The Animal Kingdom

By Enger, E.D., Ross, F.C., Bailey, D.B. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

WHAT IS AN ANIMAL? THE E !L"TI!N !# ANIMALS TEM$E%AT"%E %E&"LATI!N '!() $LANS* S)MMET%) '!() $LANS* EM'%)!NI+ +ELL LA)E%S '!() $LANS* '!() +A ITIES '!() $LANS* SE&MENTATI!N '!() $LANS* S,ELET!NS -!!$LAN,T!N NE,T!N 'ENTHI+ ANIMALS $!%I#E%A.S$!N&ES +NI(A%IA./ELL)#ISH0 +!%ALS0 AN( SEA ANEM!NES +TEN!$H!%A.+!M' /ELLIES $LAT)HELMINTHES.#LATW!%MS NEMAT!(A.%!"N(W!%MS ANNELI(A.SE&MENTE( W!%MS M!LL"S+A A%TH%!$!(A E+HIN!(E%MATA +H!%(ATA TE%%EST%IAL A%TH%!$!(S AM$HI'IANS %E$TILES 'I%(S MAMMALS

WHAT IS AN ANIMAL? Ani1als are eukar2otic0 1ulticellular organis1s whose cells lack cell walls3 Like plants0 ani1als ha4e cells that are speciali5e6 for specific purposes3 #unctions such as ingesting foo60 e7changing gases0 an6 re1o4ing wastes are 1ore co1plicate6 in ani1als than in one8celle6 protists3 In one8celle6 organis1s0 an2 e7change between the organis1 an6 the e7ternal en4iron1ent occurs through the plas1a 1e1brane3 Howe4er0 because

ani1als are 1ulticellular0 1ost of their cells are not on the bo62 surface an60 therefore0 not in 6irect contact with the e7ternal en4iron1ent3 Thus0 ani1als 1ust ha4e speciali5e6 wa2s to e7change 1aterials between their internal an6 e7ternal en4iron1ents3 So1e si1ple ani1als0 such as sponges an6 9ell2fish0 ha4e a few kin6s of speciali5e6 cells0 whereas other0 1ore co1ple7 ani1als0 such as insects an6 1ollusks0 ha4e bo6ies co1pose6 of groups of cells organi5e6 into tissues0 organs0 an6 organ s2ste1s3 The 1ore co1ple7 ani1als ha4e gills0 lungs0 or other structures use6 to e7change gases: 4arious kin6s of structures are in4ol4e6 in capturing an6 6igesting foo6: an6 there are usuall2 special structures for getting ri6 of waste pro6ucts3 Like plants0 1an2 of the larger ani1als ha4e a 1etho6 of transporting 1aterials throughout the bo623 Ani1als are heterotrophs that eat other organis1s to obtain organic 1olecules0 an6 1an2 are speciali5e6 for consu1ing certain kin6s of foo6 organis1s3 Although there are 1an2 wa2s of capturing an6 consu1ing foo60 all of the1 in4ol4e 1o4e1ent3 Mo4e1ent is a characteristic associate6 with all ani1als: it in4ol4es speciali5e6 1uscle cells that shorten3 Man2 ani1als ha4e appen6ages ;e3g30 legs: wings: tentacles: spines: or soft0 1uscular organs< that ben6 or change shape3 !ften0 these structures are in4ol4e6 in 1o4ing the ani1al fro1 place to place0 but the2 are also use6 to capture foo60 to clean the ani1als= surfaces0 an6 to 1o4e things in the ani1als= en4iron1ent3 Se7ual repro6uction is i1portant in all groups of ani1als3 The 1etho6s 4ar2 greatl2.fro1 the release of sper1 an6 eggs into the water0 for 1an2 a>uatic organis1s0 to fertili5ation insi6e the bo620 for 1ost terrestrial organis1s3 A few kin6s0 such as bir6s an6 1a11als0 pro4i6e a great 6eal of care for their offspring3 Man2 of the 1ore pri1iti4e ani1als also repro6uce ase7uall23 Those that repro6uce ase7uall2 also repro6uce se7uall2 at other ti1es in their life c2cle3 So1e ani1als repro6uce ase7uall2 b2 a process calle6 parthenogenesis3 Ani1als also ha4e sensor2 structures on their surface that 6etect changes in the en4iron1ent3 A s2ste1 of ner4e cells integrates infor1ation about the en4iron1ent an6 coor6inates 1o4e1ents0 so that 1o4e1ents occur at appropriate ti1es an6 with a proper orientation3 #igure ?@3A shows a 4ariet2 of ani1als3

THE EVOLUTION OF ANIMALS Scientists esti1ate that the Earth is at least B3C billion 2ears ol6 an6 that life originate6 in the ocean about @3D to @3E billion 2ears ago3 The earliest ani1al8like fossils 6ate to about FGG 1illion 2ears ago3 Most of the earliest ani1als were probabl2 either s1all organis1s that floate6 or swa1 in the ocean or wor1like organis1s that crawle6 on the botto1 or through the se6i1ent on the ocean floor3 These ani1als 6i6 not re>uire special 1echanis1s to 6eal with rapi6 or e7tre1e changes in the en4iron1ent3 'ecause the2 li4e6 in water the2 6i6 not ha4e a proble1 with 6eh26ration3 'ecause the ion content of the earl2 ocean appro7i1ate6 that of the ani1als= cells0 the ani1als 6i6 not nee6 to e7pen6 energ2 to keep their cells in os1otic balance3 #urther1ore0 their bo62 te1perature was that of the water in which the2 li4e63 The earl2 e4olution of ani1als was rapi63 Scientists ha4e foun6 e7a1ples of all the 1a9or groups of ani1als as far back as the +a1brian perio60 CBG to BHG 1illion 2ears ago3 The2 were all 1arine ani1als0 an6 1an2 groups0 such as sponges0 9ell2fish0 1ollusks0 crustaceans0 starfish0 an6 1an2 kin6s of fish .are still pri1aril2 1arine ani1als3 The e4olution of organis1s that inhabit

freshwater an6 terrestrial en4iron1ents is a 1ore recent 6e4elop1ent3 The first terrestrial ani1als ;arthropo6s< are foun6 in the fossils of the Silurian perio60 BB@ to BAE 1illion 2ears ago3 Ma9or changes in the kin6s of terrestrial ani1als occurre6 after that ti1e3 Two groups.arthropo6s ;particularl2 the insects< an6 4ertebrates ;especiall2 reptiles0 bir6s0 an6 1a11als<.were e7tre1el2 successful in terrestrial habitats3 It is co11on to 6i4i6e ani1als into two categories* in4ertebrates an6 4ertebrates3 Ani1als with backbones 1a6e of 4ertebrae are calle6 vertebratesan6 inclu6e 4arious kin6s of fishes0 a1phibians0 reptiles0 bir6s0 an6 1a11als3 Those without backbones are calle6 invertebrates3 All earl2 ani1als lacke6 backbones0 an6 in4ertebrates still constitute HH3HI of all ani1al species in e7istence to6a23 The subse>uent e4olution of ani1als le6 to great 6i4ersit20 an6 to6a2 ani1als are a6apte6 to li4e in 9ust about an2 en4iron1ent3 The2 li4e in all the oceans0 on the shores of oceans0 an6 in shallow freshwater3 The2 li4e in the bitter col6 of the Arctic0 the 6r2ness of the 6esert0 an6 the 6ri4ing rains of tropical forests3 So1e ani1als eat onl2 other ani1als0 so1e are parasites0 so1e eat both plants an6 other ani1als0 an6 so1e fee6 onl2 on plants3 The2 show a re1arkable 4ariet2 of for10 function0 an6 acti4it23 The2 can be foun6 in an a1a5ing 4ariet2 of si5es0 colors0 an6 bo62 shapes3 The e4olution of ani1als is co1ple7 an6 often 6ifficult to interpret3 #igure ?@3? shows the current knowle6ge of how 4arious groups of ani1als are relate63

TEMPERATURE REGULATION The te1perature of an organis1 affects the rate at which its 1etabolic reactions take place3 So1e ani1als 6o little to regulate their te1perature0 whereas others e7pen6 consi6erable energ2 to 1aintain a constant te1perature3 Poikilot er!s are organis1s whose bo62 te1perature 4aries with the en4iron1ental te1perature3 When the water or air te1perature changes0 so 6oes the te1perature of the organis13 All 1icrobes an6 plants an6 1ost ani1als0 inclu6ing insects0 wor1s0 an6 reptiles0 are poikilother1s3 This is significant because0 at col6er bo62 te1peratures0 poikilother1s ha4e lower 1etabolic rates: at higher bo62 te1peratures0 the2 ha4e higher 1etabolic rates3 Ho!eot er!s are ani1als that 1aintain a constant bo62 te1perature that is generall2 higher than the en4iron1ental te1perature0 regar6less of the e7ternal te1perature ;figure ?@3@<3 These ani1als.bir6s an6 1a11als .ha4e high 1etabolic rates0 because the2 use 1etabolic energ2 to 1aintain their constant bo62 te1perature3 This 1eans that ho1eother1s ha4e higher foo6 6e1an6s than poikilother1s but are able to re1ain acti4e at low

en4iron1ental te1peratures3 A1ong ho1eother1s0 the s1aller ani1als ha4e higher bo62 te1peratures an6 higher 1etabolic rates than the larger ani1als3 This is in part because s1all ani1als lose heat faster than large ani1als0 because s1all ani1als ha4e a larger surface area co1pare6 to their 4olu1e3 So1eti1es0 the ter1s ectotherm an6 endotherm are use6 to 6escribe the sa1e relationship fro1 a slightl2 6ifferent point of 4iew3 E"tot er!s are organis1s whose bo62 te1peratures 6epen6 on the e7ternal te1perature0 an6en#ot er!s are ani1als that ha4e internal heat8generating 1echanis1s an6 can 1aintain a relati4el2 constant bo62 te1perature in spite of wi6e 4ariations in the te1perature of their en4iron1ent3 Howe4er0 poikilother1s or ectother1s are not necessaril2 totall2 at the 1erc2 of their en4iron1ent3 Man2 poikilother1s use beha4ioral 1eans to regulate bo62 te1perature3 !ne si1ple 1etho6 is to position the bo62 so that it absorbs heat fro1 its surroun6ings3 Man2 kin6s of reptiles an6 insects JsunK the1sel4es3 '2 placing the1sel4es in the Sun or on rocks or other surfaces that ha4e been heate6 b2 the Sun0 the2 can raise their bo62 te1perature abo4e that of their en4iron1ent3 Si1ilarl20 1an2 poikilother1s can generate heat b2 contracting their 1uscles3 In col6 weather0 bu1blebees often beat their wings prior to fl2ing0 raising their bo62 te1perature3 'o62 te1perature is i1portant0 because the rate at which the wings can beat is 6eter1ine6 b2 bo62 te1perature3

$O%& PLANS' S&MMETR& S211etrical ob9ects ha4e si1ilar parts that are arrange6 in a particular pattern3 #or e7a1ple0 the parts of a 6ais2 flower an6 a bic2cle are arrange6

s211etricall23 As(!!etr( is a con6ition in which there is no pattern to the in6i4i6ual parts3 As211etrical bo62 for1s are rare an6 occur onl2 in certain species of sponges0 which are the si1plest kin6s of ani1als3 Ra#ial s(!!etr( occurs when a bo62 is constructe6 aroun6 a central a7is3 An2 6i4ision of the bo62 along this a7is results in two si1ilar hal4es3 Although 1an2 ani1als with ra6ial s211etr2 are capable of 1o4e1ent0 the2 6o not alwa2s lea6 with the sa1e portion of the bo62: that is0 there is no anterior0 or hea60 en63 Starfish an6 9ell2fish are e7a1ples of organis1s with ra6ial s211etr23 $ilateral s(!!etr( e7ists when an ani1al is constructe6 with e>ui4alent parts on both si6es of a plane3 Ani1als with bilateral s211etr2 ha4e a hea6 an6 a tail region3 There is onl2 one wa2 to 6i4i6e bilateral ani1als into two 1irrore6 hal4es3 Ani1als with bilateral s211etr2 1o4e hea6 first0 an6 the hea6 t2picall2 has sense organs an6 a 1outh3 The feature of ha4ing an anterior hea6 en6 is calle6 cephalization3 Most ani1als ha4e bilateral s211etr2 ;figure ?@3B<3

$O%& PLANS' EM$R&ONI) )ELL LA&ERS

Ani1als 6iffer in the nu1ber of la2ers of cells of which the2 are co1pose63 When we look at the 6e4elop1ent of e1br2os we fin6 that the e1br2os of the si1plest ani1als ;sponges< 6o not for1 6istinct0 tissuelike la2ers3 Howe4er0 9ell2fishes an6 their relati4es ha4e e1br2os that consist of two la2ers3 Thee"to#er! is the outer la2er an6 the en#o#er! is the inner la2er3 'ecause their e1br2os are co1pose6 of two la2ers0 these ani1als are sai6 to be#i*loblasti"3 In a6ults0 these e1br2onic cell la2ers gi4e rise to an outer0 protecti4e la2er an6 an inner la2er that for1s a pouch an6 is in4ol4e6 in processing foo63 All the other 1a9or groups of ani1als are triploblastic3 Tri*loblasti"ani1als ha4e three la2ers of cells in their e1br2os3 San6wiche6 between the ecto6er1 an6 en6o6er1 is a thir6 la2er0 the !eso#er!3 In the a6ult bo620 the ecto6er1 gi4es rise to the skin or other surface co4ering0 the en6o6er1 gi4es rise to the lining of the 6igesti4e s2ste10 an6 the 1eso6er1 gi4es rise to 1uscles0 connecti4e tissue0 an6 other organ s2ste1s in4ol4e6 in the e7cretion of waste0 the circulation of 1aterial0 the e7change of gases0 an6 bo62 support ;figure ?@3C<3

$O%& PLANS' $O%& )AVITIES A "oelo! is a bo62 ca4it2 that separates the outer bo62 wall of the organis1 fro1 the gut an6 internal organs3 Si1ple ani1als0 such as 9ell2fish an6 flatwor1s0 are a"oelo!ate0 which 1eans that the2 ha4e no space separating their outer surface fro1 their internal organs3 More a64ance6 ani1als0 such as earthwor1s0 insects0 reptiles0 bir6s0 an6 1a11als0 ha4e a coelo13 The coelo1 in a turke2 is the ca4it2 where 2ou stuff the 6ressing3 In the li4ing bir6 this ca4it2 contains a nu1ber of organs0 inclu6ing those of the 6igesti4e0 e7cretor20 an6 circulator2 s2ste1s3 The 6e4elop1ent of the coelo1 was significant in the e4olution of ani1als3 In coelo1ates0 there is less crow6ing of organs an6 less interference a1ong the13 !rgans such as the heart0 lungs0 sto1ach0 li4er0 an6 intestines ha4e

a1ple roo1 to grow0 1o4e0 an6 function3 The coelo1 allows for the separation of the inner organs fro1 the bo628wall 1usculature: thus0 the internal organs 1o4e in6epen6entl2 of the outer bo62 wall3 This results in organ s2ste1s that are 1ore highl2 speciali5e6 than those in acoelo1ate organis1s3 !rgans are not loose in the coelo1: the2 are hel6 in place b2 sheets of connecti4e tissue calle6 !esenteries3 Mesenteries also support the bloo6 4essels connecting the 4arious organs3 So1e ani1als ha4e a kin6 of coelo1 calle6 a pseudocoelom3 A*se+#o"oelo! 6iffers fro1 a true coelo1 in that it is locate6 between the lining of the gut an6 the outer bo62 wall3 In other wor6s0 ani1als with a pseu6ocoelo1 6o not ha4e 1uscles aroun6 their 6igesti4e s2ste13 Ne1ato6e wor1s an6 se4eral relate6 groups of ani1als ha4e a pseu6ocoelo1 ;figure ?@3F<3

$O%& PLANS' SEGMENTATION Man2 kin6s of bilaterall2 s211etrical organis1s ha4e seg1ente6 bo6ies3Se,!entation is the separation of an ani1al=s bo62 into a nu1ber of recogni5able units fro1 its anterior to its posterior en63 Seg1entation is associate6 with the speciali5ation of certain parts of the bo623 Three co11on groups of ani1als show seg1entation* anneli6 wor1s0 arthropo6s0

an6 chor6ates3 Anneli6 wor1s ha4e a series of 4er2 si1ilar seg1ents with 1inor 6ifferences between the13 Seg1entation in arthropo6s is 1o6ifie6 so that se4eral seg1ents are speciali5e6 as a hea6 region an6 1ore posterior seg1ents are less speciali5e63 Man2 of the posterior seg1ents ha4e legs an6 other appen6ages3 A1ong the arthropo6s0 insects show a great 6eal of speciali5ation of seg1ents3 In chor6ates0 the seg1entation is of a 6ifferent sort but is ob4ious in the arrange1ent of 1uscles an6 the 4ertebral colu1n ;figure ?@3E<3

$O%& PLANS' S-ELETONS A skeleton is the part of an organis1 that pro4i6es structural support3 Most ani1als ha4e a skeleton3 It ser4es as strong scaffol6ing0 to which other organs can be attache63 In particular0 the skeleton pro4i6es places for 1uscle attach1ent an60 if the skeleton has 9oints0 the 1uscles can 1o4e one part of the skeleton with respect to others3 So1e a>uatic organis1s0 such as sea ane1ones an6 1an2 kin6s of wor1s0 are generall2 supporte6 b2 the 6ense 1e6iu1 in which the2 li4e an6 lack well86e4elope6 skeletons3 Howe4er0 1ost a>uatic ani1als ha4e a skeleton3 Most terrestrial ani1als ha4e a strong structure that supports the1 in the thin 1e6iu1 of the

at1osphere3 There are two 1a9or t2pes of skeletons* internal skeletons ;en#oskeletons< an6 e7ternal skeletons ;e.oskeletons< ;figure ?@3D<3 The 4ertebrates ;fish0 a1phibians0 reptiles0 bir6s0 1a11als< ha4e internal skeletons3 The 4arious organs are attache6 to an6 surroun6 the skeleton0 which grows in si5e as the ani1al grows3 Arthropo6s ;crustaceans0 spi6ers0 insects0 1illipe6es0 centipe6es< ha4e an e7ternal skeleton0 which surroun6s all the organs3 It is generall2 har6 an6 has 9oints3 These ani1als acco11o6ate growth b2 she66ing the ol6 skeleton an6 pro6ucing a new0 larger one3 This perio6 in the life of an arthropo6 is 6angerous0 because for a short perio6 it is without its har60 protecti4e outer la2er3 Man2 other ani1als ha4e structures that ha4e a supporti4e or protecti4e function ;such as cla1s0 snails0 an6 corals< an6 these are so1eti1es calle6 skeletons0 but the2 6o not ha4e 9oints3 So1e organis1s use water as a kin6 of supporti4e skeleton3 Anneli6 wor1s an6 so1e other ani1als ha4e flui68fille6 coelo1s3 'ecause water is not co1pressible0 but it is 1o4able0 co1pressi4e forces b2 1uscles can cause the ani1al=s shape to change3 This is si1ilar to what happens with a water8 fille6 balloon: co1pression in one place causes it to bulge out so1ewhere else3

/OOPLAN-TON -ooplankton is a 1i7ture of 6ifferent kin6s of s1all ani1als that 6rift with currents an6 fee6 on ph2toplankton an6 other 5ooplankton3 +rustaceans 1ake up appro7i1atel2 EGI of the 5ooplankton3 These inclu6e copepo6s0 krill ;s1all0 shri1plike organis1s<0 an6 other kin6s of crustaceans3 In a66ition0 9ell2fish an6 co1b 9ellies are co11on3 !ther kin6s of 5ooplankton inclu6e proto5oa0 se4eral kin6s of wor1s0 a group of 1ollusks0 an6 the lar4ae of 1an2 ani1als0 inclu6ing fish an6 pri1iti4e chor6ate relati4es3 NE-TON Nekton inclu6es 1an2 kin6s of a>uatic ani1als that are large enough an6 strong enough to be able to swi1 against currents an6 ti6es an6 go where the2 want to3 The2 are carni4ores that fee6 either on plankton or other nekton3 Like the 5ooplankton0 this is a 6i4erse group of organis1s0 inclu6ing so1e acti4el2 swi11ing 9ell2fish0 s>ui6 an6 cuttlefish0 shri1p0 sharks0 bon2 fish0 turtles0 sea snakes0 bir6s ;penguins0 cor1orants0 an6 other 6i4ing bir6s<0 an6 se4eral kin6s of 1a11als ;whales0 porpoises0 seals0 sea otters0 walruses0 an6 so on<3 $ENTHI) ANIMALS A 1a9or ecological niche in the oceans inclu6es large nu1bers of botto18 6welling ;benthic< organis1s3 A1ong the benthic organis1s are such ani1als as the seg1ente6 wor1s: cla1s an6 snails: lobsters0 crabs0 an6 shri1p: starfish an6 sea urchins: an6 1an2 kin6s of fish3 'enthic 1arine organis1s fall into two general categories* those that 1o4e about in search of foo6 an6 those that are filter fee6ers3 +o11on ani1als that 1o4e about the botto1 are crabs0 1an2 wor1s0 fish0 starfish an6 so1e 1olluscs3 #ilter fee6ers are sessile.per1anentl2 attache6 to the substrate3 The2 fee6 b2 creating water currents with cilia or appen6ages that bring foo6 to the13 Sponges0 corals0 tube wor1s0 cla1s0 barnacles0 an6 crinoi6s are e7a1ples of filter fee6ers3 %epro6uction presents special proble1s for sessile ani1als0 because the2 cannot 1o4e to fin6 1ates3 Howe4er0 because the2 are in an a>uatic en4iron1ent0 the sper1 can swi1 to the egg an6 fertili5e it3 The fertili5e6 egg 6e4elops into a lar4al stage.the 9u4enile stage ;figure ?@3H<3 The lar4ae are usuall2 ciliate6 or ha4e appen6ages that enable the1 to 1o4e0 e4en though the a6ults are sessile3 The free8swi11ing lar4al stages allow the

ani1al to 6isperse through its en4iron1ent3 The lar4a 6iffers fro1 the sessile a6ult not onl2 because it is free8 swi11ing but also because it usuall2 uses a 6ifferent source of foo6 an6 often beco1es part of the plankton co11unit23 The lar4al stages of 1ost organis1s are sub9ecte6 to pre6ation0 an6 the 1ortalit2 rate is high3 The lar4ae 1o4e to new locations0 settle 6own0 an6 6e4elop into a6ults3 E4en 1an2 1arine ani1als that 6o not ha4e sessile stages pro6uce free8 swi11ing lar4ae3 #or e7a1ple0 crabs0 starfish0 an6 eels 1o4e about freel2 an6 pro6uce free8swi11ing lar4ae3

PORIFERA0SPONGES E4en though sponges are classifie6 as 1ulticellular0 in 1an2 wa2s the2 are si1ilar to colonial proto5oa3 There are two la2ers of cells0 but 1ost of the cells are in 6irect contact with the en4iron1ent3 All a6ult sponges are sessile ;per1anentl2 attache6< filter fee6ers with ciliate6 cells that cause a current of water to circulate through the organis13 The in6i4i6ual cells obtain their nutrients 6irectl2 fro1 the water ;figure ?@3AG<3 Although so1e sponges are ra6iall2 s211etrical0 1ost sponges are as211etrical3 Sponges ha4e structures0 calle6 spicules0 in a 9ell2like 1aterial between the two la2ers of cells3 So1e species ha4e spicules of calciu1 carbonate0 others of silicon

6io7i6e0 an6 so1e of a protein 1aterial3 It is the skeletons co1pose6 of protein spicules that are use6 as washing sponges3 ;Actuall20 1ost sponges we bu2 are 1anufacture6 fro1 4arious for1s of plastic3< Ase7ual repro6uction in sponges can occur b2 frag1entation3 Wa4e action 1a2 tear off a part of a sponge0 which e4entuall2 settles 6own0 attaches itself0 an6 begins to grow3 Sponges also repro6uce b2 b+##in,0 a t2pe of ase7ual repro6uction in which the new organis1 is an outgrowth of the parent3 Se7ual repro6uction in4ol4es e7ternal fertili5ation in which the sper1 an6 egg unite in the water3 The fertili5e6 egg 6e4elops into a free8swi11ing0 ciliate6 lar4al stage3 The lar4a swi1s in the plankton an6 e4entuall2 settles to the botto10 attaches0 an6 grows into an a6ult sponge3

)NI%ARIA01ELL&FISH2 )ORALS2 AN% SEA ANEMONES +ni6arians inclu6e the 9ell2fish0 corals0 an6 sea ane1ones3 Like 1an2 sponges0 the2 ha4e two la2ers of cells3 There is a 9ell2like 1aterial between the two la2ers of cells: it is 4er2 thick in 9ell2fishes3 +ni6arians show ra6ial s211etr20 an6 all species ha4e a single opening lea6ing into a saclike 6igesti4e ca4it23 Surroun6ing the opening is a series of tentacles ;figure ?@3AA<3 These long0 fle7ible0 ar1like tentacles ha4e speciali5e6 cells that pro6uce structures calle6nematocysts0 which can sting an6 paral25e s1all organis1s3 Ne1atoc2sts are uni>ue to the +ni6aria3 The cells that pro6uce

the ne1atoc2sts are known as cni6oc2tes an6 are responsible for the na1e of the group.+ni6aria3 E4en though the2 are pri1iti4e organis1s0 cni6arians are carni4orous3 Man2 species of +ni6aria e7hibit alternation of generations an6 ha4e both se7ual an6 ase7ual stages of repro6uction3 The !e#+sa is a free8swi11ing a6ult stage that repro6uces se7uall23 The *ol(* is a sessile lar4al stage that repro6uces ase7uall2 ;figure ?@3A?<3 Sea ane1ones an6 corals are pol2ps an6 so1e species lack a 1e6usa stage3 /ell2fish are 1e6usas: the2 often pro6uce s1all pol2p stages 6uring their life c2cle3

)TENOPHORA0)OM$ 1ELLIES +tenophorans are si1ilar to cni6arians in that the2 are 6iploblastic an6 ha4e ra6ial s211etr23 The2 swi1 b2 rows of cilia0 an6 1an2 ha4e two long0

ar1like appen6ages0 which help the1 gather foo6 ;figure ?@3A@<3

PLAT&HELMINTHES0FLATWORMS The si1plest bilaterall2 s211etrical ani1als are the flatwor1s3 'ecause the2 are also triploblastic0 the2 represent a 1a9or increase in co1ple7it2 o4er the sponges an6 cni6arians3 The2 are consi6ere6 1ore pri1iti4e than other bilaterall2 s211etrical0 triploblastic ani1als0 because the2 lack a coelo1 an6 ha4e onl2 one opening to the gut3 The2 ha4e no circulator2 or respirator2 s2ste13 Their flat structure allows for the 6iffusion of gases between their en4iron1ent an6 the internal cells3 There are three basic t2pes of flatwor1s.free8li4ing flatwor1s ;often calle6planarians< an6 two groups that are parasitic: flukes an6 tapewor1s that constitute the 1a9orit2 of species of flatwor1s ;figure ?@3AB<3 We 1a2 consi6er this for1 of nutrition rather unusual0 but of all the kin6s of ani1als in the worl60 1ore are parasites than not3 Planarians are free8li4ing flatwor1s that are botto1 6wellers in 1arine waters or freshwater3 A few species are foun6 in 1oist terrestrial habitats3 The2 are carni4ores or sca4engers that fee6 on 6ea6 organis1s3 The foo6 that enters the gut is partl2 broken 6own: then0 the foo6 particles are engulfe6 b2 the cells that line the gut3 Flukes are co11on parasites3 So1e of the flukes are e7ternal parasites on the gills an6 scales of fish0 but 1ost are internal parasites in the gut0 li4er0 or lungs of 4ertebrate hosts3 Most flukes ha4e a co1ple7 life c2cle in4ol4ing

1ore than one host3 "suall20 the lar4al stage infects an in4ertebrate host0 whereas the a6ult parasite infects a 4ertebrate host3 #or e7a1ple0 the 6isease schistoso1iasis is cause6 b2 a6ult Schistosoma mansoni flukes0 which li4e in the bloo6 4essels of the hu1an 6igesti4e s2ste13 This 6isease is co11on in tropical countries: the presence of the wor1s in the bo62 causes 6iarrhea0 li4er 6a1age0 ane1ia0 an6 a lowering of the bo62=s resistance to other 6iseases3 #ertili5e6 eggs pass out with the feces3 Eggs release6 into the water hatch into free8swi11ing lar4ae3 If a lar4a infects a snail0 it un6ergoes a66itional ase7ual repro6uction an6 pro6uces a secon6 lar4al stage3 A single infecte6 snail 1a2 be the source of thousan6s of lar4ae3 These new lar4ae swi1 freel2 in the water3 If the2 encounter a hu1an0 the lar4ae bore through the skin an6 enter the circulator2 s2ste10 which carries the1 to the bloo6 4essels of the intestine ;figure ?@3AC<3 In North A1erica0 people often encounter this kin6 of parasite as swi11er=s itch3 Swi11er=s itch is cause6 b2 the lar4al stages of a fluke burrowing into the skin3 Howe4er0 the nor1al hosts for the wor1 are species of 6ucks3 Hu1ans are not 6ucks0 so the lar4ae that ha4e burrowe6 into the skin 6ie an6 a rash often 6e4elops3 In sensiti4e in6i4i6uals0 the reaction can be e7tre1e an6 re>uire 1e6ical attention3 Tapeworms are parasites that ha4e a co1pletel2 6ifferent structure an6 wa2 of life fro1 flukes3 The life c2cle in4ol4es two hosts3 !ne of the hosts is an herbi4ore an6 the other is an o1ni4ore or a carni4ore3 'oth hosts are usuall2 4ertebrate ani1als3 An herbi4ore eats tapewor1 eggs that ha4e been passe6 fro1 an infecte6 carni4ore host through its feces3 The eggs are eaten along with the 4egetation the herbi4ore uses for foo63 An egg 6e4elops into a lar4al stage0 which 1igrates to the herbi4ore=s 1uscle an6 for1s a c2st3 When the herbi4ore is eaten b2 a carni4ore0 the tapewor1 c2st 6e4elops into the a6ult for1 in the carni4ore=s intestine3 The a6ult wor1 is highl2 speciali5e63 It has no 6igesti4e s2ste10 but it has hooks an6 suckers for hol6ing onto the intestine of its host3 It pro6uces a series of sections0 calle6 proglotti6s0 b2 ase7ual repro6uction3 Each proglotti6 has a co1plete set of repro6ucti4e organs3 It is i1portant not to confuse proglotti6s with the seg1ents seen in other kin6s of organis1s3 $roglotti6s are not seg1ents0 but are ase7uall2 pro6uce6 bu6s3 Mating takes place between proglotti6s within the intestine0 an6 the proglotti6s beco1e fille6 with fertili5e6 eggs3

The en6 proglotti6s break off an6 pass out with the feces3 Thus0 the eggs can be easil2 6isperse6 in the feces ;figure ?@3AF<3

NEMATO%A0ROUN%WORMS Me1bers of the Ne1ato6a are e7tre1el2 co11on ani1als0 often calle6 roun6wor1s or ne1ato6es3 The2 ha4e a si1ple0 unseg1ente60 elongate6 bo62 structure0 which consist of an outer epi6er1is co4ere6 b2 a thick0 fle7ible cuticle3 The cuticle is she6 perio6icall2 as the ani1al grows3

Ne1ato6es are triploblastic an6 ha4e a pseu6ocoelo1 ;figure ?@3AE<3 Their gut is continuous0 with a 1outh at one en6 an6 an anus at the other3 #ew ani1als are foun6 in as 1an2 6i4erse habitats or in such nu1bers as the roun6wor1s3 The2 li4e in water0 1oist soil0 an6 1an2 li4e within other organis1s as parasites3 Soil ne1ato6es are e7tre1el2 co11on3 Although 1ost roun6wor1s are free8li4ing0 1an2 are econo1icall2 i1portant parasites3 So1e are parasitic on plants0 whereas others infect ani1als: collecti4el20 the2 6o billions of 6ollars worth of 6a1age to crops an6 li4estock3 %oun6wor1 parasites of ani1als range fro1 the relati4el2 har1less hu1an intestinal pinwor1s Enterobius0 which 1a2 cause irritation but 6o no serious har10 to Dirofilaria0 which can cause heartwor1 6isease in 6ogs3 If untreate60 this infection can be fatal3 !ften0 the a1ount of 6a1age inflicte6 b2 roun6wor1s is 6irectl2 proportional to their nu1ber3 #or e7a1ple0 hookwor1s ;figure ?@3AD< fee6 on the host=s bloo63 A slight infestation often results in 1il6 ane1ia0 but a hea42 infestation of hookwor1s can result in 1ental or ph2sical retar6ation in chil6ren because of the se4ere ane1ia it causes3

ANNELI%A0SEGMENTE% WORMS The anneli6 wor1s are bilaterall2 s211etrical an6 ha4e a bo62 structure consisting of repeating seg1ents ;figure ?@3AH<3 Anneli6s are the first e4olutionar2 group to 6ispla2 seg1entation3 Most of the seg1ents are 4er2 si1ilar to one another0 although there is usuall2 so1e speciali5ation of anterior seg1ents into a hea60 an6 there 1a2 be speciali5ation relate6 to repro6uction an6 6igestion3 Each seg1ent has a coelo1ic ca4it23 The2 ha4e well86e4elope6 1uscular0 circulator20 6igesti4e0 e7cretor20 an6 ner4ous s2ste1s3 There are three 1a9or t2pes of anneli6 wor1s ;figure ?@3?G<3 Polychaetes are pri1aril2 benthic0 1arine wor1s that ha4e pa66lelike appen6ages on each seg1ent3 The2 ha4e a well86e4elope6 hea6 region with

sense organs an6 a 1outh3 So1e li4e in tubes an6 are filter fee6ers3 !thers burrow in 1u6 or san6: so1e swi1 in search of foo63 Most pol2chaetes ha4e separate se7es an6 release eggs an6 sper1 into the ocean0 where fertili5ation takes place3 The fertili5e6 egg 6e4elops into a ciliate6 lar4a known as a trochophore lar4a: it is planktonic an6 e4entuall2 1eta1orphoses into the a6ult for1 of the wor13 Oligochaetes li4e in 1oist soil or freshwater3 The 1ost co11onl2 seen 1e1bers of this group are the 4arious kin6s of earthwor1s3 The2 6iffer fro1 pol2chaetes in that the2 6o not ha4e appen6ages an6 a well86e4elope6 hea6 region3 The2 are also her1aphro6itic ;ha4e both sets of se7 organs in the sa1e in6i4i6ual<3 Mating between two earthwor1s results in each recei4ing sper1 fro1 the other3 Earthwor1s are e7tre1el2 i1portant soil organis1s3 The2 eat organic 1atter in the soil or co1e to the surface to eat 6ea6 lea4es an6 other organic 1atter3 As the2 burrow through the soil0 the2 create spaces0 which allow water an6 air to penetrate the soil3 The2 are also i1portant foo6 organis1s to 1an2 other ani1als3 Leeches li4e in freshwater or 1oist terrestrial en4iron1ents3 The2 ha4e suckers0 which allow the1 to hol6 on to ob9ects3 So1e are free8swi11ing carni4ores0 but 1an2 fee6 on the bloo6 of 4arious 4ertebrates3 The2 attach to their 4icti1s0 rasp a hole through the skin0 an6 suck bloo63 The2 pro6uce an anticoagulant0 which ai6s in their bloo68fee6ing lifest2le3

MOLLUS)A

Like 1ost other for1s of ani1al life0 the 1olluscs originate6 in the ocean0 an60 e4en though so1e for1s ha4e 1a6e the 1o4e to freshwater an6 terrestrial en4iron1ents0 1ost still li4e in the oceans3 The 1e1bers of this ph2lu1 6ispla2 a true bo62 ca4it20 a coelo13 %epro6uction is generall2 se7ual: so1e species ha4e separate se7es an6 others are her1aphro6itic3 The2 range fro1 1icroscopic organis1s to the giant s>ui60 which is up to AD 1eters long3 A pri1ar2 characteristic of 1ollusks is the presence of a soft bo62 enclose6 b2 a har6 shell3 The2 are not seg1ente6 but ha4e three 6istinct bo62 regions* the 1antle0 the foot0 an6 the 4isceral 1ass3 The 1antle pro6uces a shell an6 is in4ol4e6 in gas e7change0 the foot is in4ol4e6 in 1o4e1ent0 an6 the 4isceral 1ass contains the organs of 6igestion0 circulation0 an6 repro6uction3 Most of the 1ollusks ha4e a tonguelike structure known as a ra6ula0 which has teeth on it3 The2 use the ra6ula like a rasp to scrape awa2 at foo6 1aterials an6 tear the1 to tin2 particles that are ingeste6 ;figure ?@3?A<3 There are se4eral kin6s of 1ollusks: the 1ost co11onl2 obser4e6 are the chitons0 bi4al4es0 snails0 an6 octopuses an6 s>ui6s ;figure ?@3??<3 The chitons ha4e a series of shells along their back: the2 li4e attache6 to rocks along the seashore0 where the2 fee6 on algae on the rocks3 arious kin6s of snails ha4e a coile6 shell3 Most snails are 1arine0 but so1e li4e in freshwater an6 1oist terrestrial habitats3 Slugs are a kin6 of snail that 6oes not ha4e a shell3 The bi4al4es ;cla1s0 o2sters0 an6 1ussels< ha4e two shells3 The2 also 6iffer fro1 other 1ollusks in that the2 are filter fee6ers an6 lack a ra6ula3 In the s>ui6s an6 octopuses0 there is no e7ternal shell that ser4es as a for1 of support structure0 although a relate6 organis1.the nautilus.has a shell3 E7cept for the s>ui6s an6 octopuses0 1ollusks are slow81o4ing benthic ani1als3 So1e are herbi4ores an6 fee6 on 1arine algae: others are sca4engers an6 fee6 on 6ea6 organic 1atter3 A few are e4en pre6ators of other slow81o4ing or sessile neighbors3 As with 1ost other 1arine ani1als0

the 1ollusks pro6uce free8swi11ing lar4al stages0 which ai6 in 6ispersal3

ARTHROPO%A The arthropo6s are the 1ost successful group of ani1als on Earth3 The earliest arthropo6s were 1arine0 an6 to6a2 arthropo6s are foun6 as

plankton0 nekton0 an6 benthic ani1als3 Howe4er0 the 1ost successful group of ani1als is the terrestrial insects3 !4er three8fourths of the species of ani1als are arthropo6s0 an6 o4er three8fourths of the arthropo6s are insects3 Arthropo6s ha4e an e7ternal skeleton co1pose6 of chitin3 Their bo6ies are seg1ente60 but the seg1entation is highl2 1o6ifie60 co1pare6 with that of the anneli6s3 There is generall2 a hea6 region0 an6 the seg1ents that follow 1a2 be 1o6ifie6 into regions as well3 Man2 of the seg1ents ha4e paire6 appen6ages3 'oth the bo62 an6 the appen6ages are 9ointe63 'ecause the2 ha4e an e7oskeleton0 in or6er to grow the2 1ust she6 their skeleton an6 1anufacture a new0 larger one at inter4als3 The2 ha4e well8 6e4elope6 ner4ous0 1uscular0 respirator20 circulator20 an6 repro6ucti4e s2ste1s ;figure ?@3?@<3 There are 1an2 t2pes of arthropo6s* crustaceans0 1illipe6es0 centipe6es0 arachni6s0 an6 insects ;figure ?@3?B<3 Nearl2 all crustaceans are a>uatic ;both 1arine an6 freshwater< but range in si5e fro1 large crabs an6 lobsters to tin20 planktonic organis1s an6 sessile barnacles3 +rustaceans are t2picall2 o1ni4ores0 which fee6 on a 4ariet2 of li4ing an6 6ea6 1aterials3 Millipe6es an6 centipe6es ha4e long bo6ies with 1an2 legs0 an6 all the posterior seg1ents are si1ilar to one another3 The earliest fossils of terrestrial ani1als are of this t2pe3 The arachni6s are the scorpions0 spi6ers0 1ites0 an6 ticks3 The2 are 4er2 successful as lan6 ani1als3 Mites are e7tre1el2 co11on as soil organis1s3 Spi6ers are carni4ores0 an6 1ost ticks are bloo6 fee6ers3 Insects are terrestrial ani1als with a bo62 6i4i6e6 into three regions* hea60 thora70 an6 ab6o1en3 The2 ha4e three pairs of legs0 an6 1ost species ha4e wings3

E)HINO%ERMATA The echino6er1s represent a co1pletel2 6ifferent line of e4olution fro1 other in4ertebrates3 The2 are actuall2 1ore closel2 relate6 to the 4ertebrates than to other in4ertebrates3 Echino6er1s0 along with chor6ates0 ha4e an e1br2ological 6e4elop1ent0 in which the anus is the first opening of the gut to for13 Such ani1als are calle6 6euterosto1es3 In all other triploblastic organis1s0 the 1outh is the first opening of the gut to for1: these are calle6 protosto1es3 All echino6er1s are 1arine benthic ani1als an6 are foun6 in all regions0 fro1 the shoreline to the 6eep portions of the ocean3 Echino6er1s are the 1ost co11on t2pe of ani1al on 1uch of the ocean floor3 Most species are free81o4ing an6 either are carni4ores or fee6 on 6etritus3 The2 are uni>ue a1ong the 1ore a64ance6 in4ertebrates in that the2 6ispla2 ra6ial s211etr23 The2 ha4e a fi4e8part ra6ial s211etr2: thus0 the2

ha4e fi4e ar1s or regions of the bo62 that pro9ect fro1 a central a7is3 Howe4er0 the lar4al stage has bilateral s211etr20 lea6ing 1an2 biologists to belie4e that the echino6er1 ancestors were bilaterall2 s211etrical3 Another uni>ue characteristic of this group is their water 4ascular s2ste1 ;figure ?@3?C<3 In this s2ste10 water is taken in through a structure on the top si6e of the ani1al an6 then 1o4es through a series of canals3 The passage of water through this water 4ascular s2ste1 is in4ol4e6 in the organis1=s loco1otion3 The2 ha4e a har60 9ointe6 internal skeleton co4ere6 b2 a thin skin3 Man2 of the1 ha4e spines that are part of the skeleton an6 pro9ect fro1 the ani1al3 There are fi4e 1a9or t2pes of echino6er1s* starfish0 brittle stars0 sea urchins0 sea cucu1bers0 an6 crinoi6s ;figure ?@3?F<3 Starfish0 brittle stars0 an6 sea urchins 1o4e slowl2 along the ocean botto1 an6 fee6 pri1aril2 on 6etritus3 So1e starfish are carni4ores that eat cla1s3 +rinoi6s are sessile0 an6 1an2 of the1 are stalke63 'ecause the2 ha4e fi4e ar1s0 that are often feather8like0 the2 are often calle6 sea lilies or feather stars3 The2 are filter fee6ers3 Sea cucu1bers are sausage8shape6 organis1s that lie on the botto1 or burrow in the 1u63 So1e are 6etritus fee6ers an6 so1e are filter fee6ers3

)HOR%ATA The chor6ates are a 6i4erse group of ani1als3 The2 ha4e a hollow ner4e cor6 6own the back of the bo62: the2 ha4e a fle7ible ro6 9ust below the ner4e cor60 known as the notochor6: the2 ha4e a tail0 which e7ten6s be2on6 the anus: an6 the2 ha4e a region posterior to the 1outh0 known as a phar2n70 that has pouches in it3 The 1ost pri1iti4e chor6ates are s1all 1arine organis1s that ha4e a notochor6 but no backbone3 The2 are ranchiostoma ;for1erl2 na1e6!mphio"us< an6 tunicates3 ranchiostoma has a notochor6 as an a6ult0 but the tunicates ha4e onl2 a notochor6 in the tail region 6uring the lar4al stage ;figure ?@3?E<3 Howe4er0 1ost chor6ates are 4ertebrates ;ani1als with a backbone< an6 onl2 ha4e a notochor6 6uring their e1br2onic stages3 In the a>uatic chor6ates the pouches in the phar2n7 region for1 gill slits3 In terrestrial 4ertebrates0 these pouches are ob4ious in e1br2os but are highl2 1o6ifie6 in the a6ults3 There are se4eral kin6s of 4ertebrates that ha4e alwa2s been a>uatic organis1s an6 are co11onl2 calle6 fishes3 Hagfish an6 la1pre2s lack 9aws

an6 are the 1ost pri1iti4e of the fish3 Hagfish are strictl2 1arine for1s an6 are sca4engers: la1pre2s are 1ainl2 1arine but can also be foun6 in freshwater ;figure ?@3?D<3 A6ult la1pre2s suck bloo6 fro1 their larger fish hosts3 La1pre2s repro6uce in freshwater strea1s0 where the eggs 6e4elop into filter8fee6ing lar4ae3 After se4eral 2ears0 the lar4ae change to a6ults an6 1igrate to open water3 Sharks an6 ra2s are 1arine ani1als that ha4e an internal skeleton 1a6e entirel2 of cartilage ;figure ?@3?H<3 These ani1als ha4e no swi1 bla66er to a69ust their bo62 6ensit2 in or6er to 1aintain their position in the water: therefore0 the2 1ust constantl2 swi1 or the2 will sink3 %a2s fee6 b2 gli6ing along the botto1 an6 6re6ging up foo60 usuall2 in4ertebrates3 Sharks are pre6ator2 an6 fee6 pri1aril2 on other fish3 The2 tra4el great 6istances in search of foo63 !f the BG species of sharks0 onl2 E are known to attack people3 Most sharks grow no longer than a 1eter3 The whale shark0 the largest0 grows to AF 1eters0 but it is strictl2 a filter fee6er3 The bon2 fish are the class 1ost fa1iliar to us ;figure ?@3@G<3 Their skeleton is co1pose6 of bone3 Most species ha4e a swi1 bla66er an6 can regulate the a1ount of gas in the bla66er to control their 6ensit23 Thus0 the fish can re1ain at a gi4en le4el in the water without e7pen6ing large a1ounts of energ23 'on2 fish are foun6 in 1arine an6 freshwater habitats0 an6 so1e0 such as sal1on0 can li4e in both3 There are 1an2 kin6s of bon2 fish3 So1e are botto186welling0 whereas others are wi6e8ranging in the open water3 So1e fish are highl2 territorial an6 re1ain in a s1all area their entire li4es3 !f the 1an2 kin6s0 so1e fee6 pri1aril2 on algae an6 6etritus3 Howe4er0 1an2 are pre6ators3 The re1aining groups of 4ertebrates ;a1phibians0 reptiles0 bir6s0 an6 1a11als< all are terrestrial ani1als3 The a1phibians are transitional organis1s0 which 1ust return to water to repro6uce an6 ha4e a>uatic lar4al stages3 %eptiles0 bir6s0 an6 1a11als ha4e beco1e 4er2 successful terrestrial ani1als3

TERRESTRIAL ARTHROPO%S The first terrestrial ani1als were scorpion8like organis1s0 which are known fro1 the fossil recor6 fro1 o4er BGG 1illion 2ears ago3 The e7oskeleton of arthropo6s was i1portant in allowing the1 to a6apt to lan63 It pro4i6es the support nee6e6 in the less buo2ant air an6 ser4es as a surface for 1uscle attach1ent that per1its rapi6 1o4e1ent3 The e7oskeleton of terrestrial

arthropo6s is waterproof0 which re6uces water loss3 Terrestrial arthropo6s ha4e an internal respirator2 s2ste1 that pre4ents the loss of water fro1 their respirator2 surface3 Insects an6 spi6ers ha4e a tracheal s2ste1 of thin8walle6 tubes e7ten6ing into all regions of the bo620 thus pro4i6ing a large surface area for gas e7change ;figure ?@3@Aa<3 These tubes ha4e s1all openings to the outsi6e0 which re6uce the a1ount of water lost to the en4iron1ent3 Another i1portant 1etho6 of conser4ing water in insects an6 spi6ers is the presence of Malpighian tubules0 thin8walle6 tubes that surroun6 the gut an6 reabsorb water fro1 nitrogenous wastes prior to their e7cretion ;figure ?@3@Ab<3 Internal fertili5ation is t2pical of terrestrial arthropo6s3 It in4ol4es copulation in which the sper1 is place6 into the repro6ucti4e tract of the fe1ale ;insects< or the pro6uction of special sper1 containing sacs that are picke6 up b2 the fe1ale ;spi6ers<3 This is i1portant because both the sper1 an6 egg are protecte6 fro1 6r2ing3 Terrestrial arthropo6s ha4e e4ol4e6 a nu1ber of 1eans of sur4i4al un6er hostile en4iron1ental con6itions3 Their rapi6 repro6ucti4e rate is one 1eans3 Most of a population 1a2 be lost because of an unsuitable en4iron1ental change0 but0 when fa4orable con6itions return0 the re1aining in6i4i6uals can >uickl2 increase in nu1ber3 Man2 ha4e co1ple7 life c2cles that in4ol4e lar4al stages that occup2 6ifferent niches fro1 the a6ults3 #or e7a1ple0 butterflies ha4e lar4al stages that fee6 on the lea4es of plants an6 grow rapi6l23 The a6ults fee6 on the nectar of flowers an6 are pri1aril2 in4ol4e6 in se7ual repro6uction that in4ol4es 1ating an6 la2ing of the eggs on appropriate host plants ;figure ?@3@?<3 The terrestrial arthropo6s occup2 an incre6ible 4ariet2 of niches3 Man2 are herbi4ores that co1pete 6irectl2 with hu1ans for foo63 The2 are capable of 6eci1ating plant populations that ser4e as hu1an foo63 Man2 far1ing practices0 inclu6ing the use of pestici6es0 are 6irecte6 at controlling insect populations3 !ther kin6s of terrestrial arthropo6s are carni4ores that fee6 pri1aril2 on herbi4orous insects3 Insects ha4e e4ol4e6 in concert with the flowering plants: their role in pollination is well un6erstoo63 'ees0 butterflies0 an6 beetles transfer pollen fro1 one flower to another as the2 4isit the flowers in search of foo63 Man2 kin6s of crops rel2 on bees for pollination0 an6 far1ers e4en rent beehi4es to ensure a6e>uate pollination for fruit pro6uction3

AMPHI$IANS A1phibians are onl2 1ini1all2 a6apte6 to a terrestrial life3 Although the2 ha4e lungs the2 6o not ha4e an efficient 1etho6 of breathing3 The2 swallow air to fill the lungs an6 are able to acco1plish so1e e7change of o72gen an6 carbon 6io7i6e3 Howe4er0 1ost gas e7change occurs through their 1oist skin3 In a66ition to nee6ing water to keep their skin 1oist0 a1phibians 1ust repro6uce in water3 When the2 1ate0 the fe1ale releases eggs into the water0 an6 the 1ale releases sper1 a1i6 the eggs3 E7ternal fertili5ation occurs in the water0 an6 the fertili5e6 eggs 1ust re1ain in water or the2 will 6eh26rate3 Thus0 a1phibians li4e on J6r2K lan6 but are not foun6 far fro1 water0 because the2 lose water through their 1oist skin an6 repro6uction 1ust occur in water3 The 1ost co11on present86a2 a1phibians are frogs0

toa6s0 an6 sala1an6ers ;figure ?@3@@<3

REPTILES #or BG 1illion 2ears0 a1phibians were the onl2 4ertebrate ani1als on lan63 Howe4er0 e4entuall2 the2 were replace6 b2 reptiles0 which were better a6apte6 to life on lan63 In a66ition to ha4ing internal lungs0 reptiles ha4e a waterproof skin an6 water8conser4ing ki6ne2s to re6uce water loss3 #urther1ore0 their repro6uction in4ol4es internal fertili5ation0 which protects the egg an6 sper1 fro1 6r2ing3 Howe4er0 the 2oung still re>uire a 1oist en4iron1ent in which to 6e4elop3 %eptiles beca1e co1pletel2 in6epen6ent of an a>uatic en4iron1ent with the 6e4elop1ent of the a1niotic egg0 which protects the 6e4eloping 2oung fro1 in9ur2 an6 6eh26ration ;figure ?@3@B<3 The co4ering on the egg retains 1oisture an6 protects the 6e4eloping 2oung fro1 6eh26ration while allowing

for the e7change of gases3 The reptiles were the first ani1als to 6e4elop such an egg3 The 6e4elop1ent of a 1eans of internal fertili5ation an6 the a1niotic egg allowe6 the reptiles to sprea6 o4er 1uch of the Earth an6 occup2 a large nu1ber of pre4iousl2 unfille6 niches3 #or about ?GG 1illion 2ears0 the2 were the onl2 large 4ertebrate ani1als on lan63 The e4olution of reptiles increase6 co1petition with the a1phibians for foo6 an6 space3 The a1phibians generall2 lost in this co1petition: conse>uentl20 1ost beca1e e7tinct3 So1e e4ol4e6 into present86a2 frogs0 toa6s0 an6 sala1an6ers3 In a si1ilar fashion0 as bir6s an6 1a11als e4ol4e60 1an2 kin6s of reptiles beca1e e7tinct3 Howe4er0 there are still 1an2 kin6s of reptiles present to6a23 The2 inclu6e turtles0 li5ar6s0 snakes0 croco6iles0 an6 alligators ;figure ?@3@C<3

$IR%S The reptiles ga4e rise to two other groups of 4ertebrates* bir6s an6 1a11als3 About FC 1illion 2ears ago0 a 1ass e7tinction of 1an2 kin6s of reptiles occurre63 At that ti1e0 bir6s an6 1a11als began to 6i4ersif2 an6 beca1e the 6o1inant for1s of 4ertebrates on lan63 Like the structures of their reptile ancestors0 the skin0 lungs0 an6 ki6ne2s of bir6s re6uce water loss0 an6 repro6uction in4ol4es internal fertili5ation an6 the shelle6 a1niotic egg3 The2 also ha4e a6aptations that allow the1 to be successful as lan6 ani1als3 'ir6s are ho1eother1ic an6 ha4e feathers3 As ho1eother1s0 the2 ha4e a high bo62 te1perature an6 a 1ore rapi6 1etabolic rate than reptiles3 #eathers ser4e two pri1ar2 functions in bir6s3 The2 for1 an insulating la2er0 which helps pre4ent heat loss0 an6 the2 pro4i6e structural surfaces enabling the bir6s to fl23 There are se4eral 4alues to flight3 Ani1als that fl2 are able to

tra4el long 6istances in a short ti1e an6 use less energ2 than ani1als that 1ust walk or run3 The2 are able to cross barriers0 such as strea1s0 lakes0 oceans0 bogs0 ra4ines0 or 1ountains0 that other ani1als cannot easil2 cross3 The2 can also escape 1an2 kin6s of pre6ators b2 taking flight >uickl23 The e7ploitation of flight has shape6 the entire structure an6 function of bir6s3 The foreli1bs are 1o6ifie6 into wings for flight0 although it is actuall2 the flight feathers that pro4i6e 1ost of the flight surface3 Large breast 1uscles pro4i6e the power for flight3 #eathers help pro4i6e a strea1line6 shape3 Ho1eother1is1 enables a high constant te1perature0 which allows for the rapi6 wing beats t2pical of 1ost bir6s3 In a66ition0 the skeleton is re6uce6 in weight an6 the 9aws lack teeth an6 are 1o6ifie6 into a beak3 'ir6s ha4e successfull2 occupie6 1an2 niches3 So1e are nectar fee6ers0 so1e are carni4ores0 so1e are see6eaters0 so1e are a>uatic0 an6 so1e ha4e e4en lost their abilit2 to fl2 ;figure ?@3@F<3 'ecause the2 are ho1eother1s0 bir6s= eggs 1ust be kept at a war1 te1perature3 Thus0 bir6s buil6 nests0 incubate their eggs0 an6 care for their

2oung3

MAMMALS The first 1a11als appeare6 about ?GG 1illion 2ears ago0 when reptiles were at their 1ost 6i4erse3 Like bir6s0 1a11als are ho1eother1s0 with a high constant bo62 te1perature3 Like reptiles an6 bir6s0 the2 ha4e a waterproof skin an6 water8conser4ing lungs an6 ki6ne2s3 Howe4er0 the2 6iffer fro1 bir6s in se4eral respects3 Their insulating co4ering is hair0 rather than feathers0 an6 the2 pro4i6e nourish1ent to their 2oung with 1ilk pro6uce6 b2 special glan6s3 There are three categories of 1a11als3 Monotre1es ;plat2pus an6 echi6na< are egg8la2ing 1a11als whose 2oung still 6e4elop in an e7ternal egg3 #ollowing hatching0 the 1other pro4i6es nourish1ent in the for1 of 1ilk3 The 1ilk glan6s are wi6el2 6istribute6 on her un6ersi6e0 an6 the 2oung

lap up the 1ilk fro1 her fur3 Marsupials ;pouche6 1a11als< ha4e internal 6e4elop1ent of the 2oung3 Howe4er0 the 2oung are born in a 4er2 i11ature state an6 6e4elop further in an e7ternal pouch in the bell2 region of the fe1ale3 In the pouch0 the 2oung attach to a nipple3 The2 continue their 6e4elop1ent an6 e4entuall2 begin to lea4e the pouch for perio6s of ti1e until the2 are able to forage for the1sel4es3 $lacental 1a11als ha4e a for1 of 6e4elop1ent in which the 2oung re1ain within the fe1ale 1uch longer3 The e1br2o is attache6 to the wall of the uterus b2 an organ known as a placenta3 In the placenta0 capillaries fro1 the circulator2 s2ste1s of the 1other an6 e1br2o are a69acent to one another3 This allows for the e7change of 1aterials between the 6e4eloping 2oung an6 the 1other0 an6 the 2oung are born in a 1ore a64ance6 stage of 6e4elop1ent than is t2pical for 1arsupials3 The 2oung rel2 on 1ilk as a source of foo6 for so1e ti1e before the2 begin to fee6 on their own ;figure ?@3@E<3

The Plant Kingdom

By Enger, E.D., Ross, F.C., Bailey, D.B. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

WHAT IS A $LANT? ALTE%NATI!N !# &ENE%ATI!NS THE E !L"TI!N !# $LANTS THE M!SS LI#E +)+LE ,IN(S !# N!N AS+"LA% $LANTS THE SI&NI#I+AN+E !# AS+"LA% TISS"E %!!TS STEMS LEA ES THE #E%N LI#E +)+LE ,IN(S !# SEE(LESS AS+"LA% $LANTS &)MN!S$E%MS AN&I!S$E%MS* #L!WE% ST%"+T"%E AN&I!S$E%MS* THE LI#E +)+LE !# A #L!WE%IN& $LANT AN&I!S$E%MS* $!LLINATI!N ST%ATE&IES AN&I!S$E%MS* #%"IT AN&I!S$E%MS* AN&I!S$E%M (I E%SIT) THE &%!WTH !# W!!() $LANTS T%!$ISMS SEAS!NAL %ES$!NSES %ES$!NSES T! IN/"%) THE +!E !L"TI!N !# $LANTS AN( ANIMALS

WHAT IS A PLANT? $lants are eukar2otic0 1ulticellular organis1s that ha4e chloroph2ll a an6 chloroph2ll ban6 carr2 on photos2nthesis3 Their cells ha4e cellulose cell walls3 $lants also ha4e speciali5ations for life on lan63 $lants are0 for the 1ost part0 terrestrial organis1s that can li4e in 9ust about an2 en4iron1ent0 inclu6ing 6eserts0 arctic regions0 an6 swa1ps ;figure ??3A<3 Man2 plants li4e in shallow freshwater ;e3g30 water lilies0 cattails<0 an6 a few li4e in shallow oceans ;e3g30 eelgrass0 1angro4es<3 Within the 1ore than ?CG0GGG species0 plants show a re1arkable 4ariet2 of for10 function0 an6 acti4it23 $lants range in si5e fro1 tin20 floating 6uckwee6 the si5e of a pencil eraser to re6woo6

trees o4er AGG 1eters tall3 There are plants that lack chloroph2ll an6 are parasites0 plants that 6igest ani1als0 an6 plants that ha4e 1utualistic relationships with ani1als3

ALTERNATION OF GENERATIONS $lants ha4e a life c2cle that in4ol4es two 6istinctl2 6ifferent generations* thesporophyte generation an6 the gametophyte generation3 The s*oro* (te ,eneration is 6iploi6 ;?n< an6 has plant parts in which 1eiosis takes place to pro6uce haploi6 ;n< spores3 The wor6 spore is use6 se4eral 6ifferent wa2s3 There are structures calle6 spores in bacteria0 algae0 proto5oa0 fungi0 an6 plants3 Each is 6istinct fro1 the others3 In our 6iscussion of plants0 the wor6 sporerefers to a haploi6 cell pro6uce6 b2 1eiosis that ger1inates to gi4e rise to a 1ulticellular haploi6 generation known as the gametophyte generation3 The,a!eto* (te ,eneration is haploi6 an6 6e4elops structures that pro6uce ga1etes* eggs an6 sper13 'ecause the ga1etoph2te is alrea62 haploi60 eggs an6 sper1 are pro6uce6 b2 1itosis3 When haploi6 ga1etes unite0 a 6iploi6 52gote is for1e63 The 52gote is the first cell in a new sporoph2te generation3 The 52gote 6i4i6es b2 1itosis0 an6

a new 1ulticellular sporoph2te generation results3 %ecall that the ter1 alternation of generations is use6 to 6escribe this kin6 of life c2cle0 in which plants c2cle between two stages in their life.the 6iploi6 sporoph2te an6 the haploi6 ga1etoph2te ;figure ??3?<3

THE EVOLUTION OF PLANTS At one ti1e0 all life was a>uatic3 Therefore0 it is logical to look for the ancestors of plants a1ong the a>uatic0 photos2nthetic algae3 Most scientists feel that the ancestor of plants was a freshwater 1e1ber of the green algae3 The strongest e4i6ence for this is that green algae ha4e the sa1e kin6s of chloroph2ll ;chloroph2ll a an6 chloroph2ll b< an6 the sa1e kin6s of chloroplasts as plants3 +o1parison of the (NA of plants an6 green algae also supports this conclusion3 The e4olution of plants shows two general tren6s3 !ne is towar6 greater speciali5ation for li4ing in a 6r2 en4iron1ent: the other is towar6 a 1ore pro1inent role for the sporoph2te generation in the life c2cle3 The 1ost pri1iti4e plants lack 4ascular tissue to help carr2 water3 Thus0 1ost non4ascular plants are li1ite6 to 1oist habitats3 The 1ore a64ance6 4ascular plants ha4e speciali5e6 cells that help transport water an6 other

1aterials throughout the plant3 A secon6 1a9or 6e4elop1ent that allowe6 a64ance6 plants to e7ploit terrestrial habitats was the e4olution of see6s that coul6 resist 6r2ing3 In the 1ore pri1iti4e plants0 the ga1etoph2te generation is the 6o1inant generation0 whereas0 in 1ore a64ance6 groups0 the sporoph2te generation is 6o1inant3 The ta7ono12 of plants is base6 on these tren6s ;figure ??3@<3 Subse>uent sections will 6iscuss the 1a9or groups of plants an6 show how life c2cles an6 the capacit2 to li4e in a 6r2 en4iron1ent e4ol4e63

THE MOSS LIFE )&)LE

The 1oss plant that 2ou co11onl2 recogni5e is the ga1etoph2te generation3 %ecall that the ga1etoph2te generation is haploi6 an6 is the ga1ete8pro6ucing stage in the plant life c2cle3 Although the cells of the ga1etoph2te ha4e the haploi6 nu1ber of chro1oso1es ;the sa1e as ga1etes<0 not all of the1 function as ga1etes3 At the top of the 1oss ga1etoph2te are two kin6s of structures that pro6uce ga1etes* the antheridium an6 the archegonium3 The ant eri#i+! is 1a6e up of a 9acket of cells surroun6ing the 6e4eloping sper13 The ar" e,oni+! is a flask8shape6 structure that pro6uces the egg: it has a tubular channel lea6ing to the egg at its base ;figure ??3B<3 There is usuall2 onl2 one egg cell in each archegoniu13 When the sper1 are 1ature0 the outer 9acket of the antheri6iu1 splits open0 releasing the flagellate6 sper13 The sper1 swi1 through a fil1 of 6ew or rainwater to the archegoniu1 an6 continue 6own the channel of the archegoniu1 to fertili5e the egg3 When the sper1 an6 egg nuclei fuse0 a 6iploi6 52gote is pro6uce63 The 52gote is the first cell of the sporoph2te generation3 The 52gote begins to grow within the archegoniu1 an6 e4entuall2 6e4elops into a 1ature sporoph2te0 which grows out of the top of the ga1etoph2te3 The sporoph2te consists of a long stalk with a capsule on the en6 of it3 Within the capsule0 1eiosis takes place0 pro6ucing haploi6 spores3 These spores are release6: when the2 ger1inate0 the2 gi4e rise to a 1ulticellular fila1ent known as a protone1a3 The protone1a 6e4elops into a 1ature ga1etoph2te plant3 Thus0 in 1osses an6 other non4ascular plants0 the ga1etoph2te generation is the 6o1inant stage an6 the sporoph2te is

6epen6ent on the ga1etoph2te3

-IN%S OF NONVAS)ULAR PLANTS The 1osses are the 1ost co11on non4ascular plants3 Mosses grow as a carpet of 1an2 in6i4i6ual ga1etoph2te plants3 Each 1oss plant is co1pose6 of a central stalk less than C centi1eters tall0 with short0 leaflike structures that are the sites of photos2nthesis3 There are o4er AG0GGG species of 1osses0 an6 the2 are foun6 an2where there is a6e>uate 1oisture3 The ga1etoph2tes of li4erworts an6 hornworts are flat sheets onl2 a few la2ers of cells thick3 The na1e li4erwort co1es fro1 the fact that these plants rese1ble the 1oist surface of a li4er3 There are about D0GGG species of li4erworts3 Hornworts 6eri4e their na1e fro1 the presence of a long0 slen6er sporoph2te0 which protru6es fro1 the flat ga1etoph2te plants3 Their cells are unusual a1ong plants0 because the2 contain onl2 one0 large chloroplast in each cell0 whereas other plants ha4e 1an2 chloroplasts per

cell3 There are about BGG species of hornworts foun6 throughout the worl63 #igure ??3C shows e7a1ples of non4ascular plants3

THE SIGNIFI)AN)E OF VAS)ULAR TISSUE A 1a9or step in the e4olution of plants was the 6e4elop1ent of 4ascular tissue3 $lants like ferns0 pines0 flowering plants an6 1an2 others ha4e 4ascular tissue3Vas"+lar tiss+e consists of tube8like cells that allow plants to efficientl2 transport water an6 nutrients about the plant3 The presence of 4ascular tissue is associate6 with the 6e4elop1ent of roots0 lea4es0 an6 ste1s3 Roots are un6ergroun6 structures that anchor the plant an6 absorb water an6 1inerals3 Lea4es are structures speciali5e6 for carr2ing out the process of photos2nthesis3Ste!s are structures that connect the roots with the lea4es an6 position the lea4es so that the2 recei4e sunlight3 There are two kin6s of 4ascular tissue* "ylem an6 phloem3 3(le! consists of a series of 6ea60 hollow cells arrange6 en6 to en6 to for1 a tube3 The walls of these JcellsK are strengthene6 with e7tra 6eposits of cellulose an6 a co1ple7 1aterial calle6 lignin3 The plant=s roots absorb water an6 1inerals fro1 the soil into the roots3 The 72le1 carries water an6 1inerals up fro1 the roots through the ste1 to the lea4es3 There are two kin6s of 72le1 cells* 4essel ele1ents an6 trachei6s3 essel ele1ents are essentiall2 6ea60 hollow cells0 up to G3E 11 in 6ia1eter0 in which the en6walls are 1issing3 Thus0 4essel ele1ents for1 long tubes si1ilar to a series of pieces of pipe hooke6 together3 Trachei6s are s1aller in 6ia1eter an6 consist of cells with o4erlapping0 tapere6 en6s3 Holes in the walls allow water an6 1inerals to

1o4e fro1 one trachei6 to the ne7t ;figure ??3F<3 P loe! carries the organic 1olecules ;pri1aril20 sugars an6 a1ino aci6s< pro6uce6 in the lea4es to other parts of the plant where growth or storage takes place3 &rowth takes place at the tips of roots an6 ste1s an6 in the pro6uction of repro6ucti4e structures ;cones0 flowers0 fruits<3 The roots are t2picall2 the place where foo6 is store60 but so1e plants store foo6 in their ste1s3 The phloe1 consists of two kin6s of cells* sie4e tube ele1ents an6 co1panion cells3 The sie4e tube ele1ents lack a nucleus an6 1ost organelles but retain a kin6 of c2toplas13 In a66ition0 the sie4e tube ele1ents ha4e holes in the en6walls that allow the flow of water an6 6issol4e6 nutrients3 The co1panion cells ha4e 6irect connections to the sie4e tube ele1ents an6 assist in the 1o4e1ent of sugars an6 a1ino aci6s b2 acti4e transport fro1 cells in the lea4es into the sie4e tube ele1ents ;figure ??3E<3 To be well a6apte6 to a 6r2 en4iron1ent0 plants nee6 a waterproof la2er on their surface in a66ition to 4ascular tissue3 This la2er re6uces the a1ount of water the2 lose0 an6 the presence of 4ascular tissue allows for the eas2 replace1ent of the water that is lost3 'ecause 4ascular tissue allows for the 1ore efficient transport of 1aterials throughout the plant0 it allows for an increase in plant si5e3 Although not all 4ascular plants are large0 1an2 are able to beco1e large0 because 4ascular tissue allows the1 to transport water an6 nutrients efficientl23

ROOTS Roots are the un6ergroun6 parts of plants that anchor the plants in the soil an6 absorb water an6 nutrients0 such as nitrogen0 phosphorus0 potassiu10

an6 other inorganic 1olecules fro1 the soil3 ascular tissue allows these 1aterials to be 6istribute6 for use b2 other parts of the plant3 The 4ascular tissue in the roots transports water an6 nutrients to the ste1 an6 recei4es 1aterials fro1 the ste13 %oots grow fro1 their tips3 '2 growing constantl20 roots e7plore new territor2 for a4ailable nutrients an6 water3 As a plant beco1es larger0 it nee6s 1ore root surface to absorb water an6 nutrients an6 to hol6 the plant in place3 The acti4el2 growing portions of the root near the tips ha4e 1an2 s1all0 fu5520 hairlike cell e7tensions calle6 root airs0 which pro4i6e a large surface area for the absorption of nutrients an6 water3 Most roots are i1portant storage places for the foo6 pro6uce6 b2 the abo4e8groun6 parts of the plant3 Man2 kin6s of plants store foo6 in their roots 6uring the growing season an6 use this foo6 to sta2 ali4e 6uring the winter3 The foo6 also pro4i6es the raw 1aterials necessar2 for growth for the ne7t growing season3 Although hu1ans 6o not eat the roots of plants such as 1aple trees0 rhubarb0 an6 grasses0 their roots are as i1portant to the1 in foo6 storage as are those of carrots0 turnips0 an6 ra6ishes ;figure ??3H<3

STEMS

Ste1s are0 in 1ost cases0 the abo4e8groun6 structures of plants that support the light8catching lea4es in which photos2nthesis occurs3 Howe4er0 ste1s can 4ar2 consi6erabl23 Trees ha4e ste1s that support large nu1bers of branches: 4ines ha4e ste1s that re>uire support: so1e plants0 such as 6an6elions0 ha4e 4er2 short ste1s0 with their lea4es flat against the groun6: an6 so1e ste1s are actuall2 un6ergroun63 Ste1s ha4e two 1ain functions* A3 The2 support the lea4es3 ?3 The2 transport raw 1aterials fro1 the roots to the lea4es an6 1anufacture6 foo6 fro1 the lea4es to the roots3 The support that ste1s pro4i6e is possible because of the nature of plant cell walls3 #irst0 all plant cells are surroun6e6 b2 a cell wall 1a6e of cellulose fibers interwo4en to for1 a bo70 within which the plant cell is containe63 'ecause the cell wall consists of fibers0 it is like a wicker basket3 There are spaces between cellulose fibers through which 1aterials pass relati4el2 easil23 Howe4er0 the cellulose fibers 6o not stretch: if the cell is full of water an6 other cellular 1aterials0 it beco1es >uite rigi63 %e1e1ber that the process of os1osis results in cells ha4ing an internal pressure3 It is this pressure against the nonstretchable cell wall that 1akes the cell rigi63 Man2 kin6s of s1all plants0 calle6 herbaceous plants0 rel2 pri1aril2 on this 1echanis1 for support3 The secon6 wa2 ste1s pro4i6e support in4ol4es the thickening of cell walls3#oody plants ha4e especiall2 thick cell walls0 which pro4i6e a66itional support3 The 72le1 of woo62 plants has thick cell walls an6 lignin 6eposite6 in the cell walls that pro4i6es strength an6 bin6s cell walls to one another3 This co1bination of thick cell walls with strengthening lignin is such an effecti4e support 1echanis1 that large trees an6 bushes are supporte6 against the pull of gra4it2 an6 can withstan6 strong win6s for centuries3 So1e of the ol6est trees on Earth ha4e been growing for se4eral thousan6 2ears3 Another i1portant function of the ste1 is to transport 1aterials between the roots an6 the lea4es ;figure ??3AG<3 A cross section of a ste1 e7a1ine6 un6er a 1icroscope re4eals that a large proportion of the ste1 consists of 4ascular tissue3 In a66ition to support an6 transport0 the ste1s of so1e plants ha4e a66itional functions3 So1e ste1s store foo63 This is true of sugar cane0 2a1s0 an6 potatoes3 In a66ition0 1an2 plant ste1s are green an60 therefore0

are in4ol4e6 in photos2nthesis3 Ste1s also ha4e a waterproof la2er on the outsi6e3 In the case of herbaceous plants0 it is usuall2 a wa72 la2er3 In the case of woo62 plants0 there is a tough outer waterproof bark3

LEAVES Lea4es are the speciali5e6 parts of plants that are the 1a9or sites of photos2nthesis3 To carr2 out photos2nthesis0 lea4es 1ust ha4e certain characteristics ;figure ??3AA<3 'ecause it is a solar collector0 a leaf shoul6 ha4e a large surface area3 Also0 1ost lea4es are relati4el2 thin0 co1pare6 with other plant parts3 Thick lea4es woul6 not allow the penetration of light to the 1a7i1u1 nu1ber of photos2nthetic cells3 Throughout the leaf are bun6les of 4ascular tissue0 which transport water an6 1inerals to the photos2nthesi5ing cells an6 sugars an6 other 1olecules fro1 these cells3 The thick walls of the cells of 4ascular tissue also pro4i6e support for the leaf3 In a66ition0 the lea4es of 1ost plants are arrange6 so that the2 6o not sha6e one another3 This assures that the 1a7i1u1 nu1ber of cells in the leaf will be e7pose6 to sunlight3 A 6rawback to ha4ing large0 flat0 thin lea4es is an increase in water loss through e4aporation3 To help slow water loss0 the outer1ost la2er of cells0

known as the epi6er1al la2er0 has a wa720 waterproof coat on its outer surface3 Howe4er0 so1e e7change of gases an6 water 1ust take place through the leaf3 When water e4aporates fro1 the leaf0 it creates a negati4e pressure0 which ten6s to pull a66itional water an6 6issol4e6 1inerals through the 72le1 into the leaf0 a process calle6 transpiration3 'ecause too 1uch water loss can be 6ea6l20 the leaf 1ust regulate transpiration3 The a1ount of water0 carbon 6io7i6e0 an6 o72gen 1o4ing into an6 out of the lea4es of 1ost plants is regulate6 b2 1an2 tin2 openings in the epi6er1is0 calle6 stomates ;figure ??3A?<3 The sto1ates can close or open to control the rate at which water is lost an6 gases are e7change63 !ften 6uring perio6s of 6rought or 6uring the hottest0 6riest part of the 6a20 the sto1ates are close60 re6ucing the rate at which the plant loses water3

THE FERN LIFE )&)LE Although there are 6ifferences in the 6etails of the life c2cles of see6less 4ascular plants0 we will use the life c2cle of ferns as a general 1o6el3 The conspicuous part of the life c2cle is the 6iploi6 sporoph2te generation3 The lea4es of 1ost ferns are co1ple70 branche6 structures co11onl2 calle6 fron6s3 The sporoph2te pro6uces haploi6 spores b2 1eiosis in special structures of the lea4es3 The spore8pro6ucing parts are t2picall2 on the un6ersi6e of the lea4es in structures calle6 sori3 Howe4er0 so1e species ha4e speciali5e6 structures whose sole function is the pro6uction of spores3 The spores gi4e rise to a haploi6 heart8shape6 ga1etoph2te0 which has archegonia an6 antheri6ia3 The sper1 swi1s to the archegoniu1 an6 fertili5es the egg3 T2picall20 the sper1 fertili5es an egg of a 6ifferent ga1etoph2te plant3 #ollowing fertili5ation of the egg0 the 6iploi6 52gote 6eri4es nourish1ent fro1 the ga1etoph2te an6 begins to grow3 E4entuall20 a new sporoph2te grows fro1 the ga1etoph2te to begin the life c2cle again3

#igure ??3A@ illustrates the life c2cle of the fern3

-IN%S OF SEE%LESS VAS)ULAR PLANTS

Ferns are the 1ost co11on of the see6less 4ascular plants3 There are about A?0GGG species of ferns in the worl63 The2 range fro1 the co11on bracken fern0 foun6 throughout the worl60 to tree ferns0 seen to6a2 in so1e tropical areas ;figure ??3AB<3 Along with horsetails an6 club 1osses0 tree ferns were i1portant 1e1bers of the forests of the +arboniferous perio63 #hisk ferns are o66 plants that lack roots an6 lea4es3 The2 appear to be relate6 to ferns3 The2 are anchore6 in the soil b2 an un6ergroun6 ste10 which has fila1ents growing fro1 it that absorb water an6 soil nutrients3 It has flattene6 structures si1ilar to lea4es0 but the2 are not consi6ere6 lea4es because the2 lack 4ascular tissue3 Whisk ferns are 1ost co11on in war10 1oist en4iron1ents3 There are about A? species3 The spores are pro6uce6 at the en6s of branches: the spores pro6uce a ga1etoph2te in the soil3 $orsetails are low8growing plants with 9ointe6 ste1s3 The lea4es are tin2 an6 encircle the ste1 at the 9oints3 Much of the photos2nthesis actuall2 occurs in the green ste13 There are about @G species3 The2 store silicon 6io7i6e in their cell walls an60 so0 feel rough3 The2 often are calle6 scouring rushes because pioneers use6 the1 to clean pots an6 pans3 The spores are pro6uce6 in structures at the en6 of the ste1s3 The spores gi4e rise to ga1etoph2tes0 which pro6uce either eggs or sper13 Tree8si5e6 1e1bers of this group are well known fro1 the fossil recor6 of the +arboniferous perio6 @CB to ?HG 1illion 2ears ago3 %lub mosses are usuall2 e4ergreen0 bright green0 low8growing0 branching plants3 'ecause the2 are e4ergreen an6 ha4e a slight rese1blance to s1all pine trees0 so1e kin6s are calle6 groun6 pines3 Their lea4es are s1all an6 ha4e onl2 a single bun6le of 4ascular tissue3 !4er A0GGG species are ali4e to6a23 Like the whisk ferns an6 horsetails0 the2 pro6uce spores in structures at the en6 of ste1s3 The spores gi4e rise to ga1etoph2tes3 Like the horsetails0 these plants were pro1inent trees8like plants in ancient +arboniferous forests3 #igure ??3AC shows e7a1ples of whisk ferns0 club 1osses0 an6 horsetails3

G&MNOSPERMS Se4eral kin6s of woo62 plants pro6uce see6s that are not enclose63 T2picall20 their see6s are pro6uce6 in woo62 structures calle6 "ones3 The see6s are pro6uce6 on the surface of flat0 woo62 parts of the cone ;figure ??3AF<3 'ecause the see6s are not enclose60 the2 are sai6 to be naked3 Thus0 these cone8pro6ucing plants0 such as conifers0 are calle6 gymnosperms0 which 1eans nake6 see6 plants3 Howe4er0 there are se4eral 6istinct kin6s of plants in this group* the c2ca6s0 ginkgos0 an6 conifers3 All are woo62 perennial plants3 We will e7a1ine the life c2cle of the pine tree to illustrate the life c2cle of a g21nosper13 T e Pine Li4e )("le

The 6o1inant portion of the pine life c2cle is the large0 6iploi6 sporoph2te generation3 $ines pro6uce two kin6s of cones0 which are part of the sporoph2te generation but pro6uce separate haploi6 1ale an6 fe1ale ga1etoph2tes3 The conspicuous cones on pines are the fe1ale cones0 which pro6uce the fe1ale ga1etoph2te generation3 The fe1ale ga1etoph2te consists of se4eral thousan6 cells an6 pro6uces se4eral archegonia0 each of which contains an egg3 The s1all 1ale cones are locate6 on the en6s of branches3 The 1ale cones pro6uce pollen3 Each of these s1all0 6ustlike pollen grains contains haploi6 nuclei0 which function as sper13 The process of getting the pollen fro1 the 1ale cone to the fe1ale cone is calle6 *ollination3 +onifers are win6 pollinate63 $ollen is release6 in such large >uantities that clou6s of pollen can be seen in the air when su66en gusts of win6 shake the branches of the trees3 !nce the pollen grain ;1ale ga1etoph2te< is in the 4icinit2 of the fe1ale ga1etoph2te it begins to grow a tubelike structure0 which enters the archegoniu1 an6 releases a sper1 nucleus0 which fertili5es the egg3 The processes of pollination an6 fertili5ation are separate e4ents3 $ollination occurs with the transfer of pollen to the fe1ale cone3 #ertili5ation occurs when the sper1 cell fro1 the pollen unites with the egg cell in the archegoniu13 #ertili5ation in g21nosper1s 1a2 occur 1onths or e4en 2ears following pollination3 The fertili5e6 egg ;52gote< is 6iploi6 an6 6e4elops into an e1br2o within a see63 Man2 kin6s of bir6s an6 1a11als use the see6s of pines an6 relate6 trees for foo63 In 1ost pines0 the see6s are release6 fro1 the cone when the scales of the cone fol6 back3 The winge6 see6s are carrie6 b2 win6 an6 fall to the groun63 The see6 ger1inates an6 gi4es rise to a new sporoph2te plant0 an6 the life c2cle continues3 #igure ??3AE re4iews the life c2cle of the pine3 Thus0 in a66ition to 4ascular tissue0 the pine life c2cle has two significant inno4ations that re6uce the plant=s 6epen6ence on water3 The see6 contains an e1br2o sporoph2te plant along with so1e store6 foo60 surroun6e6 b2 a see6 coat that re6uces water loss3 Thus0 the see6 can withstan6 6r2 perio6s3 The pro6uction of pollen an6 the process of pollination also re6uce the nee6 for water3 The sper1 6o not nee6 to swi1 to the egg3 The entire 1ale ga1etoph2te ;pollen< is transporte6 to the fe1ale ga1etoph2te b2 win63 Then0 the 1ale ga1etoph2te transfers the sper1 nucleus to the egg0 when the pollen grain grows a tube that releases a sper1 nucleus to fertili5e the

egg3 -in#s o4 G(!nos*er!s %ycads are stout0 woo62 g21nosper1s that ha4e a ring of fernlike lea4es at the top3 The2 li4e in tropical regions an6 are 1inor parts of the lan6scape3 (uring the /urassic perio6 ;ABB to ?A@ 1illion 2ears ago<0 c2ca6s were 1a9or organis1s in the forests3 The see6s are pro6uce6 in tough0 woo620 conelike structures3 There are about @GG species0 an6 half of the1 are in 6anger of e7tinction3 &inkgo trees were co11on in the /urassic0 but to6a2 there is onl2 one species ;&inkgo biloba<3 It is a tree with fan8shape6 lea4es3 Hu1ans eat the see6s0 an6 the lea4es are use6 in 1an2 herbal 1e6icines3 %onifers are the co11on trees an6 shrubs that bear see6s in cones3 Most conifers ha4e nee6le8shape6 lea4es3 'ecause the2 retain their lea4es throughout the 2ear0 the2 are often calle6 e4ergreens3 Although the2 ha4e nee6les throughout the 2ear0 the2 6o she6 nee6les a few at a ti1e throughout the 2ear0 as e4i6ence6 b2 the 1at of nee6les un6er a conifer3 A few conifers.for e7a1ple0Lari" ;ta1arack< an6 Ta"odium ;bal6 c2press<0 lose their lea4es all at once in the fall3 There are o4er FGG species of conifers0 an6 about half are consi6ere6 threatene63 Man2 kin6s of conifers are i1portant in the pro6uction of lu1ber3 #igure ??3AD shows the three t2pes of g21nosper1s3

ANGIOSPERMS' FLOWER STRU)TURE A 4lo5er is the structure0 co1pose6 of highl2 1o6ifie6 lea4es0 that is responsible for se7ual repro6uction3 At the center of a t2pical flower is the*istil0 which is co1pose6 of the stigma0 style0 an6 o'ary3 The o4ar2 pro6uces the fe1ale ga1etoph2te plant3 Surroun6ing the pistil are the sta!ens0 which consist of a long filament with anthers at the top3 The

anther pro6uces the pollen ;1ale ga1etoph2te plant<3 Petals are a whorl of 1o6ifie6 lea4es surroun6ing the sta1ens an6 pistil3 In 1an2 flowering plants0 the petals are large an6 show23 !utsi6e the petals is another whorl of 1o6ifie6 lea4es0 known as se*als3 Man2 kin6s of flowers pro6uce o6ors an6 a sugar2 li>ui60 known as nectar3 #igure ??3AH shows the arrange1ent of parts in a t2pical flower3 There is a great 6egree of speciali5ation of flowers3 So1e are large an6 show20 such as the flowers of roses an6 1agnolias3 !thers are s1all an6 inconspicuous0 such as the flowers of grasses an6 birch trees3 In a66ition0 so1e plants ha4e two kin6s of flowers3 !ne kin6 has a pistil0 whereas a 6ifferent flower has the sta1ens3 An2 flower that has both pistil an6 sta1ens is calle6 a *er4e"t 4lo5er: a flower containing 9ust a pistil or 9ust sta1ens is calle6 an i!*er4e"t 4lo5er3

ANGIOSPERMS' THE LIFE )&)LE OF A FLOWERING PLANT The life c2cle of a flowering plant has both sporoph2te an6 ga1etoph2te generations3 The sporoph2te is the 6o1inant stage of the life c2cle0 an6 the 1ale an6 fe1ale ga1etoph2tes are pro6uce6 within the flower3 As in g21nosper1s0 the 1ale ga1etoph2te is the pollen3 The fe1ale ga1etoph2te is foun6 within the o4ar2 of the pistil an6 consists of onl2 eight cells3 !ne of the cells is an egg cell3 $ollination occurs when pollen is transferre6 fro1 an anther to the stig1a of the pistil3 In so1e cases0 pollination 1ust be between flowers of 6ifferent plants of the sa1e species: this is calle6 cross8pollination3 Howe4er0 so1e

species of plants are able to pollinate the1sel4es: this is calle6 self8 pollination3 The pollen grain ger1inates an6 pro6uces a pollen tube0 which grows 6own through the tissue of the st2le to the o4ar20 where the fe1ale ga1etoph2te is locate63 The pollen tube releases two sper13 !ne fertili5es the egg nucleus an6 gi4es rise to the 52gote3 The other sper1 nucleus co1bines with two other nuclei in the fe1ale ga1etoph2te an6 pro6uces a triploi6 nucleus0 which 6e4elops into en6osper13 The en6osper1 is the store6 foo6 of the see63 'ecause two sper1 nuclei are in4ol4e60 each fertili5ing 6ifferent cells0 this is often calle6 double fertilization3 'oth the e1br2o an6 the en6osper1 grow0 an6 a see6 coat 6e4elops aroun6 the1 to pro6uce the 1ature see63 The wall of the o4ar2 6e4elops into a speciali5e6 see68containing structure known as a fruit ;figure ??3?G<3

ANGIOSPERMS' POLLINATION STRATEGIES $lants use se4eral strategies to ensure pollination3 Most plants that ha4e inconspicuous flowers are win6 pollinate63 The2 pro6uce large nu1bers of flowers an6 huge a1ounts of pollen3 This is necessar2 because the 6istribution of pollen b2 win6 is a ran6o1 process3 '2 pro6ucing large a1ounts of pollen0 the plant increases the chances that pollen will be transferre6 successfull23 &rasses0 se6ges0 an6 so1e other herbaceous plants are win6 pollinate63 Man2 trees0 such as aspens0 birches0 an6 oaks0 are also win6 pollinate63 It is the pollen fro1 win68pollinate6 plants that is responsible for Jha2 fe4er0K an allergic reaction to the presence of air borne pollen3 Most tree

species pro6uce pollen in the spring0 so people who ha4e ha2 fe4er s21pto1s in the spring are usuall2 reacting to the pollen of certain trees3 &rasses an6 other herbaceous plants t2picall2 pro6uce their pollen in late su11er or fall3 %agwee6 is a co11on plant that pro6uces pollen late in the growing season3 $lants with large0 show2 flowers are t2picall2 pollinate6 b2 ani1als3 Although 1an2 show2 flowers are pollinate6 b2 insects0 such as bees0 others are constructe6 to be pollinate6 b2 bir6s or s1all 1a11als3 The ani1als fee6 on the nectar pro6uce6 b2 the flower: in the process0 the2 are 6uste6 with pollen an6 carr2 it to another flower of the sa1e species3 Man2 flowers pro6uce o6ors to help the ani1als fin6 the plants3 This is a 1utualistic relationship between the flowers0 which are pollinate60 an6 the ani1als0 which recei4e foo6 in the for1 of nectar or pollen ;figure ??3?A<3

ANGIOSPERMS' FRUIT 'ecause plants cannot 1o4e0 the2 1ust ha4e a 1etho6 of 6ispersing their see6s to new locations3 Most fruits are in4ol4e6 in the 6ispersal of plants3 So1e fruits.for e7a1ple0 apples0 water1elon0 to1atoes0 an6 raspberries .contain large a1ounts of nutritious 1aterials3 The nutrients are not for the plant=s use but0 rather0 attract ani1als that eat the see6s along with the fruit3 The see6s pass through the ani1als= 6igesti4e tract unhar1e60

6ispersing the plant=s offspring3 !ther fruits.such as cottonwoo6s0 1ilkwee6s0 an6 6an6elions.release fluff2 see6s0 which are carrie6 b2 the win63 Man2 trees.such as 1aples an6 ashes.pro6uce fruits with wings0 which ai6 their 6ispersal b2 win63 The fruits of so1e plants ha4e hooks or stick2 surfaces0 which beco1e attache6 to the fur or feathers of passing ani1als3 #igure ??3?? shows se4eral kin6s of fruits3

ANGIOSPERMS' ANGIOSPERM %IVERSIT& #lowering plants are the 1ost 6i4erse group of plants0 with about ?FG0GGG species3 'otanists classif2 angiosper1s into two groups* dicots or monocots3 The na1es dicot an6 monocot refer to structures in the see6s of these plants calle6 cot2le6ons3 )ot(le#ons0 also known as see6 lea4es0 are e1br2onic lea4es that ha4e foo6 store6 in the13 The2 are the first lea4es that e1erge when a see6 ger1inates3 A !ono"ot has one cot2le6on0 an6 a #i"ot has two cot2le6ons ;figure ??3?@<3 A peanut is a 6icot0 as are li1a beans an6 apples3 &rasses0 lilies0 pal1s0 an6 orchi6s are 1onocots3 #igure ??3?B lists

the 6ifferences between 1onocots an6 6icots3 E4en with this separation into 1onocots an6 6icots0 the 6i4ersit2 is staggering3 Although so1e 1onocots are woo62 species0 such as 2uccas an6 pal1s0 1ost 1onocots are herbaceous3 Man2 of these plants grow fro1 un6ergroun6 structures0 in which the2 store foo63 Man2 i1portant foo6 plants are 1onocots0 inclu6ing wheat0 rice0 corn0 2a1s0 onions0 an6 bananas3 ;How Science Works ??3A< +o11on herbaceous 6icots0 such as 1ints0 carrots0 cabbages0 1ustar6s0 to1atoes0 potatoes0 an6 peppers0 are i1portant foo6 plants3 About half of the 6icots are woo62 trees an6 shrubs0 such as aspen trees an6 sagebrush3 These plants a66 la2ers of new 72le1 an6 phloe1 each 2ear0 as the ste1 an6 root of the plant get larger in 6ia1eter3 The phloe1 is in the outer1ost part of the ste1 calle6 the bark3 (icot trees an6 shrubs generall2 pro6uce broa60 flat lea4es3 In col6er parts of the worl60 1ost woo62 6icots lose all their lea4es 6uring the fall3 Such trees are sai6 to be #e"i#+o+s ;figure ??3?C<3 Howe4er0 there are e7ceptions3 So1e are non6#e"i#+o+s0 keeping their lea4es an6 sta2ing green throughout the winter.for e7a1ple0 A1erican holl2 ;(le" opaca<3 In tropical an6 se1itropical regions0 1an2 of these trees she6 lea4es one at a ti1e0 so the2 retain their lea4es throughout the 2ear3 In areas that ha4e pronounce6 changes in rainfall0 1an2 trees an6 shrubs lose their lea4es 6uring the 6r2 part of the 2ear3

THE GROWTH OF WOO%& PLANTS All g21nosper1s an6 a large proportion of the 6icots are woo62 plants3 Although these two groups of plants ha4e 6ifferent e4olutionar2 histories0 the2 share the abilit2 to grow continuousl2 for 1an2 2ears3 The trees get taller an6 larger in 6ia1eter each 2ear3 'oth the ste1s an6 the roots grow fro1 their tips an6 a66 to their length3 In a66ition0 the2 increase in 6ia1eter b2 a66ing new 72le1 an6 phloe1 to the outsi6e of the ste13 As a tree beco1es larger0 the strengthening tissue in the ste1 beco1es 1ore an6 1ore i1portant3 A la2er of cells in the ste10 calle6 the vas"+lar "a!bi+!0 is responsible for this increase in 6ia1eter3 The 4ascular ca1biu1 is between the 72le1 an6 the phloe13 L2le1 tissue is the inner1ost part of the tree trunk or li1b0 an6 phloe1 is outsi6e3 The bark of

the tree0 containing the phloe10 is i1portant in protecting the un6erl2ing tissues3 +a1biu1 cells go through a 1itotic cell 6i4ision0 an6 two cells for13 !ne cell re1ains ca1biu1 tissue0 an6 the other speciali5es to for1 4ascular tissue3 If the cell is on the insi6e of the ca1biu1 ring0 it beco1es 72le1: if it is on the outsi6e of the ca1biu1 ring0 it beco1es phloe13 As ca1biu1 cells 6i4i6e again an6 again0 one cell alwa2s re1ains ca1biu10 an6 the other beco1es 4ascular tissue3 Thus0 the tree constantl2 increases in 6ia1eter ;figure ??3?F<3 The accu1ulation of the 72le1 in the trunk of g21nosper1s an6 woo62 angiosper1s is calle6 5oo#3 Woo6 is one of the 1ost 4aluable biological resources of the worl63 We get lu1ber0 paper pro6ucts0 turpentine0 an6 1an2 other 4aluable 1aterials fro1 the woo6 of g21nosper1s an6 angiosper1s3 As 2ou can see fro1 this 6iscussion0 both angiosper1s an6 g21nosper1s ha4e 1e1bers that are woo623 Therefore the ter1 woody cuts across ta7ono1ic lines3

TROPISMS A tro*is! is a growth 1o4e1ent towar6 or awa2 fro1 a sti1ulus3 #or e7a1ple0 plants orient the1sel4es towar6 light3 This is known as phototropism3 The 4alue of this response is ob4ious0 because plants nee6

light to sur4i4e3 The 1echanis1 that allows this response in4ol4es a hor1one known as au7in3 The growing tip of the ste1 pro6uces au7in0 which is transporte6 6own the ste1s3 Au7in sti1ulates cells to 6i4i6e0 grow0 an6 elongate3 If the growing tip of a plant recei4es 1ore light on one si6e0 the sha6e6 si6e pro6uces 1ore au7in than 6oes the lighte6 si6e3 The larger a1ount of au7in on the sha6e6 si6e causes greater growth in that area0 an6 the tip of the ste1 ben6s towar6 the light3 When all the si6es of the ste1 are e>uall2 illu1inate60 the ste1 grows e>uall2 on all si6es an6 grows straight3 House plants near a win6ow 1ust be turne6 regularl20 or the2 will grow 1ore on one si6e than the other ;figure ??3?E<3 Man2 kin6s of cli1bing 4ines are able to wrap stringlike tendrils aroun6 stur62 ob9ects in a 1atter of 1inutes3 This kin6 of growth response is calle6thigmotropism3 As the ten6rils grow0 the2 slowl2 wa4e about3 When the2 encounter an ob9ect0 their tropic response is to wrap aroun6 it an6 anchor the 4ine3 !nce attache60 the ten6rils change into har6 structures that bin6 the 4ine to its attach1ent3 Sweet peas0 grape4ines0 an6 i42 attach in this 1anner3 I42 can cause great 6a1age as it grows0 an6 its ten6rils loosen si6ing an6 ser4e as a ha4en for the growth of other 6estructi4e organis1s ;figure ??3?D<3 $lants also ha4e growth responses to gra4it2 an6 the presence of water3 Ste1s grow up: roots grow 6own an6 towar6 water in the soil3

SEASONAL RESPONSES $lants li4e in a seasonal worl60 an6 the2 respon6 accor6ingl23 $lants that li4e in te1perate regions e7perience changes in te1perature an6 the a1ount of sunlight3 The 6a2s are longest in the su11er an6 shortest in the winter3 $lants are able to 1easure 6a2 length an6 1anufacture hor1ones that cause changes in the growth an6 6e4elop1ent of specific parts of the plant3 So1e plants pro6uce flowers onl2 when the 6a2s are getting longer0 so1e onl2 when the 6a2s are getting shorter0 an6 so1e onl2 after the 6a2s ha4e reache6 a specific length3 In 6eci6uous trees0 the shortening 6a2 length in

the fall triggers a response that causes the tree to pro6uce a wall of waterproof tissue between the lea4es an6 the ste13 'ecause the lea4es no longer recei4e water0 the2 6ie an6 fall to the groun63 !ther plants store foo6 1aterials in un6ergroun6 structures such as bulbs an6 tubers3 The abo4e8groun6 part of the plant 6ies back0 but the un6ergroun6 portion re1ains3 In the spring0 as the soil war1s0 these structures sen6 up new growth3 In both of these cases0 the plant goes into a 6or1ant state3 A portion of the plant is still ali4e0 but it is not acti4el2 photos2nthesi5ing3 Man2 parts of the worl6 e7perience seasonal rainfall3 %ain is abun6ant for se4eral 1onths an6 totall2 absent 6uring others3 $lants= responses to these con6itions are si1ilar to those of plants that respon6 to seasonal changes in te1perature3 (uring the 6r2 season0 the lea4es fall fro1 trees an6 1an2 s1aller plants beco1e 6or1ant3 When it rains0 the plants respon6 b2 growing0 flowering0 an6 fruiting3 RESPONSES TO IN1UR& $lants are attacke6 b2 a 4ariet2 of 6isease8causing organis1s an6 b2 plant8 eating herbi4ores3 $lants respon6 to 6isease in 1uch the sa1e wa2 as ani1als 6o3 When infecte6 with a 6isease organis10 the2 ha4e an innate abilit2 to fight the infection3 $lants also repair woun6s b2 growing a for1 of scar tissue o4er the woun6e6 area3 Attack b2 herbi4ores is han6le6 in a 6ifferent wa23 Man2 plants pro6uce to7ic 1aterials0 which interfere with the 1etabolis1 of ani1als that eat plants3 When the lea4es of plants are eaten b2 ani1als0 the new lea4es pro6uce6 to replace those lost often contain higher a1ounts of to7ic 1aterials than the original lea4es3 $lants 1a2 e4en ha4e the abilit2 to co11unicate with one another3 An e7peri1ent carrie6 out in a greenhouse pro6uce6 so1e interesting results3 So1e of the plants ha6 their lea4es 1echanicall2 JeatenK b2 an e7peri1enter0 whereas nearb2 plants were not har1e63 Not onl2 6i6 the cut plants pro6uce new lea4es with 1ore to7ins0 but the new growth on neighboring0 non1utilate6 plants ha6 increase6 to7in le4els as well3 This raises the possibilit2 that plants co11unicate in so1e wa20 perhaps b2 the release of 1olecules that cause changes in the recei4ing plant3 Man2 of the to7ic che1icals pro6uce6 b2 plants ha4e been use6 as

1e6ications3 Muinine has been use6 to fight 1alaria3 (igitalis is use6 to strengthen heartbeat3 Ta7ol is an anticancer 6rug3 THE )OEVOLUTION OF PLANTS AN% ANIMALS The first terrestrial organis1s were plants3 Shortl2 after the plants beca1e establishe6 on lan60 ani1als0 such as insects an6 a1phibians0 arri4e63 Thus0 terrestrial plants an6 ani1als ha4e a long histor2 of interaction0 which has ha6 an influence on the e4olution of each group3 There are 1an2 e7a1ples of their coe4olution3 Most flowering plants are pollinate6 b2 insects or other ani1als3 Insect8 pollinate6 plants pro6uce flowers that are show20 ha4e nectar0 an6 pro6uce o6ors3 Man2 flowers that are pollinate6 b2 bir6s are re6 an6 pro6uce 1uch nectar3 So1e flowers bloo1 onl2 at night an6 are pollinate6 b2 1oths or bats3 &rasses an6 gra5ers ha4e coe4ol4e63 &rasses ha4e silica in their cell walls3 This is a 4er2 har6 1aterial0 an6 it ten6s to wear 6own the teeth of gra5ers3 Most gra5ing ani1als ha4e 4er2 long teeth0 which can acco11o6ate a lifeti1e of wear3 &rasses also 6iffer fro1 1ost other plants in that their lea4es an6 ste1s grow fro1 the base of the plant rather than fro1 the tip3 Thus0 the2 can withstan6 regularl2 ha4ing the tips of their lea4es chewe6 off3 Man2 kin6s of flowering plants pro6uce large0 nutritious fruits0 which ani1als use for foo60 in the process 6istributing the see6s3 There are e4en see6s that will not ger1inate unless the2 ha4e passe6 through the gut of an ani1al3 'ir6s eat s1all fruits an6 their see6s0 which are 6isperse6 when the bir6s 6efecate3 In tropical forests0 1an2 trees ha4e 4er2 large fruits0 which are eaten b2 1onke2s3 The2 eat the flesh2 part of the fruit an6 6rop the see6s3 'rowsers are ani1als that eat the lea4es an6 s1all twigs of woo62 plants3 Man2 kin6s of woo62 plants ha4e thorns0 1aking this task 1ore 6ifficult0 but browsers ha4e techni>ues or structures that allow the1 to put up with the prickl2 6eterrents3 $lants pro6uce a 4ariet2 of che1icals3 So1e of these che1icals are to7ic or irritating an6 6eter certain ani1als fro1 eating portions of the plant3 !thers che1icals pro6uce o6ors that help ani1als locate flowers or fruits3 These attracti4e o6ors ai6 the plant b2 assuring that pollination an6 see6

6ispersal will take place3 Hu1ans use 1an2 of these plants an6 the che1icals the2 pro6uce as spices an6 fla4orings3

Cell Structure and Function

By Enger, E.D., Ross, F.C., Bailey, D.B. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

THE (E EL!$MENT !# THE +ELL THE!%)* S!ME HIST!%) $%!,A%)!TI+ AN( E",A%)!TI+ +ELLS +ELL SI-E THE ST%"+T"%E !# +ELL"LA% MEM'%ANES $LASMA MEM'%ANE EN(!$LASMI+ %ETI+"L"M &!L&I A$$A%AT"S L)S!S!MES $E%!LIS!MES A+"!LES AN( ESI+LES

N"+LEA% MEM'%ANE THE EN(!MEM'%ANE S)STEM. INTE%+!N E%SI!N !# MEM'%ANES ENE%&) +!N E%TE%S.MIT!+H!N(%IA AN( +HL!%!$LASTS %I'!S!MES MI+%!T"'"LES0 MI+%!#ILAMENTS0 AN( INTE%ME(IATE #ILAMENTS +ENT%I!LES +ILIA AN( #LA&ELLA IN+L"SI!NS N"+LEA% +!M$!NENTS (I##"SI!N !SM!SIS +!NT%!LLE( METH!(S !# T%ANS$!%TIN& M!LE+"LES $%!,A%)!TI+ +ELL ST%"+T"%E E",A%)!TI+ +ELL ST%"+T"%E

THE %EVELOPMENT OF THE )ELL THEOR&' SOME HISTOR& The first person to use the ter1 cell was %obert Hooke ;AF@CNAEG@< of Englan63 He use6 a si1ple kin6 of 1icroscope to stu62 thin slices of cork fro1 the bark of a cork oak tree3 He saw 1an2 cubicles fitting neatl2 together0 which re1in6e6 hi1 of the barren roo1s ;cells< in a 1onaster2 ;figure B3A<3 He use6 the ter1 cell when he 6escribe6 his obser4ations in AFFF in the publication )icrographia3 The tin2 bo7es Hooke saw were0 in fact0 onl2 the cell walls that surroun6e6 the once li4ing portions of plant cells3 We now know that the cell wall of a plant cell is pro6uce6 on the outsi6e of the cell an6 is co1pose6 of the co1ple7 carboh26rate calle6 cellulose3 It pro4i6es strength an6 protection to the li4ing contents of the cell3 Although the cell wall appears to be a rigi60 soli6 la2er of 1aterial0 it is actuall2 co1pose6 of 1an2 interwo4en stran6s of cellulose 1olecules3 Thus0 1ost kin6s of 1olecules pass easil2 through it3 Anton 4an Leeuwenhoek ;AF@?NAE?@<0 a (utch 1erchant who sol6 cloth0 was one of the first in6i4i6uals to carefull2 stu62 1agnifie6 cells3 He apparentl2 saw a cop2 of Hooke=s )icrographia an6 began to 1ake his own 1icroscopes0 so that he coul6 stu62 biological speci1ens3 He was intereste6 in 1agnif2ing glasses0 because 1agnifiers were use6 to count the nu1ber of threa6s in cloth3 He use6 a 4er2 si1ple kin6 of 1icroscope that ha6 onl2 one lens3 'asicall20 it was a 4er2 powerful 1agnif2ing glass ;figure B3?<3 What 1a6e his 1icroscope better than others of the ti1e was his abilit2 to grin6 4er2 high8>ualit2 lenses3 He use6 his skill at lens grin6ing to 1ake about BGG lenses 6uring his lifeti1e3 !ne of his lenses was able to 1agnif2 ?EG ti1es3

He use6 his keen e2esight an6 lens81aking skills to pursue his intense curiosit2 about tin2 li4ing things3 He 1a6e thousan6s of obser4ations of 1an2 kin6s of 1icroscopic ob9ects3 He also 1a6e 4er2 6etaile6 sketches of the things he 4iewe6 with his si1ple 1icroscopes an6 co11unicate6 his fin6ings to %obert Hooke an6 the %o2al Societ2 of Lon6on3 His work sti1ulate6 further in4estigation of 1agnification techni>ues an6 6escriptions of cell structures3 When 4an Leeuwenhoek 6isco4ere6 that he coul6 see things 1o4ing in pon6 water using his 1icroscope0 his curiosit2 sti1ulate6 hi1 to look at a 4ariet2 of other things3 He stu6ie6 1an2 things such as bloo60 se1en0 feces0 pepper0 an6 tartar0 for e7a1ple3 He was the first to see in6i4i6ual cells an6 recogni5e the1 as li4ing units0 but he 6i6 not call the1 cells3 The na1e he ga4e to the Jlittle ani1alsK he saw 1o4ing aroun6 in the pon6 water was animalcules3 Although Hooke0 4an Leeuwenhoek0 an6 others continue6 to 1ake obser4ations0 nearl2 ?GG 2ears passe6 before it was generall2 recogni5e6 that all li4ing things are 1a6e of cells an6 that these cells can repro6uce the1sel4es3 In AD@D0 Mathias /akob Schlei6en of &er1an2 state6 that all plants are 1a6e up of s1aller cellular units3 In AD@H0 Theo6or Schwann0 another &er1an0 publishe6 the i6ea that all ani1als are co1pose6 of cells3 Soon after the ter1 cell caught on0 it was recogni5e6 that the cell wall of plant cells was essentiall2 lifeless an6 that it was reall2 the contents of the cell that ha6 Jlife3K This li4ing 1aterial was ter1e6 protoplasm0 which 1eans first*formed substance3 Scientists use6 the ter1 protoplas1 to 6istinguish between the li4ing portion of the cell an6 the nonli4ing cell wall3 As better 1icroscopes were 6e4elope60 people began to 6istinguish two 6ifferent regions of protoplas13 !ne region0 calle6 the nucleus0 appeare6 as a central bo62 within a 1ore flui6 1aterial surroun6ing it3 To6a20 we know the nucleus is the part of a cell that contains the genetic infor1ation3 +2toplas1 was the na1e gi4en to the flui6 portion of the protoplas1 surroun6ing the nucleus3 Although the ter1protoplasm is sel6o1 use6 to6a20 the ter1 cytoplasm is still co11onl2 use63 The 6e4elop1ent of special staining techni>ues0 better light 1icroscopes0 an6 ulti1atel2 powerful electron 1icroscopes re4eale6 that the c2toplas1 contains 1an2 structures0 calle6 organelles ;little organs+ ;figure B3@<3 #urther research has shown that each kin6 of organelle has certain functions relate6 to its structure3

PRO-AR&OTI) AN% EU-AR&OTI) )ELLS

All li4ing things are cells or co1pose6 of cells0 which ha4e an outer 1e1brane0 c2toplas10 an6 genetic 1aterial3 In a66ition0 the cells of so1e organis1s ha4e a cell wall surroun6ing these 1aterials3 To6a20 biologists recogni5e two 4er2 6ifferent kin6s of cells3 The 6ifferences are foun6 in the 6etails of their structure3 Prokar(oti" "ells are structurall2 si1ple cells that lack a nucleus an6 1ost other cellular organelles3 The fossil recor6 shows that prokar2otic cells were the first kin6 of cells to 6e4elop about @3C billion 2ears ago3 To6a20 we recogni5e that the organis1s co11onl2 calle6 bacteria are prokar2otic cells3 E+kar(oti" "ells are 1uch 1ore structurall2 co1ple7 cells that ha4e a nucleus an6 1an2 kin6s of organelles3 The2 are also t2picall2 1uch larger than prokar2otic cells3 The first eukar2otic cells show up in the fossil recor6 about A3D billion 2ears ago3 The cells of plants0 ani1als0 fungi0 proto5oa0 an6 algae are eukar2otic ;figure B3B<3

)ELL SI/E +ells of 6ifferent kin6s 4ar2 greatl2 in si5e ;figure B3C<3 In general0 the cells of prokar2otic organis1s are 1uch s1aller than those of eukar2otic organis1s3 $rokar2otic cells are t2picall2 AN? 1icro1eters in 6ia1eter0 whereas

eukar2otic cells are t2picall2 AGNAGG ti1es larger3 So1e basic ph2sical principles 6eter1ine how large a cell can be3 A cell 1ust transport all of its nutrients an6 all of its wastes through its outer 1e1brane to sta2 ali4e3 +ells are li1ite6 in si5e because0 as a cell beco1es larger0 a6e>uate transport of 1aterials through the 1e1brane beco1es 1ore 6ifficult3 The 6ifficult2 arises because0 as the si5e of a cell increases0 the a1ount of li4ing 1aterial ;the cell=s 4olu1e< increases 1ore >uickl2 than the si5e of the outer 1e1brane ;the cell=s surface area<3 As cells grow0 the a1ount of surface area increases b2 the s>uare ;L?< but 4olu1e increases b2 the cube ;L@<3 This 1athe1atical relationship between the surface area an6 4olu1e is calle6 thesurface area*to*'olume ratio an6 is shown for a cube in figure B3F3 Notice that0 as the cell beco1es larger0 both surface area an6 4olu1e increase3 Most i1portant0 4olu1e increases more >uickl2 than surface area0 causing the surface area8to84olu1e ratio to 6ecrease3 As the cell=s 4olu1e increases0 the cell=s 1etabolic re>uire1ents increase but its abilit2 to satisf2 those re>uire1ents are li1ite6 b2 the surface area through which the nee6e6 1aterials 1ust pass3 +onse>uentl20 1ost cells are 4er2 s1all3 There are a few e7ceptions to this general rule0 but the2 are easil2 e7plaine63 #or e7a1ple0 what we call the 2olk of a chicken=s egg cell is a single cell3 Howe4er0 the onl2 part of an egg cell that is 1etabolicall2 acti4e is a s1all spot on its surface3 The largest portion of the egg cell is si1pl2 inacti4e store6 foo6 calle6 yolk3 Si1ilarl20 so1e plant cells are 4er2 large but consist of a large0 centrall2 locate6 region fille6 with water3 Again0 the 1etabolicall2 acti4e portion of the cell is at the surface0 where e7change of 1aterials with the surroun6ings is possible3

THE STRU)TURE OF )ELLULAR MEM$RANES !ne feature co11on to all cells is the presence of "ell+lar !e!branes0 thin sheets co1pose6 pri1aril2 of phospholipi6s an6 proteins3 The current 1o6el of how cellular 1e1branes are constructe6 is known as the fluid* mosaic model3 The 4l+i#6!osai" !o#el0 consi6ers cellular 1e1branes to consist of two la2ers of phospholipi6 1olecules an6 that the in6i4i6ual phospholipi6 1olecules are able to 1o4e about within the structure of the 1e1brane ;How Science Works B3A<3 Man2 kin6s of proteins an6 so1e other 1olecules are foun6 a1ong the phospholipi6 1olecules within the 1e1brane an6 on the 1e1brane surface3 The in6i4i6ual 1olecules of the 1e1brane re1ain associate6 with one another because of the ph2sical interaction of its 1olecules with its surroun6ings3 The phospholipi6 1olecules of the 1e1brane ha4e two en6s0 which 6iffer che1icall23 !ne en60 which contains phosphate0 is soluble in water an6 is therefore calle6 (#ro* ili" ;hydro O water: phile O lo4ing<3 The other en6 of the phospholipi6 1olecule consists of fatt2 aci6s0 which are not soluble in water0 an6 is calle6 (#ro* obi" ;phobia O fear<3 In 6iagra1s0 phospholipi6 1olecules are co11onl2 represente6 as a balloon with two strings ;figure B3E<3 The balloon represents the water8soluble phosphate portion of the 1olecule an6 the two strings represent the ? fatt2

aci6s3 +onse>uentl20 when phospholipi6 1olecules are place6 in water0 the2 for1 a 6ouble8la2ere6 sheet0 with the watersoluble ;h26rophilic< portions of the 1olecules facing awa2 fro1 each other3 This is co11onl2 referre6 to as aphospholipid bilayer ;figure B3D<3 If phospholipi6 1olecules are shaken in a glass of water0 the 1olecules auto1aticall2 for1 6ouble8la2ere6 1e1branes3 It is i1portant to un6erstan6 that the 1e1branes for1e6 are not rigi6 but0 rather0 rese1ble a hea42 oli4e oil in consistenc23 The co1ponent phospholipi6 1olecules are in constant 1otion as the2 1o4e with the surroun6ing water 1olecules an6 sli6e past one another3 !ther 1olecules foun6 in cell 1e1branes are cholesterol0 proteins0 an6 carboh26rates3 'ecause cholesterol is not water8soluble0 it is foun6 in the 1i66le of the 1e1brane0 in the h26rophobic region3 It appears to pla2 a role in stabili5ing the 1e1brane an6 keeping it fle7ible3 There are 1an2 6ifferent proteins associate6 with the 1e1brane3 So1e are foun6 on the surface0 so1e are partiall2 sub1erge6 in the 1e1brane0 an6 others tra4erse the 1e1brane an6 protru6e fro1 both surfaces3 These proteins ser4e a 4ariet2 of functions0 inclu6ing helping transport 1olecules across the 1e1brane0 ser4ing as attach1ent points for other 1olecules0 an6 ser4ing as i6entit2 tags for cells3 +arboh26rates are t2picall2 attache6 to the 1e1branes on the outsi6e of cells3 The2 appear to pla2 a role in cell8to8cell interactions an6 are in4ol4e6 in bin6ing with regulator2 1olecules3

PLASMA MEM$RANE The outer li1iting boun6ar2 of both prokar2otic an6 eukar2otic cells is known as the *las!a !e!brane0 or "ell !e!brane3 It is co1pose6 of a phospholipi6 bila2er an6 ser4es as a barrier between the cell contents an6 the e7ternal en4iron1ent3 Howe4er0 it is not 9ust a ph2sical barrier3 It has 1an2 6ifferent functions3 In 1an2 wa2s0 it functions in a 1anner analogous to a bor6er between countries0 which 6eli1its countries but also allows for so1e restricte6 1o4e1ent across the bor6er3 The plas1a 1e1brane has se4eral i1portant features3 Metaboli" A"tivities 'ecause the plas1a 1e1brane is part of a li4ing unit0 it is 1etabolicall2 acti4e3 Man2 i1portant che1ical reactions take place within the 1e1brane

or on its insi6e or outsi6e surface3 Man2 of these che1ical reactions in4ol4e transport of 1olecules3 Move!ent o4 Mole"+les A"ross t e Me!brane 'ecause cells 1ust continuousl2 recei4e nutrients an6 ri6 the1sel4es of waste pro6ucts0 there is a constant traffic of 1olecules across the 1e1brane3 See section B3E for a 6etaile6 6iscussion of the 1an2 wa2s b2 which 1olecules enter an6 lea4e cells3 Man2 of the proteins that are associate6 with the plas1a 1e1brane are in4ol4e6 in 1o4ing 1olecules across the 1e1brane3 So1e proteins are capable of 1o4ing fro1 one si6e of the plas1a 1e1brane to the other an6 shuttle certain 1olecules across the 1e1brane3 !thers e7ten6 fro1 one si6e of the 1e1brane to the other an6 for1 channels through which substances can tra4el3 So1e of these channels operate like bor6er checkpoints0 which open an6 close when circu1stances 6ictate3 So1e 1olecules pass through the 1e1brane passi4el20 whereas others are assiste6 b2 1etabolic acti4ities within the 1e1brane3 Insi#e an# O+tsi#e The insi6e of the plas1a 1e1brane is 6ifferent fro1 its outsi6e3 The presence of specific proteins or carboh26rates is i1portant in establishing this 6ifference3 The carboh26rates that are associate6 with the plas1a 1e1brane are usuall2 foun6 on the outsi6e of the 1e1brane0 where the2 are boun6 to proteins or lipi6s3 Man2 i1portant acti4ities take place on onl2 one of the surfaces of the plas1a 1e1brane because of the wa2 the two si6es 6iffer3 I#enti4i"ation The outsi6e surface of the plas1a 1e1brane has 1an2 proteins0 which act as recognition 1olecules3 Each organis1 has a uni>ue co1bination of these 1olecules3 Thus0 the presence of these 1olecules enables one cell or one organis1 to recogni5e cells that are like it an6 those that are 6ifferent3 #or e7a1ple0 if a 6isease organis1 enters 2our bo620 the cells of 2our i11une s2ste1 use the proteins on the in4a6er=s surface to i6entif2 it as being foreign3 I11une s2ste1 cells can then 6estro2 the in4a6er3 In hu1ans0 there is a group of such protein 1olecules0 collecti4el2 known ashistocompatibility antigens ;histo O tissue<3 Each person has a specific co1bination of these proteins3 It is the presence of these antigens that is responsible for the re9ection of transplante6 tissues or organs fro1 6onors that are Jinco1patible3K In large part0 a person=s pattern of

histoco1patibilit2 antigens is here6itar2: for instance0 in i6entical twins0 the cells of both in6i4i6uals ha4e 4er2 si1ilar proteins3 Therefore0 in transplant situations0 the cells of the i11une s2ste1 woul6 see the cells of the 6onor twin to be the sa1e as those on the cell surfaces of the recipient twin3 When closel2 relate6 6onors are not a4ailable0 ph2sicians tr2 to fin6 6onors whose histoco1patabilit2 antigens are as si1ilar as possible to those of recipients3 Atta" !ent Sites So1e 1olecules on the outsi6e surface of the plas1a 1e1brane ser4e as attach1ent sites for specific che1icals0 bacteria0 proto5oa0 white bloo6 cells0 an6 4iruses3 Man2 6angerous agents cannot stick to the surface of cells an6 therefore 6o not cause har13 #or this reason0 cell biologists e7plore the e7act structure an6 function of these cell surface 1olecules3 The2 are also atte1pting to i6entif2 1olecules that can interfere with the bin6ing of 4iruses an6 bacteria to cells in the hope of controlling infections3 #or e7a1ple0 hu1an i11uno6eficienc2 4irus ;HI < attaches to specific 1olecules on the surface of certain i11une s2ste1 cells an6 ner4e cells3 If these attach1ent sites coul6 be 1aske60 the 4irus woul6 not be able to attach to the cells an6 cause 6isease3 (rugs that function this wa2 are calle6 Jblockers3K Si,nal Trans#+"tion Another wa2 in which attach1ent sites are i1portant is in signal trans6uction3Si,nal trans#+"tion is the process b2 which cells 6etect specific signals an6 trans1it these signals to the cell=s interior3 These signals can be ph2sical ;electrical or heat< or che1ical3 So1e che1icals are capable of passing 6irectl2 through the 1e1brane of specific target cells3 !nce insi6e0 the2 can pass on their 1essage to regulator proteins3 These proteins then enter into che1ical reactions0 which result in a change in the cell=s beha4ior3 #or e7a1ple0 estrogen pro6uce6 in one part of the bo62 tra4els through the bloo6strea1 an6 passes through the tissue to 1ake 6irect contact with specific target cells3 !nce the hor1one passes through the plas1a 1e1brane of the target cells0 the 1essage is co11unicate6 to begin the process of fe1ale se7 organ 6e4elop1ent3 This is like a person s1elling the cologne of his or her 6ate through a curtain3 The aro1a 1olecules pass through the curtain to the person=s nose an6 sti1ulate a response3 Howe4er0 1ost signal 1olecules are not capable of entering cells in such a 6irect 1anner3 Most signal 1olecules re1ain outsi6e their target

cells3 When the2 arri4e at the cell0 the2 attach to a receptor site 1olecule e1be66e6 in the 1e1brane3 The signal 1olecule is often calle6 the primary messenger3 The receptor.signal 1olecule co1bination initiates a se>uence of e4ents within the 1e1brane that trans1its infor1ation through the 1e1brane to the interior0 generating internal signal 1olecules0 calle6 secondary messengers3 In 1an2 other cases0 the receptor 1olecule is a protein that spans the cell 1e1brane3 This protein is capable of bin6ing the signal 1olecule outsi6e of the cell an6 then generates a secon6ar2 1essenger insi6e the cell3 The secon6ar2 1essengers are 1olecules or ions that begin a casca6e of che1ical reactions that causes the target cell to change how it functions3 This is like 2our 1other sen6ing 2our little brother to tell 2ou it is ti1e for 6inner3 )our 1other pro4i6es the pri1ar2 1essage0 2our little brother pro4i6es the secon6ar2 1essage0 an6 2ou respon6 b2 going to the 6inner table3 In a cell0 such signal trans6uction results in a change in the cell=s che1ical acti4it23 !ften0 this is acco1plishe6 b2 turning genes on or off3 #or e7a1ple0 when a signal 1olecule calle6 epidermal growth factor ;E&#< attaches to the receptor protein of skin cells0 it triggers a chain of e4ents insi6e the plas1a 1e1brane of the cells3 These changes within the plas1a 1e1brane pro6uce secon6ar2 1essengers0 ulti1atel2 lea6ing to gene action0 which in turn causes cell growth an6 6i4ision3 EN%OPLASMI) RETI)ULUM There are 1an2 other organelles in a66ition to the plas1a 1e1brane0 that are co1pose6 of 1e1branes3 Each of these 1e1branous organelles has a uni>ue shape or structure associate6 with its particular functions ;figure B3H<3 !ne of the 1ost co11on organelles foun6 in cells0 the en#o*las!i" reti"+l+!;ER<0 consists of fol6e6 1e1branes an6 tubes throughout the cell3 This s2ste1 of 1e1branes pro4i6es a large surface on which che1ical acti4ities take place3 'ecause the E% has an enor1ous surface area0 1an2 che1ical reactions can be carrie6 out in an e7tre1el2 s1all space3 $icture the 4ast surface area of a piece of newspaper cru1ple6 into a tight little ball3 The surface contains hun6re6s of thousan6s of ti6bits of infor1ation in an or6erl2 arrange1ent0 2et it is packe6 into a 4er2 s1all 4olu1e3 $roteins on the surface of the E% are acti4el2 in4ol4e6 in controlling an6 encouraging che1ical acti4ities.whether the2 are reactions in4ol4ing cell growth an6 6e4elop1ent or reactions resulting in the accu1ulation of

1olecules fro1 the en4iron1ent3 The arrange1ent of the proteins allows the1 to control the se>uences of 1etabolic acti4ities0 so that che1ical reactions can be carrie6 out 4er2 rapi6l2 an6 accuratel23 !n close e7a1ination with an electron 1icroscope0 it is apparent that there are two t2pes of E%.rough an6 s1ooth3 The rough E% appears rough because it has ribosomes attache6 to its surface3 Riboso!es are non1e1branous organelles that are associate6 with the s2nthesis of proteins fro1 a1ino aci6s3 The2 are Jprotein81anufacturing 1achines3K Therefore0 cells with an e7tensi4e a1ount of rough E%.for e7a1ple0 hu1an pancreas cells.are capable of s2nthesi5ing large >uantities of proteins3 S1ooth E% lacks attache6 riboso1es but is the site of 1an2 other i1portant cellular che1ical acti4ities0 inclu6ing fat 1etabolis1 an6 6eto7ification reactions in4ol4e6 in the 6estruction of to7ic substances0 such as alcohol an6 6rugs3 Hu1an li4er cells are responsible for 6eto7ification reactions an6 contain e7tensi4e s1ooth E%3 In a66ition0 the spaces between the fol6e6 1e1branes ser4e as canals for the 1o4e1ent of 1olecules within the cell3 This s2ste1 of 1e1branes allows for the rapi6 6istribution of 1olecules within a cell3

GOLGI APPARATUS

Another organelle co1pose6 of 1e1brane is the Gol,i a**arat+s3 Ani1al cells contain se4eral such structures an6 plant cells contain hun6re6s3 The t2pical &olgi apparatus consists of C to ?G flattene60 s1ooth0 1e1branous sacs0 which rese1ble a stack of flattene6 balloons ;figure B3AG<3 The &olgi apparatus has se4eral functions3 It 1o6ifies 1olecules shippe6 to it fro1 elsewhere in the cell0 it 1anufactures so1e pol2sacchari6es an6 lipi6s0 an6 it packages 1olecules within sacs3 There is a constant traffic of 1olecules through the &olgi apparatus3 Tin20 1e1branous sacs calle6 'esicles 6eli4er 1olecules to one surface of the &olgi apparatus3 Man2 of these 4esicles are for1e6 b2 the en6oplas1ic reticulu1 an6 contain proteins3 These 4esicles co1bine with the sacs of the &olgi apparatus an6 release their contents into it3 Man2 kin6s of che1ical reactions take place within the &olgi apparatus3 "lti1atel20 new sacs0 containing Jfinishe6 pro6ucts0K are pro6uce6 fro1 the other surface of the &olgi apparatus3 The &olgi apparatus pro6uces 1an2 kin6s of 4esicles3 Each has a 6ifferent function3 So1e are transporte6 within the cell an6 co1bine with other 1e1brane structures0 such as the en6oplas1ic reticulu13 So1e 1igrate to the plas1a 1e1brane an6 co1bine with it3 These 4esicles release 1olecules such as 1ucus0 cellulose0 gl2coproteins0 insulin0 an6 en521es to the outsi6e of the cell3 In plant cells0 cellulosecontaining 4esicles are in4ol4e6 in pro6ucing new cell wall 1aterial3 #inall20 so1e of the 4esicles pro6uce6 b2 the &olgi apparatus contain en521es that can break 6own the 4arious 1olecules of the cell0 causing its 6estruction3 These 4esicles are known as lysosomes3

L&SOSOMES L(soso!es are tin2 4esicles that contain en521es capable of 6igesting carboh26rates0 nucleic aci6s0 proteins0 an6 lipi6s3 'ecause cells are co1pose6 of these 1olecules0 these en521es 1ust be controlle6 in or6er to pre4ent the 6estruction of the cell3 This control is acco1plishe6 4er2 si1pl23 The en521es of l2soso1es function best at a pH of about C3 The 1e1brane0 which is the outer co4ering of the l2soso1e0 transports h26rogen ions into the l2soso1e an6 creates the aci6ic con6itions these en521es nee63 Since the pH of a cell is generall2 about E0 these en521es will not function if release6 into the cell c2toplas13 The functions of l2soso1es are basicall2 6igestion an6 6estruction3 #or e7a1ple0 in 1an2 kin6s of proto5oa0 such as Paramecium an6 !moeba0 foo6 is taken into the cell in the for1 of a 1e1brane8enclose6 foo6 4acuole3 L2soso1es co1bine with foo6 4acuoles an6 break 6own the foo6 particles into s1aller 1olecular units0 which the cell can use3 In a si1ilar fashion0 l2soso1es 6estro2 6isease8causing 1icroorganis1s0 such as bacteria0 4iruses0 an6 fungi3 The 1icroorganis1s beco1e surroun6e6 b2 1e1branes fro1 the en6oplas1ic reticulu13 L2soso1es co1bine with the 1e1branes surroun6ing these in4a6ers an6 6estro2 the13 This kin6 of acti4it2 is co11on in white bloo6 cells that engulf an6 6estro2

6isease8causing organis1s3 L2soso1es are also in4ol4e6 in the break6own of worn8out cell organelles b2 fusing with the1 an6 6estro2ing the1 ;figure B3AA<3

PERO3ISOMES Another organelle that consists of 1an2 kin6s of en521es surroun6e6 b2 a 1e1brane is the pero"isome3 Pero.iso!es were first i6entifie6 b2 the presence of an en521e0 catalase0 that breaks 6own h26rogen pero7i6e ;H?!?<3 $ero7iso1es 6iffer fro1 l2soso1es in that pero7iso1es are not for1e6 b2 the &olgi apparatus an6 the2 contain 6ifferent en521es3 It appears that the 1e1brane surroun6ing pero7iso1es is for1e6 fro1 the en6oplas1ic reticulu1 an6 the en521es are i1porte6 into this sac8like container3 The en521es of pero7iso1es ha4e been shown to be i1portant in 1an2 kin6s of che1ical reactions0 inclu6ing the break6own of longchain fatt2 aci6s to shorter 1olecules0 the s2nthesis of cholesterol an6 the bile aci6s pro6uce6 fro1 cholesterol0 an6 the s2nthesis of specific lipi6 1olecules present in the plas1a 1e1branes of speciali5e6 cells0 such as ner4e cells3

VA)UOLES AN% VESI)LES There are 1an2 kin6s of 1e1braneenclose6 containers in cells known as'acuoles an6 'esicles3 Va"+oles are the larger structures an6 4esicles are the s1aller ones3 The2 are fre>uentl2 6escribe6 b2 their function3 In 1ost plants0 there is one huge0 centrall2 locate60 water8fille6 4acuole3 Man2 kin6s of proto5oa ha4e speciali5e6 water 4acuoles calle6 contractile 'acuoles which are able to forcefull2 e7pel e7cess water that has accu1ulate6 in the c2toplas13 The contractile 4acuole is a necessar2 organelle in cells that li4e ;figure B3A?< in freshwater because water constantl2 6iffuses into the cell3 Ani1al cells t2picall2 ha4e 1an2 s1all 4acuoles an6 4esicles throughout the c2toplas13

NU)LEAR MEM$RANE /ust as a roo1 is a place create6 b2 walls0 a floor0 an6 a ceiling0 a cell=s nucleus is a place create6 b2 the n+"lear !e!brane3 If the nuclear 1e1brane were not for1e6 aroun6 the cell=s genetic 1aterial0 the organelle calle6 the nucleus woul6 not e7ist3 This 1e1brane separates the genetic 1aterial ;(NA< fro1 the c2toplas13 'ecause the2 are separate60 the c2toplas1 an6 the nuclear contents can 1aintain 6ifferent che1ical co1positions3 The nuclear 1e1brane is co1pose6 of two la2ers of 1e1brane3 It has large openings through this 6ouble81e1brane structure0

calle6 nuclear pore comple"es ;figure B3A@<3 The nuclear pore co1ple7es consist of proteins0 which collecti4el2 for1 barrelshape6 pores through the 1e1brane3 These pores allow relati4el2 large 1olecules0 such as %NA0 to pass through the nuclear 1e1brane3 Thousan6s of 1olecules 1o4e in an6 out through these pores each secon63

THE EN%OMEM$RANE S&STEM0 INTER)ONVERSION OF MEM$RANES It is i1portant to re1e1ber that all 1e1branous structures in cells are co1pose6 of two la2ers of phospholipi6 with associate6 proteins an6 other 1olecules3 #urther1ore0 all of these 1e1branous organelles can be con4erte6 fro1 one for1 to another ;figure B3AB<3 #or e7a1ple0 the plas1a 1e1brane is continuous with the en6oplas1ic reticulu1: as a cell beco1es larger0 so1e of the en6oplas1ic reticulu1 1o4es to the surface to beco1e plas1a 1e1brane3 Si1ilarl20 the nuclear 1e1brane is connecte6 to the en6oplas1ic reticulu13 %e1e1ber also that the &olgi apparatus recei4es 1e1brane8enclose6 packages fro1 the en6oplas1ic reticulu1 an6 pro6uces l2soso1es that co1bine with other 1e1brane8enclose6 structures an6 secretor2 4esicles that fuse with the plas1a 1e1brane3 Thus0 this entire set of 1e1brane 1aterial is in a constant state of flu73

ENERG& )ONVERTERS0MITO)HON%RIA AN% )HLOROPLASTS Two other organelles co1pose6 of 1e1branes are mitochondria an6chloroplasts3 'oth t2pes of organelles are associate6 with energ2 con4ersion reactions in the cell3 Mitochon6ria an6 chloroplasts are 6ifferent fro1 other kin6s of 1e1branous structures in four wa2s3 #irst0 their 1e1branes are che1icall2 6ifferent fro1 those of other 1e1branous organelles: secon60 the2 are co1pose6 of 6ouble la2ers of 1e1brane.an

inner an6 an outer 1e1brane: thir60 both of these structures ha4e riboso1es an6 (NA that are si1ilar to those of bacteria: fourth0 these two structures ha4e a certain 6egree of in6epen6ence fro1 the rest of the cell. the2 ha4e a li1ite6 abilit2 to repro6uce the1sel4es but 1ust rel2 on (NA fro1 the cell nucleus for assistance3 It is i1portant to un6erstan6 that cells cannot 1ake 1itochon6ria or chloroplasts b2 the1sel4es3 The (NA of the organelle is necessar2 for their repro6uction3 Mito" on#rion The !ito" on#rion is an organelle that contains the en521es responsible for aerobic cellular respiration3 It consists of an outer 1e1brane an6 an inner fol6e6 1e1brane3 The in6i4i6ual fol6s of the inner 1e1brane are known as"ristae ;figure B3ACa<3 Aerobi" "ell+lar res*iration is the series of en521e8controlle6 reactions in4ol4e6 in the release of energ2 fro1 foo6 1olecules an6 re>uires the participation of o72gen 1olecules3

So1e of the en521es responsible for these reactions are 6issol4e6 in the flui6 insi6e the 1itochon6rion3 !thers are incorporate6 into the structure of the 1e1branes an6 are arrange6 in an or6erl2 se>uence3 The nu1ber of 1itrochon6ria per cell 4aries fro1 less than ten to o4er A0GGG 6epen6ing on the kin6 of cell3 +ells in4ol4e6 in acti4ities that re>uire large a1ounts of energ20 such as 1uscle cells0 contain the 1ost 1itochon6ria3 When properl2 staine60 the2 can be seen with a co1poun6 light 1icroscope3 When cells are functioning aerobicall20 the 1itochon6ria swell with acti4it23 When this acti4it2 6i1inishes0 though0 the2 shrink an6 appear as threa6like structures3 ) loro*last The " loro*last is a 1e1branous saclike organelle responsible for the process of photos2nthesis3 +hloroplasts contain the green pig1ent0 " loro* (ll0 an6 are foun6 in cells of plants an6 other eukar2otic organis1s that carr2 out photos2nthesis3 The cells of so1e organis1s contain one large chloroplast: others contain hun6re6s of s1aller chloroplasts3 P otos(nt esis is a 1etabolic process in which light energ2 is con4erte6 to che1ical bon6 energ23 +he1ical8bon6 energ2 is foun6 in foo6 1olecules3

A stu62 of the ultrastructure.that is0 the structures seen with an electron 1icroscope.of a chloroplast shows that the entire organelle is enclose6 b2 a 1e1brane3 Insi6e are other 1e1branes throughout the chloroplast0 for1ing networks an6 structures of fol6e6 1e1brane3 As shown in figure B3ACb0 in so1e areas0 these 1e1branes are stacke6 up or fol6e6 back on the1sel4es3 +hloroph2ll 1olecules are attache6 to these 1e1branes3 These areas of concentrate6 chloroph2ll are calle6 t (lakoi# 1e1branes an6 are stacke6 up to for1 the ,rana of the chloroplast3 The space between the grana0 which has no chloroph2ll0 is known as the stro!a3

RI$OSOMES

%iboso1es are non1e1branous organelles responsible for the s2nthesis of proteins fro1 a1ino aci6s3 The2 are co1pose6 of %NA an6 protein3 Each riboso1e is co1pose6 of two subunits.a large one an6 a s1all one ;figure B3AF<3 %iboso1es assist in the process of 9oining a1ino aci6s together to for1 proteins3 Man2 riboso1es are attache6 to the en6oplas1ic reticulu13 'ecause E% that has attache6 riboso1es appear rough when 4iewe6 through an electron 1icroscope it is calle6 rough E%3 Areas of rough E% are acti4e sites of protein pro6uction3 Man2 riboso1es are also foun6 floating freel2 in the c2toplas1 where4er proteins are being asse1ble63 +ells that are acti4el2 pro6ucing protein ;e3g30 li4er cells< ha4e great nu1bers of free an6 attache6 riboso1es3

MI)ROTU$ULES2 MI)ROFILAMENTS2 AN% INTERME%IATE FILAMENTS The interior of a cell is not si1pl2 fille6 with li>ui6 c2toplas13 A1ong the 1an2 t2pes of non1e1branous organelles foun6 there are elongate6 protein structures known as !i"rot+b+les2 !i"ro4ila!ents 7a"tin 4ila!ents82an6 inter!e#iate 4ila!ents3 All three t2pes of organelles interconnect an6 so1e are attache6 to the insi6e of the plas1a 1e1brane0 for1ing the"(toskeleton of the cell ;figure B3AE<3 These cellular co1ponents pro4i6e the cell with shape0 support0 an6 the abilit2 to 1o4e3 Think of the c2toskeleton co1ponents as the internal supports an6 cables re>uire6 to construct a circus tent3 The shape of the fle7ible can4as co4er

;i3e30 the plas1a 1e1brane< is 6eter1ine6 b2 the location of internal tent poles ;i3e30 1icrotubules< an6 the tension place6 on the1 b2 attache6 wire or rope cables ;i3e30 inter1e6iate fila1ents an6 1icrofila1ents<3 /ust as in the tent analog20 when one of the 1icrofila1ents or inter1e6iate fila1ents is a69uste60 the shape of the entire cell changes3 #or e7a1ple0 when a cell is place6 on a surface to which it cannot stick0 the internal tensions create6 b2 the c2toskeleton co1ponents can pull together an6 cause the cell to for1 a sphere3 (uring cell 6i4ision0 1icrotubules an6 1icrofila1ents are in4ol4e6 in 1o4ing the chro1oso1es that contain the (NA an6 1aking other a69ust1ents nee6e6 to 1ake two cells fro1 one3 Microfila1ents an6 1icrotubules of the c2toskeleton also transport organelles fro1 place to place within the c2toplas13 In a66ition0 infor1ation can be transporte6 through the c2toskeleton3 En521es attache6 to the c2toskeleton are acti4ate6 when the cell is touche63 So1e of these e4ents e4en affect gene acti4it23

)ENTRIOLES An arrange1ent of two sets of 1icrotubules at right angles to each other 1akes up a structure known as a "entriole3 Each set of 1icrotubules is co1pose6 of nine groups of short 1icrotubules arrange6 in a c2lin6er ;figure B3AD<3 The centrioles of 1an2 cells are locate6 in a region calle6 the centrosome3 The centroso1e is often referre6 to as the 1icrotubule

organi5ing center an6 is usuall2 locate6 close to the nuclear 1e1brane3 (uring cell 6i4ision0 centrioles are responsible for organi5ing 1icrotubules into a co1ple7 of fibers known as the spindle3 The in6i4i6ual 1icrotubules of the spin6le are calle6 spindle fibers3 The spin6le is the structure to which chro1oso1es are attache60 so that the2 can be separate6 properl2 6uring cell 6i4ision3 !ne curious fact about centrioles is that the2 are present in 1ost ani1al cells but not in 1an2 t2pes of plant cells0 although plant cells 6o ha4e a centroso1e3 !ther structures0 calle6 basal bodies0 rese1ble centrioles an6 are locate6 at the base of cilia an6 flagella3

)ILIA AN% FLAGELLA Man2 cells ha4e 1icroscopic0 hairlike structures known as cilia an6 flagella0 pro9ecting fro1 their surfaces ;figure B3AH<3 These structures are co1pose6 of 1icrotubles an6 are co4ere6 b2 plas1a 1e1brane3 In general0 4la,ella are long an6 few in nu1ber an6 1o4e with an un6ulating whiplike 1otion: "ilia are short an6 1ore nu1erous an6 1o4e back an6 forth like oars on a boat3 'oth function to 1o4e the cell through its en4iron1ent or to 1o4e the en4iron1ent past the cell3 'oth cilia an6 flagella are constructe6 of a c2lin6er of nine sets of 1icrotubules si1ilar to those in the centriole0 but the2 ha4e an a66itional two 1icrotubules in the center3 This is often referre6 to as the H P ? arrangement of 1icrotubules3

The cell can control the action of these 1icrotubular structures0 enabling the1 to be 1o4e6 in a 4ariet2 of wa2s3 The proto5oan Paramecium is co4ere6 with thousan6s of cilia0 which 1o4e in a coor6inate60 rh2th1ic wa2 to 1o4e the cell through the water3 A Paramecium can stop when it encounters an obstacle0 re4erse its 6irection0 an6 then 1o4e forwar6 in a new 6irection3 Si1ilarl20 the cilia on the cells that line the hu1an trachea beat in such a wa2 that the2 1o4e 1ucus an6 particles trappe6 in the 1ucus fro1 the lungs3 Man2 single8celle6 algae ha4e flagella that beat in such a wa2 that the cells swi1 towar6 a source of light3 So1e kin6s of prokar2otic cells also ha4e flagella3 Howe4er0 their structure an6 the wa2 the2 function are >uite 6ifferent fro1 those of eukar2otic cells3 IN)LUSIONS In"l+sions are collections of 1aterials that 6o not ha4e as well 6efine6 a structure as the organelles we ha4e 6iscusse6 so far3 The2 1ight be concentrations of store6 1aterials0 such as starch grains0 sulfur0 or oil 6roplets0 or the2 1ight be a collection of 1iscellaneous 1aterials known as ,ran+les3 "nlike organelles0 which are essential to the sur4i4al of a cell0 inclusions are generall2 onl2 te1porar2 sites for the storage of nutrients an6 wastes3 So1e inclusion 1aterials are har1ful to other cells3 #or e7a1ple0 rhubarb leaf cells contain an inclusion co1pose6 of o7alic aci60 an organic aci63 Nee6le8shape6 cr2stals of calciu1 o7alate can cause in9ur2 to the ki6ne2s of an organis1 that eats rhubarb lea4es3 The sour taste of this co1poun6 ai6s in the rhubarb plant=s sur4i4al b2 6iscouraging ani1als fro1 eating it3 Si1ilarl20 certain bacteria store0 in their inclusions0 cr2stals of a substance known to be har1ful to insects3 Spra2ing plants with these bacteria is a biological 1etho6 of controlling the insect pest population while not interfering with the plant or with hu1ans3 In the past0 cell structures such as riboso1es0 1itochon6ria0 an6 chloroplasts were also calle6 granules because their structure an6 function were not clearl2 known3 As scientists learn 1ore about inclusions an6 other uni6entifie6 particles in the cells0 the20 too0 will be na1e6 an6 1ore full2 6escribe63

NU)LEAR )OMPONENTS !ne of the first structures to be i6entifie6 in cells was the nucleus3 If the nucleus is re1o4e6 fro1 a cell or the cell loses its nucleus0 the cell can li4e

onl2 a short ti1e3 #or e7a1ple0 hu1an re6 bloo6 cells begin life in bone 1arrow0 where the2 ha4e nuclei3 'efore the2 are release6 into the bloo6strea1 to carr2 o72gen an6 carbon 6io7i6e0 the2 lose their nuclei3 As a conse>uence0 re6 bloo6 cells are able to function onl2 for about A?G 6a2s before the2 6isintegrate3 The nucleus is surroun6e6 b2 a 6ouble la2er of 1e1brane which has pores3 The nucleus contains (NA3 Since the (NA contains the instructions nee6e6 b2 the cell0 the 1o4e1ent of 1olecules fro1 the nucleus through the pores of the nuclear 1e1brane is i1portant for controlling the acti4ities of the cell3 'ecause (NA has the 6irections for buil6ing the proteins a cell nee6s to function0 it is eas2 to un6erstan6 wh2 a cell lacking a nucleus 6ies3 When nuclear structures were first i6entifie60 it was note6 that certain 62es staine6 so1e parts of the nuclear contents 1ore than others3 The parts that staine6 1ore hea4il2 were calle6 " ro!atin0 which 1eans colore6 1aterial3 To6a20 we know that chro1atin is co1pose6 of long 1olecules of (NA0 along with proteins3 Most of the ti1e0 the chro1atin is arrange6 as a long0 tangle6 1ass of threa6s in the nucleus3 Howe4er0 6uring cell 6i4ision0 the chro1atin beco1es tightl2 coile6 into short0 6ense structures calle6 " ro!oso!es;chromo , color: some O body<3 +hro1atin an6 chro1oso1es are reall2 the sa1e 1olecules0 but the2 6iffer in structural arrange1ent3 In a66ition to chro1oso1es0 the nucleus 1a2 also contain one0 two0 or se4eralnucleoli3 A n+"leol+s is the site of riboso1e 1anufacture3 Specific parts of the cell=s (NA are in4ol4e6 in the 1anufacture of riboso1es3 These (NA regions beco1e organi5e6 at a particular place within the nucleus an6 pro6uce riboso1es3 The nucleolus is co1pose6 of this (NA0 specific granules an6 fibers use6 in the 1anufacture of riboso1es0 an6 partiall2 co1plete6 riboso1es3 The final co1ponent of the nucleus is its li>ui6 1atri70 calle6 then+"leo*las!3 It is a colloi6al 1i7ture co1pose6 of water0 nucleic aci6s0 the 1olecules use6 in the construction of riboso1es0 an6 other nuclear 1aterial ;figure B3?G<3

%IFFUSION Molecules are in a constant state of 1otion3 Although in soli6s 1olecules ten6 to 4ibrate in place0 in li>ui6s an6 gases the2 are able to 1o4e past one

another3 'ecause the 1otion of 1olecules is ran6o10 there is a natural ten6enc2 in gases an6 li>ui6s for 1olecules of 6ifferent t2pes to 1i7 co1pletel2 with each other3 +onsi6er a bottle of a11onia3 When 2ou open the bottle0 the a11onia 1olecules an6 air 1olecules begin to 1i7 an6 2ou s1ell the a11onia3 A11onia 1olecules lea4e the bottle an6 enter the bottle3 Molecules fro1 the air enter an6 lea4e the bottle3 Howe4er0 1ore a11onia 1olecules lea4e the bottle than enter it3 This o4erall 1o4e1ent is ter1e6 net !ove!ent0 the 1o4e1ent in one 6irection 1inus the 1o4e1ent in the opposite 6irection3 The 6irection in which the greatest nu1ber of 1olecules of a particular kin6 1o4es ;net 1o4e1ent< is 6eter1ine6 b2 the 6ifference in concentration of the 1olecules in 6ifferent places3 %i44+sion is the net 1o4e1ent of a kin6 of 1olecule fro1 a place where that 1olecule is in higher concentration to a place where that 1olecule is less concentrate63 The 6ifference in concentration of the 1olecules o4er a 6istance is known as a "on"entration ,ra#ient or #i44+sion ,ra#ient ;figure B3?A<3 When no concentration gra6ient e7ists0 the 1o4e1ent of 1olecules is e>ual in all 6irections0 an6 the s2ste1 has reache6 a state of #(na!i" e9+ilibri+!3 There is an e>uilibriu1 because there is no longer a net 1o4e1ent ;6iffusion<0 because the 1o4e1ent in one 6irection e>uals the 1o4e1ent in the other3 It is 62na1ic0 howe4er0 because the s2ste1 still has energ20 an6 the 1olecules are still 1o4ing3 The rate at which 6iffusion takes place is 6eter1ine6 b2 se4eral factors3 (iffusion occurs faster if the 1olecules are s1all0 if the2 are 1o4ing rapi6l20 an6 if there is a large concentration gra6ient3 %i44+sion in )ells (iffusion is an i1portant 1eans b2 which 1aterials are e7change6 between a cell an6 its en4iron1ent3 #or e7a1ple0 cells constantl2 use o72gen in 4arious che1ical reactions3 +onse>uentl20 the o72gen concentration in cells alwa2s re1ains low3 The cells0 then0 contain a lower concentration of o72gen than 6oes the en4iron1ent outsi6e the cells3 This creates a concentration gra6ient0 an6 the o72gen 1olecules 6iffuse fro1 the outsi6e of the cell to the insi6e3 (iffusion can take place onl2 as long as there are no barriers to the free 1o4e1ent of 1olecules3 In the case of a cell0 the plas1a 1e1brane surroun6s the cell an6 ser4es as a partial barrier to the 1o4e1ent of

1olecules through it3 Howe4er0 the 1e1brane is co1pose6 of phospholipi6 an6 protein 1olecules that are in constant 1otion an6 for1 te1porar2 openings that allow so1e s1all 1olecules to cross fro1 one si6e of the 1e1brane to the other3 !ther 1olecules are unable to pass through the 1e1brane b2 6iffusion3 If a 1olecule is able to pass through the 1e1brane0 the 1e1brane is per1eable to the 1olecules3 'ecause the plas1a 1e1brane allows onl2 certain 1olecules to pass through it0 it is sele"tivel( *er!eable3 A 1olecule=s abilit2 to pass through the 1e1brane 6epen6s on its si5e0 electrical charge0 an6 solubilit2 in the phospholipi6 1e1brane3 In certain cases0 the 1e1brane 6ifferentiates on the basis of 1olecular si5e: that is0 the 1e1brane allows s1all 1olecules0 such as o72gen or water0 to pass through but pre4ents the passage of larger 1olecules3 The 1e1brane 1a2 also regulate the passage of ions3 If a particular portion of the 1e1brane has a large nu1ber of positi4e ions on its surface0 positi4el2 charge6 ions in the en4iron1ent will be repelle6 an6 pre4ente6 fro1 crossing the 1e1brane3 Molecules that are able to 6issol4e in phospholipi6s0 such as 4ita1ins A an6 (0 can pass through the 1e1brane rather easil2: howe4er0 1an2 1olecules cannot pass through at all3 The cell has no control o4er the rate or 6irection of 6iffusion3 The 6irection of 6iffusion is 6eter1ine6 b2 the relati4e concentration of specific 1olecules on the two si6es of the 1e1brane0 an6 the energ2 that causes 6iffusion to occur is supplie6 b2 the kinetic energ2 of the 1olecules the1sel4es ;figure B3??<3 (iffusion is a passi4e process0 which 6oes not re>uire an2 energ2 e7pen6iture on the part of the cell3 %i44+sion in Lar,e Or,anis!s In large ani1als0 1an2 cells are burie6 6eep within the bo62: if it were not for the ani1als= circulator2 s2ste1s0 cells woul6 ha4e little opportunit2 to e7change gases or other 1olecules 6irectl2 with their surroun6ings3 !72gen can 6iffuse into bloo6 through the 1e1branes of the lungs0 gills0 or other 1oist surfaces of an ani1al=s bo623 The circulator2 s2ste1 then transports the o72gen8rich bloo6 throughout the bo620 an6 the o72gen auto1aticall2 6iffuses into cells3 This occurs because the concentration of o72gen insi6e cells is lower than that of the bloo63 The opposite is true of carbon 6io7i6e3 Ani1al cells constantl2 pro6uce carbon 6io7i6e as a waste pro6uct0 so there is alwa2s a high concentration of it within the cells3 These 1olecules 6iffuse fro1 the cells into the bloo60 where the concentration of carbon 6io7i6e is

kept constantl2 low0 because the bloo6 is pu1pe6 to the 1oist surfaces ;e3g30 gills0 lungs< an6 the carbon 6io7i6e again 6iffuses into the surroun6ing en4iron1ent3 In a si1ilar 1anner0 1an2 other t2pes of 1olecules constantl2 enter an6 lea4e cells3 The health of persons who ha4e 6ifficult2 getting enough o72gen to their cells can be i1pro4e6 b2 increasing the concentration gra6ient3 !72gen 1akes up about ?G percent of the air3 If this concentration is artificiall2 raise6 b2 suppl2ing a special source of o72gen0 6iffusion fro1 the lungs to the bloo6 will take place 1ore rapi6l23 This will help assure that o72gen reaches the bo62 cells that nee6 it0 an6 so1e of the person=s s21pto1s can be controlle63

OSMOSIS Water 1olecules easil2 6iffuse through cell 1e1branes3 !s1osis is the net 1o4e1ent ;6iffusion< of water 1olecules through a selecti4el2 per1eable 1e1brane3 Although os1osis is i1portant in li4ing things0 it will take place in an2 situation in which there is a selecti4el2 per1eable 1e1brane an6 a 6ifference in water concentration in the solutions on opposite si6es of the 1e1brane3 #or e7a1ple0 consi6er a solution of HGI water an6 AGI sugar separate6 b2 a selecti4el2 per1eable 1e1brane fro1 a sugar solution of FGI water an6 BGI sugar ;figure B3?@<3 The 1e1brane allows water 1olecules to pass freel2 but pre4ents the larger sugar 1olecules fro1 crossing3 There is a higher concentration of water 1olecules in one solution0 co1pare6 with the concentration of water 1olecules in the other0 so 1ore of the water 1olecules 1o4e fro1 the solution with HGI water to the other solution0 with FGI water3 'e sure that 2ou recogni5e ;A< that os1osis is reall2 6iffusion in which the 6iffusing substance is water an6 ;?< that the regions of 6ifferent concentrations are separate6 b2 a 1e1brane that is 1ore per1eable to water than the substance 6issol4e6 in the water3 It is i1portant to un6erstan6 that0 when one a66s so1ething to a water

solution0 the percentage of the water in the solution 6eclines3 #or e7a1ple0 pure water is AGGI water3 If 2ou a66 salt to the water0 the solution contains both water an6 salt an6 the percentage of water is less than AGGI3 Thus0 the 1ore 1aterial 2ou a66 to the solution0 the lower the percentage of water3 Os!osis in )ells A proper a1ount of water is re>uire6 if a cell is to function efficientl23 Too 1uch water in a cell 1a2 6ilute the cell contents an6 interfere with the che1ical reactions necessar2 to keep the cell ali4e3 Too little water in the cell 1a2 result in a buil6up of poisonous waste pro6ucts3 As with the 6iffusion of other 1olecules0 os1osis is a passi4e process0 because the cell has no control o4er the 6iffusion of water 1olecules3 This 1eans that the cell can re1ain in balance with an en4iron1ent onl2 if that en4iron1ent 6oes not cause the cell to lose or gain too 1uch water3 If cells contain a concentration of water an6 6issol4e6 1aterials e>ual to that of their surroun6ings0 the cells are sai6 to be isotoni" to their surroun6ings3 #or e7a1ple0 the ocean contains 1an2 kin6s of 6issol4e6 salts3 !rganis1s such as sponges0 9ell2fishes0 an6 proto5oa are isotonic to the ocean0 because the a1ount of 1aterial 6issol4e6 in their cellular water is e>ual to the a1ount of salt 6issol4e6 in the ocean=s water3 If an organis1 is to sur4i4e in an en4iron1ent that has a 6ifferent concentration of water than 6oes its cells0 it 1ust e7pen6 energ2 to 1aintain this 6ifference3 !rganis1s that li4e in freshwater ha4e a lower concentration of water ;a higher concentration of 6issol4e6 1aterials< than their surroun6ings an6 ten6 to gain water b2 os1osis 4er2 rapi6l23 The2 are sai6 to be (*ertoni" to their surroun6ings0 an6 the surroun6ings are (*otoni"0 co1pare6 with the cells3 These two ter1s are alwa2s use6 to co1pare two 6ifferent solutions3 The h2pertonic solution is the one with 1ore 6issol4e6 1aterial an6 less water: the h2potonic solution has less 6issol4e6 1aterial an6 1ore water3 The concept of os1osis is i1portant in 1e6ical situations3 !ften0 people are gi4en 1aterials b2 intra4enous in9ections3 Howe4er0 the solutions a66e6 1ust ha4e the right balance between water an6 6issol4e6 substances0 or re6 bloo6 cells 1a2 be in9ure6 ;figure B3?B<3 Si1ilarl20 6uring surger2 organs are bathe6 in a solution that is isotonic to the cells of the bo623 Re,+latin, Water $alan"e If an organis1 is to sur4i4e in an en4iron1ent that has a 6ifferent

concentration of water than 6oes its cells0 it 1ust e7pen6 energ2 to 1aintain this 6ifference3 !rganis1s whose cells gain water b2 os1osis 1ust e7pen6 energ2 to eli1inate an2 e7cess if the2 are to keep fro1 swelling an6 bursting3 Man2 kin6s of freshwater proto5oa ha4e special organelles calle6 contractile 4acuoles that fill with water an6 perio6icall2 collapse0 forcing the water fro1 the cell3 The ki6ne2s of freshwater fish are 6esigne6 to get ri6 of the water the2 constantl2 recei4e as a result of os1osis fro1 their surroun6ings3 Si1ilarl20 organis1s that are h2potonic to their surroun6ings ;ha4e a higher concentration of water than their surroun6ings< 1ust 6rink water or their cells will shrink3 Most ocean fish are in this situation3 The2 lose water b2 os1osis to their salt2 surroun6ings an6 1ust 6rink seawater to keep their cells fro1 shrinking3 'ecause the2 are taking in a66itional salt with the seawater the2 6rink0 the2 1ust e7pen6 energ2 to e7crete this e7cess salt3 Since terrestrial ani1als like us are not bathe6 in a water2 solution0 we 6o not gain an6 lose water through our surfaces b2 os1osis3 Howe4er0 we 6o lose water 6ue to e4aporation3 Thus0 we 1ust 6rink water to replace that lost3 !ur 6esire to 6rink is 6irectl2 relate6 to the os1otic con6ition of the cells in our bo623 If we are 6eh26rate60 we 6e4elop a thirst an6 6rink so1e water3 This is controlle6 b2 cells in the brain3 "n6er nor1al con6itions0 when we 6rink s1all a1ounts of water0 the cells of the brain swell a little0 an6 signals are sent to the ki6ne2s to ri6 the bo62 of e7cess water3 '2 contrast0 persons who are 6eh26rate60 such as 1arathon runners0 1a2 6rink large >uantities of water in a 4er2 short ti1e following a race3 This rapi6 a66ition of water to the bo62 1a2 cause abnor1al swelling of brain cells0 because the e7cess water cannot be gotten ri6 of rapi6l2 enough3 If this happens0 the person 1a2 lose consciousness or e4en 6ie because the brain cells ha4e swollen too 1uch3 Water $alan"e in Plant )ells $lant cells also e7perience os1osis3 If the water concentration outsi6e the plant cell is higher than the water concentration insi6e0 1ore water 1olecules enter the cell than lea4e3 This creates internal pressure within the cell3 'ut plant cells 6o not burst0 because the2 are surroun6e6 b2 a strong cell wall3 Lettuce cells that are crisp are ones that ha4e gaine6 water so that there is high internal pressure3 Wilte6 lettuce has lost so1e of its water to its surroun6ings0 so that it has onl2 slight internal pressure3 !s1osis occurs

when 2ou put sala6 6ressing on a sala63 'ecause the 6ressing has a 4er2 low water concentration0 water fro1 the lettuce 6iffuses fro1 the cells into the surroun6ings3 Sala6 that has been J6resse6K too long beco1es li1p an6 unappeti5ing ;table B3A<3

)ONTROLLE% METHO%S OF TRANSPORTING MOLE)ULES So far0 we ha4e consi6ere6 onl2 situations in which cells ha4e no control o4er the 1o4e1ent of 1olecules3 +ells cannot rel2 solel2 on 6iffusion an6 os1osis0 howe4er0 because 1an2 of the 1olecules the2 re>uire either cannot pass through the plas1a 1e1brane or occur in relati4el2 low concentrations in the cell=s surroun6ings3 Fa"ilitate# %i44+sion So1e 1olecules 1o4e across the 1e1brane b2 co1bining with specific carrier proteins3 When the rate of 6iffusion of a substance is increase6 in the presence of a carrier0 it is calle6 4a"ilitate# #i44+sion3 'ecause this 1o4e1ent is still 6iffusion0 the net 6irection of 1o4e1ent is in accor6ance with the concentration gra6ient3 Therefore0 this is consi6ere6 a passi'e transport 1etho60 although it can occur onl2 in li4ing organis1s with the necessar2 carrier proteins3 !ne e7a1ple of facilitate6 6iffusion is the 1o4e1ent of glucose 1olecules across the 1e1branes of certain cells3 In or6er for the glucose 1olecules to pass into these cells0 specific proteins are re>uire6 to carr2 the1 across the 1e1brane3 The action of the carrier 6oes not re>uire an input of energ2 other than the 1olecules= kinetic energ2 ;figure B3?C<3 A"tive Trans*ort When 1olecules are 1o4e6 across the 1e1brane fro1 an area

of lowconcentration to an area of high concentration0 the cell 1ust e7pen6 energ23 This is the opposite 6irection 1olecules 1o4e in os1osis an6 6iffusion3 The process of using a carrier protein to 1o4e 1olecules up a concentration gra6ient is calle6 a"tive trans*ort ;figure B3?F<3 Acti4e transport is 4er2 specific* !nl2 certain 1olecules or ions can be 1o4e6 in this wa20 an6 the2 1ust be carrie6 b2 specific proteins in the 1e1brane3 The action of the carrier re>uires an input of energ2 other than the 1olecules= kinetic energ2: therefore0 this process is ter1e6 acti'e transport3 #or e7a1ple0 so1e ions0 such as so6iu1 an6 potassiu10 are acti4el2 pu1pe6 across plas1a 1e1branes3 So6iu1 ions are pu1pe6 out of cells up a concentration gra6ient3 $otassiu1 ions are pu1pe6 into cells up a concentration gra6ient3 En#o"(tosis an# E.o"(tosis Larger particles or collections of 1aterials can be transporte6 across the plas1a 1e1brane b2 being wrappe6 in 1e1brane0 rather than passing through the 1e1brane 1olecule b2 1olecule3 When 1aterials enter a cell in this 1anner0 it is calle6 en#o"(tosis3 When 1aterials are transporte6 out of cells in 1e1branewrappe6 packages0 it is known as e.o"(tosis ;figure B3?E<3 En6oc2tosis can be 6i4i6e6 into three sorts of acti4ities* phagoc2tosis0 pinoc2tosis0 an6 receptor 1e6iate6 en6oc2tosis3 P a,o"(tosis is the process of engulfing large particles0 such as cells3 #or e7a1ple0 proto5oa engulf foo6 an6 white bloo6 cells engulf bacteria b2 wrapping the1 with 1e1brane an6 taking the1 into the cell3 'ecause of this0 white bloo6 cells often are calle6 phagocytes3 When phagoc2tosis occurs0 the 1aterial to be engulfe6 touches the surface of the cell an6 causes a portion of the outer plas1a 1e1brane to be in6ente63 The in6ente6 plas1a 1e1brane is pinche6 off insi6e the cell to for1 a sac containing the engulfe6 1aterial3 %ecall that this sac0 co1pose6 of a single 1e1brane0 is calle6 a 4acuole3 !nce insi6e the cell0 the 1e1brane of the 4acuole fuses with the 1e1brane of l2soso1es0 an6 the en521es of the l2soso1es break 6own the contents of the 4acuole3 Pino"(tosis is the process of engulfing li>ui6s an6 the 1aterials 6issol4e6 in the li>ui6s3 In this for1 of en6oc2tosis0 the sacs that are for1e6 are 4er2 s1all0 co1pare6 with those for1e6 6uring phagoc2tosis3 'ecause of their s1all si5e the2 are calle6 4esicles3 In fact0 an electron 1icroscope is nee6e6 in or6er to see 4esicles3

Re"e*tor !e#iate# en#o"(tosis is the process in which 1olecules fro1 the cell=s surroun6ings bin6 to receptor 1olecules on the plas1a 1e1brane3 The 1e1brane then fol6s in an6 engulfs these 1olecules3 'ecause receptor 1olecules are in4ol4e60 the cell can gather specific necessar2 1olecules fro1 its surroun6ings an6 take the 1olecules into the cell3 E7oc2tosis occurs in the sa1e 1anner as en6oc2tosis3 Me1branous sacs containing 1aterials fro1 the cell 1igrate to the plas1a 1e1brane an6 fuse with it3 This results in the sac contents= being release6 fro1 the cell3 Man2 1aterials0 such as 1ucus0 6igesti4e en521es0 an6 1olecules pro6uce6 b2 ner4e cells0 are release6 in this 1anner3

PRO-AR&OTI) )ELL STRU)TURE $rokar2otic cells0 the Eubacteria an6 Archaea0 6o not ha4e a t2pical nucleus boun6 b2 a nuclear 1e1brane0 nor 6o the2 contain 1itochon6ria0 chloroplasts0 &olgi0 or e7tensi4e networks of E%3 Howe4er0 prokar2otic cells contain (NA an6 en521es an6 are able to repro6uce an6 engage in 1etabolis13 The2 perfor1 all of the basic functions of li4ing things with fewer an6 si1pler organelles3 Although so1e Eubacteria ha4e a t2pe of green photos2nthetic pig1ent an6 carr2 on photos2nthesis0 the2 6o so without chloroplasts an6 use so1ewhat 6ifferent che1ical reactions3 Most Eubacteria are surroun6e6 b2 a capsule0 or sli1e la2er0 which is co1pose6 of a 4ariet2 of co1poun6s3 In certain bacteria0 this la2er is responsible for their abilit2 to stick to surfaces ;inclu6ing host cells< an6 to resist phagoc2tosis3 Man2 bacteria also ha4e fi1briae0 hairlike protein structures0 which help the cell stick to ob9ects3 Those with flagella are

capable of propelling the1sel4es through the en4iron1ent3 'elow the capsule is the rigi6 cell wall0 co1prise6 of a uni>ue proteinQcarboh26rate co1ple7 calle6 pepti6ogl2can3 This gi4es the cell the strength to resist os1otic pressure changes an6 gi4es it shape3 /ust beneath the wall is the plas1a 1e1brane3 Thinner an6 with a slightl2 6ifferent che1ical co1position fro1 that of eukar2otes0 the plas1a 1e1brane carries out the sa1e functions as the plas1a 1e1brane in eukar2otes3 Most bacteria are either ro68shape6 ;bacilli<0 spherical ;cocci<0 corkscrewshape6 ;spirilla<0 or co11a8shape6 ;4ibrio<3 The genetic 1aterial within the c2toplas1 is (NA in the for1 of a loop3 The Archaea share 1an2 characteristics with the Eubacteria3 Man2 ha4e a ro6 or spherical shape0 although so1e are s>uare or triangular3 So1e ha4e flagella an6 ha4e cell walls0 but the cell walls are 1a6e of a 6ifferent 1aterial than that of Eubacteria3 !ne significant 6ifference between the cells of Eubacteria an6 Archaea is in the che1ical 1akeup of their riboso1es3 The riboso1es of Eubacteria contain 6ifferent proteins fro1 those foun6 in the cells of Eucar2a or Archaea3 'acterial riboso1es are also s1aller3 This 6isco4er2 was i1portant to 1e6icine0 because 1an2 cellular for1s of life that cause co11on 6iseases are bacterial3 As soon as 6ifferences in the riboso1es were note60 researchers began to look for wa2s in which to interfere with the bacterial riboso1e=s function0 but not interfere with the riboso1es of eukar2otic cells3 Antibioti"s0 such as strepto12cin0 are the result of this research3 This 6rug co1bines with bacterial riboso1es an6 causes bacteria to 6ie because it pre4ents pro6uction of the proteins essential to sur4i4al of bacteria3 'ecause eukar2otic riboso1es 6iffer fro1 bacterial riboso1es0 strepto12cin 6oes not interfere with the nor1al function of the riboso1es in hu1an cells3 EU-AR&OTI) )ELL STRU)TURE Eukar2otic cells contain a true nucleus an6 1ost of the 1e1branous organelles 6escribe6 earlier3 Eukar2otic organis1s can be further 6i4i6e6 into se4eral categories0 base6 on the specific co1bination of organelles the2 contain3 The cells of plants0 fungi0 proto5oa an6 algae0 an6 ani1als are all eukar2otic3 The 1ost ob4ious characteristic that sets plants an6 algae apart fro1 other organis1s is their green color0 which in6icates that the cells contain chloroph2ll in chloroplasts3 +hloroph2ll is necessar2 for photos2nthesis.the con4ersion of light energ2 into che1ical8bon6 energ2 in foo6 1olecules3 Another 6istinguishing characteristic of plant an6 algal cells

is that their cell walls are 1a6e of cellulose ;table B3?<3 The fungi are a 6istinct group of organis1s that lack chloroplasts but ha4e a cell wall3 Howe4er0 the cell wall is 1a6e fro1 a pol2sacchari6e0 calle6 chitin0 rather than cellulose3 !rganis1s that belong in this categor2 of eukar2otic cells inclu6e 2easts0 1ol6s0 1ushroo1s0 an6 the fungi that cause such hu1an 6iseases as athlete=s foot0 9ungle rot0 an6 ringwor13 Eukar2otic organis1s that lack cell walls an6 chloroplasts are place6 in separate groups3 !rganis1s that consist of onl2 one cell are calle6 proto5oans.e7a1ples are !moeba an6 Paramecium3 The2 ha4e all the cellular organelles e7cept the chloroplast: therefore0 proto5oans 1ust consu1e foo6 as 6o fungi an6 1ulticellular ani1als3 Although the 6ifferences in these groups of organis1s 1a2 see1 to set the1 worl6s apart0 their si1ilarit2 in cellular structure is one of the central the1es unif2ing the fiel6 of biolog23 !ne can obtain a better un6erstan6ing of how cells operate in general b2 stu62ing specific e7a1ples3 'ecause the organelles ha4e the sa1e general structure an6 function0 regar6less of the kin6 of cell in which the2 are foun60 we can learn 1ore about how 1itochon6ria function in plants b2 stu62ing how 1itochon6ria function in ani1als3 There is a co11onalit2 a1ong all li4ing things with regar6 to their cellular structure an6 function3

rganic !olecules"the !olecules o# $i#e

By Enger, E.D., Ross, F.C., Bailey, D.B. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

+A%'!N* THE +ENT%AL AT!M IS!ME%S THE +A%'!N S,ELET!N AN( #"N+TI!NAL &%!"$S MA+%!M!LE+"LES !# LI#E SIM$LE S"&A%S +!M$LEL +A%'!H)(%ATES THE ST%"+T"%E !# $%!TEINS WHAT (! $%!TEINS (!? N"+LEI+ A+I(S (NA %NA T%"E ;NE"T%AL< #ATS $H!S$H!LI$I(S STE%!I(S

)AR$ON' THE )ENTRAL ATOM All organic 1olecules0 whether natural or s2nthetic0 ha4e certain co11on characteristics3 The carbon ato10 which is the central ato1 in all organic 1olecules0 has so1e unusual properties3 +arbon is uni>ue in that it can co1bine with other carbon ato1s to for1 long chains3 In 1an2 cases0 the en6s of these chains 1a2 9oin together to for1 ring structures ;figure @3@<3 !nl2 a few other ato1s ha4e this abilit23 Also unusual is that these bon6ing sites are all locate6 at e>ual 6istances fro1 one another3 If 2ou were to stick four nails into a rubber ball so that the nails were e>uall2 6istribute6 aroun6 the ball0 2ou woul6 ha4e a goo6 i6ea of the three86i1ensional arrange1ent of the bon6s ;figure @3B<3 These bon6ing sites are arrange6 this wa2 because0 in the carbon ato10 there are B electrons in the outer1ost energ2 le4el3 Howe4er0 these B electrons 6o not sta2 in stan6ar6 positions3 The2 6istribute the1sel4es 6ifferentl2.that is0

into four propeller8shape6 electron paths3 This allows the1 to be as far awa2 fro1 each other as possible3 +arbon ato1s are usuall2 in4ol4e6 in co4alent bon6s3 'ecause carbon has four places it can bon60 the carbon ato1 can co1bine with four other ato1s b2 for1ing four separate0 single co4alent bon6s with other ato1s3 This is the case with the 1ethane 1olecule0 which has four h26rogen ato1s attache6 to a single carbon ato1 ;re4iew figure @3B<3 $ure 1ethane is a colorless0 o6orless gas that 1akes up HCI of natural gas3 The aro1a of natural gas is the result of 1ercaptan an6 tri1eth2l 6isulfi6e a66e6 for safet2 to let consu1ers know when a leak occurs3 So1e ato1s 1a2 be bon6e6 to a single ato1 1ore than once3 This results in a slightl2 6ifferent arrange1ent of bon6s aroun6 the carbon ato13 An e7a1ple of this t2pe of bon6ing occurs when o72gen is attracte6 to a carbon3 An ato1 of o72gen has ? electrons in its outer1ost energ2 le4el3 If it shares A of these with a carbon an6 then shares the other with the sa1e carbon0 it for1s a 6ouble bon63 A double bond is two co4alent bon6s for1e6 between two ato1s that share two pairs of electrons3 !72gen is not the onl2 ato1 that can for1 6ouble bon6s0 but 6ouble bon6s are co11on between o72gen an6 carbon3 The 6ouble bon6 is 6enote6 b2 two lines between the two ato1s*

Two carbon ato1s 1ight for1 6ouble bon6s between each other an6 then bon6 to other ato1s at the re1aining bon6ing sites3 #igure @3C shows se4eral co1poun6s that contain 6ouble bon6s3 So1e organic 1olecules contain triple co'alent bonds: the fla11able gas acet2lene0 is one e7a1ple3 !thers.such as h26rogen c2ani6e .ha4e biological significance3 This 1olecule inhibits the pro6uction of energ2 an6 can cause 6eath3

ISOMERS Although 1an2 kin6s of ato1s can be part of an organic 1olecule0 onl2 a few are co11onl2 foun63 H26rogen ;H< an6 o72gen ;!< are al1ost alwa2s present3 Nitrogen ;N<0 sulfur ;S<0 an6 phosphorus ;$< are also 4er2 i1portant in specific t2pes of organic 1olecules3 An enor1ous 4ariet2 of organic 1olecules is possible0 because carbon is able to ;A< bon6 at four 6ifferent places0 ;?< for1 long chains0 an6 ;@< co1bine with 1an2 other kin6s of ato1s3 The t2pes of ato1s in the 1olecule are i1portant in 6eter1ining the properties of the 1olecule3 The three6i1ensional arrange1ent of the ato1s within the 1olecule is also i1portant3 'ecause 1ost inorganic 1olecules are s1all an6 in4ol4e few ato1s0 a group of ato1s can be usuall2 arrange6 in onl2 one wa2 to for1 a 1olecule3 There is onl2 one arrange1ent for a single o72gen ato1 an6 two h26rogen ato1s in a 1olecule of water3 In a 1olecule of sulfuric aci60 there is onl2 one arrange1ent for the sulfur ato10 the two h26rogen ato1s0 an6 the four o72gen ato1s3

'oth the 6i1eth2l ether an6 the eth2l alcohol contain two carbon ato1s0 si7 h26rogen ato1s0 an6 one o72gen ato10 but the2 are >uite 6ifferent in their arrange1ent of ato1s an6 in the che1ical properties of the 1olecules3 The first is an ether: the secon6 is an alcohol3 'ecause the ether an6 the alcohol ha4e the sa1e nu1ber an6 kin6s of ato1s0 the2 are sai6 to ha4e the sa1e empirical formula0 which in this case can be written +?HF!3 An e1pirical for1ula si1pl2 in6icates the nu1ber of each kin6 of ato1 within the 1olecule3 The arrange1ent of the ato1s an6 their bon6ing within the 1olecule are in6icate6 in a structural formula3 #igure @3F shows se4eral structural for1ulas for the e1pirical for1ula +FHA?!F3 Molecules that ha4e the sa1e e1pirical for1ula but 6ifferent structural for1ulas are calle6 iso1ers ;How Science Works @3A<3

THE )AR$ON S-ELETON AN% FUN)TIONAL GROUPS At the core of all organic 1olecules is a carbon skeleton0 which is co1pose6 of rings or chains ;so1eti1es branche6< of carbon3 It is this carbon skeleton that 6eter1ines the o4erall shape of the 1olecule3 The 6ifferences a1ong 4arious kin6s of organic 1olecules are 6eter1ine6 b2 three factors* ;A< the length an6 arrange1ent of the carbon skeleton0 ;?< the kin6s an6 location of the ato1s attache6 to it0 an6 ;@< the wa2 these attache6 ato1s are co1bine63 These specific co1binations of ato1s0 calle6 functional groups0

are fre>uentl2 foun6 on organic 1olecules3 The kin6 of functional groups attache6 to a carbon skeleton 6eter1ine the specific che1ical properties of that 1olecule3 '2 learning to recogni5e so1e of the functional groups0 2ou can i6entif2 an organic 1olecule an6 pre6ict so1ething about its acti4it23 #igure @3E shows so1e of the functional groups that are i1portant in biological acti4it23 %e1e1ber that a functional group 6oes not e7ist b2 itself: it is part of an organic 1olecule3 !utlooks @3A e7plains how che1ists an6 biologists 6iagra1 the kin6s of bon6s for1e6 in organic 1olecules3

MA)ROMOLE)ULES OF LIFE Macromolecules ;macro O large< are 4er2 large organic 1olecules3 We will look at four i1portant kin6s of 1acro1olecules* carboh26rates0 proteins0

nucleic aci6s0 an6 lipi6s3 +arboh26rates0 proteins0 an6 nucleic aci6s are all polymers;poly O 1an2: mer O seg1ents<3 Polymers are co1binations of 1an2 s1aller0 si1ilar buil6ing blocks calle6 monomers ;mono O single< bon6e6 together ;figure @3D<3 Although lipi6s are 1acro1olecules0 the2 are not pol21ers3 A pol21er is si1ilar to a pearl necklace or a boat=s anchor chain3 All pol21ers are constructe6 of si1ilar seg1ents ;pearls or links< hooke6 together to for1 one large pro6uct ;necklace or anchor chain<3 The 1ono1ers in a pol21er are usuall2 co1bine6 b2 a 6eh26ration s2nthesis reaction ;de O re1o4e: hydro O water: synthesis O co1bine<3 This reaction occurs when two s1aller 1olecules co1e close enough to ha4e an .!H re1o4e6 fro1 one an6 an .H re1o4e6 fro1 the other3 These are co1bine6 to for1 a 1olecule of water ;H?!<0 an6 the re1aining two seg1ents are co1bine6 to for1 the 1acro1olecule3 #igure @3Ha shows the re1o4al of water fro1 between two 1ono1ers3 Notice that0 in this case0 the structural for1ulas are use6 to help i6entif2 where this is occurring3 The che1ical e>uation also in6icates the re1o4al of water3 )ou can easil2 recogni5e a 6eh26ration s2nthesis reaction0 because the reactant si6e of the e>uation shows nu1erous0 s1all 1olecules0 whereas the pro6uct si6e lists fewer0 larger pro6ucts an6 water3 The re4erse of a 6eh26ration s2nthesis reaction is known as h26rol2sis ;hydroO water: lyse O to split or break<3 H26rol2sis is the process of splitting a larger organic 1olecule into two or 1ore co1ponent parts b2 a66ing water ;figure @3Hb<3 The 6igestion of foo6 1olecules in the sto1ach is an e7a1ple of h26rol2sis3

SIMPLE SUGARS The e1pirical for1ula for a si1ple sugar is eas2 to recogni5e0 because there are e>ual nu1bers of carbons an6 o72gens an6 twice as 1an2 h26rogens. for e7a1ple0 +@HF!@ or +CHAG!C3 The en6ing 8ose in6icates that 2ou are 6ealing with a carboh26rate3 Si1ple sugars are usuall2 6escribe6 b2 the nu1ber of carbons in the 1olecule3 A triose has @ carbons0 a pentose has C0 an6 a he7ose has F3 If 2ou re1e1ber that the nu1ber of carbons e>uals the nu1ber of o72gen ato1s an6 that the nu1ber of h26rogens is 6ouble that nu1ber0 these na1es tell 2ou the e1pirical for1ula for the si1ple sugar3 Si1ple sugars0 such as glucose0 fructose0 an6 galactose0 pro4i6e the che1ical energ2 necessar2 to keep organis1s ali4e3 &lucose0 +FHA?!F0 is the 1ost abun6ant carboh26rate: it ser4es as a foo6 an6 a basic buil6ing block for other carboh26rates3 &lucose ;also calle6 de"trose< is foun6 in the sap of

plants: in the hu1an bloo6strea10 it is calle6 blood sugar3 +orn s2rup0 which is often use6 as a sweetener0 is 1ostl2 glucose3 #ructose0 as its na1e i1plies0 is the sugar that occurs in fruits0 an6 it is so1eti1es calle6 fruit sugar3 &lucose an6 fructose ha4e the sa1e e1perical for1ula but ha4e 6ifferent structural for1ulas.that is0 the2 are iso1ers3 A 1i7ture of glucose an6 fructose is foun6 in hone23 This 1i7ture is also for1e6 when table sugar ;sucrose< is reacte6 with water in the presence of an aci60 a reaction that takes place in the preparation of canne6 fruit an6 can6ies3 The 1i7ture of glucose an6 fructose is calle6 in'ert sugar- Thanks to fructose0 in4ert sugar is about twice as sweet to the taste as the sa1e a1ount of sucrose ;table @3A<3 In4ert sugar also attracts water ;is h2groscopic<3 'rown sugar feels 1oister than white0 granulate6 sugar because it contains 1ore in4ert sugar3 Therefore0 bake6 goo6s 1a6e with brown sugar are 1oist an6 chew23 +ells can use si1ple sugars as buil6ing blocks of other 1ore co1ple7 1olecules3 Sugar 1olecules are a part of other0 larger 1olecules such as the genetic 1aterial0 (NA0 an6 the i1portant energ2 transfer 1olecule0 AT$3 AT$ has a si1ple sugar ;ribose< as part of its structural 1akeup3

)OMPLE3 )AR$OH&%RATES Si1ple sugars can be co1bine6 with each other to for1 co1ple7 carboh26rates ;figure @3AG<3 When two si1ple sugars bon6 to each other0

a disaccharide ;di O two< is for1e6: when three bon6 together0 a trisaccharide ;tri , three< is for1e63 &enerall20 a complex carbohydrate that is larger than this is calle6 a polysaccharide ;poly O 1an2<3 #or e7a1ple0 when glucose an6 fructose are 9oine6 together0 the2 for1 a 6isacchari6e0 with the loss of a water 1olecule ;re4iew figure @3H<3 The 1ost co11on 6isacchari6e is sucrose0 or6inar2 table sugar3 Sucrose occurs in high concentrations in sugarcane an6 sugar beets3 It is e7tracte6 b2 crushing the plant 1aterials0 then 6issol4ing the sucrose fro1 the 1aterials with water3 The water is e4aporate6 an6 the cr2stalli5e6 sugar is 6ecolori5e6 with charcoal to pro6uce white sugar3 !ther co11on 6isacchari6es are lactose ;1ilk sugar< an6 maltose ;1alt sugar<3 All three of these 6isacchari6es ha4e si1ilar properties0 but 1altose tastes onl2 about one8thir6 as sweet as sucrose3 Lactose tastes onl2 about one8si7th as sweet as sucrose3 No 1atter which 6isacchari6e is consu1e6 ;sucrose0 lactose0 or 1altose<0 it is con4erte6 into glucose an6 transporte6 b2 the bloo6strea1 for use b2 the bo623 All the co1ple7 carboh26rates are pol2sacchari6es an6 for1e6 b2 6eh26ration s2nthesis reactions3 So1e co11on e7a1ples of pol2sacchari6es are starch an6 gl2cogen3 +ellulose is an i1portant pol2sacchari6e use6 in constructing the cell walls of plant cells3 Hu1ans cannot 6igest ;h26rol25e< this co1ple7 carboh26rate0 so we are not able to use it as an energ2 source3 !n the other han60 ani1als known as ru1inants ;e3g30 cows an6 sheep< an6 ter1ites ha4e 1icroorganis1s within their 6igesti4e tracts that 6igest cellulose0 1aking it an energ2 source for the13 $lant cell walls a66 bulk or fiber to our 6iet0 but no calories3 #iber is an i1portant a66ition to the 6iet0 because it helps control weight an6 re6uces the risk of colon cancer3 It also controls constipation an6 6iarrhea0 because these large0 water8hol6ing 1olecules 1ake these con6itions less of a proble13

THE STRU)TURE OF PROTEINS A1ino aci6s can bon6 together b2 6eh26ration s2nthesis reactions3 When two a1ino aci6s un6ergo 6eh26ration s2nthesis0 the nitrogen of the a1ino group of one is bon6e6 to the carbon of the aci6 group of another3 This co4alent bon6 is ter1e6 a peptide bond ;figure @3A?<3 )ou can i1agine that0 b2 using ?G 6ifferent a1ino aci6s as buil6ing blocks0 2ou can construct 1illions of co1binations3 Each of these co1binations is ter1e6 apolypeptide chain3 A specific pol2pepti6e is co1pose6 of a specific se>uence of a1ino aci6s bon6e6 en6 to en63 $rotein 1olecules are co1pose6 of in6i4i6ual pol2pepti6e chains or groups of chains for1ing a particular configuration3 There are four le4els0 or 6egrees0 of protein structure* pri1ar20 secon6ar20 tertiar20 an6 >uaternar2 structure3

Pri!ar( Str+"t+re A listing of the a1ino aci6s in their proper or6er within a particular pol2pepti6e is its primary structure3 The specific se>uence of a1ino aci6s in a pol2pepti6e is controlle6 b2 the genetic infor1ation of an organis13 Genes are specific portions of (NA that ser'e as messages that tell the cell to link particular amino acids in a specific order. that is/ they determine a polypeptide0s primary structure- The kinds of side chains on these amino acids influence the shape that the polypeptide forms/ as well as its function- Man2 pol2pepti6es fol6 into globular shapes after the2 ha4e been 1a6e as the 1olecule ben6s3 So1e of the a1ino aci6s in the chain can for1 bon6s with their neighbors3 Se"on#ar( Str+"t+re So1e se>uences of a1ino aci6s in a pol2pepti6e are likel2 to twist0 whereas other se>uences re1ain straight3 These twiste6 for1s are referre6 to as thesecondary structure of pol2pepti6es3 #or e7a1ple0 at this secon6ar2 le4el so1e proteins ;e3g30 hair< take the for1 of an alpha heli"* a shape like that of a coile6 spring3 Like 1ost for1s of secon6ar2 structure0 the shape of the alpha heli7 is 1aintaine6 b2 h26rogen bon6s for1e6 between 6ifferent a1ino aci6 si6e chains at 6ifferent locations within the pol2pepti6e3 These forces of attraction 6o not for1 1olecules but result in the orientation of one part of a 1olecule to another part within the sa1e 1olecule3 !ther pol2pepti6es for1 h26rogen bon6s that cause the1 to 1ake se4eral flat fol6s that rese1ble a pleate6 skirt3 This is calle6 a beta pleated sheet3 Tertiar( Str+"t+re It is possible for a single pol2pepti6e to contain one or 1ore coils an6 pleate6 sheets along its length3 As a result0 these 6ifferent portions of the 1olecule can interact to for1 an e4en 1ore co1ple7 globular structure3 This occurs when the coils an6 pleate6 sheets twist an6 co1bine with each other3 The co1ple70 three86i1ensional structure for1e6 in this 1anner is the pol2pepti6e=s tertiary;thir686egree< structure3 A goo6 e7a1ple of tertiar2 structure can be seen when a coile6 phone cor6 beco1es so twiste6 that it fol6s aroun6 an6 back on itself in se4eral places3 The o72gen8hol6ing protein foun6 in 1uscle cells0 12oglobin0 6ispla2s tertiar2 structure3 It is co1pose6 of a single ;AC@ a1ino aci6s< helical 1olecule fol6e6 back an6 bon6e6 to itself in se4eral places3

:+aternar( Str+"t+re #re>uentl20 se4eral 6ifferent pol2pepti6es0 each with its own tertiar2 structure0 twist aroun6 each other an6 che1icall2 co1bine3 The larger0 globular structure for1e6 b2 these interacting pol2pepti6es is referre6 to as the protein=s1uaternary ;fourth86egree< structure3 The in6i4i6ual pol2pepti6e chains are bon6e6 to each other b2 the interactions of certain si6e chains0 which can for1 6isulfi6e co4alent bon6s ;figure @3A@<3 Muaternar2 structure is 6ispla2e6 b2 the protein 1olecules calle6 immunoglobulins0 or antibodies0 which are in4ol4e6 in fighting infectious 6iseases0 such as the flu0 the 1u1ps0 an6 chicken po73 T e For! an# F+n"tion o4 Proteins If a protein is to 6o its 9ob effecti4el20 it 1ust ha4e a particular three8 6i1ensional shape3 The protein=s shape can be altere6 b2 changing the or6er of the a1ino aci6s0 which causes 6ifferent cross8linkages to for13 #igure @3AB shows the i1portance of the protein=s three86i1ensional shape3 #or e7a1ple0 nor1al he1oglobin foun6 in re6 bloo6 cells consists of two kin6s of pol2pepti6e chains0 calle6 the alpha an6 beta chains3 The beta chain is ABF a1ino aci6s long3 If 9ust one of these a1ino aci6s is replace6 b2 a 6ifferent one0 the he1oglobin 1olecule 1a2 not function properl23 A classic e7a1ple of this results in a con6ition known as sickle*cell anemia3 In this case0 the si7th a1ino aci6 in the beta chain0 which is nor1all2 gluta1ic aci60 is replace6 b2 4aline3 What 1ight see1 like a 1inor change causes the he1oglobin to fol6 6ifferentl23 The re6 bloo6 cells that contain this altere6 he1oglobin assu1e a sickle shape when the bo62 is 6epri4e6 of an a6e>uate suppl2 of o72gen3 In other situations0 two proteins 1a2 ha4e the sa1e a1ino aci6 se>uence but the2 6o not ha4e the sa1e three86i1ensional for13 The 6ifference in shape affects how the2 function3 Ma6 cow 6isease ;bo4ine spongifor1 encephalopath2.'SE< an6 +reut5fel6t8/akob 6isease ;+/(< are cause6 b2 rogue proteins calle6prions3 The prions that cause these 6iseases ha4e an a1ino aci6 se>uence i6entical to a nor1al brain protein but are fol6e6 6ifferentl23 The nor1al brain protein contains helical seg1ents0 whereas the correspon6ing seg1ents of the prion protein are pleate6 sheets3 When these 1alfor1e6 proteins enter the bo620 the2 cause nor1al proteins to fol6 6ifferentl23 This causes the 6eath of brain cells which causes loss of brain function an6 e4entuall2 6eath3

+hanging en4iron1ental con6itions also influence the shape of proteins3 Energ2 in the for1 of heat or light 1a2 break the h26rogen bon6s within protein 1olecules3 When this occurs0 the che1ical an6 ph2sical properties of the protein are change6 an6 the protein is sai6 to be 6enature63 ;,eep in 1in6 that a protein is a 1olecule0 not a li4ing thing0 an6 therefore cannot be Jkille63K< A co11on e7a1ple of this occurs when the gelatinous0 clear portion of an egg is cooke6 an6 the protein changes to a white soli63 So1e 1e6ications0 such as insulin0 are proteins an6 1ust be protecte6 fro1 6enaturation so as not to lose their effecti4eness3 #or protection0 such 1e6ications 1a2 be store6 in brown bottles to protect the1 fro1 light or 1a2 be kept un6er refrigeration to protect the1 fro1 heat3

WHAT %O PROTEINS %O? There are thousan6s of kin6s of proteins in li4ing things0 an6 the2 can be place6 into three categories base6 on the functions the2 ser4e3 Structural proteinsare i1portant for 1aintaining the shape of cells an6 organis1s3 The proteins that 1ake up cell 1e1branes0 1uscle cells0 ten6ons0 an6 bloo6

cells are e7a1ples of structural proteins3 The protein collagen0 foun6 throughout the hu1an bo620 gi4es tissues shape0 support0 an6 strength3 Regulator proteins0 the secon6 categor2 of proteins0 help 6eter1ine what acti4ities will occur in the organis13 %egulator proteins inclu6e en521es an6 so1e hor1ones3 These 1olecules help control the che1ical acti4ities of cells an6 organis1s3 So1e e7a1ples of en521es are the 6igesti4e en521es in the intestinal tract3 Three hor1ones that are regulator proteins are insulin0 glucagon0 an6 o72tocin3 Insulin an6 glucagon0 pro6uce6 b2 6ifferent cells of the pancreas0 control the a1ount of glucose in the bloo63 If insulin pro6uction is too low0 or if the 1olecules are i1properl2 constructe60 glucose 1olecules are not re1o4e6 fro1 the bloo6strea1 at a fast enough rate3 The e7cess sugar is then eli1inate6 in the urine3 !ther s21pto1s of e7cess JsugarK in the bloo6 inclu6e e7cessi4e thirst an6 e4en loss of consciousness3 When bloo6 sugar is low0 glucagon is release6 fro1 the pancreas to sti1ulate the break6own of gl2cogen3 The 6isease cause6 b2 i1properl2 functioning insulin is known as diabetes3 !72tocin0 a thir6 protein hor1one0 sti1ulates the contraction of the uterus 6uring chil6birth3 It is an organic 1olecule that has been pro6uce6 artificiall2 ;e3g30 $itocin<0 an6 use6 b2 ph2sicians to in6uce labor3 Carrier proteins are the thir6 categor23 These pick up an6 6eli4er 1olecules at one place an6 transport the1 to another3 #or e7a1ple0 proteins regularl2 attach to cholesterol entering the s2ste1 fro1 the 6iet0 for1ing 1olecules calle6lipoproteins0 which are transporte6 through the circulator2 s2ste13 The cholesterol is release6 at a 6istance fro1 the 6igesti4e tract0 an6 the proteins return to pick up 1ore of this so calle6 6ietar2 cholesterol3

NU)LEI) A)I%S Nucleic acids are co1ple7 organic pol21ers that store an6 transfer genetic infor1ation within a cell3 There are two t2pes of nucleic aci6s* 6eo72r2bonucleic aci6 ;(NA< an6 ribonucleic aci6 ;%NA<3 (NA ser4es as

genetic 1aterial0 whereas %NA pla2s a 4ital role in using genetic infor1ation to 1anufacture proteins3 All nucleic aci6s are constructe6 of 1ono1ers known as nucleotides3 Nucleoti6es also pro4i6e an i11e6iate source of energ2 for cellular reactions3 Each nucleoti6e is co1pose6 of three parts* ;A< a C8carbon si1ple sugar 1olecule0 which 1a2 be ribose or 6eo72ribose0 ;?< a phosphate group0 an6 ;@< a nitrogenous base3 The nitrogenous base 1a2 be one of fi4e t2pes3 Two of the t2pes are the larger0 6ouble8ring 1olecules A6enine an6 &uanine3 The s1aller bases are the single8ring bases Th21ine0 +2tosine0 an6 "racil ;i3e30 A0 &0 T0 +0 an6 "< ;figure @3AC<3 Nucleoti6es ;1ono1ers< are linke6 together in long se>uences ;pol21ers<0 so that the sugar an6 phosphate se>uence for1s a JbackboneK an6 the nitrogenous bases stick out to the si6e3 (NA has 6eo72ribose sugar an6 the bases A0 T0 &0 an6 +0 whereas %NA has ribose sugar an6 the bases A0 "0 &0 an6 + ;figure @3AF<3

%NA Deoxyribonucleic acid (DNA is co1pose6 of two stran6s0 which for1 a twiste6 la66erlike structure thousan6s of nucleoti6es long3 The two stran6s are attache6 b2 h26rogen bon6s between their bases accor6ing to the base pair rule3 The base paring rule states that !denine on one strand always pairs with thymine on the other strand/ ! with T 2in the case of 34!/ adenine always pairs with uracil.A with "< an6 &uanine always pairs with cytosine. & with+3

A T ;or A "< an6 & + A 1eaningful genetic 1essage0 a gene0 is written using the nitrogenous bases as letters along a section of a stran6 of (NA0 such as the base se>uence +ATTA&A+T ;figure @3AE<3 The stran6 that contains this 1essage is calle6 thecoding strand0 fro1 which co1es the ter1 genetic code3 To 1ake a protein0 the cell rea6s the co6ing stran6 an6 uses sets of @ bases3 In the e7a1ple se>uence0 sets of three bases are +AT0 TA&0 an6 A+T3 This s2ste1 is the basis of the genetic co6e for all organis1s3 (irectl2 opposite the co6ing stran6 is a se>uence of nitrogenous bases that are calle6 non*coding0 because the se>uence of letters 1ake no Jsense0K but this stran6 protects the co6ing stran6 fro1 che1ical an6 ph2sical 6a1age3 'oth stran6s are twiste6 into a heli7.that is0 a 1olecule turne6 aroun6 a tubular space0 like a twiste6 la66er3 The infor1ation carrie6 b2 (NA can be co1pare6 to the infor1ation in a te7tbook3 'ooks are co1pose6 of wor6s ;constructe6 fro1 in6i4i6ual letters< in particular co1binations0 organi5e6 into chapters3 In the sa1e wa20 (NA is co1pose6 of tens or thousan6s of nucleoti6es ;letters< in specific three letter se>uences ;wor6s< organi5e6 into genes ;chapters<3 Each chapter gene carries the infor1ation for pro6ucing a protein0 9ust as the chapter of a book carries infor1ation relating to one i6ea3 The or6er of nucleoti6es in a gene is 6irectl2 relate6 to the or6er of a1ino aci6s in the protein for which it co6es3 /ust as chapters in a book are i6entifie6 b2 beginning an6 en6ing state1ents0 6ifferent genes along a (NA stran6 ha4e beginning an6 en6ing signals3 The2 tell when to start an6 when to stop rea6ing the gene3 Hu1an bo62 cells contain BF stran6s ;books< of helical (NA0 each containing 1an2 genes ;chapters<3 These stran6s are calle6 chromosomes when the2 beco1e supercoile6 in preparation for cellular repro6uction3 'efore cellular repro6uction0 the (NA 1akes copies of the co6ing an6 non8co6ing stran6s0 ensuring that the offspring0 or daughter cells0 will recei4e a full co1ple1ent of the genes re>uire6 for their sur4i4al ;figure @3AD<3 A gene is a seg1ent of (NA that is able to ;A< replicate b2 6irecting the 1anufacture of copies of itself: ;?< 1utate0 or che1icall2 change0 an6 trans1it these changes to future generations: ;@< store infor1ation that 6eter1ines the characteristics of cells an6 organis1s: an6 ;B< use this infor1ation to 6irect the s2nthesis of structural0 carrier0 an6 regulator proteins3

RNA Ribon+"lei" a"i# 7RNA8 is foun6 in three for1s3 Messen,er RNA 7!RNA8 is a single8stran6 cop2 of a portion of the co6ing stran6 of (NA for a specific gene3 When 1%NA is for1e6 on the surface of the (NA0 the base pair rule applies3 Howe4er0 because %NA 6oes not contain th21ine0 it pairs " with A instea6 of T with A3 After 1%NA is for1e6 an6 peele6 off0 it links with a cellular structure calle6 the riboso1e0 where the genetic 1essage can be translate6 into a protein 1olecule3 %iboso1es contain another t2pe of %NA0 riboso!al RNA 7rRNA83 r%NA is also an %NA cop2 of (NA0 but after being for1e6 it beco1es twiste6 an6 co4ere6 in protein to for1 a riboso1e3 The thir6 for1 of %NA0trans4er RNA 7tRNA80 is also a cop2 of 6ifferent seg1ents of (NA0 but when peele6 off the surface each seg1ent takes the

for1 of a clo4erleaf3 t%NA 1olecules are responsible for transferring or carr2ing specific a1ino aci6s to the riboso1e0 where all three for1s of %NA co1e together an6 cooperate in the 1anufacture of protein 1olecules ;figure @3AH<3 Whereas the specific se>uence of nitrogenous bases correlates with the co6ing of genetic infor1ation0 the energ2 transfer function of nucleic aci6s is correlate6 with the nu1ber of phosphates each contains3 A nucleoti6e with @ phosphates has 1ore energ2 than a nucleoti6e with onl2 A or ? phosphates3 All of the 6ifferent nucleoti6es are in4ol4e6 in transferring energ2 in phosphor2lation reactions3

TRUE 7NEUTRAL8 FATS True ;neutral< fats are i1portant0 co1ple7 organic 1olecules that are use6 to pro4i6e energ20 a1ong other things3 The buil6ing blocks of a fat are a glycerol1olecule an6 fatty acids3 Glycerol is a carbon skeleton that has three alcohol groups attache6 to it3 Its che1ical for1ula is +@HC;!H<@3 At roo1 te1perature0 gl2cerol looks like clear0 lightweight oil3 It is use6 un6er the na1eglycerin as an a66iti4e to 1an2 cos1etics to 1ake the1 s1ooth an6 eas2 to sprea63

A fatty acid is a long8chain carbon skeleton that has a carbo72l functional group3 If the carbon skeleton has as 1uch h26rogen bon6e6 to it as possible0 it is calle6 sat+rate#3 The saturate6 fatt2 aci6 shown in figure @3?Ga is stearic aci60 a co1ponent of soli6 1eat fats0 such as 1utton tallow3 Notice that0 at e4er2 point in this structure0 the carbon has as 1uch h26rogen as it can hol63 Saturate6 fats are generall2 foun6 in ani1al tissues.the2 ten6 to be soli6s at roo1 te1peratures3 So1e other e7a1ples of saturate6 fats are butter0 whale blubber0 suet0 lar60 an6 fats associate6 with such 1eats as steak an6 pork chops3 A fatt2 aci6 is sai6 to be +nsat+rate# if the carbons are 6ouble8bon6e6 to each other at one or 1ore points3 The occurrence of a 6ouble bon6 in a fatt2 aci6 is in6icate6 b2 the &reek letter ;o1ega<0 followe6 b2 a nu1ber in6icating the location of the first 6ouble bon6 in the 1olecule3 +ounting begins fro1 the o1ega en60 that is the en6 farthest fro1 the carbo72lic aci6 functional group3 !leic aci60 one of the fatt2 aci6s foun6 in oli4e oil0 is co1prise6 of AD carbons with a single 6ouble bon6 between carbons H an6 AG3 Therefore0 it is che1icall2 6esignate6 +AD*IH an6 is a 1onounsaturate6 fatt2 aci63 This fatt2 aci6 is co11onl2 referre6 to as an o1ega8H fatt2 aci63 The unsaturate6 fatt2 aci6 in figure @3?Gb is linoleic aci60 a co1ponent of sunflower an6 safflower oils3 Notice that there are two 6ouble bon6s between the carbons an6 fewer h26rogens than in the saturate6 fatt2 aci63 Linoleic aci6 is che1icall2 a pol2unsaturate6 fatt2 aci6 with two 6ouble bon6s an6 is 6esignate6 +AD*?F0 an o1ega8F fatt2 aci63 This in6icates that the first 6ouble

bon6 of this AD8carbon 1olecule is between carbons F an6 E3 'ecause the hu1an bo62 cannot 1ake this fatt2 aci6 an6 1ust be taken in as a part of the 6iet0 it is calle6 an essential fatty acid3 The other essential fatt2 aci60 linolenic aci6 ;figure @3?Gc<0 is +AD*@@: it has three 6ouble bon6s3 This fatt2 aci6 is co11onl2 referre6 to as an o1ega8@ fatt2 aci63 !ne ke2 function of these essential fatt2 aci6s is the s2nthesis of the prostaglan6in hor1ones that are necessar2 in controlling cell growth an6 speciali5ation3 Man2 foo6 1anufacturers are now a66ing o1ega8@ fatt2 aci6s to their pro6ucts0 base6 on e4i6ence that these re6uce the risk of car6io4ascular 6isease3 So+r"es o4 O!e,a6; So+r"es o4 O!e,a6< Fatt( A"i#s Fatt( A"i#s +ertain fish oils +orn oil ;sal1on0 sar6ines0 herring< $eanut oil #la7see6 oil +ottonsee6 oil So2beans So2bean oil So2bean oil Sesa1e oil Walnuts Sunflower oil +anola oil Safflower oil &reen0 leaf2 4egetables Man2 unsaturate6 fats are plant fats or oils.the2 are usuall2 li>ui6s at roo1 te1peratures3 $eanut0 corn0 an6 oli4e oils are 1i7tures of true fats an6 are consi6ere6 unsaturate6 because the2 ha4e 6ouble bon6s between the carbons of the carbon skeleton3 A pol2unsaturate6 fatt2 aci6 is one that has se4eral 6ouble bon6s in the carbon skeleton3 When gl2cerol an6 @ fatt2 aci6s are co1bine6 b2 three 6eh26ration s2nthesis reactions0 a fat is for1e63 That 6eh26ration s2nthesis is al1ost e7actl2 the sa1e as the reaction that causes si1ple sugars to bon63 In nature0 1ost unsaturate6 fatt2 aci6s ha4e h26rogen ato1s that are on the sa1e si6e of the 6ouble8bon6e6 carbons3 These are calle6 cis fatt2 aci6s3 If the h26rogens are on opposite si6es of the 6ouble bon6s0 the2 are calle6 trans fatt2 aci6s3

Trans fatt2 aci6s are foun6 naturall2 in gra5ing ani1als0 such as cattle0 sheep0 an6 horses3 Therefore0 hu1ans ac>uire the1 in their 6iets in the for1 of 1eat an6 6air2 pro6ucts3 #rench fries0 6onuts0 cookies0 an6 crackers are foo6s high intrans fatt2 aci6s3 Trans fatt2 aci6s are also for1e6 6uring the hydrogenation of either 4egetable or fish oils3 The h26rogenation process breaks the 6ouble bon6s in the fatt2 aci6 chain an6 a66s 1ore h26rogen ato1s3 This can change the li>ui6 to a soli63 Man2 pro6uct labels list the ter1 h26rogenate63 This process e7ten6s shelf life an6 allows pro6ucers to con4ert oils to other soli6s0 such as 1argarine3 +linical stu6ies ha4e shown that trans fatt2 aci6s ten6 to raise total bloo6 cholesterol le4els0 but less than the 1ore saturate6 fatt2 aci6s3 (ietar2 transfatt2 aci6s also ten6 to raise the so8calle6 ba6 fats ;low86ensit2 lipoproteins0 L(Ls< an6 lower the so8calle6 goo6 fats ;high86ensit2 lipoproteins0 H(Ls< when consu1e6 instea6 of cis fatt2 aci6s3 It is suspecte6 that this increases the risk for heart 6isease3 'ecause of the i1portance of trans fatt2 aci6s in car6io4ascular health0 the "3S3 (epart1ent of Health an6 Hu1an Ser4ices ;HHS< re>uires that the a1ount of trans fatt2 aci6s in foo6s be state6 un6er the liste6 a1ount of saturate6 fat3 The HHS suggests that a person eat no 1ore than ?G gra1s of saturate6 fat a 6a2 ;about AGI of total calories<0 inclu6ing trans fatt2 aci6s3 #ats are i1portant 1olecules for storing energ23 There is 1ore than twice as 1uch energ2 in a gra1 of fat as in a gra1 of sugar.H +alories 4ersus B +alories3 This is i1portant to an organis10 because fats can be store6 in a relati4el2 s1all space 2et 2iel6 a high a1ount of energ23 #ats in ani1als also pro4i6e protection fro1 heat loss: so1e ani1als ha4e an insulating la2er of fat un6er the skin3 The thick la2er of blubber in whales0 walruses0 an6 seals

pre4ents the loss of internal bo62 heat to the col60 water2 en4iron1ent in which the2 li4e3 The sa1e la2er of fat an6 the fat 6eposits aroun6 so1e internal organs ;such as the ki6ne2s an6 heart< cushion the organs fro1 ph2sical 6a1age3 If a fat is for1e6 fro1 a gl2cerol 1olecule an6 @ attache6 fatt2 aci6s0 it is calle6 a triglyceride: if ?0 adiglyceride: if A0 a monoglyceride ;figure @3?A<3 Trigl2ceri6es account for about HCI of the fat store6 in hu1an tissue ;!utlooks @3@<3

PHOSPHOLIPI%S P os* oli*i#s are a class of co1ple70 water8insoluble organic 1olecules that rese1ble neutral fats but contain a charge6 phosphate group ;$!B< in their structure ;figure @3??<3 $hospholipi6s are i1portant because the2 are a 1a9or co1ponent of cell 1e1branes3 Without these lipi6s0 the cell contents woul6 not be separate6 fro1 the e7terior en4iron1ent3 So1e of the phospholipi6s are better known as lecithins3 #oun6 in cell 1e1branes0 lecithins help in the e1ulsification of fats.that is0 the2 help separate large portions of fat into s1aller units3 This allows the fat to 1i7 with other 1aterials3 Lecithins are a66e6 to 1an2 t2pes of foo6 for this purpose ;chocolate bars0 for e7a1ple<3 So1e people take lecithin as nutritional supple1ents because the2 belie4e it lea6s to healthier hair an6 better reasoning abilit23 'ut once insi6e the intestines0 lecithins are 6estro2e6 b2

en521es0 9ust as an2 other phospholipi6 is ;!utlooks @3B<3

STEROI%S Steroi#s0 another group of lipi6 1olecules0 are characteri5e6 b2 their arrange1ent of interlocking rings of carbon3 We ha4e alrea62 1entione6 one steroi6 1olecule* cholesterol3 Seru1 cholesterol ;the kin6 foun6 in the bloo6 an6 associate6 with lipoproteins< has been i1plicate6 in 1an2 cases of atherosclerosis3 Howe4er0 the bo62 1akes this steroi6 for use as a co1ponent of cell 1e1branes3 The bo62 also uses it to 1ake bile aci6s3 These pro6ucts of the li4er are channele6 into the intestine to e1ulsif2 fats3 +holesterol is necessar2 for the 1anufacture of 4ita1in (0 which assists in the proper 6e4elop1ent of bones an6 teeth3 +holesterol 1olecules in the skin react with ultra4iolet light to pro6uce 4ita1in (3 #igure @3?@ illustrates so1e of the steroi6 co1poun6s0 such as testosterone an6 progesterone0 that are t2picall2 1anufacture6 b2 organis1s3 +holesterol pla2s both positi4e an6 negati4e roles in 1etabolis13 %egulating the a1ount of cholesterol in the bo62 to pre4ent its negati4e effects can be 6ifficult0 because the bo62 1akes it an6 it is consu1e6 in the 6iet3 %ecall that saturate6 fats cause the bo62 to pro6uce 1ore cholesterol0 increasing the risk for 6iseases such as atherosclerosis3 '2 watching 2our 6iet0 2ou can re6uce the a1ount of cholesterol in 2our bloo6 seru1 b2 about ?GI0 as 1uch as taking a cholesterol8lowering 6rug3 Therefore0 it is best to eat foo6s that are low in cholesterol3 'ecause 1an2 foo6s that clai1 to be low8 or no8 cholesterol ha4e high le4els of saturate6 fats0 the2 shoul6 also be a4oi6e6 in or6er to control seru1 cholesterol le4els3 Man2 steroi6 1olecules are se7 hor1ones3 So1e of the1 regulate repro6ucti4e processes0 such as egg an6 sper1 pro6uction: others regulate such things as salt concentration in the bloo63

!c%ra&'(ill Ans&ers ) D*A Structure and Chromosome rgani+ation

By (yde, D.R. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

%EM"I%E( $%!$E%TIES !# A &ENETI+ MATE%IAL 8 $%!$E%T) A* +!NT%!L !# $%!TEIN EL$%ESSI!N AN( #"N+TI!N %EM"I%E( $%!$E%TIES !# A &ENETI+ MATE%IAL 8 $%!$E%T) ?* A++"%ATE %E$LI+ATI!N WITH M"TA'ILIT) %EM"I%E( $%!$E%TIES !# A &ENETI+ MATE%IAL 8 $%!$E%T) @* L!+ATI!N IN +H%!M!S!MES E I(EN+E #!% (NA AS THE &ENETI+ MATE%IAL* T%ANS#!%MATI!N E I(EN+E #!% (NA AS THE &ENETI+ MATE%IAL* T%ANS#!%MATI!N %NA AS &ENETI+ MATE%IAL THE 'ASI+ ST%"+T"%E !# N"+LEI+ A+I(S +HA%&A##=S %ATI!S (NA L8%A) (I##%A+TI!N ST"(IES THE WATS!N8+%I+, M!(EL ALTE%NATI E #!%MS !# (NA

THE E",A%)!TI+ +ELL THE E",A%)!TI+ +H%!M!S!ME* !NE (NA M!LE+"LE $E% +H%!M!S!ME

RE:UIRE% PROPERTIES OF A GENETI) MATERIAL 6 PROPERT& =' )ONTROL OF PROTEIN E3PRESSION AN% FUN)TION The growth0 6e4elop1ent0 an6 functioning of a cell are controlle6 b2 the proteins within it0 pri1aril2 its en521es3 We can therefore sa2 that the proteins within a cell control 1ost of the cell=s phenot2pe3 (ifferent cells will contain 6ifferent proteins0 which in turn confer 6ifferent functions on those cells3 #or e7a1ple0 a 1a11alian re6 bloo6 cell pri1aril2 pro6uces he1oglobin to bin6 o72gen0 while a ro6 photoreceptor cell in the e2e pri1aril2 s2nthesi5es rho6opsin to 6etect photons of light3 Most 1etabolic processes occur in pathwa2s0 with an en521e facilitating each step in the pathwa23 As an e7a1ple0 the 1etabolic pathwa2 for the con4ersion of threonine into isoleucine ;two a1ino aci6s< appears in 4i,+re >?=3 The en521e threonine 6eh26ratase con4erts threonine into R8 ketobut2ric aci63 The ne7t en521e in the pathwa20 acetolactate s2nthase0 con4erts R8 ketobut2ric aci6 into R8aceto8R8 h26ro72but2ric aci6.an6 so it continues through this fi4e8step path0 en6ing in isoleucine3 The en6 pro6uct of each step beco1es the substrate for the ne7t3 The se>uence of a1ino aci6s 6eter1ines the three6i1ensional structure of an en521e0 which is essential for its function3 ;The structure of proteins is co4ere6 in 1ore 6etail in chapter AA3< The substrate or substrates interact with a part of the en521e calle6 the acti4e site ;fig3 E3?a<3 The shape of the acti4e site allows onl2 specific substrates to enter or fit into it3 This 4iew of the wa2 an en521e interacts with its substrates is calle6 the lock*and*key model of en521e functioning3 When the substrates are in their proper position in the acti4e site of the en521e0 the particular reaction that the en521e catal25es takes place3 Alternati4el20 the induced*fit model proposes that the shape of the en521e=s acti4e site changes upon binding of the specific substrate ;fig3 E3?b<3 The altere6 confor1ation of the acti4e site is now able to catal25e the necessar2 reaction3 So1e en521es appear to function through the lock*and* key model an6 others the in6uce68fit 1o6el3 Not all of the cell=s proteins function as en521es3 So1e are structural proteins0 such as keratin0 the 1ain co1ponent of hair3 !ther proteins are regulator2.the2 control the rate at which other en521es work3 Still others are in4ol4e6 in 6ifferent functions:

albu1ins0 for e7a1ple0 help regulate the os1otic pressure of bloo63 The genetic 1aterial 1ust therefore be capable of pro6ucing proteins with a wi6e 4ariet2 of a1ino aci6 se>uences an6 structures to acco1plish an organis1=s 4ast nu1ber of bioche1ical processes3

RE:UIRE% PROPERTIES OF A GENETI) MATERIAL 6 PROPERT& @' A))URATE REPLI)ATION WITH MUTA$ILIT& The genetic 1aterial 1ust be capable of precisel2 6irecting its own replication so that e4er2 6aughter cell recei4es an e7act cop23 In their AHC@ paper0 Watson an6 +rick hinte6 at a replication process base6 on the structure of (NA3 Each stran6 of the 6oublestran6e6 (NA 1olecule coul6 ser4e as a te1plate for a new stran6 using the propose6 co1ple1entar2 basepairing3 The fi6elit2 or accurac2 of the replication process is 4er2 great0

with onl2 about one error in a billion bases3 The 6etails pertaining to the 1echanis1 of (NA replication will be 6iscusse6 in chapter H3 In contrast to this nee6 to accuratel2 preser4e the (NA se>uence fro1 generation to generation0 the genetic 1aterial 1ust be able to 1utate or change3 Mutation in the genetic 1aterial is re>uire6 o4er a perio6 of ti1e to allow organis1s to e4ol4e3 Thus0 accurate replication is re>uire6 to 1aintain the e7istence of an organis10 while 1utabilit2 pro4i6es a 1eans to intro6uce change3 RE:UIRE% PROPERTIES OF A GENETI) MATERIAL 6 PROPERT& ;' LO)ATION IN )HROMOSOMES Since the earl2 twentieth centur20 geneticists were fairl2 certain that the genetic 1aterial was locate6 in chro1oso1es within the nuclei of eukar2otic cells3 This i6ea was base6 on the correlation between the wa2 chro1oso1es beha4e6 6uring cellular 6i4ision an6 Men6el=s laws of inheritance that 6escribe6 the beha4ior of genes3 The inference was that genetic 1aterial in eukar2otes 1ust be part of chro1oso1es3 Howe4er0 it was known that chro1oso1es were co1pose6 of both nucleic aci6s an6 proteins3 #or a long ti1e0 proteins were consi6ere6 the 1ost probable genetic 1aterial because the2 possesse6 the necessar2 1olecular co1ple7it2 to enco6e the genetic infor1ation3 $roteins were co1pose6 of ?G naturall2 occurring a1ino aci6s that coul6 be co1bine6 in an al1ost unli1ite6 4ariet20 creating thousan6s upon thousan6s of 6ifferent proteins3 In contrast0 (NA was co1pose6 of onl2 four bases0 which appeare6 to pro4i6e onl2 a li1ite6 a1ount of 4ariation3 Ne4ertheless0 1an2 researchers speculate6 that (NA0 an6 not proteins0 constitute6 the genetic 1aterial3 EVI%EN)E FOR %NA AS THE GENETI) MATERIAL' TRANSFORMATION In AH?D0 #re6erick &riffith reporte6 that heat8killing one t2pe of Streptococcuspneumoniae coul6 Jtransfor1K a 6ifferent t2pe of S3 pneumoniae0 causing the latter to e7hibit traits of the first strain3 The S strain of S3 pneu1oniae pro6uces s1ooth colonies when grown on 1e6ia in a petri plate because the cells ha4e outer capsules co1pose6 of pol2sacchari6e ;fig3 E3@<3 This strain also causes a fatal bacterial infection ;pneu1onia< in 1ice3 In contrast0 the % strain lacks pol2sacchari6e capsules an6 pro6uce6 rough colonies on petri plates ;fig3 E3@<3 The % strain 6oes not ha4e a pathological effect on 1ice because bacteria of this strain are engulfe6 b2 white bloo6

cells0 whereas the pol2sacchari6e coat protecte6 the 4irulent S strain fro1 the white bloo6 cells3 &riffith foun6 that neither heat8kille6 S strain nor li4e % strain bacteria0 b2 the1sel4es0 kille6 the 1ice3 Howe4er0 if he in9ecte6 a 1i7ture of li4e % strain an6 heat8kille6 S strain bacteria into 1ice0 the 1ice 6e4elope6 pneu1onia i6entical to that cause6 b2 li4ing S strain cells ;fig3 E3B<3 #urther1ore0 li4e S strain bacteria were reco4ere6 fro1 the 6ea6 1ice3 Thus0 so1ething in the heat8kille6 S strain transfor1e6 the % strain into li4e S strain cells3 The process b2 which this trait 1o4e6 fro1 one bacterial strain to another was ter1e6trans4or!ation3 In AHBB0 !swal6 A4er20 +olin MacLeo60 an6 Macl2n Mc+art2 e7pan6e6 on this e7peri1ent an6 i6entifie6 the transfor1ing substance3 A4er2 an6 his colleagues 6i6 their work in vitro ;literall20 in glass<0 using the 1orpholog2 of the bacterial colonies on petri plates0 rather than pro6uction of pneu1onia in 1ice0 as e4i6ence of transfor1ation3 The heat8kille6 S strain was treate6 with a 4ariet2 of a66itional 1etho6s to 6estro2 6ifferent t2pes of 1olecules before 1i7ing with the li4e % strain cells3 The2 6e1onstrate6 that 6estruction of proteins0 carboh26rates0 an6 lipi6s still resulte6 in the % strain being transfor1e6 into the S strain ;fig3 E3C<3 In contrast0 6estruction of (NA blocke6 transfor1ation of the % strain into the S strain3 This pro4i6e6 the first e7peri1ental e4i6ence that (NA was the genetic 1aterial* onl2 loss of (NA pre4ente6 the transfor1ation of the non4irulent % strain of S3 pneumoniae into the 4irulent S strain3

EVI%EN)E FOR %NA AS THE GENETI) MATERIAL' TRANSFORMATION aluable infor1ation about the nature of the genetic 1aterial has also co1e fro1 4iruses3 !f particular i1portance are stu6ies of bacterial 4iruses.the bacteriophage0 or phage for short3 'ecause phage consist onl2 of nucleic aci6 surroun6e6 b2 protein0 the2 len6 the1sel4es nicel2 to the 6eter1ination

of whether the protein or the nucleic aci6 is the genetic 1aterial ;fig3 E3Fa<3 In AHC?0 Alfre6 Hershe2 an6 Martha +hase publishe6 results supporting (NA=s role in the generation of phage3 These e7peri1ents were base6 on the un6erstan6ing that all nucleic aci6s0 but not bacterial proteins0 containe6 phosphorus3 In contrast0 1ost proteins contain sulfur ;in the a1ino aci6s c2steine an6 1ethionine<0 whereas nucleic aci6s 6o not3 Hershe2 an6 +hase use6 ra6ioacti4e isotopes of sulfur ;@CS< an6 phosphorus ;@?$< to 6ifferentiall2 label the 4iral proteins an6 nucleic aci6s 6uring the infection process3 The2 labele6 the T? bacteriophage b2 infecting Escherichia coli that were being grown in culture 1e6iu1 containing either @CS or @?$ ;fig3 E3Fc<3 Hershe2 an6 +hase then 1i7e6 either the @CS8 or @?$8labele6 phage particles with unlabele6 bacteria3 The2 re1o4e6 the phage after the2 attache6 to the bacterial wall an6 i6entifie6 the phage 1aterial in9ecte6 into the cell3 It was known that the phage replicate6 insi6e the bacterial cell0 which i1plie6 that the phage=s genetic 1aterial 1ust be transferre6 into the bacterial cell3 When@?$8labele6 phage were 1i7e6 with unlabele6 E3 coli cells0 Hershe2 an6 +hase foun6 that the @?$ label entere6 the bacterial cells0 an6 that the ne7t generation of phage release6 fro1 the infecte6 cells carrie6 a significant a1ount of the @?$ label ;fig3 E3Fc<3 When @CS8labele6 phage were 1i7e6 with unlabele6 E3 coli0 the researchers foun6 that the @CS label sta2e6 outsi6e the bacteria for the 1ost part ;fig3 E3Fc<3 Hershe2 an6 +hase thus 6e1onstrate6 that the outer protein coat of a phage 6oes not enter the bacterial cell that it infects0 whereas the phage=s (NA 6oes enter the cell3 'ecause onl2 the phage (NA is foun6 insi6e the bacterial cell0 it 1ust be responsible for the pro6uction of the new phage 6uring the infection process3 This result 6e1onstrate6 that the phage=s (NA0 not the protein0 1ust be the genetic 1aterial3

RNA AS GENETI) MATERIAL In so1e 4iruses0 %NA ;ribonucleic aci6< ser4es as the genetic 1aterial3 The tobacco 1osaic 4irus that infects tobacco plants consists onl2 of %NA an6 a protein coat3 The single0 long %NA 1olecule is package6 within a ro6like structure for1e6 b2 o4er ? thousan6 copies of a single protein3 No (NA is present in tobacco 1osaic 4irus particles ;fig3 E3Ea<3 In AHCC0 Hein5 #raenkel8+onrat an6 %oble2 Willia1s showe6 that a 4irus

can be separate60 in 4itro0 into its co1ponent parts an6 reconstitute6 as a 4iable 4irus3 This fin6ing le6 #raenkel8+onrat an6 'ea Singer to reconstitute tobacco 1osaic 4irus with parts fro1 6ifferent strains ;fig3 E3Eb<3 #or e7a1ple0 the2 co1bine6 the %NA fro1 the co11on tobacco 1osaic 4irus with the protein fro1 the 1aske6 ;M< strain of tobacco 1osaic 4irus3 The2 then 1a6e the reciprocal co1bination of co11on8t2pe protein an6 M8t2pe %NA3 In both cases0 the tobacco 1osaic 4irus pro6uce6 after infection of tobacco plants correspon6e6 to the %NA t2pe0 not the protein3 Therefore0 the nucleic aci6 ;%NA in this case< was the genetic 1aterial3 Subse>uentl20 scientists rubbe6 purifie6 tobacco 1osaic 4irus %NA into plant lea4es3 Nor1al infection an6 a new generation of t2pical0 protein8 coate6 tobacco 1osaic 4irus resulte60 confir1ing %NA as the genetic 1aterial for this 4irus3 #ro1 these an6 other lan61ark e7peri1ents0 geneticists ha4e conclu6e6 that (NA ;an6 in so1e cases %NA< is the genetic 1aterial3

THE $ASI) STRU)TURE OF NU)LEI) A)I%S Nucleic aci6s are 1a6e b2 9oining nucleoti6es in a repetiti4e wa2 into long0 chainlike pol21ers3 Nucleoti6es are 1a6e of three co1ponents* ;A< a phosphate0 ;?< a sugar0 an6 ;@< a nitrogenous base ;table >?= an6 4i,? >?A<3

A n+"leosi#e0 b2 contrast0 is a sugar8base co1poun6 that lacks phosphate ;4i,? >?B<3 When incorporate6 into a nucleic aci60 a nucleoti6e contains one of each of these three co1ponents3 'ut0 when free as a 1ono1er in the cell0 a nucleoti6e usuall2 e7ists in a triphosphate for13 The energ2 hel6 in the two e7tra phosphate bon6s is use60 a1ong other purposes0 to s2nthesi5e the pol21er3 A6enosine triphosphate ;AT$<0 the 1a9or energ2 for1 in the cell0 is a nucleoti6e triphosphate3 Si1ilarl20 the nucleoti6e guanosine triphosphate ;&T$< is a 1a9or signaling 1olecule within the cell3 The sugars in (NA an6 %NA 6iffer at a single position3 In (NA0 the sugar is 6eo72ribose0 which contains a h26rogen at the ?S carbon3 The sugar in %NA is ribose0 which contains a h26ro72l at the ?S position3 ;The carbons of the sugars are nu1bere6 AS to CS3 The pri1es are use6 to a4oi6 confusion with the nu1bering s2ste1 of the bases: see fig3 E3D3< (NA an6 %NA both ha4e four bases0 two purines an6 two *(ri!i#ines0 in their nucleoti6e chains3 'oth 1olecules ha4e the purines a#enine an6,+anine an6 the p2ri1i6ine "(tosine3 (NA contains the p2ri1i6ine th21ine0 while %NA has the p2ri1i6ine +ra"il3 To su11ari5e0 (NA an6 %NA 6iffer onl2 in the ?S position of the sugar an6 a single base0 th21ine in (NA an6 uracil in %NA3 These two structural 6ifferences account for the functional 6ifferences between (NA an6 %NA3 A nucleoti6e is for1e6 in the cell when a base attaches to the AS carbon of the sugar an6 a phosphate attaches to the CS carbon of the sa1e sugar ;4i,? >?=C<: the na1e of the nucleoti6e is 6eri4e6 fro1 the base ;table >?@<3 Nucleoti6es are linke6 together ; pol21eri5e6< b2 the for1ation of a bon6 between the phosphate at the CS carbon of one nucleoti6e an6 the h26ro72l ;!H< group at the @S carbon of an a69acent 1olecule.a linkage ter1e6 a * os* o#iester bon#;4i,? >?==<3 Although the i6entities of the in6i4i6ual nucleoti6es that are pol21eri5e6 to for1 a stran6 of (NA or %NA were known0 the actual structure of the functional (NA pol21er was not 6eter1ine6 until AHC@3 The general feeling was that the biologicall2 acti4e structure of (NA ha6 to be 1ore co1ple7 than a single string of nucleoti6es linke6 together b2 phospho6iester bon6s3 Scientists throughout the worl6 were testing se4eral 6ifferent 1o6els for the structure of (NA0 with 4ariations ranging fro1 the nu1ber of stran6s in the 1olecule to the location of the sugarN phosphate backbone ;i3e30 either

interior or e7terior<3 Watson an6 +rick built potential 1o6els to 6eter1ine that (NA e7iste6 as a two8stran6e6 structure with the sugarNphosphate backbone on the e7terior3 This 1o6el pro4e6 to be correct for 1ost (NA 1olecules in that it was the 1ost consistent with the a4ailable 6ata0 na1el2 the che1ical nature of the co1ponents of (NA0 +hargaff=s ratios for base co1position0 an6 L8ra2 6iffraction 6ata3

)HARGAFFDS RATIOS "ntil Erwin +hargaff=s work0 scientists ha6 labore6 un6er the erroneoustetran+"leoti#e (*ot esis3 This h2pothesis propose6 that (NA

was 1a6e up of e>ual >uantities of the four bases: therefore0 a subunit of (NA consiste6 of one cop2 of each base3 +hargaff carefull2 anal25e6 the base co1position of (NA in 4arious species ;table >?;<3 He foun6 that although the relati4e a1ount of a gi4en nucleoti6e 6iffers between species0 the a1ount of a6enine e>uale6 that of th21ine0 an6 the a1ount of guanine e>uale6 that of c2tosine3 That is0 in the (NA of all the organis1s he stu6ie60 a A*A correspon6ence e7iste6 between the purine an6 p2ri1i6ine bases3 This relationship is known as ) ar,a44Ds r+le3 The su1 of the a1ount of a6enine an6 th21ine ;A P T<0 howe4er0 6i6 not e>ual the su1 of the a1ount of c2tosine an6 guanine ;+ P &<3 (epen6ing on the species e7a1ine60 +hargaff foun6 that the percentage of ;A P T< in (NA 4arie6 fro1 @GI to o4er FGI3 +hargaff=s obser4ations 6ispro4e6 the tetranucleoti6e h2pothesis: the four bases of (NA 6i6 not occur in a A*A*A*A ratio3 +hargaff=s results pro4i6e6 i1portant insight to Watson an6 +rick in the 6e4elop1ent of their 1o6el3

%NA 36RA& %IFFRA)TION STU%IES While Watson an6 +rick were buil6ing 1o6els to eluci6ate the structure of (NA0 %osalin6 #ranklin0 working in Maurice Wilkins= laborator2 ;4i,3 >?=@<0 was collecting critical 6ata that re4eale6 the larger structure of (NA3 The 6ata was base6 on 36ra( #i44ra"tion3 In this techni>ue0 (NA 1olecules are first isolate6 in a cr2stal0 which arranges the in6i4i6ual (NA 1olecules in an or6erl2 wa23 When a bea1 of L8ra2s hits the cr2stal0 the bea1 scatters in an or6erl2 fashion0 an6 the 6iffraction pattern can be recor6e6 on photographic fil1 or co1puter8controlle6 6e4ices3 The pattern that is pro6uce6 re4eals

i1portant structural features of the (NA in the cr2stal3 The cross in the center of the photograph in 4i,+re >?=; in6icates that the 1olecule is a heli7: the 6ark areas at the top an6 botto1 co1e fro1 the bases0 stacke6 perpen6icular to the 1ain a7is of the 1olecule3 This i1age can also be use6 to 6eter1ine the 6istance between a69acent bases an6 the nu1ber of bases in a helical unit3 The i1age also re4eale6 that the heli7 was co1pose6 of two parallel stran6s that re1aine6 an e>ual 6istance apart fro1 each other3 This i1age of the (NA 1olecule an6 the correspon6ing calculations greatl2 contribute6 to Watson an6 +rick=s un6erstan6ing of the (NA structure3

THE WATSON6)RI)- MO%EL With the 6ata a4ailable0 Watson an6 +rick began constructing 1olecular 1o6els ;4i,? >?=E<3 The2 foun6 that a possible structure for (NA was one in which two helices coile6 aroun6 one another ;a 6ouble heli7<0 with the sugarN phosphate backbones on the outsi6e an6 the bases on the insi6e3 This structure woul6 fit the 6i1ensions L8ra2 6iffraction ha6 establishe6 for (NA if the bases fro1 the two stran6s were opposite each other an6 for1e6 JrungsK in a helical Jla66erK ;4i,? >?=F<3 The 6ia1eter of the heli7 coul6 onl2 be kept constant at about ?G T ;AG angstro1 units O A n1< if one purine an6 one p2ri1i6ine base 1a6e up each rung3 Two purines per rung woul6 be too big0 an6 two p2ri1i6ines woul6 be too s1all3 After further e7peri1entation with 1o6els0 Watson an6 +rick foun6 that the h26rogen bon6ing necessar2 to for1 the rungs of their helical la66er

coul6 occur rea6il2 between certain base pairs0 na1el2 the pairs that +hargaff foun6 in e>ual fre>uencies3 Ther1o62na1icall2 stable h26rogen bon6ing occurs between th21ine an6 a6enine0 an6 between c2tosine an6 guanine ;4i,? >?=<<3 Two h26rogen bon6s connect a6enine an6 th21ine an6 three connect c2tosine an6 guanine3 The relationship is one of "o!*le!entarit(* for an2 gi4en base0 there is one an6 onl2 one other base that can opti1all2 h26rogen bon6 with it3 Another point about (NA structure relates to the *olarit( that e7ists in each stran63 That is0 one en6 of a linear (NA stran6 has a CS phosphate an6 the other en6 has a @S h26ro72l group3 Watson an6 +rick foun6 that h26rogen bon6ing woul6 occur if the polarit2 of the two stran6s ran in opposite 6irections: that is0 if the two stran6s were antiparallel ;4i,? >?=><3 Notice that the antiparallel nature re>uires knowle6ge of the opposite orientation of the two stran6s0 which coul6 not be pre6icte6 fro1 L8ra2 6iffraction 6ata3

ALTERNATIVE FORMS OF %NA Although Watson an6 +rick=s 1o6el of (NA has pro4e6 to be correct0 research has subse>uentl2 shown that (NA can be either 6ouble8stran6e6 or singlestran6e60 as in so1e (NA 4iruses3 We also now know that 6ouble8 stran6e6 (NA e7ists in three 6ifferent 1a9or for1s: A8(NA0 '8(NA0 an6 -8 (NA3 The (NA for1 base6 on Wilkins= an6 #ranklin=s L8ra2 6iffraction 6ata is calle6$6%NA3 It is a righthan6e6 heli70 that is0 it turns in a clockwise 1anner when 4iewe6 6own its a7is3 ;+url 2our fingers in 2our right han6 an6 point 2our right thu1b up3 A righthan6e6 heli7 will turn in the 6irection of 2our fingers as it 1o4es upwar63< In this for10 the bases are stacke6 al1ost e7actl2 perpen6icular to the 1ain a7is0 with about AG base pairs ;bp< per turn ;@B n1 per turn: see fig3 E3ACc<3 '8(NA represents the 1a9or for1 of

(NA that is present in a cell3 If the water content increases to about ECI0 (NA takes on another for10 A6%NA3 The A8(NA is also a right8han6e6 heli73 In contrast to '8(NA0 the bases of A8(NA are tilte6 relati4e to the a7is0 an6 there are 1ore base pairs per turn ;appro7i1atel2 AA3@ bp per turn<3 It is thought that 6ouble8 stran6e6 %NA an6 h2bri6 1olecules0 in which one stran6 is (NA an6 the other is %NA0 e7ist in the A for13 In AHEH0 Ale7an6er %ich an6 his colleagues at MIT 6isco4ere6 a left8han6e6 heli7 that the2 calle6 /6%NA because its backbone for1e6 a 5ig5ag structure ;fig3 E3AD<3 The structure of -8(NA was 6eter1ine6 in 4er2 s1all (NA 1olecules co1pose6 of repeating &N+ se>uences on one stran6 with the co1ple1entar2 +N& se>uences on the other ;alternating purines an6 p2ri1i6ines<3 -8(NA looks like '8(NA with each base rotate6 ADG 6egrees0 resulting in a 5ig5ag0 lefthan6e6 structure3 -8(NA is slightl2 1ore co1pact than either '8(NA or A8(NA0 with appro7i1atel2 A? bp per turn3 !riginall20 it was thought that -8(NA woul6 not pro4e of interest to biologists because it re>uire6 4er2 high salt concentrations to beco1e stable3 Howe4er0 it was foun6 that -8(NA can be stabili5e6 un6er ph2siologicall2 nor1al con6itions if 1eth2l groups are a66e6 to the c2tosines3 Thus0 a single (NA 1olecule 1a2 ha4e one region that contains '8 (NA an6 an a69acent region containing -8(NA0 if the -8(NA region contains alternating +N& se>uences an6 the c2tosines are 1eth2late63 -8(NA 1a2 be in4ol4e6 in regulating gene e7pression in eukar2otes0 because c2tosine 1eth2lation is one i1portant 1echanis1 in gene regulation3 We return to this topic in chapter AE3 #our a66itional for1s of right8han6e6 helical (NA ha4e been obser4e6 in the laborator23 %*D4! occurs un6er 4er2 6eh26rate6 con6itions an6 contains onl2 H3@ bp per helical turn3 D*D4! an6 E*D4! are foun6 in s2nthetic (NA 1olecules that lack guanines an6 possess onl2 E or D bp per helical turn3 P* D4!was 6isco4ere6 when (NA was stretche6 so that onl2 ?3F bp are present per helical turn3 It re1ains to be 6e1onstrate6 that these latter four for1s of (NA e7ist un6er ph2siological con6itions an6 what function0 if an20 the2 possess3 THE EU-AR&OTI) )ELL Eukar2otes0 bacteria0 an6 archaea represent the three superking6o1s of organis1s3 #ro1 a genetics stan6point0 the archaea ha4e not been as

e7tensi4el2 stu6ie6 as either bacteria or eukar2otes3 Although genetic research with prokar2otic organis1s has pro4i6e6 a great 6eal of infor1ation0 the prokar2otic s2ste1 is 6ifferent fro1 that of eukar2otes in se4eral wa2s3 The following co1parisons0 using E3 coli as a general 1o6el for prokar2otes0 6e1onstrate the greater co1ple7it2 that is obser4e6 in eukar2otes* A3 E- coli e7ists as a si1ple0 single cell3 Although so1e prokar2otes 6o aggregate0 sporulate0 an6 show a few other li1ite6 for1s of 6ifferentiation0 the2 are pri1aril2 one8celle6 organis1s3 An60 although so1e eukar2otes are single8celle6 ;e3g30 2east<0 the essence of eukar2otes is 6ifferentiation3 In hu1an beings0 a 52gote gi4es rise to e4er2 other cell t2pe in the bo62 in a relati4el2 pre6ictable 1anner3 An E- coli cell is s1all ;G3CNC3G U1 in length for bacteria<3 Eukar2otic cells are generall2 larger than prokar2otes ;AGNCG U1 in length for ani1al tissue cells<3 An E- coli cell has 4er2 little internal structure3 Eukar2otes ha4e a nu1ber of internal organelles an6 an e7tensi4e lipi6 1e1brane s2ste10 inclu6ing the nuclear en4elope itself3 The single circular E3 coli chro1oso1e contains appro7i1atel2 B3E V AGF bp of (NA3 The haploi6 hu1an geno1e0 with ?@ ;fe1ales< or ?B ;1ales< linear chro1oso1es0 contains nearl2 a thousan6 ti1es 1ore (NA3 Most E- coli genes are groupe6 as operons that are regulate6 through a co11on 1echanis1: al1ost all eukar2otic genes are separate an6 each possesses its own regulator2 ele1ents3 The chro1oso1al (NA of E3 coli is not highl2 co1ple7e6 with proteins0 although so1e histonelike proteins are foun6 in the cell3 Eukar2otic (NA0 b2 contrast0 e7ists in the for1 of nucleoprotein0 a (NANhistone protein co1ple73 'ecause of eukar2otes= greater co1ple7it20 we ne7t take a look at the structure an6 characteristics of the eukar2ote chro1oso1e3 In later chapters0 we co4er 1echanis1s of regulating gene e7pression an6 patterns of eukar2otic 6e4elop1ent3 'acterial genetics is 6escribe6 in its own chapter0 chapter AC3

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THE EU-AR&OTI) )HROMOSOME' ONE %NA MOLE)ULE PER )HROMOSOME

!c%ra&'(ill Ans&ers ) %ene E,-ression. Transcri-tion

By (yde, D.R. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

T)$ES !# %NA 'A+TE%IAL T%ANS+%I$TI!N* $%ELIMINA%IES 8 (NAN%NA +!M$LEMENTA%IT) 'A+TE%IAL %NA $!L)ME%ASE $%!,A%)!TI+ T%ANS+%I$TI!N* $%!M!TE% SEM"EN+ES AN( T%ANS+%I$TI!N INITIATI!N $%!,A%)!TI+ T%ANS+%I$TI!N* T%ANS+%I$TI!N EL!N&ATI!N TE%MINAT!% SEM"EN+ES AN( T%ANS+%I$TI!N TE%MINATI!N* %H!8(E$EN(ENT AN( %H!8 IN(E$EN(ENT TE%MINAT!%S TE%MINAT!% SEM"EN+ES AN( T%ANS+%I$TI!N TE%MINATI!N* A S"MMA%) !# 'A+TE%IAL T%ANS+%I$TI!N MEAS"%IN& %%NA +!M$!NENTS* THE S E('E%& "NIT %I'!S!MAL ST%"+T"%E AN( $%!("+TI!N T%ANS#E% %NA ST%"+T"%AL SIMILA%ITIES !# ALL T%ANS#E% %NAS T%ANS#E% %NA &ENES

T&PES OF RNA In the protein s2nthesis process0 fi4e 6ifferent kin6s of %NA ser4e critical functions3 The first t2pe is !essen,er RNA 7!RNA80 which carries the (NA se>uence infor1ation an6 will be 6irectl2 translate6 into an a1ino aci6 se>uence at theriboso!es? The secon6 t2pe is trans4er RNA 7tRNA80 which brings the a1ino aci6s to the riboso1es0 where it base8pairs with the co1ple1entar2 se>uence in the 1%NA3 The thir6 t2pe of %NA is a structural an6 functional part of the riboso1e0 calle6 riboso1al %NA ;r%NA<3 The general relationships of the roles of these three classes of %NAs are 6iagra11e6 in 4i,+re =C?@3 Although these three t2pes of %NAs are foun6 in all organis1s0 the final two t2pes are foun6 onl2 in eukar28 otic cells3 Thes!all n+"lear RNAs

7snRNAs8 are essen8 tial for the proper pro6uction of 1%NA b2 6irecting proteins to the e7onNintron 9unctions where the2 re1o4e the introns fro1 the pri1ar2 transcript to generate the 1%NA3 The final t2pe of %NA consists of !i"roRNAs 7!iRNAs80 which pla2 an i1portant role in regulating both transcription of %NAs an6 translation of proteins3

$A)TERIAL TRANS)RIPTION' PRELIMINARIES 6 %NAGRNA )OMPLEMENTARIT& In4estigators nee6e6 proof that gene8si5e6 %NAs ;not t%NAs or r%NAs< foun6 in the c2toplas1 were co1ple1entar2 to the (NA in the nucleus3 E7peri1ents 2iel6e6 at least two lines of e4i6ence supporting this h2pothesis3 #irst0 it was shown that the %NAs pro6uce6 b2 4arious organis1s ha4e base ratios 4er2 si1ilar to the base ratios in the sa1e organis1=s (NA 7table =C?=83

The secon6 line of e4i6ence ca1e fro1 e7peri1ents b2 se4eral researchers using %NAGRNA (bri#iHation3 This techni>ue 6enatures (NA b2 heating0 which causes the two stran6s of the 6ouble heli7 to separate ;4i,? =C?;<3 When the solution cools0 a certain proportion of the (NA stran6s reanneal.that is0 co1ple1entar2 stran6s Jfin6K each other an6 refor1 6ouble helices3 When %NA isolate6 fro1 the c2toplas1 was a66e6 to the 6enature6 (NA solution an6 the solution was coole6 slowl20 so1e of the %NA 1olecules for1e6 6ouble helices with one stran6 of (NA3 This woul6 occur if the %NA frag1ents were co1ple1entar2 to a section of the (NA ;see fig3 AG3@<3 The e7istence of e7tensi4e co1ple1entarit2 between (NA an6 %NA is a persuasi4e in6ication that (NA acts as a te1plate for co1ple1entar2 %NA3 In another e7peri1ent0 (NAN%NA h2bri6i5ation showe6 that infection of bacteria b2 bacteriophage le6 to the pro6uction of bacteriophage8specific 1%NAs3 %NAs were e7tracte6 fro1Escherichia coli before an6 after bacteriophage T? infection an6 were then teste6 to see whether the2 anneale6 with either the T? phage (NA or the E3 coli(NA3 The %NA in the E3 coli cell before infection was foun6 to anneal with onl2 the E3 coli (NA3 Howe4er0 a large a1ount of the %NA in the E3 coli cell after bacteriophage T? infection anneale6 to the T? phage (NA an6 not the E3 coli(NA3 #ro1 this it is appar8 ent that when the phage infects the E3 coli cell0 it starts to 1anufacture %NA co1ple1entar2 to its own (NA an6 stops the E3 coli(NA fro1 ser4ing as a te1plate3 While this supporte6 the h2pothesis that %NA is transcribe6 ;s2nthesi5e6< fro1 a (NA te1plate an6 then 6irects protein s2nthesis0 two significant >uestions beca1e apparent3 #irst0 is the %NA single8 or 6ouble8 stran6e6? Secon60 is it s2nthesi5e6 ;transcribe6< fro1 one or both stran6s of the parental (NA? !o" Many Strands Does RNA !a#e$ #or the 1ost part0 cellular %NA 6oes not e7ist as a 6ouble heli73 It can for1 6ouble8helical sections when co1ple1entar2 parts co1e into apposition ;for e7a1ple0 see figs3 AG3AA an6 AG3AE<0 but its general for1 is not a 6ouble heli73 The si1plest0 an6 1ost con4incing0 e4i6ence for this is that co1ple1entar2 bases 6o not occur in corre8 spon6ing e>ual proportions in %NA0 as the2 6o in (NA ;+hargaff=s ratios<3 That is0 in %NA0 uracil 6oes not usu8 all2 occur in the sa1e >uantit2 as a6enine0 nor 6oes c2to8 sine occur in the sa1e >uantit2 as guanine ;table =C?@<3

%s RNA &ranscribed from 'ne DNA Strand or (oth$ The answer to the secon6 >uestion is that the stran6s of an2 gi4en seg1ent of the (NA 6ouble heli7 are not both use6 to s2nthesi5e %NA0 although rare e7cep8 tions 6o occur3 Si1ilarl20 a specific %NA is not s2nthe8 si5e6 fro1 either (NA stran63 Suppose that a se>uence of nucleoti6es on one stran6 of a (NA 6uple7 specifies a se>uence of a1ino aci6s for a protein0 an6 the co1ple1entar2 nucleoti6e se>uence also specifies the a1ino aci6 se>uence for another functional protein3 'ecause 1ost en521es are @GGNCGG a1ino aci6s long0 the 4irtual i1possibilit2 of this entire region properl2 enco6ing two proteins with co1ple1entar2 nucleoti6e se>uences shoul6 be ob4ious3 #or this to occur0 the a1ino aci6 se>uence in one protein0 enco6e6 b2 the (NA0 woul6 6ictate the co1ple1entar2 nucleoti6e se>uence0 an6 therefore the a1ino aci6 se>uence of the other protein3 It was0 there8 fore0 assu1e6 that for an2 particular gene onl2 one (NA stran6 is transcribe60 while the co1ple1entar2 stran6 is not transcribe6 in that region3 +onsi6erable e4i6ence now supports this assu1ption3 The 1ost i1pressi4e e4i6ence ca1e fro1 work 6one with bacteriophage S$D0 which infects acillus subtilis3 This phage has an interesting propert2.a great 6isparit2 e7ists in the purineNp2ri1i6ine ratio between the two stran6s of its (NA3 The 6isparit2 is significant enough that the two stran6s can be separate6 using 6ensit28gra6ient ultracentrifugation ;see the Meselson an6 Stahl e7peri1ent in chapter H<3 The S$D geno1ic (NA was 6enature60 an6 the two stran6s were separate6 b2 6ensit28gra6ient ultracentrifugation3 (NAN%NA h2bri6i5ation coul6 then be carrie6 out on each in6i4i6ual (NA stran6 with the %NA pro6uce6 after the 4irus infects the bacteriu13 /ulius Mar1ur an6 his colleagues foun6 that the %NA onl2 h2bri6i5e6 to the hea4ier of the two S$D (NA stran6s3 Thus0 onl2 the hea42 stran6 acte6 as a te1plate for the pro6uction of %NA 6uring the infection process3 The (NA stran6 that is co1ple1entar2 to the %NA 1olecule is calle6 the non"o#in, orte!*late stran#3 The "o#in, or nonte!*late stran# is the (NA stran6 that is not co1ple1entar2 to the %NA 1olecule3 In the S$D (NA 1olecule0 the hea42 stran6 is the nonco6ing stran6 an6 the light stran6 is the co6ing stran63 The i6ea that onl2 one stran6 of (NA ser4es as a transcription te1plate

for %NA has also been 4erifie6 for se4eral other s1all phages3 When larger 4iruses an6 cells are e7a1ine60 howe4er0 we fin6 that either of the stran6s 1a2 be transcribe60 but onl2 one stran6 is pri1aril2 use6 as a te1plate in an2 one region ;4i,? =C?E<3 This was clearl2 shown with the TB bacterio8 phage of E3 coli0 in which certain %NAs h2bri6i5e with one (NA stran60 an6 other %NAs h2bri6i5e with the other3

$A)TERIAL RNA POL&MERASE In prokar2otes0 the en521e RNA *ol(!erase controls transcription of %NA3 We pre4iousl2 6iscusse6 %NA pol21erase 6uring (NA replication3 $ri1ase0 which is an %NA pol21erase0 transcribes a short %NA pri1er using the (NA as the te1plate3 The %NA pri1er is e7ten6e6 in a CS W @S 6irection b2 (NA pol21erase to s2nthesi5e the new (NA stran6 ;chapter H<3 "sing (NA as a te1plate0 %NA pol21erase a66s ribonucleo8 ti6e triphosphates ;ribonucleoti6es< in a CS W @S 6irec8 tion0 which is the sa1e polarit2 that (NA

pol21erase a66s 6eo72ribonucleoti6es3 %ibonucleoti6es 6iffer fro1 6eo72ribonucleo8 ti6es in two wa2s3 #irst0 ribonucleoti6es use the sugar ribose0 whereas 6eo72ribonucleoti6es use the sugar ?S8 6eo72ribose0 which 6iffers fro1 ribose b2 the absence of the h26ro72l group on the ?S carbon ;4i,? =C?F<3 Secon60 ribonucleoti6es ha4e the base uracil instea6 of th28 1ine0 which is use6 in 6eo72ribonucleoti6es ;see fig3 AG3C<3 Thus0 the %NA uracil will base8pair with a6enine through two h26rogen bon6s ;analogous to the two h26rogen bon6s between th21ineN a6enine base pairs<3 The co1plete E3 coli %NA pol21erase en521e. the holoen521e.is co1pose6 of a core en521e an6 a si,!a 7r8 4a"tor3 The core en521e is co1pose6 of four subunits* two copies of an R8subunit0 an6 one cop2 of a X an6 XS: this core is the co1ponent of the holoen521e that actuall2 carries out the %NA s2nthesis3 The Y8factor is in4ol4e6 in recogni5ing transcription start signals on the (NA3 #ollowing the initiation of transcription0 the Y8factor 6isassociates fro1 the core en521e3 Logicall20 transcription shoul6 not be a continuous process like (NA replication3 If transcription were not regulate60 then all the cells of a higher organis1 woul6 be i6entical0 an6 a bacterial cell woul6 transcribe all of its genes all of the ti1e an6 s2nthesi5e all of its proteins3 'ecause so1e en521es 6epen6 on substrates not present all of the ti1e0 an6 so1e reactions in a cell occur less fre8 >uentl2 than others0 the cell.be it a bacteriu1 or a hu1an li4er cell.nee6s to regulate its protein s2nthesis3 !ne of the 1ost efficient wa2s for a cell to e7ert the necessar2 control o4er protein s2nthesis is to reg8 ulate the a1ount of %NA that is transcribe6 fro1 each gene3 Transcription of regions outsi6e of genes or of genes co6ing for unnee6e6 en521es is wasteful3 Therefore0 %NA pol21erase shoul6 be selecti4e3 It shoul6 transcribe onl2 those (NA seg1ents ;genes or s1all groups of genes< that co6e for pro6ucts re>uire6 b2 the cell at a particular ti1e3 The 1echanis1s of transcriptional control can be e7a1ine6 in two wa2s3 #irst0 we nee6 to un6erstan6 how the beginnings an6 en6s of transcriptional units ;a single gene or a series of a69acent genes< are 1arke63 Secon60 we want to eluci6ate how the cell can selecti4el2 turn transcription either on or off at 6ifferent ti1es an6 in 6ifferent cells3 The latter issues0 which are the ke2s to transcriptional efficienc2 an6 to eukar2otic growth an6 6e4elop1ent0

are co4ere6 in later chapters3 %NA pol21erase 1ust be able to recogni5e both the beginnings an6 the en6s of genes ;or gene groups< on the (NA 6ouble heli7 in or6er to properl2 initiate an6 ter1inate transcription3 It 1ust also be able to recogni5e the correct (NA stran6 to a4oi6 transcrib8 ing the (NA stran6 that is not infor1ational3 %NA pol21erase acco1plishes those tasks b2 recogni5ing certain start an6 stop signals in (NA0 calle6 initiation an6 ter1ination se>uences0 respecti4el23

PRO-AR&OTI) TRANS)RIPTION' PROMOTER SE:UEN)ES AN% TRANS)RIPTION INITIATION The bacterial %NA pol21erase 1olecule bin6s a pro8 1oter region consisting of about FG bp of (NA3 This si5e was 6eter1ine6 b2 allowing the %NA pol28 1erase holoen521e to bin6 (NA an6 then 6igesting the co1ple7 with nucleases0 in a techni>ue known as 4oot*rintin, ;4i,? =C?<<3 The pol21erase Jprotects0K or pre4ents 6egra6ation of0 the (NA region it bin6s3 The un6igeste6 (NA is then isolate6 an6 its si5e 6eter8 1ine6 b2 gel electrophoresis3 #urther infor1ation about the nature of the pro8 1oter se>uences was

gaine6 through reco1binant (NA technolog2 an6 nucleoti6e se>uencing techni>ues ;6escribe6 in chapter A?<3 Se>uencing 1an2 pro1oters fro1 6ifferent genes re4eale6 that the2 contain co11on se>uences3 (acterial Promoter Consensus Se)uences If se4eral nucleoti6e se>uences align with one another0 an6 each has e"actly the sa1e series of nucleoti6es in a gi4en seg1ent0 we sa2 that the se>uence in that seg1ent co1prises an in4ariant0 or "onserve# se9+en"e3 If0 how8 e4er0 so1e 4ariation appears in the se>uence0 but certain nucleoti6es occur at a high fre1uency ;significantl2 greater than b2 chance<0 we refer to those nucleoti6es as 1ak8 ing up a "onsens+s se9+en"e? Surroun6ing a point inbacterial pro1oters0 about AG nucleoti6es before the first transcribe6 base0 is a consensus se>uence CS TATAAT @S3 This se>uence is known as a Pribno5 bo. after one of its 6isco4erers0 (a4i6 $ribnow ;4i,? =C?><3 The nucleoti6es in the $ribnow bo7 are 1ostl2 a6enines an6 th21ines0 so the region is pri1aril2 hel6 together b2 onl2 two h26rogen bon6s per base pair3 'ecause local (NA 6enaturation 1ust occur prior to the start of transcription so that co1ple1entar2 pairing of ribonucleoti6es with the (NA te1plate stran6 can occur0 fewer h26rogen bon6s in the (NA 1olecule 1ake this 6enaturation easier energeticall23 When the pol21erase is boun6 at the pro1oter region ;see fig3 AG3E<0 it is in position to begin pol21eri5ation FND nt 6own fro1 the $ribnow bo73 The se>uences shown in figure AG3E are those of the co6ing stran6 of (NA3 It is a general con4ention to show the co6ing stran6 because it possesses the sa1e se>uence0 substituting " for T in the (NA0 as the 1%NA3 Thus0 the se>uence of the co6ing stran6 can be use6 to 6irectl2 6eter1ine the translate6 a1ino aci6 se>uence ;see chapter AA<3 'oth the (NA co6ing stran6 an6 the 1%NA are co1ple1entar2 to the te18 plate stran6 ;also referre6 to as the non"o#in, stran#I 4i,? =C?A<3 Another con4ention use6 in 6escribing the (NA stran6s is the sense an6 antisense stran6s3 Another i1portant con4ention use6 in labeling the (NA is to in6icate the first transcribe6 base b2 the nu1ber J= an6 to use positi4e nu1bers to count farther along the (NA in the #o5nstrea! 6irection of transcription3 So0 if transcription is procee6ing to the right0 then the 6irection to the right of PA is 6own8 strea1 an6 to the left is calle6 +*strea!0 with bases in6icate6 b2 negati4e nu1bers ;4i,? =C?B<3 Notice that there is not a base

labele6 as G0 as the PA base is pre8 ce6e6 b2 NA3 "n6er this con4ention0 the $ribnow bo7 is often referre6 to as the G=C se9+en"e3 #igure AG3H shows a secon6 consensus se>uence0 CS TT&A+A @S0 which is present in 1an2 E3 coli pro1ot8 ers3 It is centere6 near position N@C an6 conse>uentl2 is referre6 to as the G;F se9+en"e3 Mutations were generate6 in the NAG an6 N@C se>uences to 6eter1ine how the2 affecte6 transcription initiation3 Mutations in either the NAG or N@C se>uences usuall2 6ecrease6 the a1ount of transcription an6 increase6 the fre8 >uenc2 of transcription initiation at positions other than PA3 The Y8factor0 which is re>uire6 for correct transcription initiation0 recogni5es an6 bin6s both the N@C an6 the N AG se>uences3 Thus0 the 1ore a NAG or N@C se>uence 6iffers fro1 the consensus se>uence0 the less efficient Y8factor an6 %NA pol21erase bin6s an6 the less fre>uentl2 that particular pro1oter initiates tran8 scription3 The Y8factor was also foun6 to be sensiti4e to the spacing between these se>uences0 with the 1ost efficient 6istance being AE bp3 #arther upstrea1 fro1 the N@C se>uence is a thir6 se>uence that is present in bacterial pro1oters0 which are 4er2 strongl2 e7presse60 such as the r%NA genes ;see fig3 AG3H<3 This +*strea! ele!ent is about ?G bp long0 is centere6 at NCG0 an6 is rich in A an6 T bases3 Mutational stu6ies ha4e shown that when this ele1ent is a66e6 at the proper location to pro1oters that 6o not nor1all2 ha4e it0 the rate of transcription of the 1o6i8 fie6 gene greatl2 increases3 !ther recognition sites ha4e been foun6 in pro8 kar2otes0 both upstrea1 an6 6ownstrea10 at which 4arious regulator2 proteins attach3 These proteins can enhance or inhibit transcription b2 6irect contact with the pol21erase ;specificall2 the R8 an6 Y8subunits<3 +hapter AF contains a 6iscussion of these proteins3 *ariable Action of +,-actors 'ecause the holoen521e recogni5es consensus se>uences in a pro1oter0 rather than bin6ing to a con8 ser4e6 se>uence0 it is not surprising that so1e pro8 1oters are boun6 1ore efficientl2 than others or that 6ifferent Y8factors e7ist within a cell3 In E3 coli0 the 1a9or Y8factor is a protein of EG0GGG ( ;6altons<0 referre6 to as Y EG 3 ;!ne 6alton is an ato1ic 1ass of A3GGGG0 appro7i1atel2 e>ual to the 1ass of a h26rogen ato13< E3 coli also possesses about fi4e less co11on Y8factors that pro4i6e the cell with a 1echa8 nis1 to transcribe 6ifferent

genes un6er 6ifferent cir8 cu1stances3 #or e7a1ple0 at higher te1peratures0 the E3 coli cell e7presses a group of new proteins0 referre6 to as eat s o"k *roteins2 which helps to protect the cell against the ele4ate6 te1peratures3 These 4arious heat shock proteins are all e7presse6 si1ultaneousl2 because their correspon6ing genes contain pro1oters that are recogni5e6 b2 the sa1e Y8factor0 one with a 1olecular weight of @?0GGG ( ;Y @? <3 The heat shock gene pro1oters are acti4el2 transcribe6 onl2 after the te18 perature increases because Y @? is onl2 pro6uce6 b2 the cell after heat shock3 'oth prokar2otic an6 eukar2otic heat shock proteins an6 other s2ste1s of transcrip8 tional control are 6escribe6 in chapters AF an6 AE3 #ro1 1utational stu6ies of pro1oters an6 the pro8 teins in the %NA pol21erase holoen521e0 we now ha4e a picture of a holoen521e that bin6s to a (NA pro8 1oter because the Y8factor recogni5es an6 bin6s the NAG an6 N @C (NA se>uences0 an6 the R8proteins recogni5e the upstrea1 ele1ent when it is present ;4i,? =C?=Ca<3 A66itionall20 the R8 an6 Y8subunits recogni5e proteins boun6 to 4arious other upstrea1 ele1ents when these ele1ents are present3 This initiation co1ple7 is initiall2 referre6 to as a "lose# *ro!oter "o!*le.because the (NA has not 6enature6 in the pro1oter region ;see fig3 AG3AGa<3 After the holoen521e in6uces the (NA to 6ena8 ture in a s1all region0 the %NA pol21erase an6 (NA for1 an o*en *ro!oter "o!*le. ;fig3 AG3AGb<3 The 6ena8 ture6 (NA can then base8pair with ribonucleoti6es an6 per1it the initiation of transcription ;fig3 AG3AGc<3 After the transcription of CNAG bases0 the Y8factor is release6 an6 transcription procee6s ;fig3 AG3AG6<3

PRO-AR&OTI) TRANS)RIPTION' TRANS)RIPTION ELONGATION Transcription0 like (NA replication0 alwa2s procee6s in the CS W @S 6irection3 That is0 a single ribonucleoti6e is a66e6 anew to the @S8!H free en6 of the %NA ;see fig3 AG3AG6<3 (ue to the antiparallel nature of 6ouble8 stran6e6

nucleic aci6s0 transcription procee6s along the (NA te1plate in a @S W CS 6irection3 "nlike (NA pol21erase0 howe4er0 prokar2otic %NA pol21erase 6oes not possess a significant @S W CSe7onuclease acti4it2 to 4erif2 the co1ple1entarit2 of the new bases a66e6 to the growing %NA stran63 This 6eficienc2 is not serious: because 1an2 1%NAs are short8li4e60 an6 because 1an2 copies are 1a6e fro1 acti4el2 transcribe6 genes0 an occasional 1istake probabl2 6oes not pro6uce per1anent or o4erwhel1ing 6a1age3 If a particular %NA is generate6 that contains a 1utation0 a new %NA will be 1a6e soon3 E4olutionaril2 speaking0 it see1s 1ore i1portant to 1ake %NA >uickl2 than to proofrea6 each %NA 1a6e3 In contrast0 if an error is 1a6e in (NA replication0 the 6aughter cell that recei4es the 1utant cop2 an6 all the subse>uent 6aughter cells will possess the 1utation3 To illustrate this 6ifference0 i1agine that a 1utation occurs in a gene 6uring (NA replication once e4er2 AGG cell 6i4isions3 If this 1utation results in the e7pression of a nonfunctional protein that causes a 1utant phenot2pe0 then this 1utant cell an6 all the subse>uent 6aughter cells will ha4e the 1utant phenot2pe3 In contrast0 if AI of the %NAs transcribe6 fro1 this gene in a wil68t2pe cell contain 1utations0 then the cell will still possess HHI of the wil68t2pe %NAs an6 will e7hibit the wil68t2pe phenot2pe3 #urther1ore0 the subse>uent 6aughter cells will still ha4e the possibilit2 of e7pressing onl2 wil68t2pe %NAs fro1 this gene because 1utations in the %NA are not inherite63 This e7a1ple shows that transcription can tolerate a higher error rate than replication3 TERMINATOR SE:UEN)ES AN% TRANS)RIPTION TERMINATION' RHO6 %EPEN%ENT AN% RHO6IN%EPEN%ENT TERMINATORS Two t2pes of ter1inator se>uences e7ist in E3 coli0 na1el2 rho86epen6ent an6 rho8in6epen6ent0 which 6iffer in their re>uire1ent for the r o 798 *rotein? R o6#e*en#ent ter!inators utili5e both the Z8protein an6 a specific %NA structure3 In the absence of the Z8protein0 %NA pol21erase continues to transcribe past the ter1inator se>uence in a process known as rea68through3R o6 in#e*en#ent ter!inators re>uire a specific %NA structure0 but not the Z8protein3 'oth t2pes of ter1inators re>uire the sa1e t2pe of %NA structure0 na1el2 a particular se>uence an6 its in4erte6 for10 separate6 b2 another short se>uence3 This inverte#6re*eat se9+en"e is shown in 4i,+re =C?==3 In

this e7a1ple0 the se>uence CS AAA&&+T++ @S is present in both the co6ing stran6 an6 the te1plate stran63 Notice that the polarit2 6ictates the orientation of the se>uence within each stran63 A B8nt se>uence ;""""< separates the in4erte6 repeats3 In4erte6 repeats can for1 a ste!6loo* str+"t+re b2 pairing co1ple1entar2 bases within the transcribe6 1%NA3 'oth rho86epen6ent an6 rho8in6epen6ent ter1ina8 tors ha4e a ste18loop structure in the %NA 9ust before the last base transcribe63 %ho8in6epen6ent ter1ina8 tors also ha4e a se>uence of uracil8containing nucleo8ti6es in the %NA after the in4erte6 repeat0 whereas rho86epen6ent ter1inators 6o not ;see fig3 AG3AA<3 Although the e7act se>uence of e4ents at the ter1i8 nator is not full2 known0 it appears that the %NA ste18 loop structure for1s an6 causes the %NA pol21erase to pause 9ust after co1pleting it3 This pause 1a2 then allow ter1ination un6er two 6ifferent circu1stances3 In rho8in6epen6ent ter1ination0 the pause 1a2 occur 9ust after the se>uence of uracils is transcribe6 ;4i,? =C?=@<3 "racilNa6enine base pairs ha4e two h26ro8 gen bon6s an6 are thus less stable ther1o62na1icall2 than guanineNc2tosine base pairs3 $erhaps 6uring the pause0 the uracilNa6enine base pairs spontaneousl2 6enature0 releasing the transcribe6 %NA an6 the %NA pol21erase0 which ter1inates transcription3 %ho86epen6ent ter1inators0 b2 contrast0 6o not ha4e the uracil se>uence after the ste18loop structure3 Here0 ter1ination 6epen6s on the presence an6 action of the rho protein ;Z<0 which bin6s to a particular se>uence in the newl2 for1ing %NA3 In an AT$86epen6ent process0 Z tra4els along the %NA in a CS W @S 6irection at a spee6 co1parable to the transcription process itself ;see fig3 AG3A?<3 $ossibl20 when %NA pol21erase pauses at the ste18loop structure0 Z catches up to the pol21erase an6 6enatures the (NAN%NA h2bri60 which releases the transcribe6 %NA an6 %NA pol21erase fro1 the (NA te1plate3 %ho can 6o this because it has (NAN%NA helicase ;unwin6ing< properties3 The process of transcription ter1ination is prob8 abl2 1ore co1ple7 than 6escribe63 Significant inter8 actions 1a2 re>uire other proteins an6 particular se>uences surroun6ing the ter1ination se>uence to be present3 This is an area of acti4e research3

TERMINATOR SE:UEN)ES AN% TRANS)RIPTION TERMINATION' A SUMMAR& OF $A)TERIAL TRANS)RIPTION Fi,+re =C?=; shows an o4er4iew of bacterial transcrip8 tion3 The infor1ation of a gene0 co6e6 in the se>uence of nucleoti6es in the (NA0 has been transcribe6 into a co1ple1entar2 se>uence of nucleoti6es in the %NA3 This %NA transcript contains a se>uence co1ple1en8 tar2 to the te1plate stran6 of the gene=s (NA an6 thus either acts as a 1essenger ;1%NA< fro1 the gene to the cell=s protein8s2nthesi5ing co1ple7 or pro6uces a functional %NA ;t%NA or r%NA< that is not translate63

An 1%NA transcript contains nucleoti6e se>uen8 ces that are to be translate6 into a1ino aci6s. co6ing seg1ents.as well as nonco6ing seg1ents before an6 after3 The translatable seg1ent0 or o*en rea#in, 4ra!e 7ORF82al1ost alwa2s begins with a three8base se>uence0 A"&0 which is known as a translation initia8 tor co6on ;4i,? =C?=E<3 The !%# en6s with one of the three8base se>uences "AA0 "A&0 or "&A0 known as translation ter1ination0 or nonsense0 co6ons3 ;We will 6iscuss these signals in chapter AA3< The portion of the 1%NA transcript that begins at the start of transcription an6 goes to the transla8 tion initiator co6on ;A"&< is referre6 to as a lea#er0 orFK +ntranslate# re,ion 7FK UTR83 The length of 1%NA fro1 the nonsense co6on ;"AA0 "A&0 or "&A< to the last nucleoti6e transcribe6 is the ;K +ntranslate# re,ion 7;K UTR83 These se>uences pla2 a role in ensur8 ing the structural stabilit2 of the 1%NA an6 regulate translation at the riboso1e3 #igure AG3AB 6iagra1s the relationship between a bacterial gene an6 its 1%NA transcript3 The pro1oter se>uences ;NAG an6 N@C< are locate6 upstrea1 of where transcription will begin ;PA< an6 are not present on the 1%NA3 The 1%NA contains a CS "T% se>uence that is locate6 upstrea1 of the translation initiator co6on ;A"&<3 The !%# is the region of the 1%NA that will be trans8 late6 an6 is followe6 b2 a @S "T% se>uence3 Notice that the se>uence of the co6ing stran6 of the (NA is analo8 gous to the 1%NA se>uence: both contain a recogni5able translation initiator co6on ;A"& in the 1%NA an6 AT& in the (NA< an6 a translation ter1ination co6on ;"AA in the 1%NA an6 TAA in the (NA<3 "nlike the pro1oter se>uence0 the transcription ter1ination signal is present in both the (NA an6 the @S en6 of the 1%NA3 In this si1plifie6 6rawing of a bacterial gene ;see fig3 AG3AB<0 the transcript represents onl2 one gene an6 has a single !%# that e7ten6s fro1 the A"& co6on to the "AA co6on3 Man2 prokar2otic transcripts0 howe4er0 contain the infor1ation for se4eral genes3 An o*eron is se4eral genes that enco6e proteins that are in4ol4e6 in a relate6 process0 which are e7presse6 on a single 1%NA that is un6er the transcriptional control of a single pro1oter3 This is a co11on 1echanis1 to e7press se4eral genes in a coor6inate6 1anner in a bacterial cell3 Now we turn our attention to the other two t2pes of bacterial %NAs* riboso1al an6 transfer %NAs3

MEASURING RRNA )OMPONENTS' THE SVE%$ERG UNIT %iboso1es an6 other s1all 1olecules an6 particles are 1easure6 in units that 6escribe their rate of se6i8 1entation 6uring 6ensit28gra6ient centrifugation in sucrose3 This techni>ue0 6e4elope6 in the AH?Gs b2 ph2sical che1ist Theo6or S4e6berg0 gi4es infor1ation on the si5e an6 shape of the particle 6ue to the spee6 of se6i1entation3 This unit of se6i1entation is na1e6 the Sve#ber, +nit2 S3 In sucrose 6ensit28gra6ient centrifugation0 the gra8 6ient is for1e6 b2 ph2sicall2 la2ering 6ecreasingl2 con8 centrate6 sucrose solutions on top of each other in a tube3 In the relate6 cesiu1 chlori6e 6ensit28gra6ient centrifu8 gation 6escribe6 in chapter H0 the gra6ient 6e4elops as a result of centrifugation0 an6 the cesiu1 chlori6e gra6i8 ent tube is spun until it reaches e>uilibriu13 The sucrose 1etho6 ten6s to be 1ore rapi6 because the gra6ient is for1e6 prior to centrifugation3 The 1olecules or par8 ticles being stu6ie60 or a 1i7ture0 are then a66e6 to the sucrose 6ensit2 gra6ient0 an6 the tube is spun in a centri8 fuge for a perio6 of ti1e3 As in cesiu1 chlori6e 6ensit2 centrifugation0 the 6ensest 1olecules ;with the highest S 4alues< will be at the botto1 of the gra6ient tube3 RI$OSOMAL STRU)TURE AN% PRO%U)TION %iboso1es in all organis1s are 1a6e of two subunits of une>ual si5e3 In E3 coli0 the se6i1entation 4alue is CGS for the large subunit an6 @GS for the s1aller one3 When together0 the subunits ha4e a se6i1entation 4alue of about EGS3 'ecause the S4e6berg 4alue corre8 spon6s to 6ensit20 si1pl2

a66ing the S 4alues for the two subunits will not accuratel2 6eter1ine the 6en8 sit2 of the protein co1ple73 Eukar2otic riboso1es 4ar2 fro1 CCS to FFS in ani1als0 an6 EGS to DGS in fungi an6 higher plants3 Most of our 6iscussion will be confine6 to the well8stu6ie6 riboso1es of E3 coli3 Each riboso1al subunit contains one or two r%NA 1olecules an6 a fi7e6 nu1ber of proteins3 The @GS subunit of E3 coli has ?A proteins an6 a AFS 1olecule of r%NA0 an6 the CGS subunit has @B proteins an6 two r%NAs* one ?@S r%NA an6 one CS r%NA ;fig3 AG3AC<3 (etails of riboso1al structure ha4e been stu6ie6 b2 iso8 lating an6 purif2ing all the proteins0 b2 e7peri1enting with the proper se>uence of asse1bl2 of subunits0 an6 through i11unological techni>ues that ha4e clarifie6 the positions of 1an2 proteins in co1plete6 riboso1al subunits3 It is belie4e6 that the r%NA is essential in catal25ing the bon6 between a69acent pepti6es 6uring protein translation3 In E3 coli0 all three r%NA genes are transcribe6 as a single long %NA 1olecule that is then clea4e6 an6 1o6ifie6 to for1 the final three r%NAs ;AFS0 ?@S0 an6 CS<3 The %NA that contains the three r%NA 1olecules also contains four t%NAs ;4i,? =C?=<<3 This %NA is transcribe6 fro1 fi4e to ten 6ifferent locations in theE- coli chro1oso1e3 The occurrence of the three r%NA seg1ents on the sa1e piece of transcribe6 %NA ensures a final ratio of A*A*A0 the ratio nee6e6 for riboso1al construc8 tion3 This transcription of three 6ifferent r%NAs as a single %NA is analogous to an operon3 It allows for the three 6ifferent r%NA genes to be regulate6 in the sa1e 1anner to ensure that the proper ratio of the gene pro6ucts ;r%NAs< is pro6uce63 Howe4er0 it is not an operon because the single %NA pro6uce6 fro1 the three genes is not translate63 Three of the four r%NAs are also initiall2 transcribe6 as a long0 single %NA that is then cut to pro6uce the three correctl2 si5e6 r%NAs0 as 6iscusse6 later in this chapter3 The r%NAs are functional 1olecules0 the2 are re>uire6 for the riboso1e to translate a protein0 the2 are not translate63 'ecause the r%NAs are not trans8 late60 the2 lack 1an2 of the ke2 co1ponents that are present in an 1%NA0 such as an !%# an6 translation initiation an6 ter1ination co6ons3 Without an !%#0 the2 also cannot possess either a CS "T% or a @S "T%3

TRANSFER RNA (uring protein s2nthesis ;see fig3 AG3?<0 an 1%NA 1olecule0 carr2ing the infor1ation transcribe6 fro1 the gene ;(NA<0 is boun6 to a riboso1e3 The transfer %NAs ;t%NAs<0 which are attache6 to specific in6i8 4i6ual a1ino aci6s0 interact with the 1%NA in the riboso1e3 The genetic co6e in the 1%NA is rea6 in groups of three a69acent nucleoti6es0 calle6 "o#ons 74i,? =C?=>a83 The nucleoti6es of the 1%NA co6on can pair with the co1ple1entar2 three bases.the anti"o#on.on a t%NA ;see fig3 AG3AEa<3 Each 6iffer8 ent t%NA carries a specific a1ino aci63 In this wa20 the t%NA recogni5es the specificit2 of the genetic co6e3 The correct a1ino aci6 is attache6 to its proper t%NA b2 one of a group of en521es calle6 a!inoa"(l6tRNA s(nt etases3 !ne specific a1inoac2l s2nthetase e7ists for e4er2 a1ino aci60 but each s2nthetase 1a2 recogni5e 1ore than one t%NA because there are 1ore t%NAs ;an6 co6ons< than there

are a1ino aci6s3 ;The genetic co6e is 6escribe6 in 6etail in the following chapter0 which focuses on translation3< %obert W3 Holle2 an6 his colleagues were the first to 6isco4er the nucleoti6e se>uence of a t%NA3 In AHFC0 the2 publishe6 the structure of the alanine t%NA in 2east ;see fig3 AG3AEa<0 which ulti1atel2 le6 to Holle2 recei4ing a Nobel $ri5e in $h2siolog2 or Me6icine in AHFD3 The a4erage t%NA is about DG nt long3 Like r%NAs0 the t%NAs are functional 1olecules an6 are not translate60 which 1eans that the2 also lack an !%#0 translation initiation an6 ter1ination co6ons0 an6 CS an6 @S "T%s3 STRU)TURAL SIMILARITIES OF ALL TRANSFER RNAS Transfer %NAs ha4e se4eral unusual properties3 !ne ob4ious feature is that the t%NA contains unusual bases ;fig3 AG3AEa<3 These bases inclu6e#i (#ro+ri#ine 7%82 inosine 7I82 !et (l,+anosine 7MG82 !et (lino6 sine 7MI82 *se+#o+ri#ine 7.82 an# ribot (!i#ine 7T8 ;4i,+re =C?=A<3 $resu1abl20 these unusual bases 6is8 rupt nor1al base pairing an6 are in part responsible for the loops the unpaire6 bases for13 A secon6 si1ilarit2 is that all the 6ifferent t%NAs ha4e the sa1e general shape3 When the t%NAs are purifie6 fro1 cells0 the heterogeneous 1i7ture of all the t%NAs can for1 4er2 regular cr2stals3 This regu8 larit2 of the shape of t%NAs 1akes sense3 (uring translation0 two t%NAs attach ne7t to each other in a riboso1e0 an6 a pepti6e bon6 for1s between the a1ino aci6s that are attache6 to each t%NA3 An2 two t%NAs 1ust therefore ha4e the sa1e general 6i1en8 sions as well as si1ilar structures so that the2 can be recogni5e6 an6 positione6 correctl2 in the riboso1e3 This regularit2 in shape is 6ue to the presence of a 6ouble8stran6e6 acceptor ste1 an6 three ste18 loop structures ;T8loop0 antico6on8loop0 an6 (8loop< to for1 a clo4erleaf shape ;see fig3 AG3AEa<3 Howe4er0 the helical twisting that results fro1 the pairing of co1ple1entar2 se>uences in the four ste1 regions pro6uces a three86i1ensional shape that ensures all t%NAs ha4e a si1ilar structure in the cell ;fig3 AG3AE0 panels b an6 c<3 The a1inoac2l8t%NA s2nthetases attach the spe8 cific a1ino aci6 to the @S8h26ro72l of the t%NA0 which is co1pose6 of the se>uence CS ++A @S3 'ecause each a1inoac2l8t%NA s2nthetase attaches a specific a1ino aci6 to a t%NA0 it woul6 appear that this en521e rec8 ogni5es the antico6on se>uence in the center loop of the t%NA3 'ecause so1e s2nthetases attach the sa1e a1ino aci6 to 1ore than one t%NA0 the2 1ust recog8 ni5e 1ore than onl2 the

antico6on se>uence0 which coul6 be 6ifferent in the 4arious t%NAs3 In realit20 each a1inoac2l8t%NA s2nthetase recogni5es se4eral points all o4er the t%NA to ensure that it is attaching the correct a1ino aci6 to the proper t%NA3 The three8 6i1ensional structure of the t%NA helps to bring the 6ifferent ste1 loops together0 which woul6 si1plif2 the s2nthetase interacting with these 4arious struc8 tures before attaching the a1ino aci63 The first loop on the @S si6e ;the T8loop or T8[8 +8loop because it contains the T8[8+8& se>uence< is belie4e6 to be in4ol4e6 in 1aking the t%NA recogni58 able to the riboso1e3 The riboso1e 1ust hol6 each t%NA in the proper orientation to check the co1ple8 1entarit2 of the antico6on of the t%NA with the co6on of the 1%NA3

TRANSFER RNA GENES When a t%NA is originall2 transcribe6 fro1 (NA0 it is about CGI longer than its final length ;EGNHG nucleo8 ti6es<3 In fact0 so1e transcripts contain two copies of the sa1e t%NA0 or so1eti1es se4eral 6ifferent t%NA genes are part of the sa1e transcript ;see fig3 AG3AF<3 The original t%NA transcript also lacks the unusual bases that are foun6 in the 1ature t%NA3 The initial transcript is processe6 6own to the final si5e of a t%NA through the action of nucleases that re1o4e trailing an6 lea6ing pieces of %NA3 An e7a1ple of this se>uential tri11ing of the %NA to pro6uce the functional E3coli t%NA that bin6s t2rosine ;t%NA T2r < is shown in 4i,+re =C?=B3 In eukar2otes0 a ++A trinucleoti6e se>uence is a66e6 at the @S en6 b2 a

nucleoti62l transferase en521e3 Then the t%NA is further 1o6ifie60 fre>uentl2 b2 the a66ition of 1eth2l groups to the bases alrea62 in the %NA ;see fig3 AG3AH<3 Earlier we consi6ere6 a rough 6efinition of a gene as a length of (NA that co6es for one protein3 'ut we ha4e 9ust encountere6 an inconsistenc2. genes co6e for both t%NAs an6 r%NAs0 2et neither is translate6 into a protein3 Their transcripts function as final pro68 ucts without e4er being translate63 We shoul6 now think of a gene as a segment of D4! that encodes a func* tional product0 either a protein or an %NA3

!c%ra&'(ill Ans&ers ) Changes in Chromosome Structure and *umber

By (yde, D.R. Edited by Paul Ducham Share on facebookShare on twitterShare on google_plusone_share Contents

A%IATI!N IN +H%!M!S!ME ST%"+T"%E* AN ! E% IEW N!TATI!N #!% +H%!M!S!ME A'N!%MALITIES (ELETI!NS IN E%SI!NS IN E%SI!NS* S"$$%ESSI!N !# %E+!M'INATI!N $%!$E%TIES !# IN E%SI!NS E !L"TI!NA%) +!NSEM"EN+ES !# IN E%SI!NS

VARIATION IN )HROMOSOME STRU)TURE' AN OVERVIEW +hro1oso1es 1a2 break 6ue to ioni5ing ra6iation0 ph2sical stress0 or che1ical co1poun6s3 E4er2 chro1ati6 break pro6uces two en6s3 These en6s ha4e been 6escribe6 as Jstick20K which 1eans that en521atic processes in the cell ten6 to re9oin broken en6s rather than attaching a broken en6 to an un6a1age6 en6 of another chro1oso1e3 If broken en6s are not brought together0 the2 will re1ain broken3 Howe4er0 this will result in the loss of so1e of the genetic 1aterial0 which will likel2 affect the phenot2pe of the cell or organis13 If broken chro1ati6 en6s are brought together0 the2 1a2 re9oin in se4eral 6ifferent wa2s3 #irst0 the two broken en6s of a single chro1ati6 can reunite3 Secon60 the broken en6 of one chro1ati6 can fuse with the broken en6 of another chro1ati60 resulting in an e7change of chro1oso1al 1aterial an6 a new co1bination of alleles3 Multiple breaks can lea6 to a 4ariet2 of alternati4e reco1binations3 T(*es o4 $reaks The t2pes of breaks an6 reunions 6iscusse6 in this chapter can be su11ari5e6 as follows*

I3 Noncentro1eric breaks A3 Single breaks A3 %estitution ?3 (eletion @3 (icentric bri6ge '3 Two breaks ;sa1e chro1oso1e< A3 (eletion ?3 In4ersion +3 Two breaks ;nonho1ologous chro1oso1es< A3 %eciprocal translocation ?3 (icentric bri6ge II3 +entro1eric breaks A3 #ission '3 #usion Single (rea.s If a single chro1oso1e breaks0 the broken en6s 1a2 re9oin in a process calle6restit+tion? This t2pe of break has no conse>uences because the original chro1oso1e is regenerate63 'ut when the en6s 6o not re9oin0 the result is ana"entri" 4ra,!ent2 without a centro1ere0 an6 a "entri" 4ra,!ent2 with a centro1ere ;4i,? A?=<3 The acentric frag1ent0 howe4er0 will fail to faithfull2 segregate properl23 It will subse>uentl2 be e7clu6e6 fro1 the nuclei for1e60 an6 e4entuall2 it 6egra6es3 In contrast0 the centric frag1ent 1igrates nor1all2 6uring 1itosis or 1eiosis because it has a centro1ere3 Howe4er0 it lacks a telo1ere0 which will pre4ent it fro1 faithfull2 replicating the broken en6 in subse>uent roun6s of (NA replication3 This will lea6 to the continual loss of larger a1ounts of (NA fro1 the 6elete6 en6 6uring each roun6 of (NA replication3 A single break can ha4e 2et another effect3 !ccasionall20 the two centric frag1ents of a single chro1oso1e 1a2 9oin0 for1ing a two8centro1ere0 or#i"entri" " ro!oso!e an6 lea4ing the two acentric frag1ents to 9oin or0 alternati4el20 re1ain as two frag1ents ;see fig3 D3A<3 The acentric frag1ents are lost0 as 1entione6 before3 'ecause the centro1eres are on sister chro1ati6s0 the 6icentric frag1ent is pulle6 to opposite en6s of a 1itotic cell0 for1ing a bri6ge: or0 if 1eiosis is occurring0 the 6icentric frag1ent is pulle6 apart 6uring the secon6 1eiotic 6i4ision3 The ulti1ate fate of this bri6ge is breakage as the spin6le fibers pull the

centro1eres to opposite poles ;or possibl2 e7clusion fro1 a new nucleus if the bri6ge is not broken<3 The 6icentric chro1oso1e 6oes not necessaril2 break in the 1i66le0 howe4er0 an6 the subse>uent offcenter break e7acerbates the genetic i1balance* 6uplications occur on one stran60 whereas 1ore 6eletions occur on the other ;4i,? A?@<3 In a66ition0 the Jstick2K en6s pro6uce6 on both frag1ents increase the likelihoo6 of repeating this breaka,eG4+sionG bri#,e "("le in each generation3 The great i1balances resulting fro1 the 6uplications an6 6eletions usuall2 cause the cell to 6ie within se4eral generations3 &"o (rea.s in the Same Chromosome Fi,+re A?; shows three possible results when two breaks occur in the sa1e chro1oso1e3 !ne alternati4e is a reunion that o1its an acentric frag1ent0 which is then lost3 The resulting chro1oso1e then has a 6eletion or loss of 1aterial ;e*f*g in fig3 D3@<3 Two breaks in the sa1e chro1oso1e can also lea6 to an inversion2 in which the 1i66le section is reattache6 but in the in4erte6 configuration ;see fig3 D3@<3 The thir6 possibilit2 is restitution of the original chro1oso1e3 &"o (rea.s in Nonhomologous Chromosomes While the abo4e rearrange1ents in4ol4e two breaks in the sa1e chro1oso1e0 it is also possible to pro6uce two breaks si1ultaneousl2 in two nonho1ologous chro1oso1es3 %eunion can then take place in 4arious wa2s3 The 1ost interesting case occurs when the en6s of two nonho1ologous chro1oso1es are switche6 with each other in a re"i*ro"al translo"ation ;4i,? A?E<3 The organis1 in which this has happene60 a reciprocal translocation hetero52gote0 retains all the genetic 1aterial3 The outco1e of a reciprocal translocation0 like that of an in4ersion0 is a new linkage arrange1ent in the translocate6 chro1oso1es3 Centromeric (rea.s An interesting 4ariant of the si1ple reciprocal translocation occurs when two acrocentric chro1oso1es 9oin at or 4er2 near their centro1eres3 The process0 which essentiall2 is the fusion of the long chro1oso1al ar1 fro1 two nonho1ologous chro1oso1es0 is calle6 a Robertsonian translo"ation or4+sion? The short chro1oso1al ar1s fro1 the two original chro1oso1es are lost because the2 both lack a centro1ere3 A %obertsonian translocation pro6uces a 6ecrease6 nu1ber of chro1oso1es because the

long ar1s of two chro1oso1es are fuse6 into one3 In hu1ans0 %obertsonian translocations can occur between an2 two of the acrocentric chro1oso1es A@0 AB0 AC0 ?A0 an6 ??3 (own s2n6ro1e occurs when the %obertsonian translocation contains chro1oso1e ?A3

NOTATION FOR )HROMOSOME A$NORMALITIES In the stan6ar6 no1enclature s2ste10 a nor1al hu1an chro1oso1e co1ple1ent is BF0LL for a fe1ale an6 BF0L) for a 1ale3 The total chro1oso1e nu1ber appears first0 then the 6escription of the se7 chro1oso1es0 an60 finall20 a 6escription of autoso1es if an autoso1al ano1al2 is e4i6ent3 Thus0 the nu1ber of an2 e7tra chro1oso1es woul6 be a66e6 to BF0 an6 the nu1ber of 1issing chro1oso1es woul6 be subtracte63 #or e7a1ple0 a 1ale with an e7tra L chro1oso1e woul6 be BE0LL)3 A fe1ale with a single L chro1oso1e woul6 be BC0L3 'ecause all the autoso1es are nu1bere60 we 6escribe their changes b2 referring to their a66ition ;P< or 6eletion ;N<3 #or e7a1ple0 a fe1ale with triso12 ?A woul6 be BE0LL0P?A3 The shorter ar1 of a chro1oso1e is 6esignate6 p0 an6 the longer ar1 as >3 When a change in part of the chro1oso1e occurs0 a plus sign ;P< after the ar1 in6icates an increase in the length of that ar10 whereas a 1inus sign ;N< in6icates a 6ecrease in its length3 #or e7a1ple0 a fe1ale with a translocation ;t< that transfers part of the short ar1 of chro1oso1e H to the short ar1 of chro1oso1e AD woul6 be 6esignate6 asBF0LL0 t;HpN:ADpP<3 The se1icolon in6icates that both

chro1oso1es kept their centro1eres3 )ou will see this notation in 6escriptions of co11on hu1an ano1alies later in this chapter3 %ELETIONS When a break pro6uces an acentric frag1ent0 it 1a2 be lost fro1 subse>uent cell 6i4isions3 The re1aining chro1oso1e will continue through cell 6i4isions an6 beco1e part of the ga1etes3 "pon fertili5ation0 the resulting 52gote will ha4e one nor1al chro1oso1ean6 one chro1oso1e 1issing 1aterial0 ter1e6 a 6eletion or 6eficienc23 An in6i4i6ual that has a 6eletion chro1oso1e can be c2tologicall2 i6entifie6 if the in6i4i6ual also possesses a nor1al ho1olog3 (uring 1eiosis0 a bulge will be present in the tetra6 if the 6elete6 section is large enough ;4i,? A?Fa<3 This s2napse6 structure is often calle6 a #eletion loo*? '2 staining the chro1oso1es0 it is possible to 6eter1ine the precise ban6s that are present in the loop0 which correspon6s to the (NA that is 1issing in the ho1olog3 This t2pe of anal2sis has per1itte6 the characteri5ation of the 6eletions associate6 with particular hu1an genetic ano1alies0 such as cri 6u chat s2n6ro1e ;see later section<3 This loop can also appear in the paire60 pol2tene giant sali4ar2 glan6 chro1oso1es of Drosophila ;fig3 D3Cb<3 Note that the presence of a 6eletion loop actuall2 signifies that one chro1oso1e possesses less (NA than its ho1olog3 In this e7a1ple0 the loop region correspon6s to the wil68t2pe chro1oso1e that contains (NA 1issing in the 6eletion chro1oso1e3 A 6iagnostic feature of a 6eletion is its inabilit2 to re4ert to wil6 t2pe3 The loss of a portion of a chro1oso1e can not be regenerate63 Pse+#o#o!inan"e (eletions e7hibit a pheno1enon calle6 pseu6o6o1inance3 Pse+#o#o!inan"eis the e7pression of the recessi4e phenot2pe when onl2 a single recessi4e allele is present3 We pre4iousl2 6escribe6 pseu6o6o1inance in chapter B0 when we 6iscusse6 the e7pression of recessi4e alleles on the L chro1oso1e in 1ales3 $seu6o6o1inance is also obser4e6 if the region absent in a 6eletion chro1oso1e correspon6s to the location of recessi4e alleles on the ho1ologous full8length chro1oso1e ;4i,? A?<<3 In contrast0 if a recessi4e 1utation correspon6s to a region that is not absent on the 6eletion chro1oso1e0 the 6o1inant phenot2pe will be obser4e6 ;assu1ing that the 6eletion chro1oso1e contains the 6o1inant

allele: see fig3 D3F<3 Thus0 it is possible to 1ap recessi4e 1utations to chro1oso1al regions using 6eletions b2 6eter1ining if the recessi4e allele on the intact chro1oso1e results in the recessi4e phenot2pe or not3 This approach pro4i6es a powerful 1etho6 to locali5e recessi4e 1utations on chro1oso1es3 If the location an6 si5e of the 6eletion is known fro1 the staine6 chro1oso1e ban6ing patterns0 then the location of the recessi4e alleles can also be locali5e63 #or e7a1ple0 the high resolution ban6ing pattern obser4e6 in Drosophilapol2tene chro1oso1es allows for a precise 6eter1ination of the c2togenetic ban6s 1issing in specific 6eletion chro1oso1es3 +o1bining this knowle6ge with the pseu6o6o1inance results0 it is possible to locali5e a recessi4e 1utation to a single pol2tene ban6 ;fig3 D3E<3 Geneti" I!balan"e A secon6 possible effect of a 6eletion is that0 6epen6ing on the length of the 6elete6 seg1ent an6 the specific loci lost0 the hetero52gote 1a2 e7hibit a genetic i1balance3 Geneti" i!balan"e is the conse>uence of ha4ing two copies of so1e genes an6 onl2 a single cop2 ;or three copies< of other genes0 which results in an unnatural ratio of gene e7pression3 The re6uction of so1e genes b2 half ;6ue to the loss of one cop2 in the 6eletion chro1oso1e< lea6s to an insufficient a1ount of e7pression fro1 the re1aining gene3 Ha*loins+44i"ien"( occurs when a 6eletion results in a lethal phenot2pe because the e7pression of a single wil68t2pe allele cannot support the nor1al phenot2pe3 In other cases0 the genetic i1balance 1a2 be 4iable0 but the resulting hetero52gote 1a2 e7press an altere6 phenot2pe3 An e7a1ple of this 4iable genetic i1balance is the 6eletion of part of chro1oso1e C in hu1ans that pro6uces cri 6u chat s2n6ro1e3 )ri #+ ) at S(n#ro!e The s2n6ro1e known as cri 6u chat ;fro1 the #rench0 1eaning cr2 of the cat< is so na1e6 because of the cat8like cr2 that about half the affecte6 infants1ake3 Microcephal2 ;an abnor1all2 s1all hea6<0 congenital heart 6isease0 an6 se4ere 1ental retar6ation are also co11on s21pto1s3 This 6isor6er arises fro1 a 6eletion in the short ar1 of chro1oso1e C: the kar2ot2pe for this s2n6ro1e is BF0LL or L)0CpN ;4i,? A?A<3 Most other 6eletions stu6ie6 ;BpN0 A@>N0 ADpN0 AD>N< also result in 1icrocephal2 an6 se4ere 1ental retar6ation3 The rarit2 of 4iable hetero52gotes possessing a large 6eletion is consistent with the fact that

4iable 1onoso1ics ;ha4ing a single chro1oso1e of a pair< are rare3 An in6i4i6ual hetero52gous for a 6eletion is0 in effect0 1onoso1ic for the 6elete6 region of the chro1oso1e3 E4i6entl20 either 1onoso12 or hetero52gosit2 for large chro1oso1e 6eletions is generall2 lethal in hu1ans3 This lethalit2 is 6ue to a co1bination of pseu6o6o1inance of recessi4e lethal or 6eleterious 1utations0 genetic i1balance0 an6 haploinsufficienc23

INVERSIONS As shown in figure D3@0 an in4ersion results fro1 two breaks in a single chro1oso1e an6 the subse>uent reorientation of the central frag1ent before re9oining the broken en6s3 As a result0 there is no net loss or gain in geno1ic (NA se>uences3 Howe4er0 the chro1oso1al breaks can occur either between or within genes3 If the break occurs between genes0 the in4erte6 chro1oso1e usuall2 6oes not create an2 new alleles ;4i,? A?B<3 If the breaks occur within a gene0 howe4er0 two outco1es are possible3 #irst0 the break coul6 6isrupt the gene an6 pro6uce a nonfunctional allele0 which is usuall2 a recessi4e 1utation ;unless it is haploinsufficient0 see pre4ious 6iscussion: fig3 D3H<3 Alternati4el20 it coul6 1o4e a promoter se1uence0 which controls (NA transcription0 near a 6ifferent gene to e7press that wil68t2pe gene in an abnor1al location or ti1e ;see fig3 D3H<3 In either outco1e0 if the in4ersion pro6uces a change in the chro1oso1al ban6ing pattern0 then it is possible to correlate the location of the 1utation with the 6efect in the c2togenetic ban6ing pattern0 an6 in this wa2 to 1ap the location of the 6efecti4e gene relati4e to the c2togenetic 1ap3 There are two 6ifferent t2pes of in4ersions3 A *eri"entri"

inversioncontains the centro1ere within the in4erte6 section ;4i,? A?=C0 left<3 A*ara"entri" inversion has the centro1ere outsi6e of the in4erte6 region ;see fig3 D3AG0 right<3 When s2napsis occurs in an in4ersion hetero52gote ;an in6i4i6ual with an in4ersion chro1oso1e an6 a wil68t2pe ho1olog<0 an in4ersion loop often for1s to acco11o6ate the point8for8point pairing along the chro1oso1es 6uring 1eiosis.or0 in Drosophila sali4ar2 glan6s0 6uring en6o1itosis ;4i,s? A?== an6 A?=@<3 A pericentric in4ersion will ha4e the centro1ere locate6 within the in4ersion loop0 an6 a paracentric in4ersion will ha4e the centro1ere locate6 outsi6e of the in4ersion loop3

INVERSIONS' SUPPRESSION OF RE)OM$INATION !ne hall1ark of an in4ersion is the suppression of reco1bination in an in4ersion hetero52gote b2 two 6ifferent 1echanis1s3 The first is a real suppression of reco1bination or the inabilit2 to co1pletel2 s2napse 6uring 1eiosis3 This results fro1 the 6ifficult2 of co1plete s2napsis between the two ho1ologs in the regions at the base of the in4ersion loop ;fig3 D3AA<3 In other wor6s0 as 2ou 1o4e closer to the actual in4ersion breakpoints0 the crosso4er fre>uenc2 approaches 5ero3 The secon6 effect is an apparent suppression of reco1bination0 which occurs fro1 crosso4ers within the in4ersion loop ;see fig3 D3AA<3 In realit20 reco1bination can occur at a fairl2 nor1al fre>uenc2 within the in4ersion loop relati4e to the sa1e region in a nor1al in6i4i6ual3 Howe4er0 the ga1etes pro6uce6 fro1 reco1bination within the in4ersion loop are usuall2 unable to pro6uce 4iable offspring3 Mechanisms of Suppression Let=s look at the 1echanis1 of the apparent suppression in an in4ersion hetero52gote with a paracentric in4ersion3 Fi,+re A?=; shows a crosso4er within the in4ersion loop3 The two nonsister chro1ati6s that are not in4ol4e6 in the crosso4er will en6 up in nor1al ga1etes ;carr2ing either the wil68t2pe

or in4erte6 chro1oso1e<3 The pro6ucts of the crosso4er0 rather than being a si1ple reco1bination of alleles0 are a 6icentric an6 an acentric chro1ati63 The acentric chro1ati6 is not incorporate6 into a ga1ete nucleus an6 this reco1binant will be lost3 The 6icentric chro1ati6 begins a breakageNfusionN bri6ge c2cle0 as the two centro1eres are pulle6 to opposite centroso1es 6uring 1eiosis I3 "lti1atel20 the 6icentric chro1oso1e ran6o1l2 breaks between the two centro1eres an6 each chro1ati60 containing 6eletions0 pro6uces a geneticall2 i1balance6 ga1ete3 Thus0 the ga1etes 6eri4e6 fro1 the reco1binant chro1ati6s are unable to pro6uce 4iable offspring3 A pericentric in4ersion also suppresses crosso4ers0 but for slightl2 6ifferent reasons ;4i,? A?=E<3 All four chro1ati6 pro6ucts fro1 a single crosso4er within the loop will ha4e centro1eres an6 are therefore incorporate6 into the nuclei of ga1etes3 Howe4er0 the two reco1binant chro1ati6s are not balance6.the2 both ha4e 6uplications an6 6eficiencies3 In the figure0 one chro1ati6 has a 6uplication for a8b8c8d an6 is 6eficient for h*i*50 whereas the other is the reciprocal.being 6eficient for a8b8c8d an6 6uplicate6 for h*i*53 These 6uplicationN6eletion ga1etes ten6 to for1 non4iable 52gotes3 Thus0 both paracentric an6 pericentric in4ersion hetero52gotes will not e7hibit reco1binant ga1etes if the crosso4er occurs within the in4ersion loop3 It shoul6 be 1entione6 that reco1bination occurs at nor1al fre>uencies outsi6e0 but not at the base0 of the in4ersion loop3 #or this reason0 reco1bination is onl2 suppresse6 4er2 near to or within the in4ersion loop in an in4ersion hetero52gote3 %n#ersions Cause Reduced -ertility 'ecause half the chro1ati6s pro6uce6 6uring reco1bination within the in4ersion loop are not balance6 an6 cannot pro6uce 4iable 52gotes0 in4ersions cause re6uce6 fertilit2 in in6i4i6uals3 'ut since reco1bination outside of the in4ersion loop is not affecte6 in an in4ersion hetero52gote0 greater than half of all ga1etes pro6uce6 are balance6 an6 will pro6uce 4iable 52gotes3 The percentage of unbalance6 ga1etes will be proportional to the si5e of the in4ersion an6 whether 1ultiple in4ersions occur on a single chro1oso1e3 (alancer Chromosomes In Drosophila0 se4eral balan"er " ro!oso!es ha4e been generate6 containing 1ultiple in4ersions along the 1a9orit2 of their length3 A balancer chro1oso1e suppresses reco1bination along the entire length of a gi4en

chro1oso1e3 This is a useful feature when characteri5ing recessi4e 1utations or tr2ing to create specific genot2pes because the arrange1ent of alleles along a specific chro1oso1e will not change between generations3 Howe4er0 the flies that carr2 these balancer chro1oso1es pro6uce low nu1bers of offspring 6ue to their reduced fertility0 which approaches CGI when the in4ersions co4er nearl2 the entire chro1oso1e3

PROPERTIES OF INVERSIONS An in4ersion has se4eral interesting properties3 #irst is the re6uce6 fertilit2 an6 suppression of reco1binant offspring that results fro1 reco1bination within the in4ersion loop of an in4ersion hetero52gote3 Secon60 in6i4i6uals who are ho1o52gous for an in4ersion show no4el linkage relationships when their chro1oso1es are 1appe6 b2 reco1bination3 'ecause both ho1ologs contain the sa1e in4ersion0 an in4ersion loop is not generate60 an6 reco1bination 6istances can be accuratel2 1appe6 along the entire length of the in4ersion chro1oso1e3 )et0 2ou can see this no4el linkage relationship in figure D3AA where the 6istance fro1 point e to h is 4er2 6ifferent in the wil68t2pe chro1oso1e ;top< an6 the in4ersion chro1oso1e ;botto1<3 Thir60 the in4ersion chro1oso1e 1a2 pro6uce a *osition e44e"t0 which is a change in the e7pression of a gene 6ue to an altere6 linkage arrange1ent3 $osition effects are either stable0 as in the ar e2e 1utant of Drosophila ;to be 6iscusse6 later<0 or 4ariegate60 as with Drosophila e2e color3 #or e7a1ple0 a hetero52gous fe1ale fl2 ;LwLP< will ha4e phenot2picall2 wil68t2pe re6 e2es3 If the whiteP locus is 1o4e6 fro1 the euchro1atin region near the en6 of the

L chro1oso1e to the heterochro1atin through an in4ersion ;fig3 D3AC<0 the fl2 shows 4ariegation.patches of the e2e are white3 The 4ariegation is 6ue to the whiteP locus on the in4ersion chro1oso1e not being e7presse6 in parts of the e2e0 so the LwLP genot2pe pro6uces either a re6 or white e2e phenot2pe3 $resu1abl2 the heterochro1atin encroaches on the whiteP allele in so1e cells to Jturn offK the e7pression of the whiteP locus3 In the hetero52gote0 if the wil68t2pe allele is turne6 off0 then the cell will e7press the nor1all2 recessi4e white e2e phenot2pe3 (epen6ing on what happens in each e2e cell0 patches of re6 an6 white e2e color result3

EVOLUTIONAR& )ONSE:UEN)ES OF INVERSIONS

In4ersions ha4e se4eral e4olutionar2 ra1ifications3 Alleles foun6 together within an in4ersion loop ten6 to be inherite6 together because of the suppresse6 reco1bination within the in4ersion3 If se4eral loci within an in4ersion affect a single trait0 the alleles are referre6 to as a s+*er,ene3 "ntil careful genetic anal2sis is 6one0 the loci in a supergene coul6 be 1istaken for a single locus: the2 affect the sa1e trait an6 are inherite6 apparentl2 as a single unit3 E7a1ples inclu6e shell color an6 pattern in lan6 snails an6 1i1icr2 in butterflies3 Supergenes can be beneficial when the2 in4ol4e fa4orable gene co1binations3 'ut at the sa1e ti1e0 their in4ersion structure pre4ents the for1ation of new allele co1binations an6 the correspon6ing phenot2pes3 Supergenes0 therefore0 ha4e e4olutionar2 a64antages an6 6isa64antages3 +hapter ?C 6iscusses these e4olutionar2 topics in 1ore 6etail3 So1eti1es the generation of in4ersions pro6uces a recor6 of the e4olutionar2 histor2 of a species3 As species e4ol4e0 in4ersions can occur on pree7isting in4ersions0 lea6ing to 4er2 co1ple7 arrange1ents of loci3 We can rea6il2 stu62 these patterns in (iptera b2 noting the change6 patterns of ban6s in sali4ar2 glan6 chro1oso1es3 Since certain geno1ic arrange1ents can onl2 be pro6uce6 fro1 a specific se>uence of in4ersions0 it is possible to 6eter1ine the or6er in which 6ifferent species e4ol4e63