Biomolecules

If we grind any living tissue, make an extract and analyse it chemically, we find two kinds of compounds. The acid-soluble pool contains small molecules of low molecular weight — amino acids, monosaccharides (sugars), nucleotides and lipids — while the acid-insoluble fraction contains the giant macromolecules: proteins, nucleic acids and polysaccharides. A frequently tested subtlety is that lipids, although they appear in the acid-insoluble fraction, have molecular weights under about 800 and are therefore not true macromolecules; they sediment there only because they form parts of membranes.

The thousands of small organic compounds in a cell are called metabolites, and NCERT divides them into two groups. Primary metabolites — amino acids, sugars, nucleotides, fatty acids — have clear, identifiable roles in normal physiology (growth, energy, structure). Secondary metabolites — alkaloids (morphine, codeine), flavonoids, rubber, essential oils, antibiotics, coloured pigments (carotenoids, anthocyanins), gums and spices — have no obvious role in basic metabolism but are of great ecological and human importance. Recognising examples of each category is a guaranteed NEET mark.

The building blocks themselves are worth knowing. Amino acids are organic acids that carry an amino group (–NH₂), a carboxyl group (–COOH) and a variable side chain (R) on the same carbon; twenty of them build all proteins, and at cellular pH they exist as dipolar zwitterions. Lipids are usually water-insoluble and include fats and oils (glycerol esterified with fatty acids) and phospholipids; fatty acids may be saturated (no double bonds) or unsaturated (with double bonds).

Carbohydrates (sugars) range from simple monosaccharides (glucose, fructose, the pentose ribose) through oligosaccharides to long polysaccharides. The most abundant biomolecule in the whole living world is in fact a polysaccharide — cellulose. These four classes of building blocks — amino acids, sugars, nucleotides and fatty acids — are the monomers from which the cell assembles its macromolecules, the subject of the next topic.

Proteins are the most abundant biomacromolecules and are polymers of amino acids joined by peptide bonds. Their roles are vast: they act as enzymes, as transporters (the glucose transporter GLUT-4), as antibodies, as some hormones and receptors, and as structural materials. The most abundant protein in the whole animal world is collagen, while the most abundant protein in the entire biosphere is the photosynthetic enzyme RuBisCO.

A protein's shape is described at four levels, a classic NEET topic. The primary structure is simply the linear sequence of amino acids, with a defined N-terminal and C-terminal end. The secondary structure is the regular local folding of that chain into shapes such as the right-handed alpha-helix or the beta-pleated sheet, held by hydrogen bonds. The tertiary structure is the overall three-dimensional folding of the whole chain into a compact shape, essential for biological activity.

The highest level, the quaternary structure, arises only when a functional protein is built from two or more polypeptide chains (subunits) assembled together — the textbook example is haemoglobin, made of four subunits (two alpha and two beta). Not every protein has a quaternary structure, but identifying haemoglobin as the standard example, and matching each level to its description, is reliably examined.

Polysaccharides are long chains of monosaccharides linked by glycosidic bonds, and three are key. Starch is the storage carbohydrate of plants: it is a helically coiled molecule (amylose plus branched amylopectin) and forms a blue-black colour with iodine because iodine slots into its helix. Glycogen is the more highly branched storage carbohydrate of animals. Cellulose is a structural polysaccharide of plant cell walls; it has no helix and no iodine colour because it is made of straight chains of β-glucose. Chitin (in fungal walls and arthropod exoskeletons) is a nitrogen-containing structural polysaccharide. Remembering 'starch = helix + iodine-blue, cellulose = straight + structural, glycogen = animal store' covers the common questions.

Nucleic acids — DNA and RNA — are the macromolecules that store and transmit genetic information. They are polymers of nucleotides, and each nucleotide has three parts: a nitrogenous base, a pentose sugar (deoxyribose in DNA, ribose in RNA) and a phosphate group. A base joined only to the sugar (no phosphate) is a nucleoside. The nucleotides are linked into a chain by phosphodiester bonds between the phosphate of one and the sugar of the next.

The nitrogenous bases fall into two groups, a guaranteed NEET fact: the double-ringed purines are adenine (A) and guanine (G), and the single-ringed pyrimidines are cytosine (C), thymine (T) (found in DNA) and uracil (U) (which replaces thymine in RNA). So DNA uses A, G, C, T while RNA uses A, G, C, U.

The Watson–Crick double helix of DNA has two strands that run antiparallel (one 5'→3', the other 3'→5') and are coiled into a right-handed helix. The strands are held together by complementary base pairing: adenine pairs with thymine through two hydrogen bonds (A=T) and guanine pairs with cytosine through three hydrogen bonds (G≡C). This is why Chargaff's rule holds — the amount of A equals T and G equals C. The B-form helix makes one full turn every 10 base pairs (pitch 3.4 nm, with 0.34 nm between adjacent base pairs).

It helps to collect the bonds of biomolecules in one place, because NEET often asks which bond joins which monomer. Peptide bonds link amino acids in proteins; glycosidic bonds link sugars in polysaccharides; phosphodiester bonds link nucleotides in nucleic acids; and weaker hydrogen bonds stabilise the secondary and higher structures of proteins and hold the two strands of DNA together. Mastering this short list resolves a whole family of questions.

Enzymes are biological catalysts that speed up the chemical reactions of life; almost all are proteins (a few RNA molecules, called ribozymes, are catalytic too). An enzyme works by lowering the activation energy needed for a reaction, so the reaction proceeds far faster without the enzyme itself being consumed. The reactant binds to a specific pocket on the enzyme called the active site, forming a transient enzyme–substrate complex that passes through an unstable transition state before products are released.

Because enzymes are proteins, their activity is sensitive to conditions, and NEET expects the standard graphs. Each enzyme has an optimum temperature and an optimum pH; above the optimum, high temperature or extreme pH denatures the protein and activity falls sharply. As substrate concentration rises, the rate increases and then plateaus at a maximum velocity (V_max) when all active sites are saturated. Some molecules slow enzymes by inhibition: in competitive inhibition, an inhibitor that resembles the substrate competes for the active site — the classic example is malonate, which competitively inhibits succinic dehydrogenase (whose true substrate is succinate).

Enzymes are grouped by the type of reaction they catalyse into six classes, which you should be able to list: oxidoreductases (oxidation–reduction), transferases (transfer of a group), hydrolases (hydrolysis), lyases (removal of groups forming double bonds, not by hydrolysis), isomerases (interconversion of isomers) and ligases (joining two molecules using ATP). A simple way to remember them is the order OTHLIL: Oxidoreductase, Transferase, Hydrolase, Lyase, Isomerase, Ligase.

Many enzymes are active only when a non-protein helper, a cofactor, is attached. The protein part on its own is the apoenzyme, and the complete, catalytically active enzyme (apoenzyme + cofactor) is the holoenzyme. Cofactors are of three kinds: tightly bound prosthetic groups (e.g. haem in peroxidase), loosely bound organic coenzymes (often derived from vitamins, such as NAD and NADP from niacin), and metal ions (e.g. zinc in carbonic anhydrase). The relations 'holoenzyme = apoenzyme + cofactor' and the malonate–succinate example are among the most frequently asked enzyme facts.