1. A Biology Primer Part I: Classification, cells and proteins Vasileios Hatzivassiloglou University of Texas at Dallas

2. Course web page http://www.hlt.utdallas.edu/~vh/Courses/F all08/DataTextMining.htmlhttp://www.hlt.utdallas.edu/~vh/Courses/F all08/DataTextMining.html Up-to-date listing of lectures, schedules, assignments, and supplemental course materials Also accessible via my home page http://www.hlt.utdallas.edu/~vh http://www.hlt.utdallas.edu/~vh

3. We will be talking about... What biology is From organisms to cells and their contents Basic building blocks: –proteins, DNA, RNA Basic cell processes: –replication, transcription, translation, regulation Goals of biology

4. What biology is about The study of living entities (organisms) and the processes that maintain life –bios (life) + logos (account) Starting at the macroscopic level, organize known life forms identifying relations between them

5. Form, Structure, and Function Form is how things look, what observable properties they have Structure is how things are built and physically put together Function is how things interact with each other and what processes they enable Function is what we are ultimately interested in, but form and structure help us understand actual and potential function

6. Biological taxonomy Multiple levels of classification Kingdom Class Phylum Genus Species

8. Historical biological classification Initial work by Aristotle (4th century BC) Refined by Ibn Rushd (1172) Kingdoms (Linnaeus, 1735) –Animalia, Vegetabilia, Mineralia Mineralia dropped Three-kingdom division introducing Bacteria (1894) Five-kingdom division introducing Fungi (1959)

9. Modern biological classification Gradually shifting from form to structural properties, including genetic evidence Major division between prokaryotes (“before the nut”, bacteria) and eukaryotes Eukaryotes include all multi-cellular organisms Modern view of three domains including Archaea (“ancients”) (1990)

10. Status of viruses At the boundary between life and non-life Not included in most taxonomic systems Their status is evolving –Mimivirus, discovered in 2006 –Originally discovered in 1992 and thought to be a bacterium –As large as a (small) bacterium –Recently observed to have functions thought to be possible only for bacteria (has genetic code for amino acid synthesis)

11. The Tree of Life

12. Exploring the Tree of Life http://tolweb.org/tree/

13. Inside an organism Organ systems –circulatory, digestive, immune,... Organs –heart, stomach, bone Tissue

14. View of a human organ

15. Tissue specialization and internals Several types of tissue (nervous, muscle, epithelium) Tissue itself consists of cells –major building blocks, much studied Cells are generally identical but “choose” to function appropriately for their tissue and organ

16. Inside the cell Cytoskeleton Membrane Cytoplasm / cytosol Organelles

17. Cell elements

18. Major organelles Nucleus –contains the genetic material, instructions for how to carry out biological processes and replication Mitochondria (energy factories) Ribosomes (protein factories) Golgi complex (traffic control) Lysosomes (acidic recycling center)

19. Functions of a cell Need to carry out chemical interactions within the cell and with nearby cells in order to fulfill the cell’s function Need to encode the contents of the cell for cell replication within the organism and for passing the information to descendants

20. Fulfilling cell function Chemical interactions –three-dimensional representation –proteins (“first thread”) Information encoding –one-dimensional representation –DNA RNA in-between DNA and proteins

21. Roles of proteins Enzymes that speed up chemical reactions –>5,000 known enzymes; lactase –anabolic processes (muscle build-up) –catabolic processes (starvation, apoptosis) –diseases as a result of malfunctioning enzymes –aspirin as enzyme inhibitor

22. Roles of proteins Signal carrying inside and outside the cell –process usually starts by outside stimulus physical, temperature, electricity –proteins control gene activation –can lead to multiple chains of events and secondary messengers –process can be completed in as little as 1 ms

23. Roles of proteins Control cell processes determining on/off status and their rate Transporters of small molecules Building material for much of the cell

24. Structure of proteins Proteins are polymers All polymers consisting of small structural blocks (monomers) and connecting infrastructure For proteins, the connecting bonds are peptide bonds and the structural blocks are amino acids

25. Peptide bonds C-N bond orientation implies protein orientation Bond can be dissolved by adding water

26. Amino acids Each protein has 20-5,000 amino acids (average 350) There are only 20 distinct amino acids Four groups according to chemical properties Some amino acids more similar to others (implications for decoding)

27. Amino acid chemical structure