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7 Organic Compounds.doc

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University of Toronto St. George
Earth Sciences
John Ferris

7 Organic Compounds 7.0 Introduction The solid material of living organisms consists of six predominant non-metallic elements – carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulphur. The relative amount of these elements varies somewhat between organisms; however, carbon and hydrogen are the universal skeletal constituents of all organic compounds and biological molecules, whereas it is the incorporation of oxygen, nitrogen, phosphorus, and sulphur that determines the physical and chemical characteristics of the molecules. A fundamental question associated with the diversity and abundance of organic compounds in aquatic environments is where do they all come from? The answer is not entirely straightforward as some highly toxic organic compounds do not occur naturally and are derived only from anthropogenic activity; however, the vast majority of organic molecules arise initially from biological activity beginning with autotrophic fixation of CO .2This is not an energetically favourable process as it involves the formation, rather than breaking, of bonds. In thermodynamic terms, the cost is an increase in entropy that can only be achieved by an input of energy. 7.1 Principle Types of Organic Molecules Although living organisms contain thousands of different kinds of organic molecules, nearly all fall into one of four categories; carbohydrates, lipids, proteins, and nucleotides. Other forms of organic compounds, such as humic substances and polyaromatic hydrocarbons, arise from the chemical degradation of biological molecules. Still others are synthesized chemically and only occur in the environment as anthropogenic pollutants (e.g., polychlorinated biphenyls, PCBs) Regardless of their source, the primary difference between these diverse groups of organic molecules relates to their molecular structure and the chemical nature of their functional groups. Some common functional groups that occur in organic molecules are illustrated in Table 7.1. In terms of molecular composition, carbohydrates are aldehydes or ketones with multiple hydroxyl groups on carbon atoms that are not part of the aldehyde or ketone functional group. The basic structural unit of carbohydrates are monosaccharides with a general formula of (CH O)2whene n is usually between 3 (e.g., glyceraldehyde) and 6 (e.g., glucose, fructose). Condensation of monosaccharides in response to the abstraction of water leads to the formation of disaccharides (e.g., sucrose is formed from glucose and fructose), as well as polysaccharide macromolecules such as starch, glycogen, or cellulose . While starch and glycogen are used for long-term energy storage in plants and animals, 1Starch, glycogen, and cellulose are all derived from glucose. Both starch and glycogen are characterized by linear α1,4 and branched α1,6 glycosidic bonds; glycogen is more highly branched than starch. On the other hand, cellulose is formed by linear β1,4 glycosidic bonds. 1 respectively, cellulose is a structural polysaccharide that makes up the cell walls of plants and many algae. Other types of polysaccharides include modified forms such as chitin 2 3 or peptidoglycan ; chitin is a major structural component in the exoskeletons of arthropods, whereas peptidoglycan is an important constituent of bacterial cell walls. Lipids include a diverse range of organic compounds that are broadly defined as being insoluble or sparingly soluble in water. They are either hydrophobic (i.e., non- polar) or amphipathic (i.e., contain both non-polar and polar regions), and are essential structural components of biological membranes. Some types of lipids, such as triacylglycerols (i.e., fats and oils), function as intracellular storage molecules for metabolic energy. Others, like steroid hormones, have highly specialized functions in regulating of metabolic and physiological processes. Figure 7.1: Structures of three C fatt18acids (A) stearate (octadecanoate), a saturated 9 fatty acid, (B) oleate (cis-Δ -octadecanote), a monounsaturated fatty acid, and (C) linoleate (cis-Δ 9,12,-octadecatrianoate), a polyunsaturated fatty acid. The simplest lipids are fatty acids with a general formula of R-COOH, where R represents a hydrocarbon chain (Fig. 7.1). Fatty acids are essential components of more complex types of lipids including triacylglycerides, phospholipids and sphingolipids. 2 3A linear polymer of N-acetylglucosamine linked by β1,4 glycosidic bonds. A mesh-like polymer consisting of linear stands of alternating β1,4 linked N-acetylglucosamine and N- acetylmuramic acid that are cross-linked by peptide chains of 3 to five amino acids. 2 Another major class of lipids are the isoprenoids, which not only include a suite of lipid vitamins (e.g., A, D, E, and K), but also encompass compounds with fused-carbon ring structures such as cholesterol, testosterone, and bile salts (e.g., sodium cholate). Waxes are non-polar esters of long chin fatty acids and long-chain monohydroxylic alcohols; for example, myricyl palmitate is a major component of bees’ wax that is an ester of 16:0 palmitate and the 30-carbon myricyl alcohol. Proteins are linear polymers of amino acids, and participate in virtually every aspect of biological activity. Many function as enzymes that catalyze nearly all chemical reactions in living organisms. Some serve as structural components that provide shape and support to cells. Others have highly specialized roles, such as transport molecules (e.g., hemaglobin binds and transports oxygen and carbon dioxide in red blood cells), hormone receptors, or immunological defence against infections. All organisms use the same 20 α-amino acids as building blocks for the assembly of proteins (Figure 7.2). The αdesignation means that an amino group and an acidic carboxyl group are attached to the C-2 carbon, which is also known as the αcarbon. In addition, a hydrogen atom and an R-group side chain are attached to the αcarbon, the later of which is unique for each amino acid. With the exception of glycine, which has a hydrogen atom in the R-group position, the attachment of four different constituents makes the αcarbon chiral, or asymmetric. This means that 19 of the 20 α-amino acids exist as stereoisomers; i.e., compounds with the same formula, but different molecular structures. The nonsuperimposable mirror images that exist for each chiral amino acid are called enantiomers., designated D for dextro (i.e., from the Latin dexter, right) and L for levo (i.e., from the Latin laevus, left) for the opposing mirror plane images. In biological systems, the L isomer of αamino acids is used almost exclusively for the biosynthesis of proteins. This makes chirality of amino acids a useful proxy indicator of biogenecity in paleobiological and paleoenvironmental investigations. Nucleotides are not only important building blocks of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), but also play a critical role in a vast number of cellular activities including energy metabolism and enzymatic catalysis. These molecules consist of a weakly basic nitrogenous compound, a five-carbon sugar, and phosphate. The bases found in nucleotides are substituted purines and pyrimidines, whereas the sugar is usually either ribose (i.e., β-D-ribofuranose) or deoxyribose (i.e., 2-dexoy-β-D- ribofuranose). The purine or pyrimidine N-glycosides of the sugars are called ribonucleosides or deoxynucleosides, respectively. Corresponding nucleotides are the phosphate esters of the nucleosides. 3 Figure 7.2: Structures of amino acids commonly found in proteins. Major R- groups include aliphatic, aromatic, sulphur-containing, alcohols, acids, bases, and amides. 4 Purines and pyrimidines are weak bases, and are relatively insoluble in water. The major purines are adenine and guanine, whereas the major pyrimidines include uracil, thymine, and cytosine (Fig. 7.3); uracil is found mainly in ribonucleosides of RNA, and thymine occurs mainly in deoxyribonucleosides of DNA. Phosphorylation of nucleosides gives rise to mono-, di- and tri-phosphorylated nucleotides that are used in many cellular reactions, including the biosynthesis of nucleic acids. Of particular note is the ribonucleotide ATP, which plays a central role in a wide range of metabolic processes, and is essential for driving many endergonic biosynthetic reactions. Figure 7.3: Chemical structures of major purines and pyrimidines. Polyaromatic hydrocarbons (PAHs) are chemical compounds that consist of fused aromatic rings and do not contain or carry substituents. They are produced as incomplete combustion products from fossil fuel and biomass burning. In addition, natural crude oil and coal deposits contain significant amounts of PAHs, arising from chemical conversion of natural product molecules, such as steroids, to aromatic hydrocarbons. As a pollutant, they are of concern because some compounds (e.g., benzo[a]pyrene) have been identified as carcinogenic and mutagenic. Among the better known anthropogenic organic pollutants are chlordane and dichloro-diphenyl-trichloroethane (DDT), both pesticides, as well as polyvinylchloride (a thermoplastic monomer) and phthalates (plastisizers). The aromatic and halogenated nature of these compounds contributes directly to their toxicity and environmental persistence, particularly as they are not normal constituents of biological metabolic pathways. 5 7.2 Autotrophic Acquisition of Carbon The most oxidized form of carbon occurs in CO , as wel2 as dissolved inorganic carbon and carbonate minerals such as calcite (i.e., CaCO ) or d3lomite (i.e., CaMg(CO ) ).3 2duction of C in CO , carboni2 acid, bicarbonate, or carbonate is not an energetically favourable process. For example, consider the reduction of CO to 2 formic acid (COOH) CO +22H + 2e = HCOOH;Eh = -0.11 V o ΔG = 193 kJ/mol(1) The reaction at standard state is highly endergonic. This implies that a prerequisite for the reduction of C and incorporation into organic matter (i.e., carbon fixation) is coupling with an exergonic reaction. For photolithoautotrophs, carbon fixation is an easier energetic undertaking thanks to photophosphorylation. By way of contrast, chemolithoautotrophs must expend a larger part of their energy budget from oxidative phosphorylation to accomplish the same task. There are four different types of carbon fixation pathways among autotrophic organisms. These include (i) the reductive pentose phosphate pathway, or Calvin cycle, (ii) the reverse citric acid cycle, (iii) the reductive acetyl-CoA pathway, and (iv) the 3- hydroxyproprionate pathway (Table 7.1). Each of the carbon fixation pathways are distinct in terms of their biochemistry and prevalence among different groups of organisms. The implication is that carbon fixation processes among autotrophs evolved independently of a common ancestral metabolic pathway. The reductive pentose phosphate pathway, or Calvin cycle, is prevalent among plants, algae, and cyanobacteria. This pathway consists of three stages; (i) carbon fixation by carboxylation of ribulose-1,5-bisphosphate by RuBisCO (ribulose- 1,5,bisphosphate carboxylase/oxidase), (ii) reduction to glyceraldehyde-3-phosphate (GAP) using NADPH, and (iii) regeneration of ribulose-1,5-bisphosphate. Some of the synthesized GAP eventually exits the cycle and is converted into fructose-6-phosphate, as well as glucose-6-phosphate, which are used in other metabolic pathways (e.g., synthesis of starch). The fixation of carbon dioxide in the reverse citric acid cycle is used by anaerobic photolithoautotrophic and chemolithoautotrophic bacteria. It begins with C 4 oxaloacetate; two sequential reductive carboxylation reactions using NADH, NADPH, 4 and ferredoxin as electron donors give rise to C citra6e. Cleavage of citrate yields acetyl-CoA and regenerates oxaloacetate as a C carbon4dioxide acceptor. Apart from being an important intermediate for directly or indirectly building other cellular constituents, such as lipids, acetyl-CoA can also be used to make oxaloacetate by reductive carboxylation with ferredoxin as the electron donor. 4 Ferredoxins are a group of small iron-sulfur proteins that mediate electron transfer in a variety of metabolic reactions. 6 Conceptually, the simplest way to construct an organic molecule is to construct it one carbon atom at a time; however, this approach is a rather unique biological process in that most biosynthetic pathways rely on the delivery of C 2nits by acetyl-CoA. In the reductive acetyl-CoA carbon fixation pathway, which is unique among autotrophic acetogenic and methanogenic bacteria, carbon fixation is accomplished by first reducing carbon dioxide or carbon monoxide to formic acid with NADPH as the electron donor. The formic acid is then reduced further by NADPH when it is attached to 5 tetrahydrofolate to form 5-methyl-tetrahydrofolate. Then acetyl-CoA is assembled sequentially on separate cobalt and nickel containing iron-sulfur proteins. Table 7.1: Major Autotrophic fixation pathways. Primary Carbon Biochemical Pathway Organisms Acceptor(s) Photolithoautotrophs Reductive pentose phosphate ribulose-1,5- (Calvin) cycle C3 – plants and algae bisphosphate Cyanobacteria Photolithoautotrophic and some chemolithoautotrophic Reverse Citric-acid cycle bacteria
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