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Held: Tuesday, 6 September 2011
Summary:
We begin to study central issues in molecular biology and the
corresponding computational problems.
Related Pages:
Notes:
- EC for Gene Gaub's concert, Thursday, 11 a.m.
- For Thursday, Read Chapter 3.
- For next Tuesday, read and respond to Altshcul et al. 1990.
- A friendly reminder for the FaceBook generation: What appears in the S&B stays on the Web for a long time. Do you want a potential employer or grad school committee to read
My goal is to make out with everyone in this house before the end of the year.
(That's better than the alcohol comments that normally appear in house profiles. However, ....)
- Pick new groups today. New partners. Still mixed background.
- You do not need to turn in a writeup for today's lab or Thursday's lab. You will, however, have to due the on-your-own project (2.65).
Overview:
- Reflection on the Chapter 1 programming lab.
- Basics of the Central Dogma
- Key Processes
- Some Related Issues
- Computational Problems
- Web Exploration
- Python or Perl?
- Executable or interactive?
- What else did you learn?
- 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
three categories:
- 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
Several
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
?
- Duplication
- Copying DNA to DNA, e.g., when cells divide
- Lots of effort to ensure accuracy of copy
- Not that important right now
- Transcription
- 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
- Translation
- 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)
- Inheritance
- Mutation
- 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.
- We're going to try the the Web exploration for Chapter 2.
- Form new groups!
- Please read through all of our lab before beginning.
- Random notes:
- Stupid tidbit: Sam is likely to have an HBB mutation
;
