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.