BIOL388/S25:Week 2

This journal entry is due on January 30, at 12:01am Pacific time.

Overview

The purpose of this assignment is:

1. To complete the student information portion of the Week 1 assignment in an alternate format than the wiki.
2. To acquaint you with three main biological databases and the information that is typically documented, gathered, or collected regarding a gene.
3. To relate a paper and pencil gene model to actual gene sequences and tools used to manipulate them on the web.

Journal Assignment Logistics

There are five parts to this Week's journal assignment to catch us up from last week.

1. Individually you will create and share a Google Doc (link to template provided on Brightspace) with the questions you need to answer from the Week 1 assignment that we didn't get to complete on the wiki.
2. Individually you will post one question each for Dr. Dahlquist and Dr. Fitzpatrick on the discussion board created for this on Brightspace.
3. Individually you will complete a paper and pencil exercise that was handed out in class on Thursday, 1/23/25. The paper copy is due at the beginning of class on Thursday, 1/29/25.
4. With your homework partner(s) you will document your answers about your assigned open reading frame (see Homework Partners below) in a single Google Doc that you share between you. Equal participation is expected from each partner.
5. Individually, you will post to the shared class journal discussion board on Brightspace.

• The electronic parts of this assignment are due by 12:01am on Thursday, January 30; the paper/pencil exercise is due in class.
• You will have two different Google Docs.
  • Share permission to edit both documents with both Dr. Dahlquist and Dr. Fitzpatrick.
  • Put the links to the Google Docs in the text submission field of the Brightspace assignments for Week 2.
    • Each homework partner should share the same link for their Week 2 work.

Homework Partners

Homework partners for this week will be the same as last week:

• Hemen & Anastasia (LacZ)
• Nikki, Peyton, and J-P (LacY)
• Andrea & Kyle (Lac A)

Week 1 Student Information

• Make a copy of the Google Doc linked on the assignment on Brightspace, fill in the requested information, give permission to edit to Dr. Dahlquist and Dr. Fitzpatrick, and copy the link in the text submission field of the Week 1 Brightspace Assignment.
• Also post one question each for Dr. Dahlquist and Dr. Fitzpatrick on the discussion board on Brightspace created for this task.

Paper and Pencil Assignment

You will turn in individually the completed paper and pencil assignment that was handed out in class on Thursday, 1/23/25. The paper copy is due at the beginning of class on Thursday, 1/30/25.

The Lac Operon

Our modeling efforts in the first half of the semester will focus on the lac operon in Escherichia coli (E. coli). The lac operon encodes three open reading frames (ORFs), LacZ, LacY, and LacA. Each set of homework partners will research information about one of these ORFs (see Homework Partners for assigned ORF) from three different biological databases as follows and contributed to a shared Google Doc for the group. For this assignment, we will use the terms "gene" and "ORF" interchangeably.

1. What is the name of the gene and name of the protein (from EcoCyc)?
2. Look up your ORF in three different databases and create a summary of what you have learned about your gene on you and your partner's shared Google Doc. The three databases are:
   • EcoCyc
   • NCBI Gene Database
   • UniProt
   • The summary should be one paragraph about the function of your gene based on what you have read in each of the three databases. This is one paragraph that synthesizes information, not one paragraph per database. Take care to paraphrase and cite the information.
3. What is the gene ID (identifier) for your gene in all three databases (EcoCyc, NCBI Gene, UniProt)?
   • Provide hyperlinks to the specific pages for your gene in each of the above databases.
4. What is the DNA sequence of your gene?
5. What is the protein sequence corresponding to your gene?
   • Go to the ExPASy tool and translate the DNA sequence of your gene. Which reading frame encodes the protein sequence? Take a screenshot of your results, display it on your Google Doc, and state which frame it is.
     • For the output format of the ExPASy tool, select "includes nucleotide sequence" and "forward and reverse" DNA strands.
6. What is the function of the protein?
7. Include an image of the 3D structure of the protein.
   • This could be captured from one of the databases, or
   • You can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software, or
   • The NCBI Structure database and RSCB Protein Databank also display structures.
   • Include a screenshot of the information in the "operon" tab of EcoCyc.
     • How does the information presented relate to the "consensus" gene model we have discussed in class?
   • Include a screenshot of the genomic context of your gene from the genome browser.
     • What genes/operons flank your gene on either side?
8. What was different about the information provided about your gene in each of the databases?
   • Were there differences in content, the information or data itself?
   • Were there differences in presentation of the information?
9. Include Acknowledgments and References sections on your Google Doc page. Both partners should sign the Academic Honesty statement by typing their name.
   • You need to cite the specific database page from which you derived your information for each of the questions.
   • When answering the free-form questions, be sure to paraphrase and cite.

Shared Journal Reflection

Individually, you will post your answers to these questions to the shared class journal discussion board on Brightspace.

1. What aspect of this assignment came most easily to you?
2. What aspect of this assignment was the most challenging for you?
3. What (yet) do you not understand?
4. Also, out of the three databases you accessed for this assignment (EcoCyc, NCBI Gene Database, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's wiki page.)