Week 2

This journal entry is due on Friday, September 6, at midnight PDT. (Thursday night/Friday morning)

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)
• 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

Readings

1. What is the biggest discovery that I made from these readings?
2. What part of the readings did I understand the least?
3. How was the genetic code solved experimentally?
4. What is the relationship between the genetic code and 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.

Wiki Catch-up

If you missed practicing any wiki skills or doing any other tasks from Week 1, wrap them up this week.

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'.