The Same Atoms, Arranged Differently

Every living organism raises an obvious question: are all living things made of the same chemicals? Elemental analysis of a plant tissue, animal tissue or microbial paste yields a list of elements, carbon, hydrogen, oxygen and others, alongside their relative abundance; performing the identical analysis on a piece of earth's crust yields, in absolute terms, the same list of elements. Every element found in earth's crust also turns up in living tissue. A closer look, though, reveals a real difference: the relative abundance of carbon and hydrogen compared to other elements is considerably higher in any living organism than in earth's crust, hydrogen making up 9.5 percent of the human body's weight against just 0.14 percent of earth's crust, carbon 18.5 percent against 0.03 percent. To identify actual organic compounds rather than just elements, scientists grind a living tissue sample in trichloroacetic acid, producing a thick slurry that, strained through cheesecloth, separates into two fractions: the filtrate, or acid-soluble pool, containing thousands of small organic compounds, and the retentate, or acid-insoluble fraction. Burning a weighed, dried tissue sample instead oxidises all its carbon compounds away as gas, leaving behind an inorganic ash containing elements like calcium and magnesium, confirming that living tissue also contains genuinely inorganic constituents like sodium, potassium and various phosphate and sulphate compounds alongside its organic ones.

Amino acids are organic compounds carrying both an amino group and an acidic carboxyl group as substituents on the same carbon, the alpha-carbon, making them alpha-amino acids; four groups occupy that carbon's four valency positions, hydrogen, carboxyl, amino, and a variable R group. Although many amino acids exist based on R group variation, only twenty types occur in proteins, glycine when the R group is simply hydrogen, alanine when it's a methyl group, serine when it's hydroxymethyl. Based on the number of amino and carboxyl groups present, amino acids are classified as acidic, glutamic acid for instance, basic, like lysine, or neutral, like valine, with a further aromatic category, tyrosine, phenylalanine and tryptophan among them; because the amino and carboxyl groups are both ionisable, an amino acid's actual structure shifts depending on the surrounding solution's pH. Fatty acids, generally water-insoluble, carry a carboxyl group attached to an R group ranging from a single methyl group up to nineteen additional carbons, palmitic acid having sixteen total carbons and arachidonic acid twenty; they may be saturated, with no double bonds, or unsaturated, with one or more. Glycerol, trihydroxy propane, often combines with esterified fatty acids to form monoglycerides, diglycerides or triglycerides, known as fats or oils depending on melting point, oils remaining liquid in winter due to a lower melting point. Some lipids incorporate phosphorus and a phosphorylated organic group, forming phospholipids like lecithin, a key component of cell membranes, while neural tissue specifically contains lipids with even more complex structures. A separate class of heterocyclic compounds, the nitrogen bases, adenine, guanine, cytosine, uracil and thymine, become nucleosides once attached to a sugar, and nucleotides once a phosphate group is further esterified onto that sugar; DNA and RNA, the genetic material of living organisms, are built entirely from nucleotides.

Compiling every biomolecule found in living organisms would produce a list of thousands of organic compounds, amino acids and sugars among them, collectively called metabolites. In animal tissue, one finds essentially the full range of these compound categories, and these are called primary metabolites, molecules with identifiable functions in normal physiological processes. Analysing plant, fungal and microbial cells, however, turns up thousands of additional compounds well beyond the primary set, alkaloids, flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents, gums and spices, collectively called secondary metabolites. Unlike primary metabolites, the precise role of many secondary metabolites in their host organism's own physiology is not yet fully understood, even though many are genuinely valuable for human welfare, rubber, drugs, spices, scents and pigments all drawn from this category, and some carry clear ecological importance of their own.

Everything in the acid-soluble pool shares one feature: molecular weights ranging from about 18 to 800 daltons. The acid-insoluble fraction, by contrast, contains only four types of organic compound, proteins, nucleic acids, polysaccharides and lipids, and with the exception of lipids these have molecular weights of ten thousand daltons and above; biomolecules under one thousand daltons are called micromolecules, while those in the insoluble fraction are called macromolecules or biomacromolecules. This raises a real puzzle: lipids, whose molecular weights never exceed 800 daltons, are genuinely small, so why do they end up classified alongside true macromolecules in the insoluble fraction? The answer lies in structure rather than size. Lipids exist in cells not just as free molecules but arranged into structures like the cell membrane; when a tissue is ground up, membranes break apart into fragments that reform as small vesicles, which are not water-soluble and so get separated together with the acid-insoluble pool. Lipids are, strictly speaking, not macromolecules at all, just molecules that happen to travel with them during extraction. Averaged across a whole cell, water dominates the total composition at 70 to 90 percent, followed by proteins at 10 to 15 percent, nucleic acids at 5 to 7 percent, carbohydrates at roughly 3 percent, lipids at roughly 2 percent, and ions making up about 1 percent.

Proteins are polypeptides, linear chains of amino acids linked by peptide bonds. Because twenty different amino acid types can appear anywhere along that chain, a protein is a heteropolymer rather than a homopolymer, which explains why certain amino acids the body cannot synthesise, the essential ones, must come from diet, while non-essential amino acids the body can make on its own. Proteins carry out an enormous range of jobs, some transporting nutrients across membranes, some fighting infection as antibodies, some acting as hormones like insulin, some as enzymes like trypsin, some as receptors detecting smell, taste or hormones, and some, like GLUT-4, enabling glucose transport into cells; collagen is the most abundant protein in the animal world, while RuBisCO holds that title across the entire biosphere. Polysaccharides, the other major class of macromolecule in the acid-insoluble fraction, are long chains of monosaccharide sugars; cellulose, made of glucose alone, is a homopolymer and the main component of plant cell walls, as well as of paper and cotton fibre. Starch, a related but distinct homopolymer, serves as the primary energy store in plant tissues and forms helical secondary structures capable of trapping iodine molecules to produce the characteristic blue starch-iodine complex, a property cellulose, lacking such helices, does not share. Glycogen is the animal equivalent energy store, and inulin is built instead from fructose; more complex polysaccharides, built from amino-sugars and chemically modified sugars like glucosamine, form structures like chitin, the material making up arthropod exoskeletons.

Biologists describe protein structure at four distinct levels. The primary structure is simply the sequence of amino acids, positional information recording which amino acid comes first, second, and so on, from the N-terminal amino acid at one end to the C-terminal amino acid at the other; a protein is never an extended rigid rod, though, and portions of that chain fold into a helix, similar to a spiral staircase, with only right-handed helices ever observed in proteins, or into other shapes, together making up the secondary structure. The long chain then folds upon itself further, like a hollow woollen ball, producing the tertiary structure, which gives the protein its actual three-dimensional shape and is absolutely necessary for most of its biological activity. Some proteins assemble from more than one folded polypeptide subunit, and the specific arrangement of those subunits relative to each other is called the quaternary structure; adult human haemoglobin, for instance, consists of four subunits, two identical alpha-type and two identical beta-type, that together constitute the functional molecule. Nucleic acids, the other true macromolecule of the acid-insoluble fraction, are polynucleotides built from three chemically distinct nucleotide components: a heterocyclic nitrogenous base, either a purine, adenine or guanine, or a pyrimidine, cytosine, uracil or thymine; a pentose sugar, either ribose or deoxyribose; and a phosphate group. A nucleic acid containing deoxyribose is deoxyribonucleic acid, DNA; one containing ribose is ribonucleic acid, RNA.

Almost all enzymes are proteins, with a primary, secondary and tertiary structure just like any other, though a few nucleic acids called ribozymes also show catalytic behaviour. When a protein's tertiary structure folds the chain back on itself repeatedly, the criss-crossing creates crevices and pockets, and one such pocket, the active site, is where a substrate fits and gets converted into product at a dramatically accelerated rate. The difference catalysis makes is genuinely enormous: the reaction converting carbon dioxide and water into carbonic acid produces only about two hundred molecules an hour without any enzyme, but with the enzyme carbonic anhydrase present, that same reaction produces roughly six hundred thousand molecules every second, an acceleration of about ten million times. Enzyme action follows a defined catalytic cycle: the substrate binds the active site, its binding induces the enzyme to alter shape and fit more tightly around it, the active site then breaks and reforms chemical bonds to produce an enzyme-product complex, and finally the product is released, freeing the enzyme to bind another substrate molecule and repeat the cycle. What actually makes this possible is a reduction in activation energy, the extra energy a substrate must reach, via an unstable transition state, before it can convert into product; enzymes lower this energy barrier substantially, making the S-to-P transition far easier than it would be uncatalysed.