1. Definition (one of many possible): (Molecular) bio – informatics: bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical chemistry) and applying "informatics techniques" (derived from disciplines such as applied math, computer science and statistics) to understand and organize the information associated with these molecules, on a large scale. In short, bioinformatics is a management information system for molecular biology and has many practical applications. What is bioinformatics?

2. Who IS IN THERE? Who IS IN THERE? What ARE THEY DOING? What ARE THEY DOING? HOW ARE THEY DOING IT? HOW ARE THEY DOING IT? The questions…

3. Sequences and strings

4. Biology is fundamentally a comparative science

5. Richard Feynman said, “ Everything that the living things do can be understood in terms of the jigglings and wigglings of atoms. ”

6. Carl Woese (1928-2012) Using 16S rRNA methods, Carl Woese famously defined the third kingdom of life, highlighting how comparison, molecular techniques, and analysis all go together. Biology is fundamentally a comparative science

7. Things you should already know…

12. Note: We’ll come back to functional groups at the end of this lecture.

18. ATP is stored chemical potential energy.

19. Organic chemistry is a tough 1-year undergrad class …yet, we are going to try to cover the basics in less than an hour From Wikipedia: Organic chemistry is a sub-discipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of carbon- based compounds, hydrocarbons, and their derivatives. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur. Organic compounds are structurally diverse. The range of application of organic compounds is enormous. They form the basis of, or are important constituents of many products (plastics, drugs, petrochemicals, food, explosives, paints, etc.) and, with very few exceptions, they form the basis of all earthly life processes.

20. Valence shell electron pair repulsion (VSEPR) theory

21. EtheneEthyne Ethane

22. Stereochemistry A chiral molecule is a type of molecule that has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom. We will come back to this later.

24. IUPAC nomenclature of organic compounds See: http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistryhttp://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry Or: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nomen1.htmhttp://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nomen1.htm

25. Common organic functional groups Presented in their relative ReDox levels Oxidation

26. Nucleophilic attack reactions The electronegative nucleophile attacks the electopositive center

27. Nucleophilic attack reactions Reality is more complicated b/c OH - is a horrible leaving group

28. Nucleophilic attack reactions The same is true for amides