Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chapter 4: CarbonThe Backbone of Biological Molecules Although cells are 7095% 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 Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Organic chemistry is the study of carbon compounds Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Vitalism, the idea that organic compounds arise only in organisms, was shown to be false when chemists synthesized many organic compounds in the laboratory Mechanism is the view that all natural phenomena are governed by physical and chemical laws Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Carbon atoms can form diverse molecules by bonding to four other atoms An atoms electron configuration is the key to its 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 In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the molecule has a flat shape Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene) Basic structures of Carbon containing molecules Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings The electron configuration of carbon gives it covalent compatibility with many different elements 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) Carbon can form bonds with atoms of many different elements Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Diversity Arises from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Length Ethane Propane Butane 2-methylpropane (commonly called isobutane) Branching Double bonds Rings 1-Butene2-Butene CyclohexaneBenzene Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 A fat molecule Mammalian adipose cells 100 m Fat droplets (red) Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 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. Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enantiomers are very 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 L -Dopa (effective against Parkinsons disease) D -Dopa (biologically Inactive) Enantiomers and medicine Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings Functional groups are the parts of molecules involved in chemical reactions 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 The functional groups of compounds are the most Important determinant in the chemistry of life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions Estradiol Testosterone Male lion Female lion The number and arrangement of functional groups give each molecule its unique properties! Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings The six 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 Functional Groups of organic molecules 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. 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 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. 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) STRUCTURE (may be written HS) NAME OF COMPOUNDS Thiols EXAMPLE Ethanethiol FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure. 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. Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings STRUCTURE EXAMPLE NAME OF COMPOUND FUNCTIONAL PROPERTIES Methyl 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. 5-Methyl cytidine Methylated compounds Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function. Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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