Apoptosis and HIV Tutorial 1.

In apoptosis the cell destroy itself from within and avoids leakage of the cell contents into the extracellular space. What might e the conse!uences if the programmed cell death were not achieved in so neat and orderly a fashion" Inflammation and severe immune response 1. #ancer $ %ollicular lymphomas $ Hormone$dependent tumors & 'reast cancer & (rostate cancer &)varian cancer *. Autoimmune disorders $ +ystemic lupus erthematosus $ Immune$mediated glomerulo$ nephritis ,. Viral infections $ Herpesviruses $ (oxviruses $ Adenoviruses *. What are the differences etween apoptosis and necrosis"

,. What is the function of caspases. -ive the categories of caspases. What are the conserved features and structural features of caspases. How are these caspases activated and inhi ited" %unction of caspase $ #leave protein at a cysteine residue within a recognition motif #ategories $ Interleukin$1 #onverting .n/yme 0I#.1$like caspase 0123241 $ Initiator caspase 0*25262171 $ .ffector caspase 0,28291 #onserved features $ %unctional caspase unit is a homodimer: large su unit 0*7k;a1 and small su unit 017k;a1 $ Homodimerisation is mediated y hydropho ic interactions2 with 8 antiparallel strands from each catalytic su unit forming a single contiguous 1*$stranded sheet $ +everal helices and short strands are located on either side of the central sheet2 giving rise to a glo ular fold $ The active sites2 formed y four protruding loops from the scaffold2 are located at two opposite ends of the sheet +tructural features $ The su strate$ inding groove is shaped y 3 surrounding loops: <1 to <3 $ <1 loop forms one side of the groove with <3 on the other $ <* loop with catalytic #ys residue is at one end of the groove2 while <, on the other side $ The side chain of #ys points along the groove2 poised for inding and catalysis

Activation $ All caspases are produced as inactive /ymogens $ They are proteolytically cleaved to give active caspase $ The activation of an effector caspase is performed y an initiator caspase through cleavage at specific internal Asp residues that separate the large and small su units

Inhi ition

3. Apoptosis is a carefully controlled process which can result in cell death. i1 ;escri e in details %as=#; 64$induced apoptosis. .xtrinsic pathway %as$ligand 0trimer1 inds to %as$< receptor2 causes oligomerisation2 activate ;; domain of the cytoplasm2 recruit %A;; 0adaptor protein1 via ;;. %A;; have ;.; that can interact with ;.; domain of pro$caspase52 activating caspase5. This is %as$mediated apoptosis ii1 ;escri e T>% receptor induced apoptosis. Intrinsic pathway T>% 0trimer1 inds to T>%$?1 receptor2 causes oligomerisation 0trimerisation12 activate ;; domain of the T?A;; in cytoplasm2 T?A;; recruit %A;; 0adaptor protein1 via ;;. %A;; have ;.; that can interact with ;.; of pro$caspase52 activating caspase5 ?ecruit ?I(2 y interaction of ;; domain of T?A;; and ;; domain of ?I( interacting with T?A;; via T?A%*2 inducing apoptosis

4. ;iscuss the regulation of anti$apoptosis=programmed cell death in cells" (ro$survival@'cl*2 'cl$x< $'cl* or clAl located at the outer mem rane of mito2 inhi it 'ax oligomerisation and maintain mito integrity (ro$Apoptosis@ 'ax2 +u family@'ik2 'lk2 'im<2 'ad $'ax is apoptotic $<igand ind2 Akt kinase activated and phosphorylate 'ad and %khr2 se!uestered in 13$,$, protein. $'ad cannot act on cl*2 action is inhi ited: apoptosis cannot occur. 'im 0apoptotic1 $ IBB phosphorylate i$k'=>f$k'. (hosphorylation of i$k'=>f$k'2 release nf$k' which inhi it apoptosis When ligand dissociate2 'ad and fkhr are dephosphorylated and released2 'ad translocate to mito and ind to cl*2 inhi iting its function leaving 'ax free to oligomerise 0enhanced y 'im12 fkhr initiate transcription including 'im in nucleus2 released to cytoskeleton. #ytoplasmic 'ax change conformation and translocate to mito. )ligomeric association of 'ax creates pore in the outer mito mem rane2 allowing cytochrome # to escape into cytoplasm. HIV 1. What are the functions of the following components to HIV" a1 ?everse transcriptase Transcri es ?>A genome into c;>A 1 Integrase cataly/e intergration of viral ;>A into host cell genome c1 (rotease .n/yme that conducts proteolysis y hydroly/ing peptide onds d1 gp31 coreceptor inding induce conformational change e1 gp1*7 ind to cd32 induce conformational change that promote secondary gp1*7 to ind to a chemokine coreceptor f1 Vif overcome inhi itory effects of unidentified host factor

inhi it cellular protein from entering the viron during udding from a host cell. These cellular protein disrupt antiviral activity of the human en/yme 0Apo$'ec1 g1 Vpu cd3 degradation2 influence viron release h1 Vpr %acilitation of pre$integration complex into the nucleus via nuclear pore complex *. What is >ef and its function in HIV infectivity" >ef $ *78aa viral protein located in cytoplasm2 plasma mem rane2 packaged into virus particles $ .xpressed early after inCection $ Attenuated 0non$virulent1 $ Interfere with cellular processes: interact with +rc kinase2 (B#2 p4, %unction $ 'ind and alter activity of +rc kinase and disrupt intracellular signaling and suppress immune response $ Induce apoptosis in ystanders cells that express %as 0#;6412 kill #T< that remove HIV$ infected cells and activate expression of %as< 0#;64<1 $ ?educe expression of H<A #lass 1 at cell surface2 preventing presentation of HIV antigens to #;5D#T< thus escape killing $ 'inds tumor suppressor p4, thus inhi iting p4,$activated apoptosis $ ;own$regulate cell surface expression of #;3 0coreceptor that assist T$cell receptor1 o >ef create a narrow T$cell receptor response which likely to optimi/e HIV$I viral production2 and generate population of the cells so that it can further infect other cells. o A+B$1 reduced2 (I,$B increased2 p4, decreased ,. ;escri e y using as many as possi le the components a ove to show how an HIV infect2 replicate and release from an infected cell" $HIV gp1*7 ind to cd32 induce conformational change that promote secondary gp1*7 to ind to chemokine coreceptor $#hemokine receptor induce conformation change in gp312 exposing fusion peptide which insert into the cell mem rane2 ena ling viral mem rane to fuse with the target cell mem rane $HIV enter the cell2 en/yme within nucleoprotein complex activated2 viral repro cycle egin $?>A genome is transcri ed into ;>A y viral reverse transcriptase. Viral ;>A enter nucleus

$%acilitation of pre$integration complex 0composed of vpr2 rt2 integrase2 matrix E cdna flap1 into the nucleus via >uclear pore complex $Viral integrase enter nucleus and cataly/e intergration of viral ;>A into host cell genome $ integrated viral dna transcri ed into m?>A2