Lecture 2, 04/09/09, thu

In this lecture we reviewed some general background in molecular biology,
particularly the central genetic process (from DNA to Proteins).
We discussed the structure, function, and string representation of DNA, proteins and RNA and started discussing the basic processes of 
gene expression (transcription and translation).

Important concepts include:
- (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)
- structure and function of proteins
- function of DNA and RNA, ribozymes (= RNA enzymes)

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)
- 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)
- DNA serves mainly for information storage
- proteins are often represented by strings over a 20 letter alphabet
- like DNA and RNA proteins have a direction;
  they are typically written down from the N terminus to the C terminus
	

Resources:

- Garret and Grisham: Biochemistry. Saunders College Publishing, 1995
	(Parts of Chapters 1-7)

- Alberts, Bray, Lewis, Raff, Roberts, Watson: Molecular Biology of the Cell.
	Garland Publishing, Inc., 1994
	(Parts of Chapters 1-7)

- Benjamin Lewin: Genes V. Oxford University Press, 1994.



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]