1. CISC 841 Bioinformatics (Fall 2007) A Primer on Molecular Biology & Bioinformatics challenges
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2. CISC841, F07, Lec2, Liao

3. 10-9
10-6
10-3
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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:
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10. Structure of the bases (Thymine is not shown here)5 1 3
Purines:A and G
Pyrimidines: C and T
Oligonucleotide: a DNA of a few tens of nucleotides
ATP, ADP, AMP
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11. Small molecules: > fatty acids
> sugar: carbohydrate
> fatty acids
> nucleotides: A, C, G, T (Purines: A and G; Pyrimidines: C and T)
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12. CISC841, F07, 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)
C with G: the pyrimidine cytosine (C) always pairs with the purine guanine (G)
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16. Polypeptide
N-terminal
C- terminal
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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 4th neighboring AA
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22. Hydrogen bond b/w carbonyl oxygen atom on one chain and NH group on the adjacent chain
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23. The Central Dogma: DNA  RNA  Protein
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24. Gene Structure
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30. Genetic Code: codons
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31. Systems Biology Regulatory networks Signaling transduction networks
Metabolic pathway networks
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32. Regulation Genes (DNA) Message (RNA) Proteins Function/ Environment
Other
Cells
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33. Operon P1 lacI P2 lacZ lacY lacA + suppressed lac operon on E. coli
protein
suppressed
RNA polymerase
LAC
Repressor protein coded by lacI, bind to P2 preventing transcription of lacZ, lacY and lacA
lac operon on E. coli
Lactose binds with lacI, allowing RNA polymerase to bind to P2 and transcribe the structural genes
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34. Boolean Networks: An example
1: induced
0: suppressed
-: forced low
+: forced high
Interpreting data
Reverse Engineering
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35. CISC841, F07, Lec2, Liao

36. High throughput technologies
Genome sequencing
DNA microarray
Yeast 2 hybrid system
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37. Sequencing DNA (Sanger’s method)
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Courtesy of Color Atlas of Biochemistry

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47. Bioinformatics data sources
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51. Bioinformatics challenges
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