Chapter 4

1. Chapter 4 Carbon and the Molecular Diversity of Life

2. Figure 4.1 • Overview: Carbon—The Backbone of Biological Molecules • All living organisms • Are made up of chemicals based mostly on the element carbon

3. Concept 4.1: Organic chemistry is the study of carbon compounds • Organic compounds • Range from simple molecules to colossal ones

4. In 1953, Stanley Miller simulated what were thought to be environmental conditions on the lifeless, primordial Earth. As shown in this recreation, Miller used electrical discharges (simulated lightning) to trigger reactions in a primitive “atmosphere” of H2O, H2, NH3 (ammonia), and CH4 (methane)—some of the gases released by volcanoes. EXPERIMENT A variety of organic compounds that play key roles in living cells were synthesized in Miller’s apparatus. RESULTS Organic compounds may have been synthesized abiotically on the early Earth, setting the stage for the origin of life. (We will explore this hypothesis in more detail in Chapter 26.) CONCLUSION Figure 4.2 • The concept of vitalism • Is the idea that organic compounds arise only within living organisms • Was disproved when chemists synthesized the compounds in the laboratory

5. Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms

6. The Formation of Bonds with Carbon • Carbon has four valence electrons • This allows it to form four covalent bonds with a variety of atoms

7. 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 C2H6 C H C H H H H H (c) Ethene (ethylene) C C C2H4 H H Figure 4.3 A-C • The bonding versatility of carbon • Allows it to form many diverse molecules, including carbon skeletons

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

9. H H C C C C H H C H H H H H H C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H (a) Length H Ethane Propane H H H H H H H H H H H C C C C C C C C H H H H (b) Branching 2-methylpropane (commonly called isobutane) Butane H H H H C H (c) Double bonds H H C C C H H C C H H C C 1-Butene 2-Butene H H C C C (d) Rings Figure 4.5 A-D Cyclohexane Benzene Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains • Form the skeletons of most organic molecules • Vary in length and shape

10. Hydrocarbons • Hydrocarbons • Are molecules consisting of only carbon and hydrogen

11. Fat droplets (stained red) 100 µm (b) Mammalian adipose cells (a) A fat molecule Figure 4.6 A, B • Hydrocarbons • Are found in many of a cell’s organic molecules

12. Isomers • Isomers • Are molecules with the same molecular formula but different structures and properties

13. H H H C H H C H H H H H H H (a) Structural isomers 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 (b) Geometric isomers X H H H CO2H CO2H C C (c) Enantiomers H H NH2 NH2 CH3 CH3 Figure 4.7 A-C • Three types of isomers are • Structural • Geometric • Enantiomers

14. L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically inactive) Figure 4.8 • Enantiomers • Are important in the pharmaceutical industry

15. Concept 4.3: Functional groups are the parts of molecules involved in chemical reactions

16. The Functional Groups Most Important in the Chemistry of Life • Functional groups • Are the chemically reactive groups of atoms within an organic molecule

17. OH CH3 Estradiol HO Female lion OH CH3 CH3 O Testosterone Male lion Figure 4.9 • Give organic molecules distinctive chemical properties

18. Six functional groups are important in the chemistry of life • Hydroxyl • Carbonyl • Carboxyl • Amino • Sulfhydryl • Phosphate

19. FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O O OH C C OH (may be written HO ) STRUCTURE 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–.) The carbonyl group( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH).  Figure 4.10 • Some important functional groups of organic compounds

20. Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Carboxylic acids, or organic acids EXAMPLE H H H H O O C C H OH C C H C H C H OH H H H H C Ethanol, the alcohol present in alcoholic beverages H H Acetic acid, which gives vinegar its sour tatste Acetone, the simplest ketone H H O H C C C H H H Propanal, an aldehyde Figure 4.10 • Some important functional groups of organic compounds

21.  Is polar as a result of the electronegative oxygen atom drawing electrons toward itself.  Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3). FUNCTIONALPROPERTIES  Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example,  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. H H O O + H+ H C H C C C OH O H H  In cells, found in the ionic form, which is called a carboxylate group. Figure 4.10 • Some important functional groups of organic compounds

22. AMINO SULFHYDRYL PHOSPHATE O H SH N P OH O (may be written HS ) H OH 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). The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. Figure 4.10 • Some important functional groups of organic compounds

23. OH O OH H H H H H O H C C C O P O N C C SH H C C HO H H H H O H H H Ethanethiol Glycine Glycerol phosphate Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. Figure 4.10 • Some important functional groups of organic compounds

24.  Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).  Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.  Acts as a base; can pick up a proton from the surrounding solution: H H N +N H H H (nonionized) (ionized)  Ionized, with a charge of 1+, under cellular conditions. Figure 4.10 • Some important functional groups of organic compounds

25. Hydroxyl

26. Carbonyl

27. Carboxyl

28. Amino

29. Sulfhydryl

30. Phosphate