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Chapter 4: Carbon—The Backbone of Biological Molecules • Although cells are 70–95% water, the rest consists mostly of carbonbased 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 atom’s 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Basic structures of Carbon containing molecules Molecular Formula Methane Ethane Ethene (ethylene) Structural Formula Ball-and-Stick Model Space-Filling Model Carbon can form bonds with atoms of many different elements • 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) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nitrogen (valence = 3) Carbon (valence = 4) Ethane Propane Butane 2-methylpropane (commonly called isobutane) Length Molecular Diversity Arises from Carbon Skeleton Variation • • Branching Carbon chains form the skeletons of most organic molecules 1-Butene Double bonds 2-Butene Carbon chains vary in length and shape Cyclohexane Rings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Benzene 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 Mammalian adipose cells A fat molecule Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fat droplets (red) 100 µm 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. cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. 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. 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 and medicine • 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 Parkinson’s disease) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings D-Dopa (biologically Inactive) 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The number and arrangement of functional groups give each molecule its unique properties! Female lion Estradiol Testosterone Male lion Functional Groups of organic molecules • 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings STRUCTURE (may be written HO—) Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS Alcohols (their specific names usually end in -ol) 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. Acetone, the simplest ketone STRUCTURE EXAMPLE Acetone, the simplest ketone NAME OF COMPOUNDS Propanal, an aldehyde Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS Carboxylic acids, or organic acids FUNCTIONAL PROPERTIES Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group. STRUCTURE EXAMPLE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. NAME OF COMPOUNDS Amine FUNCTIONAL PROPERTIES Acts as a base; can pick up a proton from the surrounding solution: (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions STRUCTURE EXAMPLE (may be written HS—) Ethanethiol NAME OF COMPOUNDS Thiols FUNCTIONAL PROPERTIES Two sulfhydryl groups can interact to help stabilize protein structure. STRUCTURE EXAMPLE Glycerol phosphate NAME OF COMPOUNDS Organic phosphates FUNCTIONAL PROPERTIES Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules. Methyl STRUCTURE Methylated compounds EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. 5-Methyl cytidine 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Arrangement of methyl groups in male and female sex hormones affects their shape and function. NAME OF COMPOUND FUNCTIONAL PROPERTIES 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings