SBI 4UW DNA Barcoding Assignment

SBI 4UW DNA Barcoding Assignment 2017 Name: / 50 This assignment must be completed and handed in on these original handouts provided. Use your own words as much as possible, ie. don’t copy word for word from the websites! Only the last part needs to be completed on separate sheets. No exceptions! 1. Research the cytochrome c oxidase enzyme complex (one of its subunits is called CO1). a) State specifically where it is found, and describe its specific activity. Google cytochrome c oxidase; the Wikipedia response is good enough for this answer  [4]

b) Read the section on “Structure.” in Wikipedia’s article. Explain briefly the level of protein structure for the protein complex as seen in the diagrams. State the two types of secondary structure seen in the diagrams. [3]

2. Research mitochondrial DNA (mtDNA), state its location, and describe its evolutionary origin and inheritance in most multicellular organisms. Again, the Wikipedia response is good enough for this answer. [3]

3. Go to the website http://ccdb.ca and click on the “About us” tab at the top of the page. a) State what the CCDB is best known for. [1]

Click on the “Solutions” tab at the top of the page. Scroll down to “International Barcode of Life” (iBOL) and read the paragraph. b) State what iBOL participants gathered within 5 years. [1] Click on the title “International Barcode of Life” which opens a new website http://ibol.org. Hover over “About Us” in the top menu bar and click on “What is DNA Barcoding?” c) Outline how DNA barcodes can be used like UPC barcodes. [1]

d) Describe the gene region being used for DNA barcoding. [1]

e) State the advantages of using CO1 (Cytochrome Oxidase 1). [2]

f) State why CO1 cannot be used in plants, and also state where genes that may be used for DNA barcoding have been located in plants. [2]

On the same page, read “The Barcode Production Pipeline.” g) List the sequence of techniques used to obtain a DNA barcode from a tissue sample. [4]

Go back to http://ibol.org. Scroll down to the “Building the Barcode Library” article and click on “Learn more”. h) State what BOLD stands for. [1]

i) State what BOLD is used for. [1]

4. Using your knowledge from class: a) Outline how the degeneracy of the genetic code plays a role in variation in protein coding gene sequences. [2]

b) If 45 nucleotides are examined in a protein coding gene, and variation as described in j) above is possible in all codons, close to a billion alternatives could exist. Show how this amount of variation could theoretically be possible. [2]

So why is all of this important?

5. Read the article “DNA Barcoding: Cracking Down on Bushmeat” found on my webpage (http://teachers.wrdsb.ca/busch/grade-12-biology/) under “Helpful Documents / Links”. Explain how this technology may be used to stop the trade in illegal bushmeat and other animal parts. [3]

6. Suggest three other applications, not outlined on this assignment, for the use of DNA barcodes. Information under the “Solutions” tab at http://ccdb.ca will help here. [3] 7. Use the BOLD Systems to search for DNA barcodes and identify species. If an individual is attempting to bring some feline pelts through customs into Canada, you can find out if any of these may be endangered species and if trade in the pelts is or may be illegal. a) Go to http://www.barcodinglife.org or http://www.boldsystems.org . b) Click on “Identification” in the top menu bar. c) The second bullet, “Species Level Barcode Records”, should be selected. d) The (FASTA) sequences for two ‘unknown’ COI gene samples can be found at http://teachers.wrdsb.ca/busch/grade-12-biology/ under “Helpful Documents / Links” e) For the first sample, copy and paste the first sequence into the box where it states “Enter sequences in FASTA format.” f) Click the “Submit” button. g) On the resulting page, use the information under the “Identification Summary” sub-title to complete the following table for the first sequence. h) Repeat steps (a) to (g) for the second FASTA sequence. [2 marks each = 4 total] Table 1. Identification Summary for the FASTA sequences and probability of placement First Sequence Second Sequence Taxonomic Level Taxon Prob. of Taxon Prob. of Assignment Placement Assignment Placement phylum class order family genus (use proper format!) species (use proper format!)

i) Research the common name of each animal identified above, where it lives, and its conservation status (ie. endangered, threatened, etc.) Explain if this animal can legally be hunted and if trade for its pelt or other body parts would be legal or not. This should be written on a new piece of paper, and organized separately for each of the two species identified above. References should be used for these answers. [4 marks for each species = 8 total] Click on “Databases” in the top menu bar, then on “Public Data Portal”. Search first for a wolf (Canis lupus) and then in a separate window or tab, search for a domestic dog (Canis familiaris) by typing the Latin name into the search field, then clicking the “Search” button. There are many sequences from which to choose under “Showing records”. Click on the blue links and scroll down to see the FASTA sequence. Copy, paste and identify a few sequences for each animal like you did for steps (e) to (g) above, then under the “Top 20 Matches” sub-title have a look at the “Similarity %” column to help you answer the question below. Note: For the Canis familiaris list only click on the links that have “Canis familiaris [COI-5P:…]” written next to them. j) In the space below (only), deduce if wolves can be considered the same species as domestic dogs. [3]