Week 2

This journal entry is due on Tuesday, September 15, at midnight PDT. (Monday night/Tuesday morning)

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 the complementary biology or computer science 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). Homework partners for this week are:

• Mary Alverson, Elena Olufson
• Nicole Anguiano, Brandon Litvak
• Brandon Klein, Emily Simso
• Josh Kuroda, Veronica Pacheco
• Ron Legaspi, Trixie Roque
• Mahrad Saeedi, Anindita Varshneya
• Jake Woodlee, Kevin Wyllie
• Erich Yanoschik, Kristen Zebrowski

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'.

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

• Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)
• Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. Trends in Biochemical Sciences 29: 46-54. (on MyLMUConnect)
• Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight. Trends in Biochemical Sciences 29: 293.
• Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on MyLMUConnect)
• Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on MyLMUConnect)

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?