Introduction to Bioorganic Chemistry

1. Introduction to Bioorganic Chemistry

2. Chemistry of Biomolecules • A biomolecule is a chemical compound that naturally occurs in living organisms. • Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur. • Other elements sometimes are incorporated but are much less common.

3. The Six Most Abundant Elements of Life THIS IS THE LEGAL CHNOPS!! 

4. Valence • Each element has a characteristic valence that determines the number of covalent bonds it can form. • A shared electron pair is called a covalent bond.

5. Name and Comments Space-Filling Model Molecular Formula Structural Formula Ball-and-Stick Model H (a) Methane CH4 C H H H H H (b) Ethane C C2H6 H C H H H H H (c) Ethene (ethylene) C C C2H4 H H Organic Molecules: Hydrocarbons Hydrocarbons the simplest organic molecules, contain only carbon and hydrogen atoms.

6. Isomers • Organic molecules exist in three-dimensional space, and the same set of atoms can be put together in many recognizably different ways, resulting in molecules called isomers. 1. Structural isomers: Variations in the position at which different atoms are joined together. 2. Geometric isomers: Variations in the placement of atoms around carbon atoms joined by double covalent bonds.

7. H H H C H H C H H H H H H H H C C C C C H H C H C C H H H H H H H H H X X X C C C C X H H H CO2H CO2H C C H H NH2 NH2 CH3 CH3 Isomers (a) Structural isomers (b) Geometric isomers

8. Polarity (review) As we already know…Many combinations of different elements result in unequal electron sharing, called polar bonding. As a result, the electron distribution is asymmetric, or polar, and the oxygen atom is said to be electronegative. This asymmetry results in regions of slight negative and positive charge in different regions of the molecule, denoted by the Greek symbol d, for "partial" charge.   

9. The Functional Groups The properties of different biological molecules depend on certain characteristic groupings of atoms called functional groups. The names of the six most important functional groups are: • Hydroxyl • Carbonyl • Aldehydes • Ketones • Carboxyl • Amino • Sulfhydryl • Phosphate

10. H H C C H OH H H Ethanol Hydroxyl Group OH • In a hydroxyl group (–OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–). • Hydroxyl groups are not highly reactive, but they readily form hydrogen bonds and contribute to making molecules soluble in water. • Alcohols and sugars are "loaded" with hydroxyl groups.

11. O C Carbonyl Group • Carbonylgroup consists of a carbon atom joined to an oxygen atom by a double bond (symbolized as C=O). • Like hydroxyl groups, carbonyl groups contribute to making molecules water-soluble. All sugar molecules have one carbonyl group, in addition to hydroxyl groups on the other carbon atoms.

12. O C H O C H C H H C H H H H O H C C C H H H Two Forms of Carbonyl Groups: Aldehydes and Ketones Propanal, an aldehyde Acetone, a ketone • Aldehyde groups, where the C=O group is at the end of an organic molecule. A hydrogen atom is also located on the same carbon atom. • Keto groups, where the C=O group is located within an organic molecule. All sugars have either a keto or an aldehyde group. • An aldehyde and a ketone may be structural isomers with different properties, as is the case for acetone and propanal.

13. O C OH H H O O + H+ H C H C C C OH O H H Carboxyl Group (Acids) Acetic Acid Acetate • The carboxyl group (symbolized as COOH) has both a carbonyl and a hydroxyl group attached to the same carbon atom, resulting in new properties. • Carboxyl groups are weak acids, dissociating partially to release hydrogen ions.

14. H H N +N H H N H H H nonionized ionized Amino Group • The amino group (–NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. • Found in amino acids

15. Sulfhydryl Group SH • The sulfhydryl group (–SH) consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. • Two sulfhydryl groups can interact to help stabilize protein structure called disulfide bond (symbolized as -S-S-).

16. O P OH O OH Phosphate Group (Acids) • In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (–OPO32-) is an ionized form of a phosphoric acid group (–OPO3H2; note the two hydrogens). • Makes the molecule of which is a part an anion (negatively charged ion). • Can transfer energy between organic molecules (e.g., ATP).

17. ATP

18. OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion The Functional Groups • Functional groups are the chemically reactive groups of atoms within an organic molecule. • Many are polar • Give organic molecules distinctive chemical properties. • Most Important in the Chemistry of Life

19. Putting things together…let’s make some MACROMOLECULES

20. Monomers & Polymers: • monomers • smaller building blocks of the polymers (macromolecules) • amino acids build proteins: • Nucleotides build nucleic acids: • monosaccharides build carbohydrates: • fatty acids & glycerol build lipids:

21. Synthesis = dehydration synthesis Removal of WATER OH + H forms water, H2O Leaves bonding sites that join monosaccharide units. 19 Aug. 2009 Chemistry.ppt 21

22. Disassembly = hydrolysis Break bond between monosaccharide units (“lysis” means “to break”) Add WATER OH + H to fill bonding sites. 19 Aug. 2009 Chemistry.ppt 22

23. Hydrolysis Putting together / Taking apart macromolecules: macromolecules: monomers <--> polymers fig 4.3 • Dehydration Synthesis

24. We will be studying four organic macromolecules… • Carboyhdrates • Lipids • Proteins • Nucleic Acids