JEE Chemistry Biomolecules Notes Set 05

Carbohydrates: Classification

Carbohydrates are polyhydroxy aldehydes or ketones, or compounds that give them on hydrolysis. By hydrolysis they are monosaccharides (cannot be hydrolysed further; three to seven carbons, most commonly pentoses and hexoses), oligosaccharides (two to ten monosaccharide units; disaccharides such as sucrose, maltose and lactose) and polysaccharides (starch, cellulose, glycogen). Monosaccharides are aldoses or ketoses according to the carbonyl group. The simplest aldose is glyceraldehyde and the simplest ketose is dihydroxyacetone. Sugars can also be grouped as reducing (free hemiacetal or hemiketal group, or capable of enolising to an aldose) and non-reducing (only acetal or ketal links), and as sugars (sweet, crystalline) and non-sugars (polysaccharides).

Stereochemistry: D and L, Epimers and Anomers

An aldohexose has four chiral carbons (C-2 to C-5), so there are \( 2^4 = 16 \) stereoisomers (8 D and 8 L); a ketohexose has three chiral carbons and 8 stereoisomers. The label D or L shows the configuration of the highest-numbered chiral carbon, compared with glyceraldehyde: in the Fischer projection (CHO at the top) D has the OH on that carbon at the right. D and L do not indicate the direction of rotation; D-glucose is dextrorotatory, D-fructose is laevorotatory. Diastereomers that differ at only one stereocentre are epimers (glucose and mannose at C-2, glucose and galactose at C-4); the mirror image of D-glucose is L-glucose, which differs at all four stereocentres.

Structure of Glucose

Evidence for the open chain: reduction with HI and red phosphorus gives n-hexane, so the six carbons form an unbranched chain; the cyanohydrin with HCN, the oxime with hydroxylamine and the osazone with phenylhydrazine show a carbonyl group; oxidation by bromine water gives gluconic acid (so the carbonyl is an aldehyde) and by nitric acid gives saccharic acid (a dicarboxylic acid, so there is also a primary alcohol group); the penta-acetate shows five hydroxyl groups. Evidence for the ring: glucose does not give the Schiff test and does not form the sodium bisulphite adduct, its penta-acetate does not react with hydroxylamine, and it forms only one mole of methyl glycoside (acetal) with methanol and dry HCl, in two forms. Ring closure between the C-1 aldehyde and the C-5 hydroxyl gives a six-membered ring (pyranose); the new stereocentre C-1 is the anomeric carbon, giving the α and β anomers.

Mutarotation. A freshly prepared solution of α-D-glucose ([α] = +112°) or β-D-glucose (+19°) slowly changes to an equilibrium value of +52.7° as the two anomers interconvert through the open-chain form (about 36% α, 64% β, traces of open chain). Only sugars with a free anomeric OH show mutarotation.

Reactions of Glucose and Fructose

Tollens' reagent, Fehling's and Benedict's solutions are all reduced by both glucose and fructose, because in the basic medium fructose enolises to an enediol and isomerises to glucose and mannose (Lobry de Bruyn-van Ekenstein transformation). Only bromine water, which is acidic, separates them: it oxidises aldoses to aldonic acids and leaves ketoses untouched. Nitric acid oxidises glucose to saccharic acid. Sodium amalgam reduction gives one alcohol (sorbitol) from glucose and two (sorbitol and mannitol) from fructose. With excess phenylhydrazine, three moles are used: one forms the phenylhydrazone, one oxidises the adjacent CHOH group (and leaves as aniline and ammonia) and one forms the osazone. Osazone formation involves only C-1 and C-2, so glucose, mannose and fructose give the same osazone; galactose, which differs at C-4, gives a different one. Methanol and dry HCl give methyl glycosides (acetals), which do not reduce Fehling's solution. Acetic anhydride gives the penta-acetate.

Disaccharides and Polysaccharides

Sucrose is α-D-glucose joined C-1 to C-2 of β-D-fructose, so both anomeric carbons are tied up: it is non-reducing and shows no mutarotation. Its hydrolysis (acid or the enzyme invertase) gives equal amounts of glucose (+52°) and fructose (-92°); the mixture rotates to the left by about 20°, so the process is called inversion and the mixture invert sugar. Maltose is two α-D-glucose units linked α-1,4 and is reducing; lactose is β-D-galactose linked β-1,4 to glucose and is reducing; cellobiose is the β-1,4 glucose dimer.

Starch is a mixture of amylose (about 20%, unbranched, α-1,4 links, gives a blue colour with iodine) and amylopectin (about 80%, branched through α-1,6 links). Glycogen, the animal reserve, resembles amylopectin but is more highly branched. Cellulose is a linear chain of β-D-glucose units joined by β-1,4 links; its chains lie side by side and are held by hydrogen bonds, giving rigid fibres. Complete hydrolysis of starch, glycogen or cellulose gives only glucose. Humans have the enzymes for α links but not for the β links of cellulose.

Amino Acids

Alpha-amino acids have the general formula \( \ce{H2N-CH(R)-COOH} \); all natural protein amino acids (except achiral glycine) have the L configuration. They are classed as neutral, acidic (aspartic and glutamic acids) or basic (lysine, arginine, histidine), and as essential (must be taken in the diet: valine, leucine, isoleucine, lysine, methionine, threonine, phenylalanine, tryptophan, histidine, and arginine in children) or non-essential. In water an amino acid exists as the dipolar zwitterion \( \ce{H3N^+-CH(R)-COO^-} \), which explains its high melting point, solubility in water and amphoteric character: in acid it takes a proton to give the cation, in base it loses one to give the anion.

Isoelectric point. The pH at which the net charge is zero (no migration in an electric field, minimum solubility) is the pI. For a neutral amino acid pI is the mean of pKa1 and pKa2 (glycine 5.97). For an acidic amino acid, average the two lowest pKa values (aspartic acid: (1.88 + 3.65)/2 = 2.77); for a basic amino acid, average the two highest (lysine: (8.95 + 10.53)/2 = 9.74). At pH below pI the molecule is a cation and migrates to the cathode; above pI it is an anion and goes to the anode.

Preparation and tests. Amino acids are made by ammonolysis of α-halo acids, by the Strecker synthesis (aldehyde, \( \ce{NH4Cl} \) and NaCN give an α-amino nitrile, which is hydrolysed) and by the Gabriel synthesis with diethyl phthalimidomalonate. Ninhydrin gives a purple (Ruhemann's purple) colour with free α-amino groups; copper(II) gives a blue complex; Sanger's reagent (2,4-dinitrofluorobenzene) labels the N-terminal amino group; nitrous acid releases nitrogen from a primary amino group (Van Slyke method; proline, a secondary amine, does not respond).

Peptides and Proteins

A peptide bond is the amide link formed when the carboxyl group of one amino acid condenses with the amino group of another, losing water; n residues have n - 1 peptide bonds. Peptides are written from the N-terminus (free NH2, left) to the C-terminus (free COOH, right); Gly-Ala and Ala-Gly are different compounds. Polypeptides with more than about 100 residues (molar mass above 10 000) are proteins. Because the nitrogen lone pair is delocalised into the carbonyl group, the peptide unit is planar with partial double bond character and is usually trans.

Levels of structure: the primary structure is the sequence of residues. The secondary structure is local folding held by hydrogen bonds between C=O and N-H groups of the backbone: the α-helix (within one chain, each C=O bonded to the N-H four residues along) and the β-pleated sheet (between chains, more stable when antiparallel). The tertiary structure is the overall three-dimensional fold, held by disulfide bridges (covalent bonds between cysteine residues), hydrogen bonds, ionic (salt) bridges and hydrophobic interactions. Quaternary structure is the arrangement of several chains (haemoglobin). Globular proteins (insulin, albumin) are soluble in water; fibrous proteins (keratin, collagen, myosin) are insoluble. Denaturation (heat, pH change, heavy metal salts, urea) destroys the secondary and tertiary structure but not the peptide bonds, for example coagulation of egg white. Hydrolysis with 6 M HCl breaks peptide bonds and gives the free amino acids. The biuret test (violet colour with alkaline copper(II) sulfate) detects two or more peptide bonds.

Enzymes

Enzymes are globular proteins that act as biological catalysts, specific for their substrate and highly efficient under mild conditions (about 310 K and pH near 7). The substrate binds to the active site (lock-and-key or induced fit), forming an enzyme-substrate complex that is converted to the product, which leaves the enzyme free. Examples: invertase (sucrose), maltase (maltose), zymase (glucose to ethanol), urease (urea), amylase or diastase (starch), pepsin and trypsin (proteins). Inhibitors that bind at or near the active site reduce activity; many drugs act as enzyme inhibitors. Some enzymes need a non-protein cofactor or coenzyme, often derived from a vitamin.

Vitamins and Lipids

Vitamins are organic compounds needed in small amounts that the body cannot make. Fat-soluble vitamins (A, D, E, K) are stored in the body; water-soluble ones (B complex and C) must be supplied regularly. Deficiency diseases: A, night blindness and xerophthalmia (carrots, cod-liver oil); B1 (thiamine), beri-beri; B2 (riboflavin), cracked lips; B6 (pyridoxine), convulsions; B12 (cyanocobalamin, contains cobalt), pernicious anaemia; C (ascorbic acid, citrus fruits), scurvy; D (calciferol), rickets and osteomalacia; E (tocopherol), loss of fertility and muscular weakness; K, delayed blood clotting. Fats and oils are triesters of glycerol with long-chain fatty acids; alkaline hydrolysis (saponification) gives glycerol and soap. Fats give about 9 kcal per gram, more than carbohydrates or proteins (about 4 kcal per gram). Phospholipids are the chief constituents of cell membranes.

Nucleic Acids

Nucleic acids are polymers of nucleotides. A nucleoside is a nitrogen base joined through an N-glycosidic bond (C-1' of the sugar) to a pentose; a nucleotide adds a phosphate ester at C-5'; nucleotides are linked by phosphodiester bonds between C-3' and C-5'. DNA contains 2-deoxy-D-ribose and the bases adenine, guanine (purines), cytosine and thymine (pyrimidines); RNA contains D-ribose with uracil in place of thymine. In both, the sugar is in the furanose form. DNA is a double helix of two antiparallel strands held by hydrogen bonds between complementary bases: A pairs with T (two bonds) and G with C (three bonds), so in DNA A = T, G = C and purines equal pyrimidines (Chargaff). RNA is usually single-stranded and is of three kinds: messenger RNA (carries the codons), transfer RNA (carries the amino acid and the anticodon) and ribosomal RNA. DNA is replicated in the cell (each round doubles the molecules) and directs protein synthesis through transcription to mRNA and translation; a triplet codon specifies one amino acid (the genetic code), and a change in the base sequence is a mutation. DNA fingerprinting uses the unique pattern of repeated sequences for identification.

Quick Facts to Remember

Pentoses: ribose, arabinose, xylose. Hexoses: glucose, galactose, mannose (aldoses) and fructose (ketose). Disaccharide formula \( \ce{C12H22O11} \). Sucrose, glucose and fructose: +66, +52, -92°. Zymase converts glucose to ethanol; invertase hydrolyses sucrose. Mutarotation needs a free anomeric hydroxyl group. Anomers differ at C-1, epimers at one other carbon. Glycosidic linkage is an acetal linkage. Cysteine contains the thiol group, and two cysteines form a disulfide bridge (cystine). Aspartame is the methyl ester of Asp-Phe.