissue-resident dendritic cells induces their migration to
lymphoid organs and enhances antigen processing

13. B cells are highly efficient at presenting antigens that bind to their surface immunoglobulin

14. Cell-adhesion molecules mediate the initial interaction of naive T cells with antigen presenting
cells