8 Organic compounds

Organic Compounds

Organic molecules underpin life’s architecture, defined by carbon-based backbones where carbon atoms form chains or rings through covalent C–C and C–H bonds. Because carbon has four valence electrons and seeks an octet, it readily shares electrons, creating stable skeletons that serve as scaffolding for the four classes of macromolecules critical to human physiology: carbohydrates, lipids, proteins, and nucleic acids. Beyond hydrocarbons, reactive functional groups attach to carbon skeletons, conferring specific chemical behaviors; Table 8.1 catalogs the five most important groups—hydroxyl, carboxyl, amino, methyl, and phosphate—and highlights their roles in polarity, acidity, and reactivity.

The Chemistry of Carbon

What makes organic compounds ubiquitous is the chemistry of their carbon core. Recall that carbon atoms have four electrons in their valence shell, and that the octet rule dictates that atoms tend to react in such a way as to complete their valence shell with eight electrons. Carbon atoms do not complete their valence shells by donating or accepting four electrons. Instead, they readily share electrons via covalent bonds.

Normally, carbon atoms share with other carbon atoms, often forming a long carbon chain referred to as a carbon skeleton. When they share, however, they do not share all their electrons exclusively with each other. Rather, carbon atoms tend to share electrons with a variety of other elements, one of which is always hydrogen. Carbon and hydrogen groupings are called hydrocarbons. If you study the figures of organic compounds in the remainder of this chapter, you will see several with chains of hydrocarbons in one region of the compound.

Many combinations are possible to fill carbon’s four “vacancies.” Carbon may share electrons with oxygen or nitrogen or other atoms in a particular region of an organic compound. Moreover, the atoms to which carbon atoms bond may also be part of a functional group. A functional group is a group of atoms linked by strong covalent bonds and tend to function in chemical reactions as a single unit. You can think of functional groups as tightly knit “cliques” whose members are unlikely to be parted. Five functional groups are important in human physiology: the hydroxyl, carboxyl, amino, methyl and phosphate groups (Table 8.1).

Carbon’s affinity for covalent bonding means that many distinct and relatively stable organic molecules readily form larger, more complex molecules. Any large molecule is referred to as macromolecule (macro- = “large”), and the organic compounds in this section all fit this description. However, some macromolecules are made up of several “copies” of single units called monomer (mono- = “one”; -mer = “part”). Like beads in a long necklace, these monomers link by covalent bonds to form long polymers (poly- = “many”). There are many examples of monomers and polymers among the organic compounds.

Monomers form polymers by engaging in dehydration synthesis (see Figure X.X.X). As was noted earlier, this reaction results in the release of a molecule of water. Each monomer contributes; one gives up a hydrogen atom and the other gives up a hydroxyl group. Polymers are split into monomers by hydrolysis (-lysis = “rupture”). The bonds between their monomers are broken, via the donation of a molecule of water, which contributes a hydrogen atom to one monomer and a hydroxyl group to the other.

Monomers, Polymers, and Reaction Mechanisms

Cells assemble and disassemble large molecules through two complementary reactions: dehydration synthesis and hydrolysis. In dehydration synthesis (Figures X.X.X), each reacting monomer donates part of a water molecule—one provides a hydrogen atom (–H), the other a hydroxyl group (–OH)—and covalent bonds form to link monomers into polymers. For example, two glucose monomers connect via a glycosidic bond, releasing H₂O. Conversely, hydrolysis inserts H₂O into a polymer’s bond, splitting it back into monomers by supplying –H to one fragment and –OH to the other. This reversible dynamic enables cells to build complex structures when energy and substrates are available, and to reclaim monomer units when needed for energy or remodeling.

Carbohydrates

Carbohydrates, or saccharides, follow the general formula (CH₂O)ₙ and serve both as immediate energy sources and structural components. Monosaccharides such as glucose, fructose, and galactose (hexoses) or ribose and deoxyribose (pentoses) (Figure 8.1) provide fuel and carbon skeletons for other molecules. Disaccharides—sucrose, lactose, and maltose—form when two monosaccharides join via glycosidic bonds (Figure 8.2), making them transportable energy forms in plants and dairy. In the digestive tract, hydrolysis splits these into monosaccharides for absorption. Polysaccharides vary in branching and linkage: plant starch comprises amylose (unbranched α‐1,4 bonds) and amylopectin (α‐1,4 with α‐1,6 branches), animal glycogen is a highly branched glucose polymer for rapid energy release, and cellulose consists of β‐1,4 linkages that humans cannot digest yet provide dietary fiber (Figure 8.3). In cells, glucose oxidation via glycolysis and the citric acid cycle produces ATP; neurons and erythrocytes rely almost exclusively on glucose, while other cells may utilize lipids or proteins when glucose is scarce. Carbohydrates also modify proteins and lipids to form membrane glycoproteins and glycolipids, critical for cell recognition and signaling.

Lipids

Lipids are hydrophobic macromolecules composed predominantly of hydrocarbon chains or rings, with few oxygen atoms. Triglycerides—glycerol esterified to three fatty acids—store long-term energy in adipose tissue. Fatty acids lack double bonds (saturated) or contain one (monounsaturated) or multiple (polyunsaturated) double bonds, creating kinked chains that influence fluidity and melting point (Figure 8.5). Saturated fats (butter, lard) are solid at room temperature; unsaturated fats (olive oil, fish oil) are liquid. Omega‐3 fatty acids, with their first double bond at the third carbon from the methyl end, promote anti-inflammatory prostaglandin synthesis. Phospholipids replace one fatty acid with a phosphate-containing head group, yielding amphipathic molecules that self-assemble into bilayers, the fundamental architecture of cell membranes (Figure 8.6a). The hydrophilic head interacts with aqueous environments, while hydrophobic tails face inward, forming selective barriers. Steroids, like cholesterol, consist of four fused hydrocarbon rings (Figure 8.6b). Cholesterol modulates membrane fluidity and serves as a precursor for bile acids and steroid hormones (estrogens, androgens, cortisol). Prostaglandins, derived from arachidonic acid (an unsaturated fatty acid), act as local mediators in inflammation, pain, and vascular tone (Figure 8.6c). Because lipids are nonpolar, they provide more energy per gram than carbohydrates when metabolized, and they facilitate absorption of fat-soluble vitamins (A, D, E, K).

Proteins

Proteins are versatile macromolecules composed of twenty amino acid monomers, each with a central α-carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and a distinctive R-group (Figure 8.7). Amino acids link via peptide bonds—covalent bonds formed by dehydration synthesis between the carboxyl of one and the amino of another (Figure 8.8)—generating polypeptide chains. Protein function derives from hierarchical folding:

1. Primary structure is the specific amino acid sequence, encoding information for higher-level folding.
2. Secondary structure arises from hydrogen bonding between backbone atoms, producing α-helices or β-pleated sheets (Figure 8.9b).
3. Tertiary structure involves interactions among R-groups (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bridges) that fold the chain into a unique 3D conformation (Figure 8.9c).
4. Quaternary structure occurs when multiple polypeptide subunits assemble, as in hemoglobin’s α₂β₂ tetramer, enabling cooperative oxygen binding (Figure 8.9d). Protein shape underlies diverse roles: enzymes catalyze reactions via active site geometry, structural proteins like collagen provide tensile strength, transport proteins (hemoglobin) shuttle molecules, hormones regulate physiology, and antibodies defend against pathogens. Denaturation—unfolding due to heat or pH shifts—destroys function, illustrating the precision of protein architecture.

Nucleotides and Nucleic Acids

Nucleotides consist of a pentose sugar (ribose in RNA, deoxyribose in DNA), one or more phosphate groups, and a nitrogenous base (adenine, cytosine, guanine, thymine or uracil) (Figure 8.10). Phosphodiester bonds between the sugar’s 3′-OH and the phosphate of another nucleotide create sugar-phosphate backbones. DNA’s double helix (Figure 8.11) forms when two antiparallel strands align via hydrogen bonds between complementary bases (A–T, C–G), storing genetic information. RNA, typically single-stranded, conveys genetic instructions from DNA to ribosomes for protein synthesis. Additionally, nucleotides like ATP (adenine + ribose + three phosphates) release energy when the terminal phosphate bond is hydrolyzed, powering cellular processes.

Integration and Physiological Relevance

Together, these organic compounds orchestrate life’s processes: carbohydrates and lipids store and supply energy; proteins catalyze biochemical reactions, form structures, and transmit signals; nucleic acids encode and express genetic information. Functional groups and specific monomer sequences determine molecular interactions, while dynamic assembly and disassembly via dehydration synthesis and hydrolysis enable adaptation and regulation. By understanding these foundational chemistries and structures, students gain insight into how cells build complex tissues, respond to their environment, and maintain homeostasis.

Adapted from Anatomy & Physiology by Lindsay M. Biga et al, shared under a Creative Commons Attribution-ShareAlike 4.0 International License, chapter 2.