worddocumentexercise8.docx

Discussion questions for Ex 8
(Note: these deviate from the manual)

There are two parts to these new discussion questions for Ex 8. In part 1, you’ll generate a short essay. In Part 2, you’ll perform ORF Finder and BLAST on a new sequence and answer 5 questions.

Both parts must be completed in full, represent your own work and be expressed using your own words. Insert all content into this MS Word document and upload saved document to Folio to the appropriate dropbox.

Part 1:
Directions: Within the ‘Lab Completion for Exercise 8’ Folio page under Discussion, choose the link to the excellent article entitled ‘NY Times article: Bad news wrapped in a protein’. This article describes various proteins encoded by the SARS-CoV-2 genome you’ve been analyzing.
· Choose one protein described in the NY Times article and write a 2 paragraph essay that has the following structure and content:
· the first paragraph (3-5 sentences) must state the name of the protein you chose and describe its function.
· the second paragraph (3-5 sentence) must describe a detail that you found most interesting about this week’s lab and briefly summarize why scientists rely on software like ORF Finder and BLAST. 

Type your 2 paragraph essay here (return to create more space, if needed):

Part 2:

Directions: Within the ‘Lab Completion for Exercise 8’ Folio page under Discussion, choose the link entitled ‘Genome sequence to analyze for discussion questions’. The file will open in a new window and contains sequence of a different section of the SARS-CoV-2 genome than the one you analyzed in parts 3-5. This section contains a different ORF which encodes for a different protein. 

· Copy the entire sequence. 
· Analyze this sequence using ORF Finder just as you did in Part three.  If you don’t remember how to do this, re-watch the video in Part 3.
· The link for ORF Finder is in the Discussion section of your Ex 8 Folio page. However, you could always Google the term ‘ORF Finder NCBI’ to locate the site containing this software.
· Answer the following four questions:

1. What is the reading frame (choose one: -1, -2, -3, +1, +2 or +3) of the largest open reading frame (ORF) within this sequence?

2. How many nucleotides (nt) are there in this ORF?

3. How many codons are there within this ORF?

4. How many amino acids are encoded by this ORF?

· Now, BLAST the amino acid sequence encoded by this ORF just as you did in Part four. Re-watch the video in part 4 if you don’t remember the steps.
· Remember, within the ORF Finder software, under the ‘BLAST database’ option, select “Non-redundant protein sequences (nr)” from the dropdown menu. 
· Then, choose the “BLAST” button (NOT SmartBLAST). 
· Answer the following question:

5. Based on the BLAST results, list the name of the protein you predict this ORF encodes for.