Week 2

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This journal entry is due on Tuesday, September 12, at 12:01 AM PDT.

Overview

The purpose of this assignment is:

  • To familiarize yourself with the decoding the genetic code in a "paper and pencil" exercise, to motivate using a computer to do such work.
  • To begin comparing the genetic code to a computer code.

Individual Journal Assignment

  • Store this journal entry as "username Week 2" (i.e., this is the text to place between the square brackets when you link to this page).
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Don't forget to add the "Journal Entry" category to the end of your wiki page.
    • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
  • For your assignment this week, you will keep an electronic laboratory notebook on your individual wiki page. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Homework Partners

For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:

  • Eddie Azinge, Hayden Hinsch
  • Eddie Bachoura, Mary Balducci
  • Blair Hamilton, Antonio Porras
  • Quinn Lanners, Nicole Kalcic
  • Arash Lari, Dina Bashoura
  • John Lopez, Emma Tyrnauer
  • Zachary Van Ysseldyk, Corinne Wong
  • Simon Wroblewski, Katherine Wright

The Genetic Code

  • Write out the complementary strand of DNA below the strand shown and be sure to label the 5’ and 3’ ends of the complementary strand.
5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’
  • There are six possible reading frames in double-stranded DNA. Using the genetic code, translate all possible reading frames of this DNA sequence, keeping in mind the following rules.
    • In RNA, the T becomes a U, so everywhere you see a T in the sequence, read it as a U.
    • The genetic code is read in the 5’ to 3’ direction.
    • Use the single-letter abbreviations for the amino acids because that is what is commonly used by computer programs.
  • Wiki Hint: if you start your line with a single space character, it will appear in the grey box surrounded by the dashed line as shown above.
  • Which of the reading frames (if any) of the reading frames you translated is an open reading frame, i.e., does not contain a stop codon?
    • By convention, the top strand frames are called +1, +2, +3, reading 5' to 3' and the bottom strand frames are called -1, -2, -3, reading 5' to 3'.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist or Dr. Dionisio (for example, via office hours), other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
  4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."
  5. Sign your acknowledgments section with your wiki signature.

References

  • In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • data
    • facts
    • images
    • documents, including the scientific literature
  • Do not include extraneous references that you do not cite or use on your page.
  • The references in this section should be accompanied by in text citations on your page that refer to these references.
  • The references should be formatted according to the APA guidelines.
  • For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
  • Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is:
LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1
  • Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 2 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
    • NOTE: you can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

Read

Reflect

  1. What is the biggest discovery that I made from these readings?
  2. What part of the readings did I understand the least?
  3. What is the relationship between the genetic code and a computer code?