Class 3: basics of molecular biology (3) and intro to bioinformatics


detailed outline:

* reproduction, evolution, and phylogeny (continued)
  - mutation: 
    - spontaneous vs. induced (uv, chemical agents)
      - lesions: depurination, deamination, oxidative damage
    - types: point mutations, insertions, deletions, replications
    - proofreading: required for high-fidelity dna replication
    - repair mechanisms: fix lesions, required for stability of genome
    - recombination, crossover [bmc p.269]:
	cause large, 'global' changes in genome (dna sequence)
	mechanism is based on hybridisation of homologous dna (sub-)strands
    - errors in chromosome distribution (trisomy 21 = down syndrome)

  - the tree of life
  - prokariotes vs. eukariotes:
	prokaryotes:
	- bacteria and related organisms,
	- evolutationary older 
	- no nucleus
	- fast replication by binary fission 
	  (e.g.,20min/division -> 20*10e7 in 11h)
	eukaroytes:
	- typically bigger than prokaria
	- compartmentalised (nucleus, ...)
	- basis for multicellular organisms
	- typically bigger genomes, more complex organisation (introns, 
  	archea: 
	- mainly bacteria,
	- mostly living under extreme conditions,
	- genetically distinct from prokaria and eukaria,
		but share properties with both
  - endosymbiont hypothesis for mit, chlor

  - sequence-based phylogeny
	mainly using common/conserved elements of cellular systems,
	e.g., r-rna, fundamental metabolic proteins


* modern biochemical techniques:
  - restriction [mbc p.292]
	content-specific cutting of dna ('digestion', 'cleavage')
	various enzymes (restriction nucleases), cleavage sequences
	staggered (sticky) / blunt ends
	restriction mapping (combinatorial problem!)
  - electrophoresis [mbc p.295]
	used for separating dna/rna/protein according to size
	various procedures for different resolutions

  - gel-transfer hybridisation:
	used for detecting complementary sequences
	southern: blot DNA (with DNA probes)
	northern: blot RNA (with DNA or RNA probes)
	(western: analogous technique for detecting protein-antibody interactions)

  - pcr [mbc p.317]
	used for amlification DNA sequences

  - sequencing [mbc p.298]
	used for detecting sequence of DNA
	two basic methods: sanger (enzymatic method / chain termination)
		maxam & gilbert (chemical method)
	(here only sanger)
	underlying idea: make partial replicas of strand to be sequenced,
		using modified nucleotides (dideoxyribonucleoside triphosphate,
		eg., ddATP) that causes chain termination when integrated into
		DNA molecule
	automation: use primers end-labeled with flourescent dye
	-> all four reaction mixtures in one lane, automated readout
		using laser, colour filter, and fluorometer
	proteins can also be sequenced, but typically their sequence
		is inferred from mRNA/DNA sequence data

  - cloning [mbc p.309]
	used for purification, amplification, and convenient
		storage of DNA sequences, expression of genes, ...
	...

  - chemical synthesis of short DNA sequences (oligonucleotides)
	used for primer construction, short probes, etc.

  - mutagenesis:
	specific (site directed), unspecific

  - in-vivo / in-vitro / in-silico techniques


  - biological models and formalisms: "exceptions are the rule"


* problems in bioinformatics (overview)
  - sequencing genomes:
	physical mapping, genome structure

  - interpreting genomic sequence data:
	sequence alignment, gene finding, sequence annotation,
	structure prediction (rna and proteins), 
	pattern discovery, classification, clustering

  - understanding the cell / organisms:
	understanding interactions between proteins, dna, rna;
	regulatory pathways and networks, simulations

  - relations between organisms and evolutionary questions:
	phylogenetic trees, computational models of evolution, simulations

  - biomolecular computing:
	dna computing, inverse folding, self-assembling structures

  - related aspects (often not counted as bioinformatics)
	- simple tools (simple motiv search, dna-rna-protein seq translations, ...)
	- computational models of organisms or biological systems
	(biocybernetics)
	- nature-inspired algorithms
	(genetic algorithms, neural networks, ant colony optimisation, ...)
	- artificial life

  - bioinformatics: 
	- cs just provides tools for biologists / biochemists
	  problems: lack of biological knowledge can lead to weaknesses in tools
	    lack of cs understanding can lead to questionable application of tools
	- cs research motivated by biological problems
	  problem: lack of biological knowledge + overabstraction leads
	    to algorithms/results with limited/no biological application
	- synergistic, interdisciplinary research
	  problem: needs close collaboration of experts in cs and molecular biology,
	    broad common basis of cs and basic biological knowledge
	  but: high potential for innovative and intriguing research and applications



sources and materials:

- Alberts, Bray, Lewis, Raff, Roberts, Watson: Molecular Biology of the Cell.
	Garland Publishing, Inc., 1994
	(Mainly parts of chapters 1,6,7)
- Garret and Grisham: Biochemistry. Saunders College Publishing, 1995
	(Parts of Chapter 4)


reading assignment:

- Baldi and Brunak, Bioinformatics - a machine learning approach, Chapter 1 
  (available from the Reading Room) 
  Remark: Sections 1.4.4 and parts of 1.4.5 are not essential.