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Bioinformatics Why Can’t It Tell Us Everything?

Bioinformatics Why Can’t It Tell Us Everything?. Bioinformatics What are our Data Sets?. Interested in information flow with cells Currently, the key information is mostly a matter of biological macromolecules

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Bioinformatics Why Can’t It Tell Us Everything?

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  1. Bioinformatics Why Can’t It Tell Us Everything?

  2. BioinformaticsWhat are our Data Sets? • Interested in information flow with cells • Currently, the key information is mostly a matter of biological macromolecules • Eventually, information of interest will also include flow of nutrients, energy, and impact of small molecules on macromolecular function

  3. BioinformaticsWhat are our Questions? • What is in there? • What does it do? • How similar is it to something else? • How does it fold? • Where does it go in a cell? • What does it interact with? • How it is regulated? • Level of confidence?

  4. * Function of organism is determined by function of its cells  * Function of cells determined by chemical reactions that take place within them  * Chemical reactions occur or not according to presence and activity of enzymes* Enzymes are proteins* Proteins are determined by genes* Therefore, genes determine organismal function BioinformaticsLogical Reasoning Behind Data Sets

  5. Genomics Proteomics

  6. Central DogmaFlow of Information

  7. Central DogmaDNA as the Blueprint for Life?

  8. Central DogmaDNA as the Blueprint for Life?

  9. Central DogmaDNA RNA Protein Genes & proteins are different molecular languages, but they are colinear

  10. Double helical DNA Basic Unit (alphabet): Nucleotide (base) Only 4: A, T, G, and C Double-stranded: A<>T and G<>C 5’..AGCTGCATGCTAGCTGACGTCA….3’ 3’..TCGACGTACGATCGACTGCAGT….5’ “Words” (genes) to encode proteins, RNA

  11. DNAStructure Connected to Information DNA Tower in Perth, AUS

  12. DNAReplication & Transcription as Algorithms • With rare exceptions, all DNA is replicated • Crucial tool is ability to go from one strand to another • Transcription uses same base-pairing rules with U instead of T, but occurs in packets

  13. Transcription = DNA to RNA Where to Start is a Big Question

  14. Protein Alphabet: amino acids There are 20amino acids Met Cys Ser Leu Ala Ala Val

  15. ProteinsNumber of Possible 100-mer Peptides? 20 possible residues at each position For 2-mers, 20 possible at position 1 and 20 possible at position 2, so 20 x 20 = 202 = 400 Same logic for 100-mers, 20100 = 2100 x 10100 = (210) 10 x 10100 = ~ (103) 10 x 10100 = 10130

  16. beta-pleated sheetProteinsFolding Starts Local alpha-helix

  17. ProteinsFolding Goes Global

  18. ProteinsPredictive Protein Folding as Holy Grail

  19. Protein Alphabet: amino acids There are 20amino acids Encoded by codons (triplets of nucleotides) ATG TGC AGC CTAGCTGCCGTC CTAGCTGCCGTC Met Cys Ser Leu Ala Ala Val

  20. Genetic Code Found on Earth:How Does It Work? 5’-UCGACCAUGGUUGACCAUUGAUUACCACG-3’

  21. Genetic Code • Triplet • Nonoverlapping • Comma-less • Redundant

  22. Bioinformatics:Mining a Mountain of Data Where are the putative genes?

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