This outline is also available in PDF.
Held: Tuesday, 8 September 2009
We begin to study central issues in molecular biology and the
corresponding computational problems.
- Reading: Chapter 2.
- Due: Writeup of Web exploration.
- Vida has been sick. That means you get to watch the
train wreck in slow motion of Sam trying to describe biology.
- There is no homework for Thursday. You may, however, want to look over Chapter 2 again.
- Lab Exercises, Continued
- Basics of the Central Dogma
- Key Processes
- Some Related Issues
- Computational Problems
- Web Exploration
- We'll use the first fifteen-twenty minutes of class to wrap up the
lab exercise from the previous class.
- We'll spend a few minutes reflecting on what you learned in the lab.
- The title of the chapter is
The Central Dogma?
- Do the authors tell us explicitly what the central dogma is?
- How would you phrase the central dogma?
- The term
The Central Dogma was coined by Francis Crick
- You should know who Francis Crick is
- The central dogma describes information transfer between the three
primary sequences we work with
- He introduced the concept in a 1958 conference paper and revisited
it in a 1970 Nature paper.
- Crick describes the dogma in this way:
once (sequential) information has passed into the protein, it cannot
get out again
- Crick also breaks the possible types of information transfer into
- General transfers, which happen for most kinds of cells:
- DNA to DNA (replication)
- DNA to RNA (transcription)
- RNA to Protein (translation)
- Special transfer, which happen in a few special cases
- DNA to protein
- RNA to RNA
- RNA to DNA
- Unknown transfers, which he postulates do not happen
- Protein to DNA
- Protein to RNA
- Protein to Protein
- Interestingly, Crick's second article on the Central Dogma is
immediately followed by an article whose thesis is
RNA tumour viruses contain an enzyme that synthesizes a DNA-RNA
hybrid using the single stranded viral RNA as template.
Hybridization experiments confirm that the DNA strand is
complementary to the viral RNA.
- Do you know any possible exceptions to the
proteins don't transfer
information to any kind of sequence?
- Copying DNA to DNA, e.g., when cells divide
- Lots of effort to ensure accuracy of copy
- Not that important right now
- Copying DNA to RNA
- Process goes from the 3' to 5' of the template strand
- A lot like DNA pairing, except that U pairs with A.
- The quick hack: Start with the coding strand, replace all T's with U's
- Starts at start codon (AUG)
- Triplets of nucleotides converted to proteins
- Stops at stop codon
- A promoter region gets everything started
- Chromosomes: 46 (22 pairs plus two sex chromosomes)
- So, what are the interesting computational problems we get from
this initial information?
- We can encode transcription and translation
- What input types?
- What output types?
- As the initial examples suggest, one interesting problem is to compare
two DNA sequences and see how close they are.
- Allows us to find asic information about mutations.
- A more interesting problem is to look at comparing partial sequences
to longer sequences.
Make sure to turn on scripting for any site you visit!
- We're going to try the Web exploration for Chapter 2.
- You'll find that some of it is similar to what we did for Chapter 1.
- But reinforcement is good.
- No, you don't need to turn it in.
- But we will compare notes at the end.
- You may want to note what you learn from the more detailed instructions.
- Here are some notes, thoughts, and questions
- Did this exploration help you find better ways to look for DNA?
- Does the FASTA file for HBB use the template sequence or the coding
sequence? How do you know?
- Can you find typos in the GenBank record?
- Stupid tidbit: Sam is likely to have an HBB mutation
- What software can you use to compare sequences?
- What procedures would we have to write to make all of this easier to