1. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Chapter 25 Organic and Biological Chemistry Chemistry, The Central Science, 11th edition Theodore L. Brown; H. Eugene LeMay, Jr.; and Bruce E. Bursten John D. Bookstaver St. Charles Community College Cottleville, MO

2. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Organic Chemistry Organic chemistry is the chemistry of carbon compounds. Carbon has the ability to form long chains. Without this property, large biomolecules such as proteins, lipids, carbohydrates, and nucleic acids could not form.

3. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Carbon Compounds There are three hybridization states and geometries found in organic compounds: –sp 3 Tetrahedral –sp 2 Trigonal planar –sp Linear

4. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Hydrocarbons There are four basic types of hydrocarbons: –Alkanes –Alkenes –Alkynes –Aromatic hydrocarbons

5. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Alkanes Alkanes contain only single bonds. They are also known as saturated hydrocarbons. –They are “saturated” with hydrogens.

6. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Formulas Lewis structures of alkanes look like this. They are also called structural formulas. They are often not convenient, though…

7. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Formulas …so more often condensed formulas are used.

8. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Properties of Alkanes The only van der Waals force is the London dispersion force. The boiling point increases with the length of the chain.

9. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Alkanes Carbons in alkanes are sp 3 hybrids. They have a tetrahedral geometry and 109.5° bond angles.

10. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Alkanes There are only  - bonds in alkanes. There is free rotation about the C—C bonds.

11. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Isomers Isomers have the same molecular formulas, but the atoms are bonded in a different order.

12. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Organic Nomenclature There are three parts to a compound name: –Base: This tells how many carbons are in the longest continuous chain.

13. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Organic Nomenclature There are three parts to a compound name: –Base: This tells how many carbons are in the longest continuous chain. –Suffix: This tells what type of compound it is.

14. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Organic Nomenclature There are three parts to a compound name: –Base: This tells how many carbons are in the longest continuous chain. –Suffix: This tells what type of compound it is. –Prefix: This tells what groups are attached to the chain.

15. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. How to Name a Compound 1.Find the longest chain in the molecule. 2.Number the chain from the end nearest the first substituent encountered. 3.List the substituents as a prefix along with the number(s) of the carbon(s) to which they are attached.

16. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. How to Name a Compound If there is more than one type of substituent in the molecule, list them alphabetically.

17. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Cycloalkanes Carbon can also form ringed structures. Five- and six-membered rings are most stable. –They can take on conformations in which their bond angles are very close to the tetrahedral angle. –Smaller rings are quite strained.

18. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Alkanes Alkanes are rather unreactive due to the presence of only C—C and C—H  -bonds. Therefore, they make great nonpolar solvents.

19. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Alkenes Alkenes contain at least one carbon–carbon double bond. They are unsaturated. –That is, they have fewer than the maximum number of hydrogens.

20. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Alkenes Unlike alkanes, alkenes cannot rotate freely about the double bond. –The side-to-side overlap in the  -bond makes this impossible without breaking the  -bond.

21. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Alkenes This creates geometric isomers, which differ from each other in the spatial arrangement of groups about the double bond.

22. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Properties of Alkenes Structure also affects the physical properties of alkenes.

23. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Nomenclature of Alkenes The chain is numbered so the double bond gets the smallest possible number. cis-Alkenes have the carbons in the chain on the same side of the molecule. trans-Alkenes have the carbons in the chain on opposite sides of the molecule.

24. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Alkenes One reaction of alkenes is the addition reaction. –In it, two atoms (e.g., bromine) add across the double bond. –One  -bond and one  -bond are replaced by two  -bonds; therefore,  H is negative.

25. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Mechanism of Addition Reactions It is a two-step mechanism: –The first step is the slow, rate-determining step. –The second step is fast.

26. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Mechanism of Addition Reactions In the first step, the  -bond breaks and the new C—H bond and a cation form.

27. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Mechanism of Addition Reactions In the second step, a new bond forms between the negative bromide ion and the positive carbon.

28. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Alkynes Alkynes contain at least one carbon–carbon triple bond. The carbons in the triple bond are sp-hybridized and have a linear geometry. They are also unsaturated.

29. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Nomenclature of Alkynes The method for naming alkynes is analogous to the naming of alkenes. However, the suffix is -yne rather than -ene. 4-methyl-2-pentyne

30. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Alkynes Alkynes undergo many of the same reactions alkenes do. As with alkenes, the impetus for reaction is the replacement of  -bonds with  -bonds.

31. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Aromatic Hydrocarbons Aromatic hydrocarbons are cyclic hydrocarbons that have some particular features. There is a p-orbital on each atom. –The molecule is planar. There is an odd number of electron pairs in the  - system.

32. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Aromatic Nomenclature Many aromatic hydrocarbons are known by their common names.

33. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Aromatic Compounds In aromatic compounds, unlike in alkenes and alkynes, each pair of  -electrons does not sit between two atoms. Rather, the electrons are delocalized; this stabilizes aromatic compounds.

34. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Aromatic Compounds Due to this stabilization, aromatic compounds do not undergo addition reactions; they undergo substitution. In substitution reactions, hydrogen is replaced by a substituent.

35. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Structure of Aromatic Compounds Two substituents on a benzene ring could have three possible relationships: –ortho-: On adjacent carbons. –meta-: With one carbon between them. –para-: On opposite sides of ring.

36. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Reactions of Aromatic Compounds Reactions of aromatic compounds often require a catalyst. Halogenation Friedel-Crafts Reaction

37. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Functional Groups The term functional group is used to refer to parts of organic molecules where reactions tend to occur.

38. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Alcohols Alcohols contain one or more hydroxyl groups, —OH. They are named from the parent hydrocarbon; the suffix is changed to -ol and a number designates the carbon to which the hydroxyl is attached.

39. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Alcohols Alcohols are much more acidic than hydrocarbons. –pK a ~15 for most alcohols. –Aromatic alcohols have pK a ~10.

40. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Ethers Ethers tend to be quite unreactive. Therefore, they are good polar solvents.

41. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Carbonyl Compounds The carbonyl group is a carbon-oxygen double bond. Carbonyl compounds include many classes of compounds.

42. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Aldehydes In an aldehyde, at least one hydrogen is attached to the carbonyl carbon.

43. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Ketones In ketones, there are two carbons bonded to the carbonyl carbon.

44. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Carboxylic Acids Acids have a hydroxyl group bonded to the carbonyl group. They are tart tasting. Carboxylic acids are weak acids.

45. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Esters Esters are the products of reactions between carboxylic acids and alcohols. They are found in many fruits and perfumes.

46. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Amides Amides are formed by the reaction of carboxylic acids with amines.

47. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Amines Amines are organic bases. They generally have strong, unpleasant odors.

48. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Chirality Carbons with four different groups attached to them are handed, or chiral. These are optical isomers or stereoisomers. If one stereoisomer is “right-handed,” its enantiomer is “left-handed.”

49. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Chirality Many pharmaceuticals are chiral. Often only one enantiomer is clinically active. S-ibuprofen

50. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Amino Acids and Proteins Proteins are polymers of  -amino acids. A condensation reaction between the amine end of one amino acid and the acid end of another produces a peptide bond.

51. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Amino Acids and Proteins Hydrogen bonding in peptide chains causes coils and helices in the chain. Kinking and folding of the coiled chain gives proteins a characteristic shape.

52. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Amino Acids and Proteins Most enzymes are proteins. The shape of the active site complements the shape of the substrate on which the enzyme acts; hence, the “lock- and-key” model.

53. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Carbohydrates Simple sugars are polyhydroxy aldehydes or ketones.

54. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Carbohydrates In solution, they form cyclic structures. These can form chains of sugars that form structural molecules such as starch and cellulose.

55. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Nucleic Acids Two of the building blocks of RNA and DNA are sugars (ribose or deoxyribose) and cyclic bases (adenine, guanine, cytosine, and thymine or uracil).

56. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Nucleic Acids These combine with a phosphate to form a nucleotide.

57. Organic and Biological Chemistry © 2009, Prentice-Hall, Inc. Nucleic Acids Nucleotides combine to form the familiar double-helix form of the nucleic acids.