4 Chapter Lecture
Organic Chemistry
Introduction
Although cells are 70-95% water, the rest consists mostly of carbon-based compounds. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements.
These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).
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1. Organic chemistry is the study of carbon compounds
The study of carbon compounds, organic chemistry, focuses on any compound with carbon (organic compounds).
While the name, organic compounds, implies that these compounds can only come from biological processes, they can be synthesized by non-living reactions. Organic compounds can range from the simple (CO2 or CH4) to complex molecules, like proteins, that may weigh over 100,000 daltons.
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The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another. However, because of carbon's versatility, these few elements can be combined to build an inexhaustible variety of organic molecules. While the percentages of major elements do not differ within or among species, variations in organic molecules can distinguish even between individuals of a single species.
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The science of organic chemistry began in attempts to purify and improve the yield of products from other organisms.
Later chemists learned to synthesize simple compounds in the laboratory, but they had no success with more complex compounds. The Swedish chemist Jons Jacob Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds from the nonliving world.
This lead early organic chemists to propose vitalism, the belief in a life outside the limits of physical and chemical laws.
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Support for vitalism began to wane as organic chemists learned to synthesize more complex organic compounds in the laboratory.
In the early 1800's the German chemist Friedrich Whler and his students were able to synthesize urea from totally inorganic starting materials.
In 1953, Stanley Miller at the University of Chicago was able to simulate chemical conditions on the primitive Earth to demonstrate the spontaneous synthesis of organic compounds.
Fig. 4.1
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Organic chemists finally rejected vitalism and embraced mechanism.
Under mechanism, all natural phenomena, including the processes of life, are governed by the same physical and chemical laws.
Organic chemistry was redefined as the study of carbon compounds regardless of origin.
Still, most organic compounds in an amazing diversity and complexity are produced by organisms. However, the same rules apply to inorganic and organic compounds alike.
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2. Carbon atoms are the most versatile building blocks of molecules
With a total of 6 electrons, a carbon atom has 2 in the first shell and 4 in the second shell.
Carbon has little tendency to form ionic bonds by loosing or gaining 4 electrons. Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds. This tetravalence by carbon makes large, complex molecules possible.
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When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles near 109o.
While drawn flat, they are actually three-dimensional.
When two carbon atoms are joined by a double bond, all bonds around the carbons are in the same plane.
They have a flat, three-dimensional structure.
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Fig. 4.2
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The electron configuration of carbon gives it compatibility to form covalent bonds with many different elements. The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules.
Fig. 4.3
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In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms.
The structural formula, O = C = O, shows that each atom has completed its valence shells. While CO2 can be classified at either organic or inorganic, its importance to the living world is clear.
CO2 is the source for all organic molecules in organisms via the process of photosynthesis.
Urea, CO(NH2) 2, is another simple organic molecule in which each atom has enough covalent bonds to complete its valence shell.
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3. Variation in carbon skeletons contributes to the diversity of organic molecules
Carbon chains form the skeletons of most organic molecules.
The skeletons may vary in length and may be straight, branched, or arranged in closed rings. The carbon skeletons may also include double bonds.
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Fig. 4.4
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Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.
Hydrocarbons are the major component of petroleum. Petroleum is a fossil fuel because it consists of the partially decomposed remains of organisms that lived millions of years ago.
Fats are biological molecules that have long hydrocarbon tails attached to a non-hydrocarbon component.
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Fig. 4.5
Isomers are that compounds have the same molecular formula but different structures and therefore different chemical properties.
For example, butane and isobutane have the same molecular formula C4H10, but butane has a straight skeleton and isobutane has a branched skeleton.
The two butanes are structural isomers, molecules with the same molecular formula but differ in the covalent arrangement of atoms.
Fig. 4.6a
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Geometric isomers are compounds with the same covalent partnerships that differ in their spatial arrangement around a carbon-carbon double bond.
The double bond does not allow atoms to rotate freely around the bond axis. The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another.
Fig. 4.6b
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Enantiomers are molecules that are mirror images of each other
Enantiomers are possible if there are four different atoms or groups of atoms bonded to a carbon. If this is true, it is possible to arrange the four groups in space in two different ways that are mirror images. They are like left-handed and right-handed versions. Usually one is biologically active, the other inactive.
Fig. 4.6c
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Even the subtle structural differences in two enantiomers have important functional significance because of emergent properties from the specific arrangements of atoms.
One enantiomer of the drug thalidomide reduced morning sickness, its desired effect, but the other isomer caused severe birth defects. The L-Dopa isomer is an effective treatment of Parkinson's disease, but the D-Dopa isomer is inactive.
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Fig. 4.7
1. Functional groups contribute to the molecular diversity of life
The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups.
Functional groups are attachments that replace one or more hydrogen atoms to the carbon skeleton of the hydrocarbon.
Each functional groups behaves consistently from one organic molecule to another. The number and arrangement of functional groups help give each molecule its unique properties.
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The basic structure of testosterone (male hormone) and estradiol (female hormone) is identical.
Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings.
These then interact with different targets in the body.
Fig. 4.8
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There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups.
All are hydrophilic and increase solubility of organic compounds in water.
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In a hydroxyl group (-OH), a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton.
Because of these polar covalent bonds hydroxyl groups improve the solubility of organic molecules. Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.
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A carbonyl group (=CO) consists of an oxygen atom joined to the carbon skeleton by a double bond.
If the carbonyl group is on the end of the skeleton, the compound is an aldelhyde. If not, then the compound is a ketone. Isomers with aldehydes versus ketones have different properties.
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A carboxyl group (-COOH) consists of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group.
Compounds with carboxyl groups are carboxylic acids. A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).
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An amino group (-NH2) consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton.
Organic compounds with amino groups are amines. The amino group acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution. Amino acids, the building blocks of proteins, have amino and carboxyl groups.
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A sulfhydryl group (-SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone.
This group resembles a hydroxyl group in shape. Organic molecules with sulfhydryl groups are thiols. Sulfhydryl groups help stabilize the structure of proteins.
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A phosphate group (-OPO32-) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond).
A phosphate group connects to the carbon backbone via one of its oxygen atoms. Phosphate groups are anions with two negative charges as two protons have dissociated from the oxygen atoms. One function of phosphate groups is to transfer energy between organic molecules.
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2. The chemical elements of life: a review
Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus. These elements are linked by strong covalent bonds. Carbon with its four covalent bonds is the basic building block in molecular architecture. The great diversity of organic molecules with their special properties emerge from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton.
Copyright 2002 Pearson Education, Inc., publishing as Benjamin Cummings