AP BIOLOGY Investigation #3 Comparing DNA Sequences to Understand - PDF document

Slide 1 / 32 New Jersey Center for Teaching and Learning Progressive Science Initiative This material is made freely available at www.njctl.org and is intended for the non-commercial use of students and teachers. These materials may not be used for any commercial purpose without the written permission of the owners. NJCTL maintains its website for the convenience of teachers who wish to make their work available to other teachers, participate in a virtual professional learning community, and/or provide access to course materials to parents, students and others. Click to go to website: www.njctl.org Slide 2 / 32 AP BIOLOGY Investigation #3 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Summer 2014 www.njctl.org Slide 3 / 32 Investigation #3: Comparing DNA Click on the topic to go to that section · Pacing/Teacher's Notes · Pre-Lab · Guided Investigation · Independent Inquiry

Slide 4 / 32 Pacing/Teacher's Notes Return to Table of Contents Slide 5 / 32 Teacher's Notes Lab procedure adapted from College Board AP Biology Investigative Labs: An Inquiry Approach Teacher's Manual Click here for CB AP Biology Teacher Manual Slide 6 / 32 Pacing General Reference Day (time) Activity to Unit Plan Notes Description Day 1 (HW) Pre-Lab EC Day 16 Pre-lab questions HW Downloaded files need to be Guided "unzipped" before use. BLAST may Day 2 (80) Steps 1-4 EC Day 17 take a few minutes to process Practice on BLAST information depending on your school's bandwidth. Copy desired gene Independent sequences Day 3 (40) EC Day 18 Investigation from Entrez Gene into BLAST Day 4 (20) Assessment Lab Quiz EC Day 19

Slide 7 / 32 Pre-Lab Return to Table of Contents Slide 8 / 32 Question/Objectives How can bioinformatic be used as a tool to determine evolutionary relationships and to better understand genetic diseases? In this lab we will: · Create cladograms that depict evolutionary relationships. · Analyze biological data with a sophisticated bioinformatics online tool. · Use cladograms and bioinformatics tools to ask other questions of your own and to test the ability to apply concept you know relating to genetics and evolution. Slide 9 / 32 Pre-Lab Questions Read the background information and answer the following questions in your lab notebook. (from pages S43-S44 of student lab manual) 1. Use the following data to construct a cladogram of the major plant groups. Organisms Vascular Tissue Flowers Seeds Mosses 0 0 0 Pine Trees 1 0 1 Flowering Plants 1 1 1 Ferns 1 0 0 Total 3 1 2

Slide 10 / 32 Pre-Lab Questions 2. GAPDH (glyceraldehyde 3-phosphate dehydrogenase) is an enzyme that catalyzes the sixth step in glycolysis, an important reaction that produces molecules used in cellular respiration. The following data table shows the percentage similarity of this gene and the protein it expression humans versus other species. Gene Percentage Protein Percentage Species Similarity Similarity Chimpanzee ( Pan troglodytes ) 99.6% 100% Dog ( Canis lupus familiaris ) 91.3% 95.2% Fruit Fly ( Drosophila melanogaster ) 72.4% 76.7% Roundworm ( Caenorhabditis elegans ) 68.2% 74.3% a. Why is the percentage similarity in the gene always lower than the percentage similarity in the protein for each species? b. Draw a cladogram depicting the evolutionary relationships among all five species (including humans) according to this percentage similarity in the GAPDH gene. Slide 11 / 32 Safety There are no safety precautions associated with this investigation. Slide 12 / 32 Guided Investigation Return to Table of Contents

Slide 13 / 32 Materials · Computer with · Laboratory notebook internet access Slide 14 / 32 Liaoning Fossil A team of scientists has uncovered this fossil specimen near Liaoning Province, China. Make some general observations about the morphology (physical structure) of the fossil, and then record your observations in your lab notebook. Slide 15 / 32 Liaoning Fossil Little is know about the fossil. It appears to be a new species. Upon careful examination of the fossil, small amounts of soft tissue have been discovered. Normally, soft tissue does not survive fossilization; however, rare situations of such preservation do occur. Scientists were able to extract DNA nucleotides from the tissue and use the information to sequence several genes. Your task is to use BLAST to analyze these genes and determine the most likely placement of the fossil species on the cladogram.

Slide 16 / 32 Liaoning Fossil Step 1 Form an initial hypothesis as to where you believe the fossil specimen should be placed on the cladogram based on the morphological observations you made earlier. Sketch your hypothesized cladogram, including the Liaoning fossil, in your notebook. Slide 17 / 32 Liaoning Fossil Step 2 Locate fossil gene files by going to: http://apcentral.collegeboard.com/apc/members/courses/ teachers_corner/218954.html Click here for gene files Unpack the zip files. Slide 18 / 32 Liaoning Fossil Step 3 Upload the gene sequence into BLAST by doing the following: a. Go to the BLAST homepage: http://blast.ncbi.nlm.nih.gov/ Blast.cgi b. Click on "Saved Strategies" from the menu at the top of the page. c. Under "Upload Search Strategy," click on "Browse" and locate one of the gene files you saved onto your computer. Click here for BLAST

Slide 19 / 32 Liaoning Fossil d. Click "View". e. A screen will appear with the parameters for your query already configured. Do not alter any of the parameters. Scroll down the page and click on the "BLAST" button at the bottom. Slide 20 / 32 Slide 21 / 32 Liaoning Fossil Step 4 The results page has two sections. The first section is a graphical display of the matching sequences.

Slide 22 / 32 Liaoning Fossil The second section lists genetic sequences identical or most similar to the gene of interest. By clicking on a particular species listed, you can view a full report of this species relationship to the gene of interest. Note: the higher the score the closer the alignment, the lower the E value the closer the alignment, and sequences with E values less than 1 x10 -4 can be considered related with an error rate of less than 0.01%. Slide 23 / 32 Liaoning Fossil By clicking on the link title "Distance tree of results" you will see a cladogram with the species with similar sequences to your gene of interest placed on the cladogram according to how closely their matched gene aligns with your gene of interest. Note: your gene of interest will be highlighted in the cladogram. Click here for cladogram Slide 24 / 32 Liaoning Fossil Repeat steps 3 and 4 with the other genes of interest.

Slide 25 / 32 Analyzing & Evaluating Results As you collect information from BLAST for each of the gene files, you should be thinking about your original hypothesis and whether the data support or cause you to reject your original placement of the fossil species on the cladogram. Analysis Questions · What species in the BLAST results has the most similar gene sequence to the gene of interest? · Where is that species located on your cladogram? · How similar is that gene sequence? · What species has the next most similar gene sequence to the gene of interest? Based on this evidence, decide where the fossil species belongs of the cladogram. If necessary, redraw the cladogram you created before. Slide 26 / 32 Independent Inquiry Return to Table of Contents Slide 27 / 32 Designing & Conducting Your Investigation Now that you are comfortable utilizing BLAST, you can explore your own gene of interest. Below is a list of some gene suggestions you could investigate using BLAST. Suggested Genes to Explore Families or Genes Studied Previously ATP synthase Enzymes Catalase Parts of ribosomes GAPDH Protein channels Keratin Myosin Pax1 Ubiquitin