Biomolecules

Carbohydrates (saccharides) are optically active polyhydroxy aldehydes or ketones, or compounds that yield such units on hydrolysis. Most have the general formula C_n(H₂O)_m, which is why they were once called "hydrates of carbon", though some carbohydrates (e.g. rhamnose, C₆H₁₂O₅) do not fit this formula while some non-carbohydrates (e.g. acetic acid, CH₃COOH) do — so the formula is only a rough guide, not a definition.

On the basis of their behaviour on hydrolysis, carbohydrates are classified into three groups:

• Monosaccharides: cannot be hydrolysed further into simpler polyhydroxy units, e.g. glucose, fructose, ribose. Classified by the number of carbons (triose, tetrose, pentose, hexose ...) and by the carbonyl group present — aldose (aldehyde group) or ketose (ketone group).
• Oligosaccharides: yield 2–10 monosaccharide units on hydrolysis; those giving two units are disaccharides (sucrose, maltose, lactose), the most common in nature.
• Polysaccharides: yield a large number of monosaccharide units on hydrolysis (starch, cellulose, glycogen). They are not sweet and are called non-sugars.

Carbohydrates are also classed as reducing sugars (reduce Fehling's solution and Tollens' reagent because a free −CHO or potentially free −C=O group is available in solution) or non-reducing sugars. All monosaccharides, and disaccharides such as maltose and lactose, are reducing sugars; sucrose is the important non-reducing disaccharide.

The open-chain structure of D-(+)-glucose, the most abundant monosaccharide, was established from a series of experimental facts: it forms a monoxime with hydroxylamine and adds one molecule of HCN (confirming a carbonyl group); on mild oxidation with bromine water it gives a six-carbon monocarboxylic acid, gluconic acid, showing the carbonyl is an aldehyde (a ketone could not be oxidised so mildly); acetylation gives glucose pentaacetate, confirming five −OH groups; and vigorous oxidation with dilute HNO₃ gives a dicarboxylic acid, saccharic acid, showing that C6 is a primary alcohol (−CH₂OH). Its stereochemistry (established by Fischer) is:

CHO−CHOH−CHOH−CHOH−CHOH−CH₂OH, with the −OH at C2, C4 and C5 on the right and at C3 on the left in the Fischer projection (C5 fixes the D-configuration).

This open-chain structure, however, fails to explain some observations: glucose does not give the 2,4-DNP test or Schiff's test readily, it does not react appreciably with NaHSO₃, and, most tellingly, freshly prepared solutions of glucose show mutarotation — the specific rotation of α-D-glucose (+111°) and β-D-glucose (+19°) both drift on standing to an equilibrium value of +52.7°. This is explained by a cyclic hemiacetal structure: the −OH at C5 attacks the C1 aldehyde to form a six-membered (pyranose) ring, generating a new stereocentre at C1 — the anomeric carbon — so that two cyclic forms (α and β anomers) exist and interconvert in solution. Fructose is the corresponding ketohexose (carbonyl at C2), which forms a five-membered (furanose) ring using the C5−OH, and also shows mutarotation and gives anomers.

Worked example: How many stereoisomers are possible for the open-chain structure of an aldohexose such as glucose? In CHO−CHOH−CHOH−CHOH−CHOH−CH₂OH, the four middle carbons C2, C3, C4 and C5 are each attached to four different groups, so each is a chiral (asymmetric) centre: n = 4. The number of possible stereoisomers is N = 2ⁿ = 2⁴ = 16 (8 belonging to the D-series and 8 to the L-series); D-(+)-glucose is just one specific member of this set of 16.

A disaccharide is formed when two monosaccharide units are joined by a glycosidic linkage — an acetal linkage formed between the anomeric carbon (the hemiacetal −OH) of one unit and an −OH group of the other, with elimination of one molecule of water.

Sucrose (cane sugar) is obtained from sugarcane and sugar beet. It is formed by linking C1 of α-D-glucose to C2 of β-D-fructose (an α,β-1,2-glycosidic linkage). Because both anomeric carbons take part in the linkage, sucrose has no free anomeric −OH and cannot reduce Fehling's/Tollens' reagent — it is a non-reducing sugar. On hydrolysis (by dilute acid or the enzyme invertase) it gives an equimolar mixture of glucose and fructose. Sucrose is dextrorotatory (+66.5°) but the hydrolysis mixture is laevorotatory (−39.9°) because the large negative rotation of fructose outweighs the positive rotation of glucose; the change of sign is called inversion and the product mixture is called invert sugar.

Maltose consists of two α-D-glucose units joined by a C1−C4 (α-1,4) glycosidic linkage; one anomeric carbon remains free, so maltose is a reducing sugar. Lactose (milk sugar) consists of β-D-galactose joined to β-D-glucose by a C1−C4 (β-1,4) linkage, and is also a reducing sugar.

Polysaccharides are polymers of many monosaccharide units joined by glycosidic linkages; they are not sweet and serve mainly as storage or structural material:

• Starch — the storage polysaccharide of plants; a polymer of α-D-glucose with two components: amylose (15–20%, a long unbranched chain with only α-1,4 linkages, coiled into a helix, gives a blue colour with iodine) and amylopectin (80–85%, a branched chain with α-1,4 linkages along the chain and α-1,6 linkages at branch points, gives a purple/red colour with iodine).
• Cellulose — a linear, unbranched polymer of β-D-glucose joined by β-1,4-glycosidic linkages; the long straight chains pack together via hydrogen bonding into strong fibres that make up plant cell walls. Humans lack the enzyme (cellulase) that can hydrolyse β-linkages, so cellulose cannot be digested by humans though it is an essential dietary fibre.
• Glycogen — the storage polysaccharide of animals ("animal starch"), stored in the liver and muscles; structurally similar to amylopectin but even more highly branched, which allows rapid release of glucose when energy is needed.

Worked example: 34.2 g of sucrose (molar mass 342 g mol⁻¹) is completely hydrolysed. Find the total mass of glucose and fructose formed.
Moles of sucrose = 34.2 g ÷ 342 g mol⁻¹ = 0.1 mol.
C₁₂H₂₂O₁₁ + H₂O → C₆H₁₂O₆ (glucose) + C₆H₁₂O₆ (fructose)
0.1 mol sucrose consumes 0.1 mol (1.8 g) of water and gives 0.1 mol glucose (0.1 × 180 = 18.0 g) and 0.1 mol fructose (18.0 g).
Total product mass = 18.0 g + 18.0 g = 36.0 g, which correctly equals 34.2 g (sucrose) + 1.8 g (water) by conservation of mass.

Amino acids are the building blocks of proteins. Each contains an amino (−NH₂) group and a carboxyl (−COOH) group; in the amino acids that make up proteins, the amino group is on the carbon next to −COOH, so they are called α-amino acids, general formula R−CH(NH₂)−COOH, where R varies from one amino acid to another.

Amino acids are classified in two useful ways. By the relative number of amino and carboxyl groups: acidic (extra −COOH, e.g. glutamic acid, aspartic acid), basic (extra −NH₂, e.g. lysine, arginine) and neutral (equal numbers, e.g. glycine, alanine). By nutritional requirement: essential amino acids (cannot be synthesised by the body and must come from the diet, e.g. valine, leucine) and non-essential amino acids (the body can synthesise them, e.g. glycine, alanine).

In the solid state and in aqueous solution, an amino acid exists mainly as a zwitterion (dipolar ion): the −COOH group transfers a proton to the −NH₂ group intramolecularly, giving H₃N⁺−CHR−COO⁻. Because it carries both an ionisable acidic group (−NH₃⁺) and an ionisable basic group (−COO⁻), an amino acid is amphoteric — it reacts with added acid (−COO⁻ accepts H⁺) and with added base (−NH₃⁺ loses H⁺). The pH at which an amino acid carries no net charge (exists purely as the zwitterion) is its isoelectric point.

Two amino acids join through a peptide linkage (an amide bond, −CO−NH−), formed between the −COOH of one molecule and the −NH₂ of another with loss of a water molecule. Chains of amino acid residues are called dipeptides, tripeptides, oligopeptides or polypeptides depending on length; a polypeptide with more than about 100 amino acid residues (molecular mass greater than 10,000) is called a protein.

The structure of a protein is described at four levels:

• Primary structure — the exact sequence of amino acids in the polypeptide chain(s); even a single change here can alter the protein's function.
• Secondary structure — the local shape the chain adopts through hydrogen bonding between the C=O and N−H of peptide linkages: the coiled α-helix or the extended, zig-zag β-pleated sheet.
• Tertiary structure — the overall three-dimensional folding of the whole chain, giving two broad classes of protein: fibrous proteins (long thread-like molecules held by hydrogen/disulphide bonds running parallel to each other, insoluble in water, e.g. keratin of hair, myosin of muscle) and globular proteins (chains fold into a compact, roughly spherical shape, generally water-soluble, e.g. insulin, albumins, most enzymes).
• Quaternary structure — the spatial arrangement of two or more polypeptide subunits relative to each other, seen in proteins made of more than one chain, e.g. haemoglobin, which is built from four polypeptide subunits.

Denaturation occurs when a protein's native (biologically active) conformation is disturbed by a change of temperature or pH: the hydrogen bonds and other weak interactions that hold the secondary and tertiary structure are broken, the globular protein unfolds into a random coil, and its biological activity (e.g. enzymic action) is lost — even though the primary structure (the peptide-bonded amino acid sequence) remains unchanged. Coagulation of egg white on boiling and curdling of milk are everyday examples of denaturation.

Worked example: A tripeptide is formed by condensing three amino acid molecules. How many peptide bonds are formed and how many water molecules are eliminated?
Joining n amino acid residues into one chain requires (n − 1) peptide-bond-forming condensations, each releasing one H₂O.
For n = 3: peptide bonds = 3 − 1 = 2, and water molecules eliminated = 2.

Enzymes are globular proteins that act as biocatalysts, speeding up the biochemical reactions occurring inside living cells without themselves being consumed. Compared with ordinary chemical catalysts, enzymes are extraordinarily efficient (they can increase reaction rates by many orders of magnitude under the mild conditions of temperature and pH found in the body) and extraordinarily specific — a given enzyme generally catalyses only one reaction, or a small set of closely related reactions, of one particular substrate.

This specificity is explained by the shape of the enzyme molecule. Each enzyme has a small three-dimensional pocket or groove, the active site, whose shape and arrangement of chemical groups exactly complements the shape of its substrate — much as a key fits a particular lock (the lock-and-key model). The substrate binds non-covalently at the active site to form a transient enzyme–substrate (ES) complex; within this complex the reaction is catalysed and proceeds far more readily than it would in free solution; the products are then released and the free enzyme is regenerated unchanged, ready to bind another substrate molecule.

The following simple sequence summarises enzyme action:

1. Substrate molecule diffuses to and binds at the active site of the free enzyme, forming the enzyme–substrate complex.
2. The bound substrate is converted to product(s) while still held at the active site (the specific chemical environment of the active site lowers the activation energy of the reaction).
3. The product(s) are released from the active site.
4. The unchanged enzyme is free to bind a fresh substrate molecule and repeat the cycle.

Enzyme activity is sensitive to conditions: every enzyme has an optimum temperature (about 37°C for most human enzymes) at which it works fastest — activity falls off at lower temperatures because molecular motion (and hence collision with substrate) slows down, and it falls sharply above the optimum because heat denatures the enzyme's tertiary structure and destroys its active site. Similarly, each enzyme has an optimum pH, since extremes of pH disturb the ionisation of groups at the active site (and can also denature the protein). Because enzymes are proteins, anything that denatures a protein — heat, extremes of pH, heavy-metal ions — will also abolish enzyme activity; even a very small change in the substrate's structure can prevent it from being recognised at the active site at all.

Vitamins are organic compounds required in the diet in small amounts to maintain normal growth, health and metabolic function. Except for small amounts of a few (such as vitamin D, made in the skin on exposure to sunlight, and vitamin K and some B vitamins made by intestinal bacteria), the body cannot synthesise them, so they must be supplied through food. A deficiency of a specific vitamin (avitaminosis) produces a specific, recognisable disease, and both deficiency and (for some vitamins) excess can be harmful.

Vitamins are classified by solubility into two groups, which also governs how the body handles them:

• Fat-soluble vitamins (A, D, E, K) dissolve in fats and oils, are absorbed along with dietary fat, and can be stored in appreciable amounts in the liver and adipose (fatty) tissue.
• Water-soluble vitamins (the B-group and vitamin C) dissolve in the aqueous fluids of the body; because they are not stored to any significant extent and are continuously lost in urine, they must be supplied regularly through the diet.

Important vitamins, dietary sources and their deficiency diseases:

• Vitamin A (retinol) — fish liver oil, carrots, milk, butter — deficiency causes xerophthalmia (hardening of the cornea) and night blindness.
• Vitamin B₁ (thiamine) — yeast, cereals, milk — deficiency causes beriberi (loss of appetite, weak muscles, enlarged heart).
• Vitamin B₂ (riboflavin) — milk, eggs, green vegetables — deficiency causes cheilosis (cracking at the corners of the mouth), digestive disorders and a burning sensation of the skin.
• Vitamin B₆ (pyridoxine) — meat, fish, egg yolk — deficiency can cause convulsions.
• Vitamin B₁₂ (cyanocobalamin) — meat, fish, curd — deficiency causes pernicious anaemia (the only water-soluble vitamin stored in the body, mainly in the liver, to a useful extent).
• Vitamin C (ascorbic acid) — citrus fruits, amla, green leafy vegetables — deficiency causes scurvy (bleeding and swollen gums, slow wound healing).
• Vitamin D (calciferol) — sunlight on skin, fish, egg yolk, milk — deficiency causes rickets in children (soft, deformed bones) and osteomalacia in adults.
• Vitamin E (tocopherol) — vegetable oils, seeds — deficiency increases fragility of red blood cells and can cause muscular weakness; it also functions as a natural antioxidant.
• Vitamin K — green leafy vegetables — deficiency increases the time taken for blood to clot (increased blood-clotting time).

Because water-soluble vitamins are excreted rather than stockpiled, deficiencies of B-group vitamins and vitamin C tend to appear relatively quickly if intake is inadequate, whereas fat-soluble vitamin deficiencies typically take longer to develop because of the body's stores — but excess fat-soluble vitamin intake can accumulate to toxic levels, which is far less likely with water-soluble vitamins.

Nucleic acids are polymers found mainly in the nucleus of the cell that carry genetic information and transmit it from one generation to the next; the two types are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

The repeating unit of a nucleic acid is the nucleotide, built from three components: a pentose sugar (2-deoxy-D-ribose in DNA, D-ribose in RNA), a nitrogenous base, and a phosphate group. A base joined to the sugar alone (no phosphate) is called a nucleoside; adding a phosphate group gives a nucleotide. The nitrogenous bases are of two kinds: purines — adenine (A) and guanine (G) — and pyrimidines — cytosine (C), and either thymine (T, found only in DNA) or uracil (U, found only in RNA, replacing thymine).

Within a nucleotide, the base is attached to C1′ of the sugar by a β-N-glycosidic linkage, and the phosphate is attached to C5′ of the sugar by a phosphoester linkage. Successive nucleotides are then joined by a phosphodiester linkage between the 3′-OH of one sugar and the 5′-phosphate of the next, building up the alternating sugar–phosphate backbone of a polynucleotide chain, with the nitrogenous bases projecting from this backbone.

DNA normally exists as the famous double helix (Watson–Crick model): two polynucleotide chains coiled around a common axis, running in opposite (antiparallel) directions and held together by hydrogen bonds between specific, complementary pairs of bases on the two strands — adenine always pairs with thymine (2 hydrogen bonds) and guanine always pairs with cytosine (3 hydrogen bonds). This complementary base pairing means the two strands are not identical but exactly complementary, which is what allows DNA to be faithfully copied (replicated) and is the molecular basis of heredity.

RNA, in contrast, is generally single-stranded and occurs in three functional types, all involved in protein synthesis: messenger RNA (m-RNA) carries the genetic code from DNA to the site of protein synthesis; ribosomal RNA (r-RNA) forms part of the ribosome; and transfer RNA (t-RNA) carries specific amino acids to the ribosome for assembly into the growing protein chain.

Worked example (Chargaff's rule): A sample of double-stranded DNA contains 20% cytosine. Find the percentage of adenine, thymine and guanine.
By the base-pairing rule, %C = %G, so %G = 20% as well; hence %C + %G = 40%.
The remaining bases, adenine and thymine, must together make up 100% − 40% = 60%, and since %A = %T, each is 60% ÷ 2 = 30%.
So: %A = 30%, %T = 30%, %G = 20%, %C = 20% (total = 100%).