Lecture 1, 03/09/09, tue

In today's lecture, after some general information on the course,
we briefly discussed the question "what is bioinformatics?"
and started going over some general background in molecular biology,
particularly the central genetic process (from DNA to Proteins).
In particular, we discussed the structure and function of DNA and RNA.

Important concepts include:
- three types of computing devices: computers, brains, cells
- computational molecular biology vs. biomolecular computing
- (complex) hierarchical structure of cells
- key role of organic macromolecules, particularly dna, rna, proteins
- prokaryotes vs. eukaryotes (the latter have organelles, e.g., nucleus)
- dna, bases, pairing of complementary bases
- rna, secondary structure
- transcription, translation
- reverse transcription
- ribosome
- messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA)

Note:
- in eukaryotic cells, DNA occurs in the nucleus as well as in 
	mitochondria / chloroplasts
- central genetic process: genomic DNA gets transcribed into mRNA 
	which is translated into proteins
- RNA uses uracil (U) instead of thymine (T)
- DNA and RNA molecules have two chemically distinct ends (called 5' and 3')
- DNA is typically double stranded, RNA single stranded
- RNA often forms secondary structure by means of baise-pairing
	interactions within the same (single stranded) molecule
  (DNA can also form secondary structure, but it typically doesn't happen, since
	DNA occurs mostly double-stranded)
- DNA serves mainly for information storage
- RNA has many different functions:
  - temporary information storage (mRNA)
  - catalytic (ribozymes, rRNA)
  - other: tRNA (adaptor molecule, key role in translation of mRNA into proteins),
		small RNAs (e.g., snoRNA play key roles in mRNA processing)


Resources:

- Alberts, Bray, Lewis, Raff, Roberts, Watson: Molecular Biology of the Cell.
	Garland Publishing, Inc., 1994
	(Parts of Chapters 1-7)
  Note: any introductory biochemistry text will cover similar information

- Baldi, Brunak: Bioinformatics - The Machine Learning Approach.
	MIT Press, 1998
	(Ch. 1)
  [Available in the ICICS Reading Room]


Assigned Reading:

- Douglas R. Hofstadter: Metamagical Themas, Chapter 27: 
	The Genetic Code: Arbitrary? Bantam Books, 1986
  [Available from the CPSC 545/445 box in the ICICS Reading Room]