1. Chap 4 Carbon and the Molecular diversity of life

2. Overview: Carbon—The Backbone of Biological Molecules All living organisms –Are made up of chemicals based mostly on the element carbon –Organic Molecules have C-H bonds. Figure 4.1

3. 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 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 H 2 O, H 2, NH 3 (ammonia), and CH 4 (methane)—some of the gases released by volcanoes. A variety of organic compounds that play key roles in living cells were synthesized in Miller’s apparatus. EXPERIMENT RESULTS CONCLUSION 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.) Figure 4.2

4. With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second (valence) shell. –Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons. –Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. –This tetravalence by carbon makes large, complex molecules possible. 2. Carbon atoms are the most versatile building blocks of molecules Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

5. Carbon is tetravalent making it very versatile

8. 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

9. 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. –While CO 2 can be classified at either organic or inorganic, its importance to the living world is clear. 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. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

10. 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. Fig. 4.5

12. Hydrocarbons are hydrophobic

13. Isomers – have the same chemical formula

14. Isomers have the same chemical formula but different structures Structural isomers differ in the covalent arrangement of the atoms Geometric isomers differ in spatial relationship Enantiomers are mirror images of each other The middle carbon is the assymetric carbon

16. Shape is important for biological function

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

18. 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 hydrogen atoms to the carbon skeleton of the hydrocarbon. Each functional groups behaves consistently from one organic molecule to another. The number and arrangement of functional groups help give each molecule its unique properties. 1. Functional groups contribute to the molecular diversity of life Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

19. The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical. Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings. –These then interact with different targets in the body. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 4.8

20. Six functional groups are important in the chemistry of life –Hydroxyl –Carbonyl –Carboxyl –Amino –Sulfhydryl –Phosphate –All are hydrophilic and increase solubility of organic compounds in water.

21. In a hydroxyl group (-OH), a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton. –Because of these polar covalent bonds hydroxyl groups improve the solubility of organic molecules. –Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.

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

23. A carboxyl group (-COOH) consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group. –Compounds with carboxyl groups are carboxylic acids. –A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H + ).

24. An amino group (-NH 2 ) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. –Organic compounds with amino groups are amines. –The amino group acts as a base because ammonia can pick up a hydrogen ion (H + ) from the solution. –Amino acids, the building blocks of proteins, have amino and carboxyl groups. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

25. A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone. –This group resembles a hydroxyl group in shape. –Organic molecules with sulfhydryl groups are thiols. –Sulfhydryl groups help stabilize the structure of proteins. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

26. 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 as two protons have dissociated from the oxygen atoms. –One function of phosphate groups is to transfer energy between organic molecules. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings