Definition (one of many possible): (Molecular) bio – informatics: bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical

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?

WhoIS IN THERE?

WhoIS IN THERE?

WhatARE THEY DOING?

WhatARE THEY DOING?

HOWARE THEY DOING IT?

HOWARE THEY DOING IT?

The questions…

Sequences and strings

Biology is fundamentally a comparative science

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

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

Things you should already know…





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

ATP is stored chemical potential energy.

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.

Valence shell electron pair repulsion (VSEPR) theory

Valence shell electron pair repulsion (VSEPR) theory

Ethene Ethyne

Ethane

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.

IUPAC nomenclature of organic compoundsSee: http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistryOr: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nomen1.htm

http://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/nomen1.htm

Common organic functional groupsPresented in their relative ReDox levels

Oxidation

Nucleophilic attack reactionsThe electronegative nucleophile attacks the electopositive center

Nucleophilic attack reactionsReality is more complicated b/c OH- is a horrible leaving group

Nucleophilic attack reactionsThe same is true for amides

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Definition (one of many possible): (Molecular) bio – informatics: bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical