Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Lab

Question Description

I need an explanation for this Biology question to help me study.

No actual lab report due but I need you to write down all the questions they ask as you read along in the different sections and then answer the question.
The copy can be pretty light so look carefully for the connecting lines especially on the tree they represent.

use file that I provide

if the copy is light, you can use the link

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Wi To sEotIENcEs roMp*nrf,roPNA -wITH rND EnsieND EvoiurLoNARY RELATT o,NEinP ffi BACKGROUND scientists Retrveen 1990-2003' BtAsT s research project knorvn llorking on an international as gen.mes of othel' theHun.ranCt'''o**"""t'u'ereableto'iat'''tif'uanclmapthe2{]'000-25'000genes ,rr" *..,;-*iutt,' *opp*r1 the io" 0."i.., a,d complete that e1e{ine * nr**'i.r]*. *'u'uJi"'li'!tia'coli'ii'e ln'atio" the rvorld to species, includi*g;;;; ';"*"' u" available for anvone in ";" ofthese in each gt"e' ofthe 'O"tL sequence access via the lnternet' j,"uctreI uudet'I'rnd gcncric diseltt- Iti \\rhyistlrisinlornrationirlportarrt?Beingabletoidentift'thelrreciselocation .il*r "g.n.r'rrltt o,rr,,,rr*n an(1 sequenc. 1* othel tn":i^".'^}',,'lt;:il$:''lt:-,i'"' the sequence of g""t' additio', leirr,ing about Nlanv oi ciur genes alnong organlsms' evolutionar,v relationships - i1 irlit a pariicular disti:'e rhar is responsible rbr ii }'iluld take i'tuttot a sitrriiar disease? t* lrrtai' Ihe same hunran genonle to trv I;::l1i;:ffi:ffie,sene tour]a i, n.**r,'o"., flies. Is that same g.n. read through th. "r-rtir. you nearl,v l0 ,veajs to n"' Jt'"tta,.' iJnt p'actitui' sequence nf t'*'"' tft'i* n-n " is treeded' tecirnological nrethod 511 3 5arpl-risticated "*'' ue:ir'ds' entire Bioinibrmaticsisa{ieldtl-ratcombinesstatistics,mathenr'.riicaiu.ldeiing,an<] and ciiflererrces' tti"."i;;;;&;tological o*.'it*toioi'fc'rrmati;s .o a.i.. genetit sir:lilrlrities Local be Basic cari ;;;;;*,."Ji: genoines stirn*s ibr :'-oi] rl.j i, er,asr, computer 'ut-,ich An exrrernely noi".rr*ibioi'tb,nati.r you can input a geilt sequ'l.ce of interest and using BLAS-1], in a rllatter of seco,ds' Alignrnent ,."r.n i"ri. or similar "qttt"ttt g"r.u*i.iiU.urlJ. for iclentical search.rr,r.. (also called Inthislaboratoryinvestigatlon,yourvilluseBLASTtocLrilpareseveralgerres, u .*r-oiog'nn'"\-ciaJogran-r ,o .or1r*o., arrd then r-rse the informatLon phylogenetic rr;.);;;;uitru,ton a simPle cladogram' "f a species' Figure ;;;';i.;;;i,-'a'r. r'i'tecln-'-" of 1 is ::a., :::. r), 10. ljnder "choose search set," select rvhether yoli n ant to search the human genome onl% mouse genome onl,v, or ail genomes avaiiabie. 11. under "Program Selection," chocse rt-hether or not you u,ant highiy si,riiar sequences or somervhat similar sequences. C}:oosing somervhat similar sequences rvrl.l provide ;-ou u..-ith more result_s. 12. Ciick BLAST. Belorv is a list oi some gcne suggcsiii-r,-r ',-orr ir,.ulci in'estigate using BLAST. As 1,ou look at a particular gene, answer tl:e iirii,:;r-ing questions: r \fhat is the functio'in hun:a,s *irh: p:"*iein produced from that gene? r \\buld 1'ou expect to find the :ame p:rr:r;: in other organisms? If so, which ones? r Is i[ possibie to find the sarne gele ii i-,rr-r iiferent kinds of organisnrs r the protein that is produced iiom ihai :lsne If you iound the same gene in ail orsanl;rt: er.,olution of this gene in the t hist*rr-,:i]ie blt not find ? ,,ili ,:,ir test, what cloes this suggest about the ;arrh? Does the use of DNA sequences ii: tl:e i;* j.; i:i e:-olutionary relationships mean that other characteristics are unimportar:r ii: riuh .tulies? Explain your ansl!,er. ! 1 g s g,srgu. 9:r-:, 1_o_ -elp rory ATP synthase Catalase GAPDH ^K;;;ii;""'" Myosin Paxl Ubiquitin Ftitt* or c?Ies StuUieC Freviousry-l Enzymes Parts of ribosomes Protein channels i ,, i Lycopodium Selaginella lsoetes Figure 1. simpre cradogram Representing Oifferenr prant species Note that the cladogram is treelike, wjth the endpoints of each branch representing a specific species' The closer trvo species are locatecl to each other, the more recentiy they share a cofilll-lon ancestor. For example, Selaginella (spikemoss) and. Isoetes (quillw.ort) share a more recent common ancestor tiran the common ancestor that is shared bv all three organisms. Figure 2 includes additional detaiis, such as the evolution ofparticular physical structures called shared derived characters. Note that the placement of the derived characters corresponds to when (in a general, not a specific, sense) that character eT,'olved; every species above the character label possesses that structure. For example, tigers and gorilla.s have hair, but larnpreys, sharks, salamanders, and lizards c1o not har.e hair. d gorilla \--t-=-Ub 7'>' 7h: ri. ' saiamander -*rft ian:pr*1 ;Qntr no tail c ' I : ..-.' hair dry skin lungs iaws Figure 2. Cladogram of Several Animal Species The c:;iiugran alrove can be used to answer several questions. lVhich organisms have lungs: "'"ihat three structures do ail lizartls possess? According to the cladogram, which stru.iitr€ dt.r skin or hair _ er,,olved first? - xffi s42 I lr,resligation 3 Historically, onl1, physical structures were used to create cladograms; horvever, r-rroriel.n-cla,v cladistics relies heavily on genetic evidence as ne1l. Chimpanzees and humans share 959,b+ of their DNA, u,hich rvould place them closeiv together on a cladograrn. Humans ancl fruit f.Iies share approximately 6096 of their DNA, xhich rcouid place thent farther apart on a cladogrirn-r. Can vou drarv a claclograrn that depicts the evolutionar,v relationship among humans, chimpanz-ees, jLliil tiuit flies, ancl mosses? tx*rr;ir*g ffi*:je*{lv*x I -fo create cladograms tliat depict evolutionary relationships o 'k: aual,vze biological clata with a sophisticated bioiirforrnatics online tool r To use cladograms and bioinformatics tools to ask ottrer questiotrs of your owu and to test your abilify io apply concepts ),ou kl1ow relating to genetics and evolution lli::{ ffi *x't*rer t Smf*{v Fr*lcma*tim*s There are no safet,v precautions associated ivith this investigation. ffi THE INVESTIGATIONS {ti{ S*${rttg $tmrt*d Your teacher ma,v assign the iblloiving questious to see how much you understaud concepts relirted to cladograms before you conduct,vour investigation: 1. Use the firilolviirg data to construct ir cladogram of the majcir plant groups: Table 1. Characteristics of Maior Plant Groups j 0rganisms Vascular fissue Flowers Mosses I 2. GAPDFI (giyceraldehycle 3-phosphate deh;,'dr-oee1r;:i. r i] irtil eilzYi-I.)e that catalyzes tire sixth step iu glycolysis, an improrttrnt reaclion I}-lal rroduces molecuies used ln cellular respiration. The following data table shr.rrt-i iiie i.erc€ntage similarlty of this gene and the protein it expresses in humans ve rsis oirer species. For example, according to the tal:le, the GAPDH gene in cirimpar:ztes i: 99.6% identical to tl-re geire found in humans, while tl-re protein is icleniical. ln,.,osliqeiion 3 S43 &ffiffi I Table 2. Percentage Similarity Between the GAPDH Gene and Protein in Humans and Other Species Species . troglldytes) Dog {Canis lupus fanilrarrs) Fruit fly lfisssspt'tr!6 neianogaster) , Chimpanzee lPan Roundworm tcaenolfab.dln: "l:s.:,1:, Gene Percentage siri'-,rg. 6% 91.390 12.4c,h 99 _. ur?,!" -. , Protein Percentage -!ilfi1g-: 100% gi.2To 76.70/o 74.3% . 3. \\'hf is the percentage similarit-rr in the gene alwavs lorver than the percentage sirnilarit,r' in the prateir for each of the species? (Hir:t: Recall hort a gcne is expressed to produce a protein.) b' Drarv a cladogram depicting the evolutionarv relationships among ali fir,e species (including humans) according to their perceiltage similerritv in the GAPIIH gene. You can also prepare 1br the Iab b1, lr,orking through the foliorving otrline activities: t "The livolution of Fliglrt in Birds" http : I / www. ucmp. be r ke I ey. ed u / ed u ea t i on I *xp I o r a t i ons/ r e s I a bl fti ght I ma i n. htm This activitv pror.ides a real-rvorld ex;rmp1e olhorv cladogr':.rnrs are used to understand er.oit"itionarl, relatioirsl:ips. r "\,Vhat did http :// l. r'er taste like?" www. ucm p. be r ke ley. ed u / e d u c a ti on / e xp I o r a lindex.html r "Journet- ir-ritr Pil..-l i-,{ene: i; S';-r iell;:.tics" www. u c rn p . be r ke I ey. ed u I c I a d / c la d4. h t tp :// ffi, html $r***dxr* -{ a ti on s / tau r s I Tr ex l;:r: ri !;}:! h;s i:lrcr-r-ered the fbssil specimen in Figure 3 near Liaoning i-'in.: \iake some generai observations alrout the rnorphology (ph,vsical Pi,'',-:::::. = :rt-rit:-ri ..i:it; :*ssi.l, and then record y.'our observations in your notebook, il::.r -: ";:1, '',"':: ;ltrut the fossil. It appears to be a neu, species. Upon careful exauination :l 2 ; Z i--'l li: dr:c. r.,:-: . s;::;ii amounts of sott iissue have been discovered. Normall,r., soft tissue li-i i':::-'-i fossilization; howeyer, rare situations o1 such preseryation clo occur. Scitnrr"li io extract DNA nucleotides from the tissue ancl use the infonnation to serlus:: ji ,.f..'ei-al genes. Your task i.s fo use BIAST' to analyz_e lhese genes anrl deterr:i;:: :i:e arost likel_v placement of tire fossil species on Figure .1. e -,'.-rrt able Figure 3. Fossil Specimen r ffi#s s44 lnvesticaticr:3 great rodents birds crocodilians opPosable thumbs feathers Palatal valve insects apes crustaceans two specialized incisors fur ex00sed mouthparts t!!o-parted limbs vertebrae heterotroPh Figure 4' Fossil Gladogram $tep believe tire tbssil specimen should be 1 Form an i,,itiirl h1,p'rht'sis as to rr4-rere ,vou pltrcedontlrecladogr,ambaseelontlrelnorp}rologicalobservtrtiorrs.vournadeearlier' I)rau: vour hlpothesis on Figr'ire'1' $tep ;;ou'tlioacl three gene fi1es 21-ocate ancl clo'vnloaci ge,e fiies. l1-re AP Biolog' Investigalir,el,abspageatAPCetltral:bttp:|/apcentral.collegeboard.comlapcl r / 2 I 89 5 4 " html' membe r s / cou rses / iea rh e r s *c or ne $tep 3 Uploahare similar genes. Ihe more similar genes tr\,o species har.e in cofillnlrn. ihe :::,rrr rt;eni their comnlon ancestor and the closer the tlvo species rr'il1 be iocatei 11 ; clad*sram. intbrmation fron: Bi dST ii,r .aci'r ol the gene files, you shoulcl be thinking about ,r,our original hrpoti"resis a;ri ',' Lelher tl:e diita support or catlse yoll to As you collect reject your original placement of the lbs:li sf e;i Purchase answer to see full attachment
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