1. CISC841, F08, Lec2, Liao CISC 841 Bioinformatics (Fall 2008) A Primer on Molecular Biology & Bioinformatics challenges

2. CISC841, F08, Lec2, Liao

3. 10 -3 10 -6 10 -9

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9. 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:

10. 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)

11. CISC841, F08, Lec2, Liao Small molecules: > sugar: carbohydrate > fatty acids > nucleotides: A, C, G, T (Purines: A and G; Pyrimidines: C and T)

12. CISC841, F08, Lec2, Liao

13. 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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16. C- terminal N-terminal Polypeptide

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21. Helix complete turn every 3.6 AAs Hydrogen bond between (-C=O) of one AA and (-N-H) of its 4 th neighboring AA

22. CISC841, F08, Lec2, Liao Hydrogen bond b/w carbonyl oxygen atom on one chain and NH group on the adjacent chain

23. The Central Dogma: DNA  RNA  Protein CISC841, F08, Lec2, Liao

24. Gene Structure

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30. Genetic Code: codons

31. Systems Biology Regulatory networks Signaling transduction networks Metabolic pathway networks CISC841, F08, Lec2, Liao

32. Regulation Other Cells Genes (DNA) Message (RNA) Proteins Function/ Environment Regulation

33. 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

34. 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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36. High throughput technologies Genome sequencing DNA microarray Yeast 2 hybrid system

37. CISC841, F08, Lec2, Liao Sequencing DNA (Sanger’s method) Courtesy of Color Atlas of Biochemistry

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44. Expression Profiles Classification

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48. Bioinformatics data sources CISC841, F08, Lec2, Liao

52. Bioinformatics challenges CISC841, F08, Lec2, Liao