• it is triggered by microbes(bacteria, fungi,and viruses) or host cells invaded by microbes 
• phagocytes recoginize parts of microbes that are not present in mammalian cells

1. Lipopolysaccharide (LPs)
2. Terminal Mannose
3. 2x stranded viral RNA
4. unmethylated CpGs(cytosine phosphodiester guanine)

• act as endotoxin and is part of the bacterial cell wall that is released when bacteria are lysed

• resides on bacterial glycoproteins
• is not seen on mammalian glyoproteins

• adjacent Cs & Gs may be methylated(contain a methyl group)

• methylation makes stretches of DNA unavailable for transcripton and translation into protein

• they are microbial membrane products
• are recognized by receptors (called pattern recognition receptors) on phagocytes
• receptors are expressed on different types of cells: phagocytes, macrophages, eosinophils, neutrophils, dendritic cells, b & t lymphoctes,

1. Toll-Like Receptors(TLRs)
2. Pathogen Assoc. Molecular Patterns(PAMPs)
3. Pattern Recognition Receptors(PRRs)

• discovered in insects and named for protein called Toll which enhances immune system in fruit flies
• protect or recognize different parts of pathogens 

  -ex. toll-like receptor-5 is specific for a particular bacterial flagellum

-signals from TLRs activate transription factors that stimulate the production of cytokines, enzymes, etc, involved in antimicrobial functons of phagocytes

2. PAMPs

(examples)

• lipopholysaccharide
• viral nucleic acids

• receptors on APCs that recognize patterns in and on the pathogens

1. toll-like receptors
2. receptors for the mannose residues in bavterial vell membranes
3. those receptors thhat recognize viral nucleic acid
4. those receptors that recognize chemokines

• chemicals that direct cells to site of infection

1. physical
2. chemical
3. cellular

• located in the skin and produces psoriasin which is a protein that has potent antimicrobial action especially against E. coli

• mucous membranes which wash away pathogens with saliva and tears

• on cells of the respiratory tract
• cilia remove microbes

-by riding in via phagocytes-

• some phagocytes(macrophages & neutrophils) fail at inracellular killing and carry the intact bacteria across the epithelium
• the specialized ability to traverse the epi. depends on the particular pathogen

-some pathogens are engulfed by macrophages and live in them, some actually attach to the epi. cells and replicate inside those cells

Connection between innate and adaptive immune system

in the innate system:

1.  pathogens breach the host
2. at that time, chemicals decide between "self(normal cells or products of metablism) and non-self(antigens)"
3. once the immune system decides that it is "nonself" PRR recognizes PAMPs
4. restriction of innate system to PAMPs on microbes prevents recognition of important non-self component of the body like an artificial joint
5. restriction(specificity) of innate system is flawless,while adaptive is flawed

• group of proteins that from aggregates(clusters) that kill cells
• producces glycoprotein that promote mictrobe uptake by phagocytes
• complement straddles or bridges innate and adaptive systems by or via production of antibody by the adaptive sys. 

*antibody stimulate compliment

• promotion of phagocytosis
  

• glycoproteins that promote phagocytosis

• possess TLRs that recognize the PAMPs
• this recognition stimulate cytokine production
• at the infection site internalize antigen and present it to cells

B-Lymphocytes and antibody production(adaptive or aquired)

Humoral response(antibody production):

• humor or humour is refered to as a mix of bodily fluids which the Greeks thought controlled health
• as part of the adaptive system, uses antibodies to neutrilize microbes and toxins

• are specific for many types of antigens while t-cells are only specific for proteinaceous antigens
• naive Bs are "activated" and divide to become plasma cells which secrete antibody
• naive Bs are membrane bound and secrete soluble antibodies
• both B-cell membrane bound and secreted antibody receptors recognize: protiens, lipids, carbs, nucleic acids, small chemical groups, part of macromolecules

1. there are "variable(v)" regions which change depending on the antigen
2. there are "constant(c)" region which are highly conserved and stay basically the same

1. Cγ(gamma)
2. Cμ(mu)
3. Cα(alpha)
4. Cδ(delta)
5. Cε(epsilon)

-the corresponding antibodies to these genes are called immunoglobins(heavy chain aka antibodies)

1. IgG
2. IgM
3. IgA
4. IgD
5. IgE

• serum proteins
• some are produced by liver while others by organs of the immune system
• term refers to adverse group of proteins with high molecular weight

1. α1
2. α2
3. β
4. γ(gamma)

• immunoglobins are a subgroup of gamma

• intravenous immunoglobin G
• it is pooled IgG for immunodeficiencies

• within the V regions there are specific antigen binding regions called hypervariable regions aka complimentary determining region(CDR)
• called CDR because it is complementary to antigen structure

*There are a limited # of genes coding for the basic structure of the antibody. The uniqueness of these antibodies derives from sequence variation in the hypervariable region

• made up of 4 polypeptide chains(2 light & 2 heavy)
• each chain has a variable and constant region
• takes on a Y - shape
•  chains are held together by disulfide bonds
• has "loops", variable, and hinge regions

• they corrspond to the location of antigen binding and is where the hypervariavle or CDR regions are found

• allows the "arms" of the Y shape to act independently in antigen binding

• area of the loops that has 3 CDRs
• CDR #3 contributes the most to antigen binding

• they were named based on fragments isloated by proteolytic enzymes using pepsin and papain(enzymes)
• these enzymes were then digested into 2 parts:

1. Fab fragment
2. Fragment Crystallizable(FC) fragment

• Fragment Antigen Binding
• specific area of antigen binding
• included the whole light chain plus the varible and the 1^st constant region of the heavy chain

• Fragment Crystallizable
• tends to crystallize in solution
• is the remaining heavy chain regions

[image]

1. Kappa(κ)
2. Lambda(λ)

• the two types are never mixed

1. IgG
2. IgM
3. IgA
4. IgD
5. IgE

1. physical properties(monomer, pentamer,..)
2. bilogical properties(half-life, conc. in serum,..)
3. effector functions(mast cell or naive b-cell maturation)

• all exept IgD 
• can secrete only one at a time

• most abundant Ig in serum
•  has 4 subclasses
• each subclass has slight differences in hinge region and location of disulfide bonds

these differences reflect ability to:

• cross placenta
• compliment activation
• mediating opsonization(promotion of phagocytosis)

• 5-10% of serum Ig
• first to be produced in response to antigen
• first to be produced by neonate(birth to 4 wks)
• efficient in binding antigens with repeating epitopes(binding sites on antigen)ex. viruses

• 10-15% of serum Ig
• prominant in:breast milk, tears, saliva, lung secretions, GI & GU tracts
• can bind to large antigens
• good defense against cholera, salmonella. gonorrhea, polio, influenza

• low serum content, but potent
• mediates immediate rxns

ex. asthma, hay fever, hives, anaphylactic shock

• widespread vasodialation which causes a lowering of blood volume(circulatory shock)
• smooth m. contraction of respiratory system(resp. shock)

1. IgE binds to basophils and mast cells
2. they degranulate, releasing histamines
3. histamines cause vasodialation to get WBCs to site of inflammation

• the major membrane bound Ig along with IgM
• is NOT secreted
• signals when naive B-cells are activated

What is antibody affinity?

-structure

ex. IgM=pentamer

• they are receptors on NK cells, neutrophils, macrophages, etc.
• they bind Fc portion of antibodies
• are respondibles for movement of antibody avross cell membrane and from mother to fetus

-they recognize different antigens

Ex.

B-cells»whole proteins, lipids, carbs, nucleic acids

T-cells»portions of proteins

• light chains can either be kappa(κ) or lambda(λ)
• they have variable(VL) and constant(CL) regions
• Vl has 2 segments which come together to form the variable region of the light chain (VL)

1. variable(V)
2. joining(j)

• through somatic recombination

• when genes are randomly selected then spliced together(only in immune sys.)

1. VDJ recombinase-enzyme that mediates rearrangement of genes(also involved in heavy chain)
2. RAG-1, RAG-2-proteins required in the first stages of cutting of the genes

• kappa gene is on chromosome 2, lambda on 22
• differ in the # of VJ genes
• kappa and lambda light chain loce also contain pseudogenes

• process of recombination is similar to kappa/lambda l.c. recomb.(VDJ recombinase and RAG 1&2 is involved)
• has a "D" segment (D=diversity) part of "V" region
• D&J segments code for the 3^rd CDR(is the most involved CDR in antigen binding)
• "c" genes that code for the "class" of isotype of antibody(all "c"s are present in a specific order with IgM&IgD first since they are the 1^st to be expressed

• allelic exclusion and somatic hyper mutation

• after VJ or VDJ is expressed, no other variable region can be selected

• point mutations that occur after antigen exposure
• increases binding affinity
• in some cases it lowers binding affinity-these cells are eliminated by apoptosis

• where an individual B-cell can switch or select an antibody to be produced
• antigen binds the antibody receptor(BCR) and the B-cell is influenced by cytokines produced by T-helper cells
• these events cause the signals for Class Switching

1. antigen binding B-cell
2. cytokine influence

(via CD40, CD40L)

1. T-cell produces cytokines
2. depending on the "type" of cytokine the DNA is loosened near the "class" gene

• loosened DNA=switch region
• switch recombinase(enzyme) rearranges the class gene to be close to VDJ

• antibodies are destined for the ER-golgi pathway due to the "L" or leader sequence(tells ribosome to drop off the antibody into the ER)
• in ER disulfide bonds are added for folding into antibodies shape
• glycosylation occurs in golgi
• antibodies are either secreted or inserted in B-cell membrane via vesicles from golgi

-----

• BiP(binding protein) binds to defunct antibody and keeps it in the ER
• in ER its labeled with ubiquitin which signals the ER vesicle to bring the defunct antibody to a proteasome which destroys the antibody and recycles it

• genes are expressed at different rates to prevent over exposure
• 2 "regulatory sequences" are involved

1. Promoters
2. Enhancers

• 3 post-transcriptional modifications must occur

1. removal of introns(unneeded RNA)
2. addition of multiple A bases on 3' end
3. G base(cap) is added to 5' end

• 2 and 3 prevent proteinn degredation

• researchers can study one antigenic molecule at a time for characteristics of antigenicity
• they attach an antigen to a "hapten"(a molecule so small it doesnt induce immune reponse)
• hapten+antigen=conjugate

• aka: immunization
• it is the use of weakened or killed pathogen or pathogen components to induce immunity
• different from innoculation which is the administration of unweakened, live pathogens
• vaccinization stimulates antibody production aginst the pathogen source in the vaccine

• small pox was the first developed
• cowpox virus was injected to provent smallpox
• cowpox is a skin blister transmitted from milking cows
• milkmaids developed immunity to smallpox by exposure to cowpox
• edward jenner coined the term "vaccination" from vaca=cow

• first given by "passive" immunization-antibodies from infected people were given
• invented by Jonas Salk 
• consisted of a weadened(attenuated) virus
• later an oral vaccine was developed

-vaccine replicates well in the stomach

-not as effective, but easy to make

1. killed or inactivated
2. attenuated
3. DNA
4. vector

1. IV=vein
2. ID=into dermis
3. SC=subcutaneous
4. IP=peritoneal(body cavity)
5. IM=muscle

-they increase response to antigen in vaccines

-they are chemicals mixed with antigen

-Freund's adjuvant

1. complete-antigen heat killed mycobacterium in H₂0 and oil
2. incomplete-antigen + H₂0 + oil

• produces localized inflammatory response by infiltration of macrophage rich granulocytes
• stimulates expression of costimulation on APCs that interact with TCR

• Al salts are used in adjuvants
• antibiotic prevent antibacterial growth
• egg protein is present from vaccine preparation 
• formaldehyde inactivates bacterial product
• MSG is a stabilizer
• Bimarsol is used as preservative and contains mercury

1. in chicken egg a whole is drilled and virus is inserted into embryotic cavity
2. egg provides stirility and nourishment
3. repicated virus is extracted with ambiotic fluid
4. process takes 6 months