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Chemistry 2


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Chemistry 2

  1. 1. - Carbon and the Molecular Diversity of Life<br />Overview: Carbon—The Backbone of Biological Molecules<br />All living organisms<br />Are made up of chemicals based mostly on the element carbon<br />
  2. 2. Organic chemistry is the study of carbon compounds<br />Organic compounds<br />Range from simple molecules to huge, complex molecules<br />Carbon has four valence electrons<br />This allows it to form four covalent bonds with a variety of atoms<br />Carbon atoms can form diverse molecules by bonding to four other atoms<br />
  3. 3. Name and Comments<br />Space-Filling Model<br />Molecular Formula<br />Structural Formula<br />Ball-and-Stick Model<br />H<br />(a) Methane<br />CH4<br />C<br />H<br />H<br />H<br />H<br />H<br />(b) Ethane<br />C2H6<br />C<br />H<br />H<br />C<br />H<br />H<br />H<br />H<br />(c) Ethene (ethylene)<br />C<br />C<br />C2H4<br />H<br />H<br />The bonding versatility of carbon<br />Allows it to form many diverse molecules, including carbon skeletons<br />
  4. 4. H<br />H<br />C<br />C<br />C<br />C<br />H<br />H<br />C<br />H<br />H<br />H<br />H<br />H<br />H<br />C<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />C<br />C<br />C<br />C<br />C<br />C<br />C<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />(a) Length<br />H<br />Ethane<br />Propane<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />C<br />C<br />C<br />C<br />C<br />C<br />C<br />C<br />H<br />H<br />H<br />H<br />(b) Branching<br />2-methylpropane<br />(commonly called isobutane)<br />Butane<br />H<br />H<br />H<br />H<br />C<br />H<br />(c) Double bonds<br />H<br />H<br />C<br />C<br />C<br />H<br />H<br />C<br />C<br />H<br />H<br />C<br />C<br />1-Butene<br />2-Butene<br />H<br />H<br />C<br />C<br />C<br />(d) Rings<br />Cyclohexane<br />Benzene<br />Molecular Diversity Arising from Carbon Skeleton Variation<br />Carbon chains<br />Form the skeletons of most organic molecules<br />Vary in length and shape<br />
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  8. 8. Fat droplets (stained red)<br />100 µm<br />(b) Mammalian adipose cells<br />(a) A fat molecule<br />Hydrocarbons are molecules consisting of only carbon and hydrogen<br />Hydrocarbons<br />Are found in many of a cell’s organic molecules<br />Are these polar or nonpolar?<br />
  9. 9. H<br />H<br />H<br />C<br />H<br />H<br />C<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />(a) Structural isomers<br />H<br />C<br />C<br />C<br />C<br />C<br />H<br />H<br />H<br />C<br />C<br />C<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />H<br />X<br />X<br />X<br />(b) Geometric isomers<br />C<br />C<br />C<br />C<br />X<br />H<br />H<br />H<br />CO2H<br />CO2H<br />(c) Enantiomers<br />C<br />C<br />H<br />H<br />NH2<br />NH2<br />CH3<br />CH3<br />Isomers are molecules with the same molecular formula but different structures and properties<br />Three types of isomers are<br />
  10. 10. L-Dopa<br />(effective against Parkinson’s disease)<br />D-Dopa<br />(biologically inactive)<br />Enantiomers<br />Are important in the pharmaceutical industry<br />
  11. 11. Carbon<br />(valence = 4)<br />Nitrogen<br />(valence = 3)<br />Hydrogen<br />(valence = 1)<br />Oxygen<br />(valence = 2)<br />O<br />H<br />N<br />C<br />The electron configuration of carbon<br />Gives it covalent compatibility with many different elements<br />
  12. 12. OH<br />CH3<br />HO<br />Estradiol<br />Female lion<br />OH<br />CH3<br />CH3<br />O<br />Testosterone<br />Male lion<br />Functional groups are the chemically reactive groups of atoms within an organic molecule<br />Give organic molecules distinctive chemical properties<br />Carbon hydrogen areas are not chemically active.<br />Functional groups attached are chemically active<br />Are these functional groups polar?<br />What about the rest of the molecule?<br />
  13. 13. Six functional groups are important in the chemistry of life<br />Hydroxyl<br />Carbonyl<br />Carboxyl<br />Amino<br />Sulfhydryl<br />Phosphate<br />
  14. 14. FUNCTIONAL<br />GROUP<br /> HYDROXYL CARBONYL CARBOXYL<br />O<br />O<br />OH<br />C<br />C<br />OH<br />(may be written HO )<br />STRUCTURE<br />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–.)<br />The carbonyl group( CO) consists of a carbon atom joined to an oxygen atom by a double bond.<br />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).<br /><br />Some important functional groups of organic compounds<br />
  15. 15. Ketones if the carbonyl group is within a carbon skeleton <br />Aldehydes if the carbonyl group is at the end of the carbon skeleton<br />NAME OF COMPOUNDS<br />Alcohols (their specific names usually end in -ol)<br />Carboxylic acids, or organic acids<br />EXAMPLE<br />H<br />H<br />H<br />H<br />O<br />O<br />C<br />C<br />H<br />OH<br />C<br />C<br />H<br />C<br />H<br />C<br />H<br />OH<br />H<br />H<br />H<br />H<br />C<br />Ethanol, the alcohol present in alcoholic beverages<br />H<br />H<br />Acetic acid, which gives vinegar its sour tatste<br />Acetone, the simplest ketone<br />H<br />H<br />O<br />C<br />C<br />C<br />H<br />H<br />H<br />H<br />Propanal, an aldehyde<br />FUNCTIONAL <br />GROUP<br />HYDROXYL CARBONYL CARBOXYL<br />
  16. 16.  A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.<br /> Is polar as a result of the electronegative oxygen atom drawing electrons toward itself.<br /> Attracts water molecules, helping dissolve organic compounds such as sugars (see Figure 5.3).<br />FUNCTIONALPROPERTIES<br /> Has acidic properties because it is a source of hydrogen ions.<br />The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example,<br />H<br />H<br />O<br />O<br />+ H+<br />H<br />C<br />H<br />C<br />C<br />C<br />OH<br />O<br />H<br />H<br /> In cells, found in the ionic form, which is called a carboxylate group.<br />HYDROXYL CARBONYL CARBOXYL<br />
  17. 17. AMINO SULFHYDRYL PHOSPHATE<br />O<br />H<br />SH<br />N<br />P<br />OH<br />O<br />(may be written HS )<br />H<br />OH<br />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).<br />The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.<br />The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape.<br />Some important functional groups of organic compounds<br />
  18. 18. OH<br />O<br />OH<br />H<br />H<br />H<br />H<br />H<br />O<br />H<br />C<br />C<br />C<br />O<br />P<br />O<br />N<br />C<br />C<br />SH<br />H<br />C<br />C<br />HO<br />H<br />O<br />H<br />H<br />H<br />H<br />H<br />H<br />Ethanethiol<br />Glycine<br />Glycerol phosphate<br />Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids.<br />Some important functional groups of organic compounds<br />AMINO SULFHYDRYL PHOSPHATE<br />
  19. 19. <ul><li>Two sulfhydryl groups can interact to help stabilize protein structure (see Figure 5.20).
  20. 20. A disulfide bond</li></ul>Makes the molecule of which it is a part an anion (negatively charged ion).<br />Can transfer energy between organic molecules.<br />ATP<br /> Acts as a base; can pick up a proton from the surrounding solution:<br />H<br />H<br />N<br />+N<br />H<br />H<br />H<br />(nonionized)<br />(ionized)<br />Ionized, with a charge of 1+, under cellular conditions.<br />Some important functional groups of organic compounds<br />AMINO SULFHYDRYL PHOSPHATE<br />
  21. 21. Nucleotides can act as short-term carriers of chemical energy<br /> ATP <br />adenosine triphosphate<br />Formed by oxidation of food. The phosphates are linked by phosphoanhydride bonds which release large amounts of useful energy when broken. The terminal phosphate is frequently split off by hydrolysis, releasing energy which drives energy-requiring reactions in the cell<br />