1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Carbon—The Backbone of Biological Molecules Although cells are 70–95% water, the rest consists mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

3. 1. Stanley Miller’s experiment

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 1. Miller’s experimental design: Gases in the “primitive atmosphere” are those that are produced by volcanoes The electrode simulated lightening, a form of energy thought to be present on the primitive earth Boiling water represented the “primordial sea”

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 2. Miller’s results A variety of organic compounds, such as amino acids, were synthesized in Miller’s apparatus Conclusion: Organic compounds may have been spontaneously generated from inorganic compounds (NH 3, CH 4, H 2, and H 2 0) on the early Earth, setting the stage for the origin of life.

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3. The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms This tetravalence makes large, complex molecules possible

7. Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene) Examples:

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 4. Carbon Skeletons Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape They can be straight chains, branched chains, or rings Carbon skeletons can also contain double bonds

9. Examples of Carbon skeletons—which of these are hydrocarbons? Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene2-Butene CyclohexaneBenzene

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 5. Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy Hydrocarbons are nonpolar and hydrophobic

11. LE 4-6 A fat moleculeMammalian adipose cells 100 µm Fat droplets (stained red)

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 6. Isomers Isomers are compounds with the same molecular formula but different structures and properties: – Structural isomers have different covalent arrangements of their atoms – Geometric isomers have the same covalent arrangements but differ in spatial arrangements – Enantiomers are isomers that are mirror images of each other

13. 7. Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Examples: Thalidomide, L-Dopa & D-Dopa 8.

15. L -Dopa (effective against Parkinson’s disease) D -Dopa (biologically Inactive)

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 9. Structure affects Function!!! Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it Certain groups of atoms are often attached to skeletons of organic molecules They are called functional groups. Example: testosterone vs. estradiol

17. 9. Estradiol Testosterone Male lion Female lion

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 10. Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 11.

20. LE 4-10aa STRUCTURE (may be written HO—) NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) Ethanol, the alcohol present in alcoholic beverages FUNCTIONAL PROPERTIES 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).

21. LE 4-10ab STRUCTURE NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton EXAMPLE Acetone, the simplest ketone A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Aldehydes if the carbonyl group is at the end of the carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde FUNCTIONAL PROPERTIES

22. LE 4-10ac STRUCTURE NAME OF COMPOUNDS Carboxylic acids, or organic acids EXAMPLE Has acidic properties because it is a source of hydrogen ions. Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H + ) tend to dissociate reversibly; for example, Acetic acidAcetate ion In cells, found in the ionic form, which is called a carboxylate group.

23. LE 4-10ba STRUCTURE NAME OF COMPOUNDS Amine EXAMPLE Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) Ionized, with a charge of 1+, under cellular conditions Glycine (ionized)

24. LE 4-10bb STRUCTURE (may be written HS—) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).

25. LE 4-10bc STRUCTURE NAME OF COMPOUNDS Organic phosphates EXAMPLE Glycerol phosphate FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings P.S. ATP: An Important Source of Energy for Cellular Processes One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Chemical Elements of Life: A Review The versatility of carbon makes possible the great diversity of organic molecules Variation at the molecular level lies at the foundation of all biological diversity