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CISC841, F08, Lec2, Liao CISC 841 Bioinformatics (Fall 2008) A Primer on Molecular Biology & Bioinformatics challenges
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CISC841, F08, Lec2, Liao
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10 -3 10 -6 10 -9
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CISC841, F08, Lec2, Liao
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DNA (double helix, hydrogen bond, complementary bases A-T, G-C) 5' end phosphate group 3' end is free 1' position is attached with the base double strand DNA sequences form a helix via hydrogen bonds between complementary bases hydrogen bond: - weak: about 3~5 kJ/mol (A covalent C-C bond has 380 kJ/mol), will break when heated - saturation: - spefic:
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CISC841, F08, Lec2, Liao 1 5 Purines: A and G Pyrimidines: C and T Oligonucleotide: a DNA of a few tens of nucleotides ATP, ADP, AMP 3 Structure of the bases (Thymine is not shown here)
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CISC841, F08, Lec2, Liao Small molecules: > sugar: carbohydrate > fatty acids > nucleotides: A, C, G, T (Purines: A and G; Pyrimidines: C and T)
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CISC841, F08, Lec2, Liao
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The rules for base pairing (Watson-Crick base pairing) : A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T)purinepyrimidine C with G: the pyrimidine cytosine (C) always pairs with the purine guanine (G)
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CISC841, F08, Lec2, Liao
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C- terminal N-terminal Polypeptide
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CISC841, F08, Lec2, Liao
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Helix complete turn every 3.6 AAs Hydrogen bond between (-C=O) of one AA and (-N-H) of its 4 th neighboring AA
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CISC841, F08, Lec2, Liao Hydrogen bond b/w carbonyl oxygen atom on one chain and NH group on the adjacent chain
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The Central Dogma: DNA RNA Protein CISC841, F08, Lec2, Liao
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Gene Structure
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CISC841, F08, Lec2, Liao
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Genetic Code: codons
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Systems Biology Regulatory networks Signaling transduction networks Metabolic pathway networks CISC841, F08, Lec2, Liao
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Regulation Other Cells Genes (DNA) Message (RNA) Proteins Function/ Environment Regulation
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CISC841, F08, Lec2, Liao Operon lac operon on E. coli Lactose binds with lacI, allowing RNA polymerase to bind to P2 and transcribe the structural genes P1lacIP2lacZlacYlacA P1lacIP2lacZlacYlacA ++++ P1lacIP2lacZlacYlacA +++ lacI protein suppressed RNA polymerase lacI LAC Repressor protein coded by lacI, bind to P2 preventing transcription of lacZ, lacY and lacA
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CISC841, F08, Lec2, Liao Boolean Networks: An example Reverse EngineeringInterpreting data 1: induced 0: suppressed -: forced low +: forced high Bayesian networks: P(0,1,2,3) = P(0)P(1)P(2|1,0)P(3|1,2)
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CISC841, F08, Lec2, Liao
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High throughput technologies Genome sequencing DNA microarray Yeast 2 hybrid system
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CISC841, F08, Lec2, Liao Sequencing DNA (Sanger’s method) Courtesy of Color Atlas of Biochemistry
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Expression Profiles Classification
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Bioinformatics data sources CISC841, F08, Lec2, Liao
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Bioinformatics challenges CISC841, F08, Lec2, Liao
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