Determination sets fate of cell Differentiation process thru which diff cell types arise Morphogenesis shapes cells

lls into organs Growth increase in size Morphogen must directly affect target cells, different concentrations = different effects

Lung and circulatory disease

Coagulation:
Extrinsic: injury/external Intrinsic: triggers not understood Most enzymes are proteases a suffix = acti!ated"

Trafficking pathways
#$ %efault exported to surface, no spec signal needed &$ regulated to storage !esicle '$ (argeting to lysosome needs signal )$ import from surface endocytosis" may need signal *ell puts proteins in transport !esicles different types w/ diff destinations", go along microtu+ules ,esicle doc-ing and fusion = receptor mediated Endocytosis types: . phagocytosis, ingestion of large particles . pinocytosis ingestion of small regions of plasma mem+rane . receptor.mediated

*holesterol transport: transported in lipoproteins coated +y phospholipid monolayer lipoprotein density changes in tissues /%/ receptors +inds apo0 in /%/ and apoE in ,/%/ mainly in li!er, fat, adrenal cells remo!es )12 plasma /%//day /ow cholesterol = up.regulation

Familial hypercholesterolaemia:
Ele!ated plasma cholesterol *holesterol deposits around joints %e!elop heart disease and death in teens 3utosomal dominant

3therosclerosis fatty deposit +uild.up around !essel walls

Initial injury/irritation, attracts /%/ as part of healing /%/ =4 oxidised, damages surrounding cells, attracts monocytes, inflammatory response Monocytes adhere to !essel, diff into macrophages Macrophages ta-e up ox5d /%/, accum cholesterol esters, +ecome foam cells %ead/dying foam cells form fatty streaExcess /%/ in 67 = acceleration 8 classes of /%/ receptor mutants that cause hypercholesterolaemia *lass # = no production *lass &.8 = functional/traffic-ing defects

*lass & 9u+stitutions/deletions :ro+lems with receptor folding :re!ented from mo!ing to ;olgi, degraded *lass ' mutation in domain #, will not +ind to /%/ *lass ) <eceptor fails to internalise #" (runcation receptor lac-s transmem+rane = cytoplasmic domain, is secreted &" truncation lac-s cytoplasmic se>uence = internalisation signal '" point mutation destroys internalisation signal *lass 1 Mutation in E;6 domain, receptor fails to release ligand in early endosome <eceptor ? ligand degraded <eceptor not recycled, lowers receptor num+ers *lass 8 Mutation in domain 1 cytosolic" <esults it in +eing mis.directed to apical surface in hepatic cells, no receptors on cell surface 67 treatment: dietary modification lower cholesterol foods drugs to lower cholesterol remo!e /%/ from +lood li!er transplant

Familial hemophagocytic lymphohistiocytosis (F L!:

;enetic, leeeeeeeeeeethal %E3(7" disorder of immune regulation 6e!er, enlarged li!er and spleen, lower @0* count, fatty acid dysfunction accumulation of *%A? ( cells and macrophages in tissues %ifficult to diagnose pre.mortem '.prong: 6e!er ? enlarged spleen /a+ tests Morphologic hemophagocytosis engulfment of +lood cells +y macrophages"

Mechanisms of "rotein Folding and #ggregation

$nfolded state inacti!e %ati&e state catalytically acti!e 3nfinsen tells us that proteins fold into their nati!e state spontaneously$ primary se>uence of proteins determine their secondary and tertiary structures ' models as to how tertiary folding happens: '( Framework 9econdary structures . sheets, helices, turns form first . diffuse together to ma-e tertiary )( %ucleation 9ome &ndary forms first, tertiary forms around it, stepwise *( ydropho+ic collapse *hains collapse around hydropho+ic residues, then &ndary forms :rotein forming = free energy funnel 3s proteins fold, intermediates form, fewer species present therefore less energy 3t +ottom, single nati!e state, low free energy$ :roteins fold to lowest energy state$ 3myloids = unfolded proteins aggregate, form pla>ue deposits and cause diseases a+out )B" 4 #&B +y protein misfolding 7untington5s inside cell Most common in 3lzheimer5s outside cell #myloids, Extracellular fi+rillar deposits associate w/ disease 9low.onset, degenerati!e %istinct from amino acid se>uence and nati!e fold . all proteins form same structure in amyloid fi+ril structure 3myloids are not +ad in all creatures just humans$ 3myloids = spider sil-C :% <eason thought it is formed hydropho+ic +its stic- together 3myloid fi+rils +eta.sheet rich, long and straight ;enerally & or ) sheets that interact closely 6rom #'2 to #BB2 of aas in!ol!ed in amyloid structure 3ggregation phases . lag phase, forms nuclei . elongation phase, exponential forming . addition of seed shortens lag phase "athogenesis of protein deposition diseases /oss of function Misfolding = incorrect function, incorrect traffic-ing 3ggregation of misfolded = loss of function ;ain of function *ellular function impaired due to aggregate and cell components /arge deposits of amyloidoses in or around !ital organs 6i+rils are non.toxic :rotofi+rils toxic ha!e hydropho+ic side chains, reacti!e

"olyglutamine (poly-.! proteins and diseases D '1 Es, fine 4 '1 Es, diseases /oss of neurones, aggregation =4 neuronal dysfunction untington/s 7untingtin protein function un-nown, present in many cell types Fnsta+le *3; repeat after #st exon :rogressi!e motor impairment, cogniti!e decline, emotional stuff GB2 onset +/w &B and 11 yrs old 3lways present in family, +oth male and female Fp to 'B2 neuronal cell loss 7untingtin and u+i>uitin in striatum and cere+ral cortex neurons :olyE 3ggregates u+i>uitinated, inhi+it u+i>uitin.proteasome from functioning %isrupt gene transcription attaches other polyglut se>uences into the aggregate 9ome of these proteins are in transcription complexes *an +ind transcriptional coacti!ators such as *0: :oly> expansion doesn5t cause structure change of protein Instead, it desta+ilises protein =4 forms aggregates ;oal sta+ilisation of nati!e state %euroserpin polymerisation Heuroserpin aggregates diff to amyloids :I/JME<9 9erpin serine proteinase inhi+itors 7as ' +eta sheets and G alpha helixes 3 sheet has 1 strands #,&,',1,8 %on5t fold to most sta+le, +ecause they are dum+ /atent form reacti!e centre loop inside 3 sheet, inacti!e %elta form partially inserted into 3 sheet :rotein inhi+ited +y deformation into those forms Dementia, *aused +y neuroserpin, found only in +rain Inhi+its t:3, which is a serine proteinase in!ol!ed in de!eloping em+ryonic and neonatal +rain, neuronal plasticity, degeneration, synaptic remodelling *orrelation +etween I0 formation and clinical se!erity :olymers formed = loss of function more sta+le Mutant pushes to polymer conformation Mutant not as acti!e t:3 more acti!e Mutant less sta+le than wild.type @hen protein polymerises, change in &ndary structure 3H9 +inds to hydropho+ic patches 6luorescence increases due to change in &ndary structure conc independent", decreases as polymerases/aggregates conc dependent", therefore fewer exposed hydropho+ic Hati!e =4 intermediate =4 polymer

0ntracellular "athogens
1higella
Mainly in de!eloping countries, children 6aecal.oral route transmission personal contact, food and water )B2 &ndary attac- within household" 6e!er, a+dominal cramps, rectal trou+le, +loody stools #12 fatality 9upporti!e therapy, ciprofloxacin Kfirst line treatment *losely related to E$ *oli tree gram neg, anaero+ic, non.motile, enteric Intracellular pathogen 9ecretes Ipa0 into medium, conditions host cell to ta-e it up ;oes into cytoplasm, reproduces there 3ctin.+ased motility Induces M.cells in intestine" L transcytosis, ma-es M.cells release 9higella under epithelial layer Multiplies, epithelial cells %IEEEEEEEEE Induces strong inflammatory response =4 tissue destruction, ulcers and mucosal a+scesses 7ost produces pro.inflam cyto-ines recruits and acti!ates neutrophils epithelial cell destruction +y neutrophils causes !omiting/intestinal emptying =4 spread to others ,irulence factors Ipa0: engages +asolateral receptors, forms pores on cell mem+ranes, macrophage pyroptosis ,ir3: degrades microtu+ules Ics0: protection from autophagocytosis ,ir;: secreted into external media, facilitates introduction into cell ;ly.rich repeats +ind H.@39:

23tracellular "athogens
Clostridia
;ram ?, anaero+ic E!erywhere in en!ironment 9pore.forming Exotoxin producing

Ma4or histocompati+ility comple35 transplantation5 autoimmunity

Transplantation 1yngeneic #llogeneic #utograft 0sograft #llograft 6enograft M C restriction own M7* - transfer cells/tissues/organs from one indi!idual to another . immunologically compati+le . immunologically incompati+le . from one +ody part to another, from same indi!idual . +/w genetically identical indi!iduals . +/w mem+ers of same species . +/w mem+ers of different species . ( cells will only recognise and -ill antigen when it5s +ound +y the host5s

;raft rejection: specificity and memory$ /i-e immunisation when first graft, first.set rejection$ If second, similar graft is gi!en second.set rejection is much faster$ In graft, & types important: 30I +lood group antigens 7istocompati+ility antigens D= focus 7isto antigens are encoded +y the major histocompati+ility complex M7*" genes 7uman M7*: 7uman leu-ocyte antigens 7/3.3, .0, .* class I" 6orm functional receptor on most cells 7/3.% class II" 6orm heterodimeric MN" protein receptors expressed on surface of antigen.presenting cells (hese present antigen peptides to (.cells Inheritance = codominant %i!ersity good for indi!idual5s immunity to many different forms of diseases as it allows presentation of many different antigen peptides, good for specific host defence :ro+lematic for transplant matching e$g In western 3frica, 7/3.01' is common$ (his can present malaria antigen to (.cells$ Is uncommon elsewhere$ 7hy two types8 9ome microorganisms exist in cytosol e$g$ !iruses" M7* class I displays internal !iral peptides on surface of cell . responded to +y *%A 9ome in extracellular space/!esicles M7* class II on surface of antigen.presenting cells macrophages, dendritic cells, etc$" responded to +y *%) (herefore *%A ( cells see M7* class I cells =4 -ill cells that are: !irally.infected infected with intracellular parasite foreign cancerous *%) see M7* c II cells, +inds to c II, *%) is helper ( cell assist *%A assist 0.cells

Ho way for ( cells to automatically +e a+le to differentiate +/w self and non.self (*<s recognise antigenic peptide ? M7* complex, one alone is insufficient %uring thymic selection positi!e selection occurs, only M7*s recognised +y (.cell sur!i!e :eptides that +ind M7* I usually A.#B aa long :eptides that +ind M7* II usually #'.#O aa long 9ole in transplantation 0oth class I and II reduce transplant sur!i!al rate +y some Memory and specificity of s-in grafts come from ( cells Major histocompati+ility matching does not necessarily mean indefinite acceptance: Minor histocompati+ility antigens allopeptides presented +y M7* of graft cell e$g$ 7.J male antigens only on males" polymorphic proteins some singular aa +/w donor and recipient Graft re4ection: (.cell directly recognises donor5s M7* on surface of tissue %onor5s antigen.presenting cells from transplant" go to local lymph node = not recognised as self, stimulate alloreacti!e recipient ( cells <ecipient5s antigen.presenting cells process proteins and produce/present peptides from the graft "re&ention Matching 30I antigens, matching M7* alleles Immunosuppressi!e drugs = lifted after a while, +ody learns to tolerate M C and autoimmunity In thymus: :ositi!e selection thymocytes that can recognise self.M7* are -ept$ @ea- recognition of class I or class II M7* ? peptide Hegati!e selection too strong +inding to M7* ? peptide are -illed %angerous to immune system/self . Hegati!e selection: not all self.antigens expressed in thymus . 3uto.reacti!e still occur "eripheral tolerance 0 cells exposed to antigen w/o (.cell help (.cells, exposure without co.stimulation =4 anergic, apoptosis (reg cells -eep auto.reacti!e ( cells under control express 6ox:', *%), *%&1

:oth central and peripheral tolerance done fucks up (ype # dia+etes autoimmune, attac-s thyroid, stomach, joins, muscles *ertain M7* genes predispose people to autoimmune diseases %ifferent M7* gene in each disease Type ' dia+etes: %E.+eta allele responsi+le for suscepti+ility Hormally has aspartic acid K position 1O important, forms salt +ridge +/w alph and +eta chains Many people w/ t# dia+etes ha!e non.acidic e$g$ serine" at 1O 7ypothesis as to why M7* in!ol!ed in autoimmune: #$ :rotecti!e types +ind to self peptides w/ high affinity &$ 9uscepti+ility haplotypes dri!e positi!e selection of autoreacti!e '$ 9uscepti+ility haplotypes promiscuous in peripheral antigen presentation Transgenic manipulations5 use to address .uestions (ransgenic gain of function -noc-.out loss of function -noc-.in change of function (ransgenic mice implantation: *onstruct transgene Mate male and female mouse, ta-e out zygote at point of fertilization, microinject transgene into male pronucleus (ransfer zygote into pseudo.pregnant mouse Iffspring screened !ia :*< or F, to chec- for transgenic mice 2(g( ' 23pression of marker proteins (like GF"!;la+elling or tagging cells e$g$ Pgreen miceQ 3llow trac-ing of mar-ed cells Mouse actin promoter attached to c%H3 encoding ;6:, therefore produce green glow under F, Fseful to tell which is transgenic 2(g( ) 23pression of neo-antigen @ant to understand what happens when immune system recognises new antigen$ e$g$ @hat happens if new antigen is only expressed in +eta cellsR 7ow can (.cell +ecome tolerant to self.antigen not expressed in thymusR /i-e !iral antigen, li-e nucleoprotein /*M, nucleoprotein H:" was attached to insulin promoter therefore only expressed in +eta cells" (ransgenic mice w/ H: expressed in pancreatic +eta cells only +eta cells, no response from (.cells @ere there auto.reacti!e to H:" (.cells in peripheryR Jes +ut not acti!ated +y self$ 0ecause of (regs 3fter +eing infected with /*M,, acti!ate antigen.presenting cells, trigger *%A lymphocytes into acti!ation, -ills !irus$ (his then trigger attac- of +eta cells +ecause of presence of H:$ (.cells follow chemo-ine signals to site of infection, only start patrolling/auto.immune acti!ation after 6urther acti!ation +y local 3:*s

2(g( < 23pression of suscepti+ility or resistance genes In M7* class II gene, 7/3.%E0 allele at position 1O, aspartate acidic residue" forms salt +ridge w/ other helix$ Hon.acidic eg serine", salt +ridge not formed$ :redisposes to (ype # dia+etes @hen functional M7* class II gene gi!en to mouse with defecti!e gene, dia+etes did not de!elop$ @hen transgenic mice made, random integration