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Algorithms for Molecular Biology

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  1. Algorithms for Molecular Biology CSCI 4314-001 Elizabeth White elizabeth.white@colorado.edu

  2. DNA, RNA are similar Image from http://en.wikipedia.org/wiki/RNA_world_hypothesis

  3. 4 kinds of RNA in the cell • Messenger RNA (mRNA) • Always ends up being translated into protein • Function: information storage • Small nuclear RNA (snRNA) • Never translated, just stays around as RNA • Function: machinery for mRNA splicing • Transfer RNA (tRNA), ribosomal RNA (rRNA) • Never translated, just stays around as RNA • Function: machinery for reading mRNA into protein

  4. mRNA specifies 3-base codons Image from http://en.wikipedia.org/wiki/Genetic_code

  5. 3-letter codons map to amino acids Image from http://www.pangloss.com/seidel/Protocols/codon.html


  6. Transfer RNAs do the mapping Image from http://cropandsoil.oregonstate.edu/classes/css430/lecture%209-07/figure-09-10.JPG

  7. Ribosomes do the work of connecting amino acids into a protein Image from http://www.modares.ac.ir/elearning/Dalimi/Proto/Lectures/week2/week2.htm

  8. Ribosomes are mostly RNA (orange) with some protein decorations (blue) Image from http://www.modares.ac.ir/elearning/Dalimi/Proto/Lectures/week2/week2.htm

  9. Translation proceeds via ribosome Image from http://www.scripps.edu/chem/wong/rna.html

  10. Overview: transcription/translation Image from http://www.cbs.dtu.dk/staff/dave/DNA_CenDog.html

  11. Protein structure • Primary: amino acid sequence • Secondary: short regions of protein form • Alpha-helix • Beta-sheet • Tertiary: helices and sheets nestle together to make a 3 dimensional shape • Quaternary: 2 or more proteins associate together

  12. Primary structure: amino acid sequence Top image from http://en.wikipedia.org/wiki/Amino_acid Bottom image from http://commons.wikimedia.org/wiki/Image:2-amino-acids.png

  13. Secondary structure: alpha-helix Left image from http://commons.wikimedia.org/wiki/Image:AlphaHelixProtein_fr.jpg Bottom image from http://www.srs.ac.uk/px/showcase/guide_files/helix4.jpg

  14. Secondary structure: beta-sheet Left image from http://www.sciencecollege.co.uk/SC/biochemicals.html Right image from http://cnx.org/content/m11614/latest/

  15. Tertiary structure: 3D shape Image from http://www.colorado.edu/chem/people/wuttked.html

  16. Quaternary structure: assembly Image from http://www.man.poznan.pl/CBB/GIF/hcc-beta.jpg

  17. Some proteins just hold stuff together Image from http://www.wellesley.edu/Chemistry/chem227/structproteins/strctprt.htm

  18. DNA-binding proteins • Recognize particular DNA sequences • Regulate which genes are transcribed into mRNA • Often act in pairs Image fromhttp://en.wikipedia.org/wiki/DNA

  19. Enzymatic proteins • Catalyze chemical reactions • Beta-lactamase enzyme inactivates penicillin Image from http://www.nersc.gov/news/annual_reports/annrep97/bash.html

  20. Open problem: protein folding • Amino acid sequence of protein determines its shape • In theory, we should be able to deduce a protein’s shape from its sequence • “Holy Grail” question for biology • Open door to “designer” proteins • Allow for faster, cheaper biomedical research

  21. Protein backbone is free to rotate Each amino acid residue in the protein can spin around phi, psi angles (but not omega)

  22. In practice? Too many choices • Levinthal paradox • Consider a 100-amino acid protein (not big) • Suppose there are 3 choices for each phi, psi angle • This means that 3200 conformations are possible • Can a protein try each one randomly? • Suppose it can test one conformation in 10-15 sec • Will take about 1080 seconds to test all • Note: the universe is about 1020 seconds old • In nature, proteins fold in seconds (or less). • Conclusion: folding is NOT a random search