Lecture 2, 03/09/11, thu

In this lecture, we reviewed some basic issues regarding
the structure and string representation of DNA, RNA, and proteins.
We then covered some more details of the basic processes
of gene expression (transcription, RNA maturation, translation),
discussed the structure and organisation of genomes
as well as fundamental controll mechanism for gene expression
and protein activity, and gave a brief overview of
some basic issues in reproduction, evolution, and phylogeny.


Important concepts include:
- structure and function of proteins
- function of DNA and RNA, ribozymes (= RNA enzymes)
- RNA maturation, splicing, introns, exons
- eukariotic genome structure, chromosomes, 
	extranuclear genomes (mitochondrial, chloroplast)
- function of genomic dna:
	protein coding, functional rna coding, centromeres, telomeres, 
	repetitive elements, transposons, ...
- gene regulation:
	transcription / translation control, 
	transport control, RNA maturation control, 
	mRNA degradation control, protein activity control;
	regulatory networks
- evolution:
	dna replication, mutations (transitions / transversions,
	insertions, deletions, transposons, chromosome recombination,
	cross-over)

Note:
- 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
- genome size / chrosome number is not strictly correlated to 
	complexity of organism
- gene regulatory relationships can have the form of 
	(noisy) logical conjunctions or disjunctions (AND/OR expressions)
	and can be modelled using standard CS concepts
	(gates, neural networks, ...)
- mutation probabilities vary across chromosomes (hot spots)
- mutations result in genomic differences that can be used to 
	estimate evolutionary relationships / distance between organisms
	

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.

- Griffiths, Miller, Suzuki, Lewontin, Gelbart: 
	An Introduction to Genetic Analysis. Freeman and Company, 1993.

- Watson, Gilman, Witkowsi, Zoller: Recombinant DNA. 
	Scientific American Books, 1992.



Assigned Reading (reminder):

- 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]