Class 1: basics of molecular biology


detailed outline:

* course intro, organisational info
  - brief intros?
  - what is bioinformatics?
      biology: a branch of knowledge that deals 
	with living organisms and vital processes
      informatics: (chiefly British): information science
    -> various views: 
	- it/cs tools for biological problems, 
	- cs/is research inspired by biological problems, 
	- information processing in biological systems,
	- ...
	- hot interdisciplinary research area with lots of 
		funding/employment/publication opportunities :-)
  - course outline and organisation
  - grades, assignments
  - course project, timetable
  - conflicts with other courses: thu 538D (Greenstreet), tue 532D (MacLean)

* the basic genetic process ("central dogma")
  - dna, rna, protein; transcription, translation;
	structure, basic components, string representations,
	directionality
  - base-pairing, complementarity, hybridisation (complementary templating)

  - dna: double strand (helix)
  - dna function: information storage,
	determined by sequence
  - protein: single backbone, polymers, interaction with 
	dna,rna,prot
  - protein function: catalytic, structural,
	determined by / dependent on 3d shape which
	is determined by / dependent on sequence
	(genotype vs. phenotype)

  - transcription: initiation, termination, 
	m-rna (stabilisation, digestion)
  - introns, exons
  - rna maturation: editing, splicing
  - translation: genetic code, codons, 
	degeneracy, wobble base, stop-codons
  - translation: ribosomes, t-rna, initiation?, termination?

  - rna: single strand, dna-rna hybrid, rna double strand
  - function of rna:
	information transfer (m-rna, t-rna),
	structural (e.g., r-rna),
	information storage (rna viruses, single and double strand),
	catalytic (rna world)

  - specific example: translation of seleno-cystein


sources and materials:

- 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.

- Gesteland, Cach, Atkins (Editors): The RNA World. 
	Cold Spring Harbor Laboratory Press, 1999. 
	(Chapter 24 - translation of selenocystein)



reading assignment:

- Douglas R. Hofstadter: Metamagical Themas, Chapter 27: The Genetic Code: Arbitrsry?
	Bantam Books, 1986