1. Chapter 4 Carbon and the Molecular Diversity of Life (aka Organic Chemistry)

2. Introduction Cells are 70-95% water, the rest consists mostly of carbon-based compounds. Living organisms consist mostly of carbon- based compounds. Proteins, DNA, carbohydrates, and other molecules are all composed of carbon atoms bonded to each other and to atoms of other elements. –These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

3. As we explore biological molecules we will find that many have a carbon backbone. –That carbon backbone refers to the links of C atoms bonded together with other atoms (such as H), or groups of atoms (functional groups) attached to the carbon backbone.

4. Organic Chemistry The study of carbon compounds, organic chemistry, focuses on any compound with carbon (organic compounds). –Organic compounds can range from the simple (CO 2 or CH 4 ) to complex molecules, like proteins, that may weigh over 100,000 Daltons. –The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform or similar from one organism to another.

5. Formation of Carbon Bonds With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell. –Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons. –Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.

6. The electron configuration of carbon –Gives it covalent compatibility with many different elements H O NC Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) Figure 4.4

7. (a) Methane (b) Ethane (c) Ethene (ethylene) Molecular Formula Structural Formula Ball-and- Stick Model Space-Filling Model H H H H H H H H H H HH H H C C C CC CH 4 C2H6C2H6 C2H4C2H4 Name and Comments Figure 4.3 A-C

8. In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms. –The structural formula, O = C = O, shows that each atom has completed its valence shells. –CO 2 is the source for all organic molecules in organisms via the process of photosynthesis. Urea, CO(NH 2 ) 2, is another simple organic molecule in which each atom has enough covalent bonds to complete its valence shell.

9. Variation in Carbon Backbones Carbon chains form the skeletons of most organic molecules. –The backbone may vary in length and may be straight, branched, or arranged in closed rings. –The carbon backbones may also include double bonds.

11. Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms. –Hydrocarbons are the major component of petroleum. –Petroleum is a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago. Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component.

12. Isomers are compounds that have the same molecular formula but different structures and therefore different chemical properties. –For example, butane and isobutane have the same molecular formula C 4 H 10, but butane has a straight skeleton and isobutane has a branched skeleton. The two butanes are structural isomers, molecules with the same molecular formula but differ in the covalent arrangement of atoms.

13. Geometric isomers (Cis-Trans Isomers) are compounds with the same covalent partnerships that differ in their spatial arrangement around a carbon-carbon double bond.

14. Enantiomers are molecules that are mirror images of each other. –Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon. –If this is true, it is possible to arrange the four groups in space in two different ways that are mirror images. –They are like left-handed and right-handed versions.

16. Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Usually only one isomer is biologically active Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

18. Figure 4.8 Drug Ibuprofen Albuterol Condition Effective Enantiomer Ineffective Enantiomer Pain; inflammation Asthma S-IbuprofenR-Ibuprofen R-Albuterol S-Albuterol

19. Functional Groups The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups. –Functional groups are attachments that replace one or more bonded hydrogen atoms. –There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups. The number and arrangement of functional groups help give each molecule its unique properties.

21. The seven functional groups that are most important in the chemistry of life: –Hydroxyl group –Carbonyl group –Carboxyl group –Amino group –Sulfhydryl group –Phosphate group –Methyl group

22. In a hydroxyl group (-OH), a hydrogen atom forms a covalent bond with an oxygen which bonds to the carbon backbone. –Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.

23. A carbonyl group (C=O) consists of an oxygen atom joined to the carbon backbone by a double bond. –If the carbonyl group is on the end, the compound is an aldelhyde. –If not, then the compound is a ketone. –Isomers with aldehydes versus ketones have different properties.

24. A carboxyl group (-COOH) consists of a carbon atom with a double bonded oxygen atom and a single bond to a hydroxyl group. –Compounds with carboxyl groups are carboxylic acids.

25. An amino group (-NH 2 ) consists of a nitrogen atom attached to two hydrogen atoms and the carbon backbone. –Organic compounds with amino groups are amines. –Amino acids, the building blocks of proteins, have amino and carboxyl groups.

26. A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the carbon backbone. –This group resembles a hydroxyl group in shape. –Organic molecules with sulfhydryl groups are thiols. –Sulfhydryl groups help stabilize the structure of proteins.

27. A phosphate group (-OPO 3 2- ) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond). –A phosphate group connects to the carbon backbone via one of its oxygen atoms. –Phosphate groups are anions with two negative charges.

28. A methyl group consits of a carbon bonded to three hydrogen atoms –Addition of methyl groups alters the expressions of genes within our DNA

30. You should be able to; 1. Discuss the variations that occur in carbon based molecules and the bonds that carbon makes with hydrogen, oxygen and nitrogen. 2. Discuss the three variations of isomers. 3. Identify and describe all discussed functional groups.