Overview Carbon The Backbone of Life 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 Organic chemistry is the study of compounds that contain carbon and such organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 2 EXPERIMENT Atmosphere CH4 Water vapor Electrode NH 3 H2 Condenser Cooled water containing organic molecules H2O sea Sample for chemical analysis Cold water Concept 4 2 Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom s characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms With four valence electrons carbon can form four covalent bonds with a variety of atoms This tetravalence makes large complex molecules possible Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 3 Name a Methane b Ethane c Ethene ethylene Molecular Formula Structural Formula Ball and Stick Model Space Filling Model Fig 4 4 The valences of carbon and its most frequent partners hydrogen oxygen and nitrogen are the building code that governs the architecture of living molecules Hydrogen valence 1 Oxygen valence 2 Nitrogen valence 3 Carbon valence 4 H O N C Carbon atoms can partner with atoms other than hydrogen for example Carbon dioxide CO2 Urea CO NH2 2 Carbon chains vary in length and shape Hydrocarbons are organic molecules consisting of only carbon and hydrogen anything with the letters h and c Many organic molecules such as fats have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 5 Ethane Propane a Length Butane b Branching 1 Butene 2 Butene c Double bonds 2 Methylpropane commonly called isobutane Cyclohexane d Rings Benzene Fig 4 6 Fat droplets stained red 100 m a Mammalian adipose cells b A fat molecule Fat has more energy than a carb Fat molecules contain hydrocarbons 9 calories from 1 gram of fat 4 from carbs and protein 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 Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 7 Pentane 2 methyl butane a Structural isomers cis isomer The two Xs are on the same side trans isomer The two Xs are on opposite sides b Geometric isomers L isomer c Enantiomers D isomer 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 Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 8 Drug Condition Ibuprofen Pain inflammation Albuterol Effective Enantiomer Ineffective Enantiomer S Ibuprofen R Ibuprofen R Albuterol S Albuterol Asthma Concept 4 3 A small number of chemical groups are key to the functioning of biological molecules Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules These chemical groups affect molecular function by being directly involved in chemical reaction and are called functional groups Estradiol Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Testosterone 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 Copyright 2008 Pearson Education Inc publishing as Pearson Benjamin Cummings Fig 4 10a CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE may be written HO NAME OF COMPOUND 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 an OH group the entire assembly of atoms is called a carboxyl group COOH Alcohols their specific names usually end in ol Ketones if the carbonyl group is within a carbon skeleton Carboxylic acids or organic acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol the alcohol present in alcoholic beverages Acetone the simplest ketone Acetic acid which gives vinegar its sour taste Propanal an aldehyde FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom A ketone and an aldehyde may be structural isomers with different properties as is the case for acetone and propanal Can form hydrogen bonds with water molecules helping dissolve organic compounds such as sugars These two groups are also found in sugars giving rise to two major groups of sugars aldoses containing an aldehyde and ketoses containing a ketone Has acidic properties because the covalent bond between oxygen and hydrogen is so polar for example Acetic acid Acetate ion Found in cells in the ionized form with a charge of 1 and called a carboxylate ion here specifically the acetate ion Fig 4 10b CHEMICAL GROUP Amino Sulfhydryl Methyl 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 The phosphate group OPO32 abbreviated P is an ionized form of a phosphoric acid group OPO3H2 note the two hydrogens A methyl group consists of a carbon bonded to three hydrogen atoms The methyl group may be attached to a carbon or to a different atom may be written HS STRUCTURE NAME OF COMPOUND Phosphate The amino group NH2 consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon