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AP Biology Chapter 4 Carbon and the Molecular Diversity of Life 1 The Importance of Carbon Organic Chemistry is the Study of Carbon Compounds Most cells comprise 70% to 95% water with the remaining portions consisting of carbon based compounds. Biological molecules consist mainly of Hydrogen, Oxygen, Nitrogen, Sulfur, and Phosphorus. Organic Chemistry is mainly the study of carbon based compounds. Jons Jakob Berzelius made the distinction between organic compounds and inorganic compounds in living organisms. Wohler made Urea from Ammonium Cyanate. Kolbe made Acetic Acid from inorganic substances. During the early study of organic chemistry the mechanism for biological life were controlled or governed by chemical laws. Carbon Atoms are the most versatile Building Blocks of Molecules The key to the characteristics of atoms is the configuration of the electrons. Classification normally starts with the hydrocarbons: compounds which contain only carbon and hydrogen. Other elements, present themselves in atomic configurations called functional groups which have decisive influence on the chemical and physical characteristics of the compound; thus those containing the same atomic formations have similar characteristics, which may be miscibility with water, acidity/ alkalinity, chemical reactivity, oxidation resistance, or others. Some functional groups are also radicals, similar to those in inorganic chemistry, defined as atomic configurations which pass during chemical reactions from one chemical compound into another without change. Some of the elements of the functional groups (O, S, N, halogens) may stand alone and the group name is not 2 strictly appropriate, but because of their decisive effect on the way they modify the characteristics of the hydrocarbons in which they are present they are classed with the functional groups, and their specific effect on the properties lends excellent means for characterisation and classification. Names of Some Organic Compounds 3 Variation in Carbon Skeletons Constitutes a Diversity of Organic Molecules Organic compounds are generally covalently bonded. This allows for unique structures such as long carbon chains and rings. The reason carbon is excellent at forming unique structures and that there are so many carbon compounds is that carbon atoms form very stable covalent bonds with one another (catenation). In contrast to inorganic materials, organic compounds typically melt, boil, sublimate, or decompose below 300°C. Neutral organic 4 compounds tend to be less soluble in water compared to many inorganic salts, with the exception of certain compounds such as ionic organic compounds and low molecular weight alcohols and carboxylic acids where hydrogen bonding occurs. Organic compounds tend rather to dissolve in organic solvents which are either pure substances like ether or ethyl alcohol, or mixtures, such as the paraffinic solvents such as the various petroleum ethers and white spirits, or the range of pure or mixed aromatic solvents obtained from petroleum or tar fractions by physical separation or by chemical conversion. Solubility in the different solvents depends upon the solvent type and on the functional groups if present. Solutions are studied by the science of Physical Chemistry. Like inorganic salts, organic compounds may also form crystals. Unique property of carbon in organic compounds is that its valency does not always have to be taken up by atoms of other elements, and when it is not, a condition termed unsaturation results. In such cases we talk about carbon carbon double bonds or triple bonds. Double bonds alternating with single in a chain are called conjugated double bonds. An aromatic structure is a special case in which the conjugated chain is a closed ring. Compounds that for the most part are hydrophobic are nonpolar. Isomers isomers are compounds with the same molecular formula but different structural formulae[1] Isomers do not necessarily share similar properties unless they also have the same functional groups. This should not be confused with a nuclear isomer, which involves a nucleus at different states of excitement. There are many different classes of isomers, like stereoisomers, enantiomers, geometrical isomers, et cetera (see graph below). A simple example of isomerism is given by propanol: it has the formula C3H8O (or C3H7OH) and occurs as two isomers: propan-1ol (n-propyl alcohol; I) and propan-2-ol (isopropyl alcohol; II) 5 Note that the position of the oxygen atom differs between the two: it is attached to an end carbon in the first isomer, and to the center carbon in the second. There is, however, another isomer of C3H8O which has significantly different properties: methoxyethane (methyl-ethyl-ether; III). Unlike the isomers of propanol, methoxyethane has an oxygen atom that is connected to two carbons rather than to one carbon and one hydrogen. This makes it an ether, not an alcohol, as it lacks a hydroxyl group, and has chemical properties more similar to other ethers than to either of the above alcohol isomers. There are two main forms of isomerism: structural isomerism and stereoisomerism. In structural isomers, the atoms and functional groups are joined together in different ways, as in the example of propyl alcohol above. This group includes chain isomerism whereby hydrocarbon chains have variable amounts of branching; position isomerism which deals with the position of a functional group on a chain; and functional group isomerism in which one functional group is split up into different ones. In stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers where different isomers are non-superimposable mirror-images of each other, and diastereomers when they are not. Diastereomerism is again subdivided into conformational isomerism (conformers) when isomers can interconvert by chemical bond rotations and cis-trans isomerism when this is not possible. Note that although conformers can be referred to as having a diastereomeric relationship, the isomers over all are not diastereomers, since bonds in conformers can be rotated to make them mirror images. In skeletal isomers the main carbon chain is different between the two isomers. This type of isomerism is most identifiable in secondary and tertiary alcohol isomers. Tautomers are structural isomers of the same chemical substance that spontaneously interconvert with each other, even when pure. They have different chemical properties, and consequently, distinct reactions characteristic to each form are observed. If the interconversion reaction is fast enough, tautomers cannot be isolated from each other. An example is when they differ by the 6 position of a proton, such as in keto/enol tautomerism, where the proton is alternately on the carbon or oxygen. In food chemistry, medicinal chemistry and biochemistry, cis-trans isomerism is always considered. In medicinal chemistry and biochemistry, enantiomers are of particular interest since most changes in these types of isomers are now known to be meaningful in living organisms. Pharmaceuti cal and academic researchers have found chromatogra phical methods to reliably separate these from each other. On an industrial scale, however, these methods are rather costly and are mostly used to filter out the potentially harmful or biologically inactive enantiomer. While structural isomers typically have different chemical properties, stereoisomers behave identically in most chemical reactions, except in their reaction with other stereoisomers. Enzymes however can distinguish between different enantiomers of a compound, and organisms often prefer one isomer over the other. Some stereoisomers also differ in the way they rotate polarized light. Other types of isomerism exist outside this scope. Topological isomers called topoisomers are generally large molecules that wind about and form different shaped knots or loops. Molecules with topoisomers include catenanes and DNA. Topoisomerase enzymes can knot DNA and thus change its topology. There are also isotopomers or isotopic isomers that have the same numbers of each type of isotopic substitution but in chemically different positions. In nuclear physics, nuclear isomers are excited states of atomic nuclei. Spin isomers have differing distributions of spin among their constituent atoms. 7 Enantiomers Enantiomers are non-superimposable mirror images of one another. Not being able to superimpose one molecule on top of the other simply means that the two molecules are not equivalent or identical. For a compound to form an enantiomeric pair, it must have chiral molecules. Chiral molecules must not have an internal plane of symmetry, and they must have a stereocenter. Each enantiomer exhibits what is called optical activity. Each isomer of the pair is capable of rotating plane polarized light. One isomer rotates this light to the right "x" number of degrees, and the other isomer of the pair rotates this light to the left for the same number of degrees. In fact, this is the only difference in the two isomers, their ability to rotate plane polarized light in opposite directions. All other physical properties are exactly the same. This makes it extremely difficult to separate the two isomers should they be mixed as often they are. If the enantiomers are crystalline salts like Pasteur's Tartrate salts, then the enantiomers will have a different appearance when observed under magnification and one can pick them out to separate them, but most enantiomeric pairs are not salts and therefore look the same. There is a way that we can separate such a mixture of enantiomers which is referred to as resolution to be disscussed in a later lesson. Another characteristic that Enantiomers exhibit is configuration. Configuration is the spacial way that non-equivalent groups arrange themselves around a stereocenter carbon. One enantiomer will be configured right handedly (R) and the other will be configured left handedly (S). Enantiomers are usually dipicted on a planar surface either as a 3dimensional structural formula, or we can show the structure as a Fisher Projection. A Fisher projection is a 2-dimensional projection of a 3-dimensional chiral molecule. A Fisher projection consists of a long vertical line representing the longest contineous chain of the molecule with a series of horizontal line intersecting this vertical line along its length. At the point where the horizontal lines intersect the vertical line there will be a carbon atom. At the ends of the horizontal lines will be atoms or groups of atoms. In a Fisher projection atoms or groups that are projected in front of the plane where the vertical line extends will be at the ends of the horizontal lines.Those atoms along the vertical line will be projected behind the plane. For example 2-Bromobutane is a chiral molecule, and therefore, will be one of an enantiomeric pair with its mirror 8 image. We can show this molecule in 3-D formula as is usually the case using solid wedges to show atoms in front of the plane and dotted wedges for atoms behind the plane with any atoms within the plane to be connected to a solid line(See Fig 1-a). Its mirror image could be projected as in Fig 1-b. On the other hand we can dipict the same chiral molecule and its mirror image using a Fisher Projection (See Fig 2). One has to be very careful about using Fisher Projections when you go and try to manipulate the projections by rotation out of plane. In fact, one cannot rotate Fisher projections of acyclic molecules out of plane without leading to incorrect conclusions concerning whether or not the mirror images are nonsuperimposable. That is because when you rotate out of plane (flip over) then you still have atoms that were at the end of horizontal 9 lines, and therefore projected forward in front of the plane at the end of horizontal lines after flipping. However the use of simple molecular models will show that when you flip a molecule out of plane 180 degrees you will project the groups that were in front to the back of the plane. This is not indicated within a Fisher projection. Suffice to say that when dealing with Fisher projections, it is best not to manipulate out of plane. Any manipulations using Fisher Projections should be done within the plane either translation or rotation within the plane. Functional Groups Functional Groups Contribute to Molecular Diversity of Life A distinctive property of an organic molecule can depend on the arrangement of the carbon skeleton structure. The Hydroxyl Group represents alcohols. The ending name is “ol”. This group is soluble in water implicating easy distribution to the cells. The Carboxyl Group consists of a double carbon oxygen bond. If this group is at the end of the carbon skeleton then the organic compounds represents aldehydes otherwise the compound will be a ketone. The simplest being Acetone. The Carboxyl Group consists of a double bonded oxygen atom off a carbon atom that is attached to an hydroxyl group. These compounds form organic acids or carboxylic acids. Formic Acid or Acetic Acid are example compounds. The Amino Group consist of a nitrogen aton bonded with 2 hydrogen atoms. These compounds are also the amines. All these compounds are the opposite of the carboxyl acids and form bases. The Sulfhydryl Group has a sulfur atom bonded to an hydrogen atom. These compounds also called “thiols” help to stabilize protein complexes. The Phosphate Group forms from the dissociation of Phosphoric Acid to give: OPO32 . This ion is then attached to a carbon skeleton. 10 Organic Functional Groups Name General Structure Example Carboxylic acid acetic acid (vinegar is aqueous soln.) Anhydride acetic anhydride Ester isoamyl acetate (banana oil) Amide propanamide Aldehyde benzaldehyde (almond smell) Ketone acetone (solvent) Alcohol ROH, R is not H CH3CH2OH ethanol, ethyl alcohol (grain alcohol) Thiol (Mercaptan) RSH, R is not H (CH3)3CSH tert-butyl mercaptan (natural gas odorant) Amine RNH2, R2NH, R3N (CH3)2NH dimethylamine Ether ROR, R is not H CH3CH2OCH2CH3 diethyl ether (solvent) Sulfide RSR, R is not H CH3CH2SCH3 ethyl methyl sulfide Aromatic toluene (in model airplane glue) Alkyne ethyne (fuel for welding torch) Alkene CH3CH2CH=CH2 1-butene Haloalkane R—Cl, R—Br, R—I, R—F CHCl3 chloroform (trichloromethane) Alkane R—H CH3CH2CH3 propane (fuel) 11 R = hydrocarbon group such as methyl (CH3), ethyl (CH3CH2). Can sometimes be H or aromatic. Where two R groups are shown in a single structure, they do not have to be the same, but they can be. Ph refers to "phenyl," the substituent name for benzene and is the same as "C 6H5"; Ar refers to a general aromatic group. 12