7 Organic Compounds
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
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
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.
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-
alcohols, acids, bases,
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
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
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,
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.
Ferredoxins are a group of small iron-sulfur proteins that mediate electron transfer in a variety of
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
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.
Biochemical Pathway Organisms
Reductive pentose phosphate ribulose-1,5-
(Calvin) cycle C3 – plants and algae bisphosphate
Reverse Citric-acid cycle bacteria