Case 1: Cystic Fibrosis Patient: Angel Age: 19 Gender: Male Diagnosis: Cystic Fibrosis Med Hx 37-yr G P A!

A!" old #ot$er% nor#al &'ll-ter# (regnancy and deli)ery !orn *it$ #econi'# ile's +$ic,ened intestinal #'co's secretions Diagnosed CF Corrected )ia s'rgery Pancreatic ins'&&iciency Gi)en s'((le#ental (ancreati)e en-y#es C$ronic sin'sitis C$ronic ear in&ections .'rgical corrections /o l'ng de&iciencies 'ntil age 10-17 Co'g$% s$ortness o& breat$% decrease acti)ity tolerance% no *$ee-ing Diagnosed as A!PA 1Allergic bronc$o('l#onary as(ergillosis2 Gi)en syste#ic corticosteroids Pse'do#onas aer'ginosa in&ection Already on in$aled +obra#ycin 3ater gi)en oral Ci(ro&loxacin Ac'te )iral res(iratory in&ections 4xacerbated l'ng &'nction Co'nter *it$ $ig$er dosage bronc$odilator and c$est co#(ression )est Age 10: G'illain-!arre syndro#e 5nde(6 Fro# CF +reated *it$ corticosteroids and 575G 1intra)eno's i##'noglob'lin2 8esol)ed -3 #ont$s a&ter*ard% no rec'rrence Age 17: Cro$n9s disease 5nde(6 Fro# CF +reated *it$ corticosteroids and 5n&lixi#ab 1i##'nos'((ressant2 Had Pyoder#a gangrenos'# co#(lication 1'lcer2 :ent a*ay b't rec'rred /e* co'rse o& 5n&lixi#ab started Age 17: CF8D 1cystic &ibrosis-related diabetes #ellit's2 D'e to corticosteroid 'se 5ns'lin &or CF8D C'rrently .een e)ery 3 #ont$s at CF Clinic Denies co'g$% *$ee-e% ($leg#% or congestion C'rrently acti)e% lost *eig$t% good a((etite /o abnor#al stool (atterns Medications 1. ;s#otic aids

a. Hy(ertonic saline 1in$aled2- re$ydrate #'co's b. P'l#o-y#e- t$ins #'co's c. <o(enex- in$aled bronc$odilator d. .aline nasal s(ray e. 8$inocort- nasal s(ray to red'ce in&la##ation 2. Digestion en$ancers a. Creon "- s'((le#ent (ancreatic en-y#es 3x#eals% xsnac,s b. Pre)acid-antacid c. Asacol- oral% red'ce intestinal in&la##ation d. Miralax- oral% &or consti(ation e. =rsodiol- oral% (ro#otes bile &lo* in li)er &or CF-related li)er disease 3. 5ns'lin-CF related diabetes a. 3ant's- s'bc'taneo's in>ection at bedti#e b. /o)alog- s'bc'taneo's in>ection (er 1?g# CH; at eac$ #eal 4. Antibotics a. +;!5 13"" #g@#l2 -in$aled antibiotic 5. P'l#icort- in$aled corticosteroid to decrease l'ng in&la##ation 6. Anti-in&la##atory a. A-it$ro#ycin- oral antibiotic &or anti-in&la##ation in CF (ts b. 8e#icade- i##'no#od'lator &or Cro$n9s disease 7. 7ita#ins a. AA'AD4B )ita#ins- )ita#ins enric$ed *it$ &at sol'ble )ita#ins b. 7ita#in 4 c. Folic Acid d. Ferro's s'l&ate- 5ron s'((le#ent Allergies: 7oricona-ole 1#edication2 Patient 5n&or#ation 4xercises reg'larly Medications and c$est ($ysiot$era(y a(x $o'rs (er day C'rrent college st'dent at =C.!% &'ll-ti#e st'dent Has roo##ates Ho#e in t$e s'##er: 3os Angeles Fa#ily Hx Fat$er 0C-yr-old no $x o& ast$#a% res(iratory allergies% or l'ng diseases *or,s at 3A< air(ort Mot$er 0"-yr-old no $x o& ast$#a% res(iratory allergies% or l'ng diseases ;lder sister 31-yr-old% $ealt$y /o &a#ily $x o& CF /o s#o,ers ;ne dog% Angel s$o*s no sy#(to#s /o $obbies t$at generate d'st or &'#es

P4 *ell-de)elo(ed% reasonably *ell no'ris$ed no ac'te distress no cyanosis% #ild digital cl'bbing (syc$ological #anner is a*a,e% alert% interacti)e% (leasant no assistance &or breat$ing reg'lar res(iratory r$yt$# t$oracic con&ig'ration $as slig$tly increase anterior-(osterior dia#eter% ot$er*ise nor#al :eig$t@Heig$t@!M5 all *it$in statistically nor#al range +e#( 306C Celsi's Heart rate 71 8es(irations: C !P: 11D@03

Microbiology C'lt're 1E2 &or Pseudomonas aeruginosa sensiti)e to all antibiotics exce(t A#i,acin no #et$icillin-resistant Staphylococcus aureus Assess#ent 1. CF 2. C$ronic CF l'ng disease 3. Pse'do#onas aer'ginosa l'ng in&ection 1. 8eacti)e air*ays disease Prior Review 1. pH of strong and weak acids Stronger acids have a lower pH than wea acids. !ea acids tend to have better b"##ering properties$ especiall% when &i'ed with wea bases. 2. pK, buffers (Henderson-Hasselbach , titration curve p(a is the acid dissociation constant$ p(b is the base dissociation constant. Stronger acids have a larger p(a. )s stolen #ro& wi ipedia$ i# an acid dissociates li e H)

*hen the

*he Henderson+Hasselbalch ,-"ation states that .a&el%$ the pH o# a sol"tion depends on the e'tent o# dissociation o# its dissolved acid /a si&ilar e-"ation e'ists #or basic sol"tions0.

) b"##er sol"tion resists change in pH #ro& the addition o# acids or bases "p to a certain point. 1t2s "s"all% a &i't"re o# a wea acid and wea base. )s &ore acid is added to the b"##er$ the wea base dissociates to raise the pH. !hen all o# the base has dissociated$ the b"##er 3brea s4. *he reverse is tr"e$ o# co"rse$ when the wea acid dissociates to resist an increase in pH. !. "eneral Properties of #$ino #cids )n a&ino acid has a carbo'%l /566+0 end$ an a&ino /.H2+0 end$ and a side chain. ,ach side chain has its own p(a. 7epending on the pH$ this will give the chain a charge. *he isoelectric point is the pH at which a speci#ic side chain will have no charge. 1n general$ a&ino acids are assigned a charge based on standard bod% pH$ altho"gh there are environ&ents in the bod% with e'tre&el% low and high pH. %. &tructure of the peptide bond *he peptide bond lin s together a&ino acids #ro& carbo'%l end to a&ino end via deh%dration s%nthesis. 1t2s a covalent bond and di##ic"lt to brea .

'earning (b)ectives 1. "eneral Properties of proteins 8"nctions9 Seen in table below. 5atal%sis$ :eg"lation$ *ransportation$ 5ontractile ele&ents$ 7e#ense$ Str"ct"ral ele&ents Si;e9 &olec"lar weight ranges #ro& 6<<< to 4<$<<<$<<< Shape9 =lob"lar /e.g. he&oglobin$ other en;%&es0$ 8ibro"s /e.g. collagen$ contrib"te to str"ct"re0$ 5on>"gated /e.g. 7.) binding proteins++co&bine 7.) with :.)0. 5harge9 7epends on a&ino acids on s"r#ace o# protein. Sol"biliti%9 7epends on location in bod%. ?lood proteins are water sol"ble$ &e&brane proteins lipid sol"ble. So&e proteins are a&phipathic. @ini&"& sol"bilit% at isoelectric point. 2. 'evels of Protein &tructure Ari&ar%9 )&ino acid chain derived directl% #ro& gene translation. ,ach "nit is connected via peptide bonds. Secondar%9 S&allest possible str"ct"re$ connection b% wea h%drogen bonds. @ost co&&on str"ct"res are the alpha heli' and B+pleated sheet. *ertiar%9 *hree+di&ensional str"ct"re o# a single protein chain. Stabili;ed b% h%drogen and ionic bonds. 8olding "s"all% needs to be done e'actl% right in order #or protein to #"nction properl%. 5haperonin proteins e'ist to re#old da&aged proteins correctl%$ "s"all% b% presenting the& with

a rapidl% alternating h%drophobic and h%drophilic environ&ent. :ibon"cleases alwa%s #old correctl% a#ter denat"ration$ while ins"lin is irreparable when denat"red. C"aternar%9 *he con>"gation o# &"ltiple tertiar% protein str"ct"res. Stabili;ation b% h%drogen$ ionic$ and h%drophobic interactions. 8or e'a&ple$ he&oglobin$ collagen. !. Protein folding and denaturation 7isc"ssed above. %. &tructure-function relationships Arotein str"ct"re is related to #"nction. =lob"lar proteins "s"all% have h%drophobic center and h%drophilic s"r#ace. ,n;%&es have a "ni-"e active site that binds to a speci#ic s"bstrate. ,'a&ples given in class9 ) point &"tation on a B+chain o# he&oglobin res"lts in a long chain instead o# a glob"lar protein. *he protein loses its sol"bilit% and sic le cell res"lts. ) &"tation in 58*: &a es it "nable to transport 5l+ and c%stic #ibrosis res"lts.

*ntro to +icro#nato$, 10 .a&e the co&ponents that &a e "p cells$ tiss"es and organs. -ells are co&prised o# three do&ains9 D ."cle"s D 1ntracisternal /inside organelles0 D 5%tosol /5%toplas& contains organelles E 1ntracisternal space0 /is e'tracell"lar space di##erentiated as a do&ainF0 o 5ontains c%tos eletal ele&ents .issues/ 5ells G 0-+ /,'tracell"lar @atri'0 D 4 *%pes o# *iss"e o 0pithelial/ closel% lin ed cells #or& a lining /re&e&ber tight >"nctions and paracell"lar &ove&ent0 o -onnective .issue/ S"pportive tiss"e can be #le'ible or rigid /cartilage vs bone0 o 1ervous .issue/ Speciali;ed #or cond"ction o -ontractile .issue/ @"scles with contractile protein #ibers (rgans/ 5o&prised o# @"ltiple *iss"e *%pes /Hs"all% all 40 D 5o&ple' str"ct"re (rgan &,ste$s 20 Iist co&&on #eat"res o# cells + 2o$ains /i.e 6rganelles0 have speci#ic #"nctions and are &eparated b, +e$branes (now9

(1 n"cleol"s (2 n"cle"s (! riboso$es (% vesicle (3 rough endoplas$ic reticulu$ (0R (4 "olgi apparatus (5 c,toskeleton (6 s$ooth 0R (7 $itochondria (18 vacuole (11 c,tosol + 7i##erent #ro& 1ncl"sions which are s"bstances stored in cell /=l%cogen$ 8at0 +e$branes/ Ahospholipid ?i+la%er establishes co&part&entali;ation J do&ains D :estricts J :eg"lates &ove&ent in and o"t o# cell D 9luid-+osaic +odel9 @e&brane has lipid and protein co&ponents /a&o"nt o# cholesterol increasesJdecreases #l"idit% o# &e&brane0 o S&all polar or charged &olec"les &ove via Arotein @ediated *ransport o Iarge @olec"les &ove thro"gh vac"oles thro"gh 0ndoc,tosis and 0:oc,tosis o *ntegral +e$brane Proteins9 contain h%drophobic do&ains are re-"ire detergent to re&ove #ro& &e&brane o Peripheral +e$brane Proteins/ 7o not co&pletel% penetrate bi+la%er and are onl% te&poraril% associated with &e&brane

D "l,cocon)ugates/ S"gars associated with &e&brane proteins o 5ell+cell interactions K :ecognition o 5ell+&atri' interactions o )l&ost ,'cl"sivel% on .on+5%tosolic Side Polarit,9 .on+:ando& distrib"tion o# organelles D .ight-;unctions ca"se polarit% in @e&brane proteins 30 ,'plain the basic processes o# tiss"e preparation and &icroscop% #or histological preparations 1 9i:ation9 5ross lin ing o# proteins with #or&aldeh%de /others li e gl"taraldeh%de preserve "ltrastr"ct"re 2 &ectioning9 8i'ed sa&ple is sliced so light can pass thro"gh it on a slide D L 5< &icrons thic #or light &icroscop% /hair is 1<< &icrons0

D o D D

,lectron &icroscop% needs 6< nano&eters ?lac and !hite Hse @icroto&e Plane of &ection

! &taining D He$ato:,lin/ Stains basophilic s"btances bl"e o 7.)$ :o"gh ,: D 0osin9 Stains acidophilic s"bstances pin o @itochondria$ 5%toplas&

Enzymes August 16, 2011 10:00AM 1. General properties of enzymes -Enzymes are a class of proteins that increase the rate of a chemical reaction. - ecause enzymes control the rates of reactions, they are use! to regulate the acti"ity of the cell. -Enzymes ha"e a specific !istri#ution $ithin su#cellular compartments an! $ithin specific organs. %As proteins, enzymes are sensiti"e to changes in temperature an! p& an! re'uire a relati"ely sta#le en"ironment in or!er to function. %Enzymes are often (ept in the inacti"e state, $here it is calle! the zymogen or proenzyme. )his allo$s enzyme acti"ity to #e strictly regulate!. -Many proenzymes re'uire a short se'uence on the *-terminus to #e clea"e! in or!er to #ecome acti"e. +or e,ample, pepsinogen is translate! an! release! #y chief cells in the stomach. )rypsin then clea"es the *-terminus, con"erting the proenzyme to its acti"e form pepsin. 2. -nteraction of enzyme $ith su#strate -.u#strates #in! to a relati"ely small region of an enzyme calle! the active site. )he #oun! su#strate fits in a specific orientation an! is fitte! through ionic #on!s, hy!rogen #on!s, an! hy!ropho#ic interactions. -)he act of the su#strate #in!ing to the enzyme can cause a conformational change in the enzyme. )his is also calle! induced fit. /. Enzyme catalysis0 Michaelis-Menten e'uation -Enzymes ha"e no effect on the thermo!ynamic properties of a gi"en reaction an! therefore al$ays mo"e the chemical reaction to$ar!s e'uili#rium. -nstea!, enzymes lo$er the energy of acti"ation, an energy #arrier re'uire! in or!er for a reaction to procee!, an! there#y increase the spee! of a reaction.

-Enzymatic reactions can procee! in the for$ar! or #ac($ar! reactions !epen!ing on $here the chemical e'uili#rium lies. -1ar#onic anhy!rase !oes the re"erse an! for$ar! reaction !epen!ing on location in the #o!y. -)he Michaelis-Menten equation allo$s one to pre!ict the rate of reaction gi"en a specific amount of su#strate. %2uring catalysis, the enzyme remains unchange! after the reaction has ta(en place. -n many cases, the enzyme forms a co"alent interme!iate. &o$e"er, this co"alent #on! is not in"ol"e! in su#strate-enzyme #in!ing. 3. Enzyme inhi#ition -Competitive inhibitors !irectly compete $ith the su#strate to #in! at the acti"e site. -A competiti"e inhi#itor $ill increase the 4m, the concentration re'uire! for half the enzymes to #e #oun! to su#strate, #ecause the competiti"e inhi#itors $ill al$ays occupy a specific portion of acti"e enzymes. -A competiti"e inhi#itor $ill lea"e "ma, unchange! #ecause a!!ing an infinite amount of su#strate $ill allo$ the enzyme to #in! to the su#strate more often than to the competitor.

-Noncompetitive inhibitors, also calle! allosteric inhibitors, #in! to a site on the enzyme some$here other than at the acti"e site. -*on-competiti"e inhi#itors $ill occupy a gi"en portion of enzymes at any gi"en time, there#y re!ucing "ma, regar!less of su#strate concentration. %-t is hypothesize! that the noncompetiti"e inhi#itor #in!s to the enzyme an! pre"ents it from achie"ing a specific conformational state, there#y ma(ing the enzyme nonfunctional.

5. Mechanism of enzyme reactions -Enzymes can ha"e a high specificity to a gi"en su#strate or can #e more non-specific 6!igesti"e enzymes7. --n a gi"en reaction $ith an enzyme, t$o reactants nee! to #ump into each other $ith the proper orientation in or!er for the reaction to ta(e place. An enzyme #in!s to these su#strates, there#y increasing effecti"e pro,imity an! placing the su#strates into the proper orientation. %An enzyme remains unchange! after performing the appropriate chemical reaction. 6. 8egulation of enzyme acti"ity -Isozymes are multiple forms of the same enzyme, often $ith !ifferent (inetic properties. -9actate !ehy!rogenase is gi"en as a specific e,ample $here the !istri#ution of lactate !ehy!rogenase is specific to !ifferent organs. -:hosphorylation can acti"ate or !eacti"ate a gi"en enzyme. -Allosteric enzymes -Multiple su#units can interact $ith each other or ha"e ligan!-in!uce! conformational change. in!ing of first su#strate can ma(e secon! su#strate easier to #in! -p& an! en"ironment

%in!icates rele"ant information co"ere! in other lectures #ut not this one
6.15.11 Redd, 21# R0P'*-#.*(1 1. 5o&pare and contrast 7.) replication in Aro ar%otes and ," ar%otes Ahase 1nitiation Prokaryotes 21# # binds to (ri- /onl% origin o# replication0 and &elts 7.) 21# < /helicase0 "nwinds 7.) .opoiso$erase * needed to nic 1 strand o# 7.) to relieve torsional stress /bc contin"o"s circle0 &ingle &trand <inding Proteins /SS?s0 bind to prevent 7.) #ro& re+binding to other parent strand RPAs bind to (re)ent D/A &ro# re-binding to (arent strand Eukaryotes Helicase1F2 binds to origin o& re(lication 1#any2 Helicase 1F2 'n*inds D/A

Ari&ing

Pri$ase recr"ited to replication #or and adds :.) pri&er to leading strand$ then to lagging strand #"rther down 7.)

Ari&ase recr"ited to replication #or and adds :.) pri&er to leading strand$ then to lagging strand #"rther down 7.) DNA Pol adds a &e* D/A n'cleotides to (ri#er 1(art o& 'nit * (ri#ase2

,longation

21# pol *** then binds /tethers with beta cla$p0 to pol%&eri;e 7.) in 52+32 direction /leading strand in contin"o"s &anner$ and lagging strand in discontin"o"s &anner w 6 a;a i #rag&ents0 7.) Aol 111 can bac trac and proo#read in 32+52 direction 21# Pol * replaces 7.) Aol 111 to re&ove :.) pri&ers

DNA pol t$en binds 1tet$ers * PCNA2 to re(licate in ?G-3G 1leading strand in contin'o's #anner% and lagging strand in discontin'o's #anner * ;,a-a,i &rag#ents2 D/A (ol H can bac,trac, and (roo&read in 3G-?G direction Fen-1 re#o)es (ri#ers 1bc no (oly#erase t$at $as ?9-39 exon'clease acti)ity2 and DNA pol re(laces ga(s * D/A DNA ligase >oins strands Telo erase 1ty(e o& re)erse transcri(tase2 creates 8/A te#(late to extend lagging strand *it$ >'n, D/A

21# ligase >oins strands *er&ination *er&inator se-"ences trap replication #or near origin site and bing .=& proteins 2nd *HS Arotein does not allow 7.) ? to pass thro"gh$ and elongation is stopped .opoiso$erase iv "nlin s the catenated strands 2.

+-loo(s &or#ed at ends

,'a&ples o# diseases that occ"r d"e to replication de#ects a. @"tation in :.) telo&erase ++M 7%s eratosis congenita9 7evelop&ental dela% b. Iow telo&erase levels ++M no *+loops N geno&ic instabilit% N increased cancer ris c. 8ragile O s%ndro&e P e'cess 5== d. @"sc"lar d%stroph% e. Spinocerebellar ata'ia #. H"ntington2s

21# +utation and Repair > +uschen 6.15.2811 7escribe the relationship between 7.) da&age$ 7.) repair$ 7.) replication$ and &"tagenesis 1. @"tagenesis P Aer&anent &"tation vs *ransient alteration a. @"tation P errors d"ring replication$ da&age ind"ced b% che&icals or irradiationQ

not consolidated "ntil ne't ro"nd o# replication b. *ransient alteration P when da&ageJerror reversed b% repair c. 7epends on the ratio o# replication9repair P *i&e #ra&e closes with replication d. 2. .or&al Ste& cells P C"iescent /slow cell c%cle0$ High #idelit% 7.) repair$ rare &"tations 3. 5ancer cells P High t"rnover$ short li#e$ error+prone 7.) repair$ &"tations drive evol"tion 4. 2nd strand so"rce o# correction recr"it&ent P red"ndanc% o# ds7.) State the &a>or so"rces o# 7.) da&age and the &a>or t%pes o# 7.) repair 1. So"rces + a. 7o"ble strand brea s &ost har&#"lQ co&ple&entarit% no longer applies$ &ore v"lnerable to deca%Jda&age b. ,ndogeno"s i. replication errors /&isincorporation$ slippage0 @ost #re-"ent$ easil% repaired ii. 7ea&ination /c%tosine P "racil0 iii. 7ep"rination /abasic site /no base0 creation0 iv. :eactive 6'%gen species /strand brea s$ base da&age0 v. 7.) reco&bination errors + Ieast #re-"ent$ di##ic"lt to repair c. ,nviron&ental i. 1: increasing reactive species /indirect &echanis&0 ii. HR generates p%ri&idine di&&ers /direct &echanis&0 iii. 5he&ical @"tagens 2. :epair P least to &ost serio"s a. Aroo#reading P d"ring replication. error rate91<S+4 T 1<S+U b. @is&atch e'cision P a#ter replication. ,rror rate 1<S+U T 1<S1< i. ,rror recognition T strand discri&ination T e'cision T res%nthesis T ligation c. ?ase e'cision repair9 7.) gl%cos%lase #lips and re&oves base T )A endon"clease c"ts phosphodiester bond T 7.) pol%&erase T ligase i. creates abasic site that can be pre&"tagenic i# not repaired on ti&e ii. 7irect reversal9 @=@* destro%s itsel# to get rid o# &eth%lation o# g"anine bases d. ."cleotide e'cision repair9 7a&age recognition T ."clease cleavage T re&oval with helicase T AolV$ AolW T 7.) ligase i. re&oves b"l % di&ersJ"nrecogni;able bases

e. Ho&ologo"s :eco&bination P less errors$ onl% available d"ring &itosis when sister chro&atid is aro"nd. :eliable repair o# do"ble strand brea s i. e'on"clease c"ts to &a e stic % ends T strand invasion b% sister chro&atid T 7.) s%nthesisJsister chro&atid e'change T "nwindingJligation/?I@ helicase0 #. .on+ho&ologo"s :eco&bination P @ore error prone$ available an% ti&e o# cell c%cle. Hnreliable P possible error in relegation$ clean "p step is waste#"l i. s%napse #or&ation to hold ends together b% ("7< and ("U< T 7.) A(cs clean "p staggered ends T Iigation b% I1=4 and O:554 proteins 7escribe the clinical conse-"ences o# &"tagenesis and o# de#ects in 7.) repair 1. 7.) repair de#icits T 5ancer 2. Ste& cell depletion T Are&at"re aging 3. 1&&"ne s%ste& T &"tagenesis needed #or adaptation to new antigens$ etc

1uclear 1. @a e a si&pli#ied sche&a o# the basic str"ct"ral co&ponents o# the n"cle"s /n"clear envelope$ pores$ n"cleol"s$ chro&atin$ n"clear &atri'0.

2. ,'plain the str"ct"re and #"nction o# the n"clear envelope and n"clear &atri'. 1uclear 0nvelope9 1s a 2+&e&brane s%ste& which #or&s a barrier between the n"cle"s and the rest o# the cell to9 + @aintain "ni-"e protein and n"cleotide environ&ent + Se-"ester &:.) s%nthesis #ro& *ranslational &achiner% + Arotect J 5ontain 7.) (uter +e$brane and *nner +e$brane are separated b% the Perinuclear cisterna. 1t is per#orated b% 1uclear Pores containing 1P- /."clear Aore 5o&ple'es0. *he inner &e&brane is s"pported b% the 'a$ina 1uclear +atri:9 ) protein lattice &ade o# #ibers /si&ilar to c%tos eleton0 which9 + )nchors 7.) replication + )nchors transcription co&ple'es + :ein#orces n"clear envelope ++M stabilit% 3. ,'plain the i&portance o# the str"ct"re o# n"clear pore co&ple'es and how this pla%s a role in n"cleoc%toplas&ic e'change. 1uclear Pore -o$ple:9 /U<+1<< n& dia&eter0 is the site o# selective n"cleoc%toplas&ic e'change. 1t creates a selective barriers #or the transport o# &acro&olec"les across the n"clear envelope /not as selective #or s&aller &olec"les0. Has a !-ring &tructure that has U spo es with a hole in the center. + -,toplas$ic Ring/ /U+s"b"nits0 with prot"sions into c%toplas& #or &ediating i&port + +iddle Ring/ U s"b"nits protr"de into Aerin"clear space o *ransport proteins

1ucleoplas$ic Ring9 8ibro"s proteins protr"de into n"cleoplas& D Serves as a doc #or i&portins and e'portins. o 1&portin J e'portin &ediated transport re-"ires energ% 4. 7escribe the organi;ation o# chro&atin and its role in s%nthesis$ processing and storage o# 7.) and :.). 5hro&atin is highl% co&pacted 7.) G Aac ing Aroteins9 + Heterochro$atin9 highl% coiled and less active =enes not transcribed in cell + 0uchro$atin/ less coiled$ &ore active 7.) 5o&position9 1ucleoso$e/ /1< n&0 7.) wrapped aro"nd U Histones /146 bpJ histone0 D 8or&s <eads on a &tring -oiled 1ucleoso$e/ /3< n&0 coiled n"cleoso&es D H1 Histone9 )ctivit% a##ects densit% o# n"cleoso&e coil *he densit% o# chro&atin pac ing deter&ines the availabilit% o# the genes #or transcription. Histone tails are sites #or activating the e'posing J coiling o# local 7.) 5. Have a general concept o# the cell c%cle and its control as well as apoptosis. "1/ 5ell =rowth & phase9 7.) replication "2 phase9 1nterval be#ore &itosis /val"able #or 7.) lesion repair0 +itosis

.ranscription and -ontrol of .ranscription 'earning (b)ectives 1. 7escribe the basic transcription &achiner%$ the basic str"ct"re o# genes /incl"ding pro&oters0 and transcription "nits$ and the basic &echanis& o# transcription in e" ar%otes. a. ?asic &achiner% needed i. R1# pol /to read %o"r te&plate 32+520 ii. &o$e bases /)*A$ =*A$ 5*A$ H*A$ all ribon"cleotides o# co"rse0 iii. 21# topoiso$erases to "nwind the heli' b. ?asic str"ct"re o# genes$ wJpro&oters X t'pn "nits

ii.

Aro&oter region 1. !here proteins bind to begin transcription. *his incl"des9 2. *nitiator se?uence /which incl"des theY0 !. .#.# bo: 4. ) &i' o# enhancer and silencer se?uences

a. 5an be in other places other than right be#ore the transcribed gene /e'. ?ehind$ in the intron$ etc.0 b. 8'n9 assist reg"lation b% allowing a speci#ic t'pn #actor to bind to it c. *his leads to activationJrepression o# transcription d. ,nviron&ental conditions can control the binding o# t'pn #actors to these enhancerJsilencer ele&ents e. Hlti&atel%$ the binding will lead to actions s"ch as phosphor%lation or bindingJdissociation o# another protein that is related to the t'pn #actor iii. *ranscribed gene 1. 0:on9 leaves the n"cle"s as &at"re &:.) a#ter &odi#ication 2. *ntron9 (ept inside the n"cle"s /altho"gh proble&s with the intron co"ld later contrib"te with &"tations and proble&s with the &at"re &:.)0 c. ?asic &echanis& o# e" t'pn i. :.) pol transcribes the 7.) ii. 7epending on the :.) we are atte&pting to transcribe$ we will "se a corresponding pol%&erase iii. ?asal t'pn #actors assist pol in recogni;ing the pro&oter and initiating t'pn iv. .6*,9 @itochondria /have :.) pol that is si&ilar to pro pol$ and transcribes their own 7.) into their own r:.)s$ &:.)s$ and t:.)s0

2.7isc"ss the roles o# transcriptional activator proteins$ enhancer ele&ents$ coactivators$ and chro&atin in reg"lation o# e" ar%otic transcription a. .ranscriptional activator proteins i.?ind basal t'pn #actors associated with :.) pol 2 to get it over to the pro&oter ii. :ecr"it coactivators to per#or& 2 #"nctions 1. 5oactivators are proteins that increase gene e'pression b% binding to an activator or t'pn #actor which contains a 7.) binding do&ain$ #acilitating the t'pn o# a desired gene 2. )lter chro$atin str"ct"re /li e "nwind it #ro& the histone0 to &a e pro&oter region &ore accessible 3. :ecr"it :.) pol 11 and its basal transcription #actors iii. 0nhancer ele$ents /gene se-"ences #ar "pstrea&Jdownstrea& #or the gene or nearb%0 are bro"ght closer to the gene we want to transcribe thro"gh co&ple'es o# transcriptional activator proteins$ coactivators$ and other transcription #actor proteins in preparation #or transcription b% :.) pol 11

3. 7escribe the cell"lar response /or signal transd"ction0 pathwa% "sed b% steroid hor&ones and list the &a>or hor&ones which interact with &e&bers o# the n"clear receptor #a&il% a.@a>or hor&ones that interact with the steroid receptor protein #a&il% also nown as the Zn"clear receptor2 #a&il% i. =l"cocorticoids$ @ineralcorticoids$ ,strogens$ )ndrogens$ Arogestins

ii. 5an also interact with steroid+related vita&ins$ a&ino acid derivatives$ and other &olec"les %et to be discovered

b.

Aathwa% i. Steroid co&es into the cell and is bo"nd b% a steroid receptor ii. *his creates a steroid+protein co&ple' that enters the n"cle"s /o#ten a di&er0$ which binds to a hor&one enhancer ele&ent on 7.) iii. *he bo"nd co&ple' G enhancer se-"ence will #old "pJ>oin the pro&oter region$ which will now begin to bind t'pn #actors$ coactivators$ and Aol 11 onto the pro&oter region. *he *)*) bo' is ill"strated in the e'a&ple above to give a #ra&e o# re#erence. iv. .ow the desired gene can be transcribed into &:.) v. *he &:.) is then &odi#ied and pac aged so it can e'it the n"cle"s and be translated into protein vi. *his protein will in t"rn create a ph%siological response

4. ,'plain wh% agonists pro&ote gene activation b% steroid receptors$ b"t antagonists inhibit steroid receptor #"nction )gonist binding steps 1. )gonist &olec"le binds to a receptor. 1n o"r notes$ the receptor is a steroid receptor. 2.:eceptor binds to enhancer se-"ence on 7.) 3.:eceptor "ndergoes a con#or&ational change$ %ielding a new binding spot )ntagonist binding steps 1. )ntagonist &olec"le binds to a receptor 2.:eceptor binds to enhancer se-"ence on 7.) 3.:eceptor "ndergoes a con#or&ational change$ ?H* there is .6 new binding site

4.) coactivator protein will bind to this new spot$ and with this binding$ will recr"it the binding o# other transcriptional #actors and :.) Aol 2 5..ow transcription can occ"r 90 5oncl"sion9 pro&otion o# activit%

4.5oactivator has no place to bind$ the t'pn apparat"s never sets "p

5..o transcription occ"rs 9[/ 5oncl"sion9 inhibited activit%

5. 7isc"ss the roles o# steroid receptors and their agonistJantagonists in the etiolog% andJor treat&ent o# breast cancer a. ?reast tiss"e develop&ent is triggered b% estrogen b. *here#ore$ estrogen is an agonist #or breast tiss"eJbreast cancer growth c. *a&o'i#en$ an anti+cancer dr"g$ is an antagonist$ changing con#or&ation and inhibiting t'pn b% den%ing coactivators and t'pn #actors a binding site /see -"estion 40 d. *his prevents the growth o# breast cancer cells

6. ,'plain how the c)@A signaling pathwa% can reg"late t'pn o# speci#ic genes /S"r#ace cell receptors0 a. ,'. =l"cagon /hor&one0 pathwa% /which signals that we need to &a e gl"cose0 i. Arotein or steroid #ro& o"tside the cell binds to a receptor. ii. *he receptor activates a = protein$ which activates aden%l%l c%clase iii. )den%l%l c%clase releases c)@A$ which binds to protein inase ) iv. Arotein inase ) enters the n"cle"s via n"clear pore$ phosphor%lating 5:,? /c)@A response ele&ent binding0 protein. .ow this is >"st li e -"estion 3\ v. 5:,? now binds to its enhancer region$ 5:, /c)@A reponse ele&ent0 vi. .6* in the notes$ b"t 1 tho"ght this was help#"l9 a coactivator called 5?A /5:,?+binding protein0 then binds to 5:, vii. .ow t'pn is activated

---------------------------------------8egulation of )ranscription-------------------------------------Initiation 1an ha"e multiple promoter an! start sites 1reates !i"ersity #y inclu!ing;e,clu!ing e,ons Also changes the <)8 length an! potential for regulation Capping 5= en! cappe! #y in"erte! guanine .ome groups are methylate! 2one #y capping enzymes associate! $ith polymerase as it transcri#es

-recognize! #y nuclear pores, necessary for proper e,port -pre"ents e,onuclease !egra!ation -promotes circularization an! translation Polyadenylation )ranscription en!s $hen it recognizes termination se'uence AA<AAA Also can ha"e multiple termination sites- pro"i!es /= en! !i"ersity >nce termination se'uence is recognize!, m8*A is cut /0 #p !o$n an! 200 a!enosines are a!!e! *ecessary for e,port of the m8*A 9in( to cap to help promote translation :re"ents /= en! e,onuclease !egra!ation Splicing -ntrons out, E,ons in Alternati"e splicing creates great #io!i"ersity 6$hen intentional7 )emporal;spatial regulation 1onsensus site is strong for introns

5=

G<??..A?..1;< rich?.AG

/=

E,cise! structure is terme! @lariat= Ahen acci!ental or mis-splice!, can #e harmful to cell 2ominant negati"e forms :rotein comple,es 6sn8*:s7 remain on m8*A, cells can tell if intron is left in )en! not to #e e,porte! 1ryptic sites- sites 6sometimes mutations7 that #ecome splice acceptor;!onor sites that are not the normal sites for splicing
:ortuguese family $ith cystic fi#rosis cryptic splice site BB frameshift mutation ur(itt=s 9ymphoma chromosomal translocation shortens /= <)8, remo"ing se'uences necessary for m8*A !o$nregulation ranslation 17 2escri#e the principle of m8*A translation an! e,plain the !egeneracy of genetic co!e 27 <n!erstan! an! #e a#le to summarize the general steps of translation /7 E,plain ho$ a#errant translation can play a role in human: C .plicing mutations; frameshift changes C )he role of nonsense-me!iate! m8*A !ecay C Aminoglycosi!e anti#iotics;!eafness