Constructing Evolutionary Lineages using DNA BLAST

Part A - Essential Knowledge Background In or!ation - Read the background information in the student lab manual on pages 41-42. Define the vocabulary and answer the questions based on the background information in your lab notebook. s well! list the three learning ob"ectives in your lab notebook. Key "oca#ulary #uman $enome %ro"ect $enome &ioinformatics &' () *ladogram *ommon ncestor Derived *haracteristics *ladistics
http122ephraimgregor.com2html2print2logo/3.html

$uestions #ow is information from the human genome pro"ect used in bioinformatics+ ,hat kind of information is obtained from a &' () search and how can it be used+ #ow are cladograms that are currently being created different from cladograms that were created in the 1-./s+

Learning %#&ectives )o create a cladogram that depicts evolutionary relationships. )o analy0e biological data with a sophisticated bioinformatics online tool. )o use cladograms and bioinformatics tools to ask other questions of your own and to test your ability to apply concepts you know relating to genetics and evolution.

Part B ' Con ir!ation Skill Develo(!ent )Part *+ - %ractice constructing cladograms by completing the two questions on pages 43-44 of the student lab manual in your lab book. 4ou must have the instructor check your answers to these questions before proceeding. Skill Develo(!ent )Part ,+ - *hoose one of the following websites to gain more background in regard to how cladistics can be applied to evolutionary studies. *ite the website and write a summary of what occurred in the online activity presented in the website in your lab notebook. Evolution of Flight in Birds http122www.ucmp.berkeley.edu2education2e5plorations2reslab2flight2main.htm What did T. rex Taste Like? http122www.ucmp.berkeley.edu2taste2 Part C ' Structured In-uiry Procedure )Part *+ 6 7ake a sketch of the cladogram shown below 89igure 4:. 9ollow the directions on pages 44-4; in the student lab manual! and mark your prediction for the placement of the fossil shown below 89igure 3: on the cladogram using a dot labeled 8(: for structural evidence. s well! briefly e5plain the reasons for your prediction in your lab book.

Procedure )Part ,+ 6 9ollow the directions listed on pages 4;-4< in the student lab manual and use the clarifying information specified in =>ote? bullets below to carry out the &' () search. )he websites required are also listed below and may be accessed

clicking on the web address listed. s well! collect the information indicated in the &' () D ) card below for each of the four gene sequences during the &' () search and record it in your lab notebook. >ote1 @n step 2! download all four gene files rather than "ust three. >ote1 @n step 3! you must click on =nucleotide blast? located under =&asic &last? before you click on =(aved (trategies? )he printed directions do not indicate this! but 9igure ; in the student lab manual implies that this must be done. >ote1 @n step 3! the =*hoose 9ile? button shown in 9igure A will allow you to browse saved files. )here is no button labeled =&rowse?. College Board .ene /iles 6 use this site to download the four D> sequences necessary for the first part of the investigation. http122blogging4biology.edublogs.org22/1/2/<22<2college-board-lab-files2 Blast 6 use this website to compare gene sequences with genomic D> from representative organism in a data base. http122blast.ncbi.nlm.nih.gov2&last.cgi NCBI .ene 6 use this website to obtain gene sequences for analysis. http122www.ncbi.nlm.nih.gov2gene

BLAST DATA
(equence B CCCCCCC %rotein %roduced by (equence CCCCCCCCCCCCCCCCCCCCCCCCC 7ost *losely Related Drganism CCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCC 8Genus) (species:

CCCCCCCCCCCCCCCCCCC 8common name:

Distance )ree Results - (ketch of *ladogram showing at least 3 closely related species.

Data Analysis 6 )he section entitled = naly0ing Results? on page 4< of the student lab manual does not provide procedures that allow the data to be correctly analy0ed. @nstead!

use the procedure indicated by the two bullets below to analy0e your data. fter you are completely done with this structured inquiry! revisit the = naly0ing Results? section in the student lab manual and see if you can figure out what is wrong with the basic premise used for analy0ing the data. 0a((ing .ene Se-uences on t1e Cladogra! - fter collecting data from all four &' () searches! add four additional dots to the cladogram you created in %rocedure 8%art 1: to show the position of the specimen based on the four gene sequences analy0ed. &e sure to label each dot with its sequence number. 2eig1ting Data 6 @n cladistics! not all data is equal in terms of importance. @n general! molecular data is considered more important than structural data. #owever! not all molecular data is of equal importance. )o determine the importance of each of the gene sequences studied! follow the steps below. 1. Ese a Google search to research the function of each protein as well as the range of living organisms known to possess the protein. @f information on range of species is not available online! you may return to the =Distance )ree? option in the &' () program to obtain this information. Record this information in your lab book using the e5ample below.

Google Data
(equence B CCCCCCC %rotein %roduced by (equence CCCCCCCCCCCCCCCCCCCCCCCCC %resumed 9unction of the %rotein CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC )ypes of organisms in which protein is e5pressed CCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 2. Ese the information from the Google search to rank the importance of each of the gene sequences from most to least important. s well! consider the importance of the structural evidence in regard to each of the four gene sequences. Record the rankings you assign to the data in your lab book and also provide the reason for your ranking scheme using the e5ample below. 7ost @mportant 1 2 3 4 'east @mportant ;

Conclusion )3evise t1e 0odel+ 6 &ased on your data analysis! draw a revised version of the cladogram that indicates only the position 8or range of positions: where the unknown

specimen should be placed in your lab book. s well! e5plain your reasoning for choosing the position or range on the cladogram in your lab book.

Peer-Persuasion - %repare a mini-poster presentation of your findings and be able to e5plain and "ustify all components of this investigation. )o construct a mini-poster! tape two manila folders together to make a 3-panel display board that can stand alone on the counter. )he panels should be organi0ed according to the diagram below.
$roup 7ember >ames and 'ogo @ntroduction including - %rimary Fuestion - &ackground *onte5t - #ypothesis 'iterature *ited 7ethodology and G5perimental Design *onclusions and @nterpretation of Results )itle bstract Results - including graphs! tables! charts! and statistical analysis.

Part D ' .uided In-uiry

>ote1 ll procedures! data! and conclusions involved in this guided inquiry should be documented in your lab notebook. 1. Ese the procedure for =Designing and *onducting 4our @nvestigation? on pages 4--;/ in the student lab manual to research =human actin?. @n doing so! use the search parameters bulleted below. naly0e all geno!es available. 'ook for 1ig1ly si!ilar sequences.

2. (ketch the &' () =Distance )ree? cladogram with the five most similar species and collect any other data that you feel is pertinent. 3. G5amine all the suggested genes listed in the first column of the table shown to the right using &' (). )o do so! use the same procedures that are listed for the analysis of =human actin? above. >ote1 ,hen searching! be sure to put the word 41u!an5 in front of the protein. 9or e5ample! search for =human )% (ynthase?. 4. fter the data for all the genes is compiled! consider the function and importance of each of the sequences2proteins! )hen! create a final composite cladogram that reflects all the data you have collected. s well! provide an e5planation of the reasoning you used to create your final composite cladogram. Suggested .enes to E6(lore )% (ynthase *atalase $ %D# Heratin 7yosin %a51 Ebiquitin

Part E ' %(en In-uiry *hoose a protein8s: and organism8s: to study using bioinformatics. (tate your goal and decide if you will search all genomes or only highly similar sequences. *ollect and analy0e your data! before creating and e5plaining your final composite cladogram. Brain Stor!ing Starter /a!ilies o .enes Gn0ymes %arts of Ribosomes %rotein *hannels

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