Download SBI 4UW DNA Barcoding Assignment 2015 / 50 marks

SBI 4UW DNA Barcoding Assignment 2015
/ 50 marks
Name:________________________________________________________
This assignment must be completed and handed in on these original handouts provided. Try to use your
own words and not 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.” State and explain briefly the level of structure for the protein
complex, also 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 read the introductory paragraphs.
a) List the sciences involved in DNA barcoding. [1]
Select “Research” in the top menu bar. Read “Primer on DNA Barcoding.”
b) Outline how DNA barcodes can be used like UPC barcodes. [1]
Scroll up to “International Barcode of Life (iBOL) and read the paragraph.
c) State what iBOL participants will gather within 5 years. [1]
Click on the title “International Barcode of Life (iBOL)” which opens a new website
http://ibol.org. Go down to “Building the Barcode Library” and select “Learn more”
d) State what BOLD stands for. [1]
e) State what BOLD is used for. [1]
Select “About Us” in the top menu bar and go to “What is Barcoding?”
f) Describe the gene region being used for DNA barcoding. [1]
g) State the advantages of using CO1. [2]
h) 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]
Read “The Barcode Production Pipeline.”
i) List the sequence of techniques used to obtain a DNA barcode from a tissue sample. [4]
1.
2.
3.
4.
j) Using your knowledge from class, outline how the degeneracy of the genetic code plays a role
in variation in protein coding gene sequences. [2]
k) 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?
1. Read the article provided DNA Barcoding: Cracking Down on Bushmeat found at
teachers.wrdsb.ca/cdrung under SBI 4UW. To access the article, follow the same
instructions given on the last page using step 4, except choose the article above to download
instead of the fasta sequences.
Explain how this technology may be used to stop the trade in illegal bushmeat and other
animal parts. [3]
2. Suggest three other applications, not outlined on this assignment, for the use of DNA
barcodes. A link at http://ccdb.ca at the bottom of the page for Species ID Services will help
here. [3]
Using the BOLD Systems to search for DNA barcodes and identify species: a hypothetical
situation
An individual is attempting to bring some feline pelts through customs into Canada. You have
been assigned to find out if any of these may be endangered species, and if trade in the pelts is
or may be illegal.
1.
2.
3.
4.
Go to http://www.barcodinglife.org
Select Identification in the top menu bar.
Select the second bullet “Species Level Barcode Records.”
The fasta sequences for two COI gene samples can be found at teachers.wrdsb.ca/cdrung under
SBI 4UW. Select “Fasta sequences” in order to download the fasta sequences.
5. For the first sample, copy and paste the first fasta sequence into the box where it states
Enter sequences in fasta format.
6. Select Submit.
7. This will open an Identification Summary for the fasta sequence submitted. Complete the
following table for the first sample. Repeat the process for the second fasta sequence.
[2 each = 4 total]
Table 1. Identification Summary for the first fasta sequence and probability of placement
Taxonomic Level
Taxon Assignment
Probability of Placement
phylum
class
order
family
genus (use proper format!)
species (use proper format!)
Table 2. Identification Summary for the second fasta sequence and probability of placement
Taxonomic Level
Taxon Assignment
Probability of Placement
phylum
class
order
family
genus (use proper format!)
species (use proper format!)
8. Research the common name of each animal, where it lives, and its conservation status (e.g.
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 done on a separate piece of
paper, and organized separately for each of the two species identified above.
[4 marks for each species = 8 total] References should be used for these answers. [1]
9. Explain if the wolf (Canis lupus) and the domestic dog (Canis familiaris) are possibly the
same species. Provide concrete evidence in the answer from the BOLD systems. Complete
this answer below. [3]