Slide 1 / 32 Slide 2 / 32 New Jersey Center for Teaching and Learning AP BIOLOGY Progressive Science Initiative This material is made freely available at www.njctl.org and is intended for the non-commercial use of Investigation #3 students and teachers. These materials may not be used for any commercial purpose without the written Comparing DNA Sequences to Understand permission of the owners. NJCTL maintains its Evolutionary Relationships with BLAST 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. Summer 2014 www.njctl.org Click to go to website: www.njctl.org Slide 3 / 32 Slide 4 / 32 Pacing/Teacher's Notes Investigation #3: Comparing DNA Click on the topic to go to that section · Pacing/Teacher's Notes · Pre-Lab · Guided Investigation · Independent Inquiry Return to Table of Contents Slide 5 / 32 Slide 6 / 32 Pacing Teacher's Notes General Reference Lab procedure adapted from College Board AP Biology Day (time) Activity to Unit Plan Notes Description Investigative Labs: An Inquiry Approach Teacher's Manual Day 1 (HW) Pre-Lab EC Day 16 Pre-lab questions HW Downloaded files need to be Click here for CB "unzipped" before use. BLAST may Guided Day 2 (80) Steps 1-4 Practice on EC Day 17 take a few minutes to process AP Biology BLAST information depending on your Teacher Manual 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 Slide 8 / 32 Pre-Lab 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. Return to Table of Contents Slide 9 / 32 Slide 10 / 32 Pre-Lab Questions Pre-Lab Questions 2. GAPDH (glyceraldehyde 3-phosphate dehydrogenase) is an enzyme that catalyzes the sixth step in glycolysis, an important Read the background information and answer the following reaction that produces molecules used in cellular respiration. The questions in your lab notebook. (from pages S43-S44 of student lab following data table shows the percentage similarity of this gene manual) and the protein it expression humans versus other species. 1. Use the following data to construct a cladogram of the major plant groups. Gene Percentage Protein Percentage Species Similarity Similarity Organisms Vascular Tissue Flowers Seeds Chimpanzee ( Pan troglodytes ) 99.6% 100% Mosses 0 0 0 Dog ( Canis lupus familiaris ) 91.3% 95.2% Pine Trees 1 0 1 Fruit Fly ( Drosophila melanogaster ) 72.4% 76.7% Flowering Plants 1 1 1 Roundworm ( Caenorhabditis elegans ) 68.2% 74.3% Ferns 1 0 0 a. Why is the percentage similarity in the gene always lower than the Total 3 1 2 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 Slide 12 / 32 Safety Guided Investigation There are no safety precautions associated with this investigation. Return to Table of Contents
Slide 13 / 32 Slide 14 / 32 Materials Liaoning Fossil · Computer with · Laboratory notebook A team of scientists has internet access 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 Slide 16 / 32 Liaoning Fossil Liaoning Fossil Little is know about the fossil. It appears to be a new species. Step 1 Form an initial hypothesis as to where you believe the Upon careful examination of the fossil, small amounts of soft fossil specimen should be placed on the cladogram based on tissue have been discovered. Normally, soft tissue does not the morphological observations you made earlier. Sketch your survive fossilization; however, rare situations of such hypothesized cladogram, including the Liaoning fossil, in your preservation do occur. notebook. 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 17 / 32 Slide 18 / 32 Liaoning Fossil Liaoning Fossil Step 2 Locate fossil gene files by going to: Step 3 Upload the gene sequence into BLAST by doing the following: http://apcentral.collegeboard.com/apc/members/courses/ teachers_corner/218954.html 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 Click here for page. gene files c. Under "Upload Search Strategy," click on "Browse" and locate one of the gene files you saved onto your computer. Unpack the zip files. Click here for BLAST
Slide 19 / 32 Slide 20 / 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 21 / 32 Slide 22 / 32 Liaoning Fossil Liaoning Fossil The second section lists genetic sequences identical or most Step 4 The results page has two sections. The first section is a similar to the gene of interest. graphical display of the matching sequences. 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 Slide 24 / 32 Liaoning Fossil Liaoning Fossil By clicking on the link title "Distance tree of results" you will see Repeat steps 3 and 4 with the other genes of interest. 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
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