Food Science & Technology · Foundations · also Biochemistry, Fundamentals of Biochemistry, Principles of Biochemistry
The structure of biomolecules and the metabolic pathways that turn food into energy and body tissue. Food chemistry (phase 2) describes how these molecules behave in a food; this subject explains how they behave in the body and in living raw materials such as respiring fruit and post-mortem muscle.
In the exams: ICAR AIEEA-PG Code 18 Unit I (metabolism of carbohydrates, lipids and protein; BV and PER)
Biochemistry is the chemistry of living things: the structures of the molecules that cells are made of, and the networks of enzyme-catalysed reactions that build, break down and convert them. For a food scientist it matters in two directions. Food is eaten, and biochemistry explains how its carbohydrates, fats and proteins are digested, absorbed and turned into energy and body tissue, why some proteins are worth more than others, and why vitamins are needed in milligram or microgram amounts. And food is made from living or recently living material: a harvested apple still respires, a carcass continues glycolysis for hours after slaughter, a wheat grain germinates, a cheese ripens through enzyme action. Understanding those living processes is the basis of post-harvest technology, meat science and fermentation.
This subject covers the structure of biomolecules; enzymes and their kinetics; coenzymes and the vitamins they come from; bioenergetics, ATP and the electron transport chain; the metabolism of carbohydrates, lipids and proteins, including the urea cycle and the measures of protein quality; nucleic acids and the flow of genetic information; hormonal regulation of metabolism; the biochemistry of post-harvest respiration and post-mortem muscle; and the laboratory techniques used to separate and measure biomolecules. Food chemistry explains how the same molecules behave in a food; this subject explains how they behave in a cell.
Biochemistry is examined in postgraduate entrance examinations in food science, which ask about metabolic pathways, enzyme kinetics and protein quality indices such as biological value and protein efficiency ratio; in life-science graduate entrance examinations; in university entrance tests in the biological sciences; and in teaching-eligibility and research-fellowship examinations in food science and nutrition. The questions with this manual follow those patterns and show working for each calculation.
Carbohydrates are polyhydroxy aldehydes or ketones and their polymers. Monosaccharides are classified by the number of carbons (trioses, pentoses, hexoses) and by their carbonyl group (aldoses such as glucose and galactose, ketoses such as fructose). In water, pentoses and hexoses exist mostly as five-membered (furanose) or six-membered (pyranose) rings, with α and β anomers at the new stereocentre. Monosaccharides join through glycosidic bonds to form disaccharides: sucrose (glucose α1→β2 fructose, non-reducing because both anomeric carbons are bound), lactose (galactose β1→4 glucose) and maltose (glucose α1→4 glucose), both reducing. Polysaccharides store energy or give structure: starch, with amylose (linear α1→4) and amylopectin (α1→4 with α1→6 branches), is the plant store; glycogen, more highly branched, is the animal store; cellulose, linear β1→4 glucose, forms plant cell walls and is not digested by human enzymes; chitin is the structural polymer of fungi and arthropods.
Lipids are biomolecules that dissolve in non-polar solvents. Fatty acids are carboxylic acids with long hydrocarbon chains, saturated or with cis double bonds; triacylglycerols, three fatty acids esterified to glycerol, are the main energy store, yielding about 37 kJ per gram. Phospholipids, such as phosphatidylcholine (lecithin), have two fatty acids and a phosphate-containing polar head, so they are amphipathic and form the bilayers of cell membranes. Sterols, such as cholesterol in animals and phytosterols in plants, are rigid ring structures that regulate membrane fluidity and are precursors of steroid hormones, bile acids and vitamin D. Waxes are esters of long-chain fatty acids and long-chain alcohols that protect fruit surfaces.
Proteins are polymers of 20 standard L-α-amino acids linked by peptide bonds. Each amino acid has an amino group, a carboxyl group and a side chain (R group) that classes it as non-polar (glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan), polar uncharged (serine, threonine, cysteine, asparagine, glutamine, tyrosine), acidic (aspartate, glutamate) or basic (lysine, arginine, histidine). At physiological pH amino acids are zwitterions, and each has an isoelectric point at which its net charge is zero. Protein structure is described at four levels: primary (the amino-acid sequence), secondary (α-helices and β-sheets held by backbone hydrogen bonds), tertiary (the folded three-dimensional shape, held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulphide bridges between cysteines) and quaternary (the assembly of several subunits, as in haemoglobin's four chains). Function depends on shape: denaturation by heat, acid, alkali, salts or solvents destroys the higher levels without breaking peptide bonds, which is why cooked egg white cannot be uncooked but its amino acids remain nutritionally available.
Nucleic acids are polymers of nucleotides, each made of a nitrogenous base, a pentose sugar and a phosphate. DNA contains deoxyribose and the bases adenine, guanine, cytosine and thymine; RNA contains ribose and uracil in place of thymine. Nucleotides are joined by 3′→5′ phosphodiester bonds into a strand with a direction. Nucleotides also act alone as energy carriers (ATP, GTP), in coenzymes (NAD⁺, FAD, coenzyme A) and as signals (cyclic AMP). In foods, nucleotides matter for flavour: inosine monophosphate and guanosine monophosphate give the savoury umami taste and act synergistically with glutamate, which is why they are used as flavour enhancers and why the breakdown of ATP in fish muscle is a measure of freshness (chapter 10).
Enzymes are biological catalysts, almost all proteins (some are catalytic RNAs), that speed reactions by factors often of millions or more without changing the equilibrium. The International Union of Biochemistry and Molecular Biology classifies them by the reaction catalysed into seven classes, each with an EC number: EC 1 oxidoreductases (dehydrogenases, oxidases such as polyphenol oxidase and glucose oxidase), EC 2 transferases (aminotransferases, kinases), EC 3 hydrolases (amylases, proteases, lipases, lactase), EC 4 lyases (pectate lyase, decarboxylases), EC 5 isomerases (glucose isomerase used to make high-fructose syrups), EC 6 ligases (synthetases that use ATP) and EC 7 translocases, added in 2018 for enzymes that move ions or molecules across membranes.
The substrate binds at the active site, a cleft formed by a few amino-acid residues. The lock-and-key model emphasised complementary shapes; the induced-fit model recognises that binding changes the enzyme's shape. Enzymes lower the activation energy by stabilising the transition state more than the substrate, by bringing reactants together in the right orientation, and by acid-base catalysis, covalent catalysis (as in the serine proteases) and metal-ion catalysis. Activity depends on temperature, rising until the enzyme begins to denature and then falling, and on pH, through the ionisation of active-site groups. Each enzyme has an apparent optimum that depends on the assay time and conditions. Food processing exploits both: blanching vegetables inactivates enzymes such as peroxidase, lipoxygenase and polyphenol oxidase that would otherwise cause off-flavours and browning in frozen storage, and peroxidase, one of the most heat-stable, is used as an indicator of adequate blanching.
For an enzyme E that binds substrate S to form a complex ES, which gives product P, the initial rate follows the Michaelis-Menten equation v = Vmax[S]/(Km + [S]). Vmax is the rate when the enzyme is saturated, and Km, the Michaelis constant, is the substrate concentration at which v = Vmax/2; a low Km means the enzyme reaches half its maximum rate at low substrate concentration (often read as high affinity). At [S] much less than Km, the rate is nearly proportional to [S] (first order); at [S] much greater than Km, it approaches Vmax (zero order). The turnover number kcat = Vmax/[E]total is the number of substrate molecules converted per active site per second, and kcat/Km measures catalytic efficiency. Because the curve is hyperbolic, the Lineweaver-Burk double-reciprocal plot, 1/v = (Km/Vmax)(1/[S]) + 1/Vmax, was traditionally used to estimate the constants: its y-intercept is 1/Vmax and its x-intercept is −1/Km. Non-linear regression on the untransformed data is now preferred because the reciprocal plot magnifies errors at low [S].
Reversible inhibitors are distinguished by their effect on the constants. A competitive inhibitor resembles the substrate and binds the active site: apparent Km increases, Vmax is unchanged, and on a Lineweaver-Burk plot the lines meet on the y-axis; high substrate overcomes it. A pure non-competitive inhibitor binds elsewhere equally well to E and ES: Vmax falls, Km is unchanged, and the lines meet on the x-axis. An uncompetitive inhibitor binds only ES: both Vmax and Km fall in proportion, giving parallel lines. Mixed inhibitors change both constants unequally. Irreversible inhibitors, such as organophosphorus compounds acting on acetylcholinesterase or heavy metals binding sulphydryl groups, inactivate the enzyme permanently. Allosteric enzymes, often with several subunits, give sigmoidal rather than hyperbolic curves and are regulated by molecules binding at sites other than the active site; feedback inhibition of the first committed step of a pathway by its end product is the common pattern.
Many enzymes need a non-protein partner, a cofactor, to work. The protein part alone is the apoenzyme; with its cofactor it is the holoenzyme. Cofactors are either metal ions or organic molecules called coenzymes; a coenzyme bound tightly or covalently is a prosthetic group. Most water-soluble vitamins are precursors of coenzymes, which is why they are needed only in small amounts: they are recycled, not consumed, in the reactions they serve.
Thiamine (vitamin B1) forms thiamine pyrophosphate, the coenzyme of oxidative decarboxylations (pyruvate dehydrogenase, α-ketoglutarate dehydrogenase) and of transketolase in the pentose phosphate pathway; deficiency causes beriberi, historically common where diets relied on polished rice. Riboflavin (B2) forms flavin mononucleotide and flavin adenine dinucleotide, carriers of hydrogen atoms in dehydrogenases and the electron transport chain. Niacin (B3) forms NAD⁺ and NADP⁺; NAD⁺ is the main electron acceptor in catabolism and NADPH the reductant of biosynthesis. Deficiency causes pellagra, historically common where maize was the staple without alkaline processing; niacin can also be made from tryptophan, about 60 mg of tryptophan giving 1 mg of niacin. Pantothenic acid (B5) is part of coenzyme A, the carrier of acyl groups. Pyridoxine (B6) forms pyridoxal phosphate, the coenzyme of transamination, amino-acid decarboxylation and glycogen phosphorylase. Biotin (B7) is the coenzyme of carboxylases (acetyl-CoA carboxylase, pyruvate carboxylase); the protein avidin in raw egg white binds biotin tightly, and cooking denatures it. Folate (B9) as tetrahydrofolate carries one-carbon units for nucleotide and amino-acid synthesis, and deficiency causes megaloblastic anaemia and, around conception, raises the risk of neural tube defects, the reason many countries fortify flour with folic acid. Cobalamin (B12) is needed by methylmalonyl-CoA mutase and methionine synthase; it is made only by microorganisms and is found naturally in animal foods, so people on vegan diets need fortified foods or supplements.
Several other vitamins have cofactor roles. Ascorbic acid (vitamin C) keeps the iron of prolyl and lysyl hydroxylases in the reduced state; these enzymes hydroxylate collagen, and their failure in deficiency gives the fragile capillaries, bleeding gums and poor wound healing of scurvy. Vitamin K is the cofactor of the carboxylase that converts glutamate residues of clotting factors into γ-carboxyglutamate, which binds calcium; without it blood clotting fails. Lipoic acid, not a vitamin for humans because it is synthesised, carries acyl groups and electrons in the pyruvate and α-ketoglutarate dehydrogenase complexes, which together need five cofactors: thiamine pyrophosphate, lipoic acid, coenzyme A, FAD and NAD⁺. Vitamins A, D and E act mainly as hormones, pigments or antioxidants rather than as enzyme cofactors: retinal is the light-sensitive pigment of vision, calcitriol (from vitamin D) regulates calcium absorption, and tocopherols protect membrane lipids from oxidation.
Metal ions serve as cofactors in perhaps a third of enzymes. Magnesium binds ATP in almost every kinase reaction. Zinc is the catalytic metal of carbonic anhydrase, alcohol dehydrogenase and carboxypeptidase, and it stabilises the structure of many other proteins. Iron and copper carry electrons in cytochromes and in cytochrome c oxidase; iron in haem also carries oxygen in haemoglobin and myoglobin. Selenium, as selenocysteine, is at the active site of glutathione peroxidase, which removes hydrogen peroxide and lipid hydroperoxides; molybdenum is the cofactor of xanthine oxidase; manganese is used by arginase and some superoxide dismutases. Food processing affects the supply of these cofactors: thiamine is lost in milling and destroyed by heat at neutral or alkaline pH and by sulphite; riboflavin is destroyed by light, which is why milk is packed in opaque containers; folate and vitamin C are lost by leaching and oxidation. The human-nutrition subject treats requirements and deficiency in detail.
Living cells run on the same thermodynamics as any chemical system: a reaction proceeds spontaneously only if its free-energy change ΔG is negative. Biochemists use the standard free-energy change at pH 7, ΔG°′, and the actual ΔG in the cell, which depends on concentrations: ΔG = ΔG°′ + RT ln([products]/[reactants]). An unfavourable reaction can be driven by coupling it to a favourable one through a shared intermediate, and the universal coupling agent is adenosine triphosphate. Hydrolysis of ATP to ADP and inorganic phosphate has ΔG°′ of about −30.5 kJ/mol, and under cellular conditions the actual ΔG is more negative, often around −50 kJ/mol. ATP is called a high-energy compound not because its bonds are unusually strong but because its hydrolysis products are more stable, through relief of charge repulsion, resonance stabilisation of phosphate and hydration.
ATP is made in two ways. Substrate-level phosphorylation transfers a phosphate directly from a compound with a higher phosphoryl-transfer potential, such as 1,3-bisphosphoglycerate and phosphoenolpyruvate in glycolysis, or uses the energy of succinyl-CoA in the TCA cycle. Oxidative phosphorylation, which supplies most ATP in aerobic cells, uses the energy released as electrons pass from NADH and FADH₂ to oxygen. Muscle also keeps a small reserve of phosphocreatine, which regenerates ATP within seconds through creatine kinase, a reserve that matters both in sprinting and in the first hours after slaughter (chapter 10). NAD⁺ and FAD carry electrons from fuel oxidation; NADP⁺ carries them into biosynthesis.
The electron transport chain, in the inner mitochondrial membrane of eukaryotes and the plasma membrane of aerobic bacteria, is a series of carriers of increasing reduction potential. NADH passes its electrons to complex I (NADH dehydrogenase); FADH₂ from succinate enters through complex II (succinate dehydrogenase), which is also a TCA-cycle enzyme. Both deliver electrons to ubiquinone (coenzyme Q), which carries them to complex III (cytochrome bc₁); cytochrome c carries them to complex IV (cytochrome c oxidase), which reduces oxygen to water. As electrons flow through complexes I, III and IV, protons are pumped from the matrix to the intermembrane space.
Peter Mitchell's chemiosmotic theory explains how this makes ATP: the proton gradient (the proton-motive force, combining a pH difference and a membrane potential) drives protons back through ATP synthase (sometimes called complex V), whose rotating mechanism synthesises ATP from ADP and phosphate. Current estimates give about 2.5 ATP per NADH and 1.5 per FADH₂ (the P/O ratio); older textbooks used 3 and 2, which is why the total yield of ATP from one glucose is given as about 30 to 32 in modern texts and 36 to 38 in older ones. Inhibitors and uncouplers show how tightly the steps are linked. Rotenone blocks complex I, antimycin A complex III, and cyanide, azide and carbon monoxide complex IV, stopping both electron flow and ATP synthesis. Oligomycin blocks ATP synthase, which also stops electron flow because the gradient cannot be dissipated. Uncouplers such as 2,4-dinitrophenol carry protons across the membrane, so electron flow continues at a high rate but the energy is released as heat; brown adipose tissue uses a natural uncoupling protein, thermogenin, to generate heat in newborn and cold-adapted mammals.
Glycolysis, in the cytosol of virtually all cells, converts one glucose into two pyruvate in ten steps. The first phase invests two ATP: hexokinase (glucokinase in liver) phosphorylates glucose to glucose 6-phosphate, which is isomerised to fructose 6-phosphate and phosphorylated again by phosphofructokinase-1 to fructose 1,6-bisphosphate; aldolase splits this into two triose phosphates. The second phase oxidises glyceraldehyde 3-phosphate, generating NADH, and makes four ATP by substrate-level phosphorylation (phosphoglycerate kinase and pyruvate kinase). The net yield is two ATP and two NADH per glucose. The three irreversible steps, catalysed by hexokinase, phosphofructokinase-1 and pyruvate kinase, are the control points; phosphofructokinase-1, activated by AMP and fructose 2,6-bisphosphate and inhibited by ATP and citrate, is the main one.
The fate of pyruvate depends on oxygen and the organism. With oxygen, it enters the mitochondrion and is oxidised by the pyruvate dehydrogenase complex to acetyl-CoA, CO₂ and NADH. Without oxygen, NADH must be reoxidised so that glycolysis can continue: animal muscle and lactic acid bacteria reduce pyruvate to lactate (lactate dehydrogenase), and yeast decarboxylates it to acetaldehyde and reduces that to ethanol (pyruvate decarboxylase and alcohol dehydrogenase), the basis of bread, beer and wine. Homofermentative lactic acid bacteria give mainly lactate; heterofermentative ones also give CO₂ and ethanol or acetate. The pentose phosphate pathway, branching from glucose 6-phosphate, produces NADPH for biosynthesis and ribose 5-phosphate for nucleotides.
The tricarboxylic acid (citric acid, Krebs) cycle in the mitochondrial matrix oxidises acetyl-CoA completely. Acetyl-CoA condenses with oxaloacetate to form citrate, which is isomerised to isocitrate and oxidatively decarboxylated twice (isocitrate dehydrogenase and α-ketoglutarate dehydrogenase) to succinyl-CoA; succinyl-CoA gives succinate and one GTP or ATP; succinate is oxidised to fumarate (FADH₂), fumarate hydrated to malate, and malate oxidised back to oxaloacetate. Each turn yields 3 NADH, 1 FADH₂, 1 GTP (or ATP) and 2 CO₂. The cycle is also a hub: its intermediates feed amino-acid, haem and fatty-acid synthesis, and anaplerotic reactions such as pyruvate carboxylase refill them. Commercially, citric acid for food use is produced by moulds that overflow this cycle.
Gluconeogenesis makes glucose from non-carbohydrate precursors, mainly in the liver and kidney, during fasting. It reverses glycolysis but bypasses the three irreversible steps: pyruvate carboxylase (biotin-dependent) and phosphoenolpyruvate carboxykinase convert pyruvate to phosphoenolpyruvate; fructose 1,6-bisphosphatase replaces phosphofructokinase-1; and glucose 6-phosphatase releases free glucose. The precursors are lactate (returned from muscle in the Cori cycle), glycerol from triacylglycerols, and the carbon skeletons of glucogenic amino acids such as alanine; even-chain fatty acids cannot give net glucose in animals because the two carbons of acetyl-CoA are lost as CO₂ in the TCA cycle.
Glycogen is stored mainly in liver and muscle. Glycogen synthase adds glucose from UDP-glucose by α1→4 bonds and a branching enzyme forms α1→6 branches; glycogen phosphorylase, with pyridoxal phosphate, releases glucose 1-phosphate, and a debranching enzyme removes the branches. Liver glycogen maintains blood glucose because the liver has glucose 6-phosphatase; muscle lacks it, so muscle glycogen fuels only the muscle itself, a fact central to post-mortem glycolysis.
Fatty acids released from triacylglycerols by lipases are the richest fuel. In the cytosol they are activated to fatty acyl-CoA by acyl-CoA synthetase, at the cost of two high-energy phosphate bonds (ATP → AMP + PPi). Long-chain acyl groups enter the mitochondrion by the carnitine shuttle: carnitine palmitoyltransferase I on the outer membrane, the rate-controlling step, transfers the acyl group to carnitine, and carnitine palmitoyltransferase II restores acyl-CoA inside. Malonyl-CoA, the first intermediate of fatty-acid synthesis, inhibits carnitine palmitoyltransferase I, so synthesis and oxidation do not run at the same time.
Each round of β-oxidation removes two carbons as acetyl-CoA in four steps: oxidation by acyl-CoA dehydrogenase (FADH₂), hydration, oxidation by a dehydrogenase (NADH) and thiolytic cleavage. Palmitate (C16) needs seven rounds, giving 8 acetyl-CoA, 7 FADH₂ and 7 NADH. With modern P/O ratios, the 8 acetyl-CoA give 80 ATP through the TCA cycle and oxidative phosphorylation, 7 FADH₂ give 10.5 and 7 NADH give 17.5, a total of 108, less 2 for activation: 106 ATP per palmitate. Unsaturated fatty acids need an isomerase (and for some double bonds a reductase); odd-chain fatty acids leave a final propionyl-CoA, which is converted via methylmalonyl-CoA (a vitamin B12-dependent step) into succinyl-CoA, a glucogenic product. Very-long-chain fatty acids are first shortened in peroxisomes.
When fatty-acid oxidation in the liver outpaces the TCA cycle, as in prolonged fasting, very-low-carbohydrate diets or uncontrolled type 1 diabetes, acetyl-CoA is diverted into ketone bodies: acetoacetate, β-hydroxybutyrate and acetone. Heart, muscle and, after adaptation, brain use acetoacetate and β-hydroxybutyrate as fuels; in excess they cause ketoacidosis. In dairy cattle, ketosis in early lactation reflects the same imbalance.
Fatty-acid synthesis takes place in the cytosol, mainly in liver, adipose tissue and the lactating mammary gland, when energy and carbohydrate are plentiful. Acetyl-CoA formed in mitochondria leaves as citrate and is regenerated in the cytosol by ATP-citrate lyase. Acetyl-CoA carboxylase, a biotin enzyme, carboxylates acetyl-CoA to malonyl-CoA; this is the committed and main regulated step, activated by citrate and insulin and inhibited by long-chain acyl-CoA, glucagon and adrenaline. The multifunctional fatty-acid synthase then builds the chain two carbons at a time from malonyl-CoA, releasing CO₂ at each condensation and using two NADPH per cycle, until palmitate (C16:0) is released. Making one palmitate needs 7 malonyl-CoA (7 ATP) and 14 NADPH, the NADPH coming from the pentose phosphate pathway and malic enzyme. Longer chains are made by elongases in the endoplasmic reticulum, and desaturases introduce cis double bonds.
Mammals can insert double bonds at Δ9 (making oleic acid from stearic acid) but not beyond Δ9 towards the methyl end, so they cannot make linoleic acid (C18:2 n−6) or α-linolenic acid (C18:3 n−3). These two are the essential fatty acids and must come from the diet; from them the body makes longer, more unsaturated fatty acids, arachidonic acid from linoleic acid and, less efficiently, eicosapentaenoic and docosahexaenoic acids from α-linolenic acid, the precursors of eicosanoid signalling molecules. Fish and algal oils supply the long-chain n−3 acids directly. The fat of ruminant milk and meat has a distinctive composition because rumen microbes hydrogenate dietary unsaturated fatty acids, producing saturated and trans fatty acids including conjugated linoleic acid, and because the mammary gland synthesises short- and medium-chain fatty acids such as butyric acid, a marker of milk fat. Cholesterol is synthesised from acetyl-CoA through HMG-CoA, and HMG-CoA reductase, the rate-limiting enzyme, is the target of the statin drugs.
Body proteins are continuously broken down and resynthesised, and dietary amino acids beyond the needs of synthesis are used as fuel or converted to glucose or fat; the body has no protein store comparable to glycogen or fat. The first step in catabolism of most amino acids is transamination: an aminotransferase, with pyridoxal phosphate, transfers the amino group to α-ketoglutarate, forming glutamate and the corresponding α-keto acid. Alanine aminotransferase and aspartate aminotransferase are the best known; their activity in blood is a clinical marker of liver or muscle damage. Glutamate is then oxidatively deaminated in liver mitochondria by glutamate dehydrogenase, releasing ammonia and regenerating α-ketoglutarate.
Ammonia is toxic, and terrestrial mammals convert it into urea in the liver. In the urea cycle, carbamoyl phosphate synthetase I in the mitochondria combines ammonia, bicarbonate and two ATP into carbamoyl phosphate; this step is activated by N-acetylglutamate. Ornithine transcarbamoylase transfers the carbamoyl group to ornithine, forming citrulline, which moves to the cytosol. Argininosuccinate synthetase condenses citrulline with aspartate (using ATP → AMP + PPi), argininosuccinate lyase splits the product into arginine and fumarate, and arginase hydrolyses arginine into urea and ornithine. Each urea carries two nitrogens, one from ammonia and one from aspartate, and its synthesis uses four high-energy phosphate bonds. Fish excrete ammonia directly and birds and reptiles uric acid. The carbon skeletons left after deamination are glucogenic (yielding pyruvate or TCA intermediates) or ketogenic (yielding acetyl-CoA or acetoacetate); leucine and lysine are purely ketogenic, and several, such as phenylalanine, tyrosine, isoleucine and tryptophan, are both. Amino acids are also precursors of important molecules: tyrosine of catecholamines and melanin, tryptophan of serotonin and niacin, histidine of histamine, glycine of haem and creatine, and arginine of nitric oxide.
Nine amino acids cannot be synthesised by humans in adequate amounts and are essential (indispensable): histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Others, such as arginine, cysteine and tyrosine, are conditionally essential in some life stages or diseases. The nutritional quality of a dietary protein therefore depends on how well its essential amino-acid pattern matches human needs and on how much of it is digested. Cereal proteins are limited mainly by lysine and legume proteins by the sulphur amino acids (methionine and cysteine), so a mixture of the two complements each other, the basis of traditional cereal-legume combinations on several continents.
Nitrogen balance studies give the classic indices. Biological value (BV) is the percentage of absorbed nitrogen that is retained in the body: BV = retained N/absorbed N × 100, where absorbed N = intake − (faecal N − endogenous faecal N) and retained N = absorbed N − (urinary N − endogenous urinary N). Whole egg protein has one of the highest biological values and has served as a reference. Net protein utilisation (NPU) is the percentage of nitrogen intake that is retained, NPU = BV × true digestibility. The protein efficiency ratio (PER), measured in growing rats, is the weight gain divided by the protein eaten over a standard period, usually with a 10 per cent protein diet; results are often adjusted to a casein reference value of 2.5 because PER varies between laboratories. For example, rats that gain 60 g while eating 25 g of protein give a PER of 2.4. Because rat growth needs differ from human needs, international expert bodies replaced PER with amino-acid scores corrected for digestibility: the protein digestibility-corrected amino acid score (PDCAAS), the limiting amino acid ratio multiplied by faecal protein digestibility and capped at 1.0, and, recommended by FAO in 2013, the digestible indispensable amino acid score (DIAAS), which uses true ileal digestibility of each amino acid and is not capped. Processing affects these indices: heat damage and the Maillard reaction reduce available lysine, while inactivating trypsin inhibitors in legumes improves digestibility.
DNA is a double helix of two antiparallel strands held together by hydrogen bonds between complementary bases: adenine pairs with thymine through two hydrogen bonds, and guanine with cytosine through three. Chargaff's rules follow: the amount of A equals T and G equals C, so a DNA with 20 per cent adenine has 20 per cent thymine and 30 per cent each of guanine and cytosine. Because G-C pairs are held by three hydrogen bonds and stack more strongly, DNA with more G + C has a higher melting temperature. The B form of DNA, the common one in cells, is a right-handed helix with about 10.5 base pairs per turn and major and minor grooves. Prokaryotes usually have a single circular chromosome plus plasmids; eukaryotes package linear DNA with histones into chromatin in the nucleus, with smaller genomes in mitochondria and chloroplasts.
Replication is semi-conservative, as Meselson and Stahl showed: each new double helix has one old and one new strand. Helicase unwinds the helix, single-strand binding proteins keep it open, and topoisomerases relieve the twisting ahead of the fork. DNA polymerases add nucleotides only to a 3′ end, so synthesis runs 5′→3′, and they need a primer, laid down as short RNA by primase. The leading strand is made continuously towards the fork; the lagging strand is made discontinuously as Okazaki fragments, whose primers are removed and gaps filled and sealed by DNA ligase. Proofreading by the polymerase's 3′→5′ exonuclease activity and later mismatch repair keep the error rate very low. The polymerase chain reaction (PCR) copies this process in a tube with a heat-stable polymerase, cycling between denaturation, primer annealing and extension, so that a target sequence doubles each cycle; it is the basis of the detection of genetically modified material, species identification of meat and fish, and rapid detection of pathogens in food.
In transcription, RNA polymerase copies one DNA strand (the template) into RNA, starting at a promoter and running 5′→3′; the RNA has the same sequence as the other, coding strand, with U in place of T. Bacteria use one RNA polymerase with a sigma factor that recognises promoters; eukaryotes have three, with RNA polymerase II making messenger RNA. In eukaryotes the primary transcript is processed: a 5′ cap and a 3′ poly(A) tail are added, and introns are removed by splicing, leaving the exons. Ribosomal RNA and transfer RNA are also transcripts, and they do the work of translation.
The genetic code is read in non-overlapping triplets, codons, from a fixed starting point. Of the 64 codons, 61 specify amino acids and three (UAA, UAG, UGA) are stop signals; AUG codes for methionine and is the usual start codon. The code is degenerate (most amino acids have several codons, often differing in the third base, which allows wobble pairing with tRNA anticodons) and nearly universal, with a few exceptions in mitochondria and some microbes. Transfer RNAs carry amino acids, attached by aminoacyl-tRNA synthetases that check both partners; the anticodon of each tRNA pairs with a codon of the mRNA on the ribosome. Ribosomes are 70S in bacteria (50S and 30S subunits) and 80S in the eukaryotic cytosol (60S and 40S); the ribosomal RNA catalyses peptide-bond formation. Translation proceeds through initiation, elongation (with GTP-using elongation factors) and termination at a stop codon. Many antibiotics act on the bacterial ribosome. Gene expression is regulated mainly at transcription: in the lac operon of Escherichia coli, the repressor blocks transcription of the lactose-using genes unless lactose (as allolactose) is present, and glucose further reduces their expression through catabolite repression, a model for how fermentation organisms switch between sugars. Changes in DNA sequence (mutations) may be silent, missense or nonsense, and recombinant DNA technology, treated in the fermentation and biotechnology subject, uses these mechanisms to make enzymes and ingredients.
Metabolism in a multicellular animal is coordinated by hormones that tell each tissue whether fuel is plentiful or scarce. After a meal, rising blood glucose stimulates the β cells of the pancreatic islets to secrete insulin. Insulin acts through a receptor tyrosine kinase and a cascade of protein kinases and phosphatases. In muscle and adipose tissue it moves the GLUT4 glucose transporter to the cell surface, increasing glucose uptake; in liver and muscle it activates glycogen synthase and inhibits glycogen phosphorylase; in liver it promotes glycolysis and fatty-acid synthesis (through acetyl-CoA carboxylase) and suppresses gluconeogenesis; in adipose tissue it promotes triacylglycerol storage and inhibits lipolysis; and it promotes protein synthesis. Insulin is the hormone of storage.
Between meals and in fasting, falling glucose stimulates the α cells to secrete glucagon. Glucagon acts mainly on the liver through a G-protein-coupled receptor that activates adenylate cyclase; the second messenger cyclic AMP activates protein kinase A, which phosphorylates key enzymes, activating glycogen phosphorylase and inhibiting glycogen synthase, and lowering fructose 2,6-bisphosphate so that gluconeogenesis is favoured over glycolysis. Glucagon also promotes fatty-acid oxidation and ketone-body formation. The ratio of insulin to glucagon, rather than either hormone alone, sets the direction of liver metabolism. In diabetes mellitus this control fails: in type 1 diabetes insulin is not produced, and in type 2 diabetes tissues respond poorly to insulin; either way, blood glucose rises and, in type 1 without treatment, fat breakdown runs unchecked and ketoacidosis can develop. The glycaemic index of foods, a ranking of how much a portion of available carbohydrate raises blood glucose compared with a reference, reflects how quickly glucose reaches the blood and hence the insulin demand.
Adrenaline (epinephrine) from the adrenal medulla and noradrenaline from sympathetic nerves prepare the body for sudden activity. Through β-adrenergic receptors and cyclic AMP they activate glycogen breakdown in muscle and liver and lipolysis in adipose tissue (through hormone-sensitive lipase), raising blood glucose and fatty acids within seconds. Cortisol from the adrenal cortex acts over hours to days through nuclear receptors that change gene transcription: it promotes gluconeogenesis, the breakdown of muscle protein to supply amino acids, and fat mobilisation, which is why chronic stress or steroid treatment causes muscle wasting and high blood glucose. Thyroid hormones (thyroxine and triiodothyronine), whose synthesis needs iodine, raise the basal metabolic rate and are essential for growth and brain development; iodine deficiency causes goitre and, in pregnancy, impaired development of the child, the reason for salt iodisation programmes in many countries. Growth hormone promotes protein synthesis and fat mobilisation.
Appetite and long-term energy balance are signalled by hormones from the gut and fat tissue. Leptin, secreted by adipose tissue in proportion to fat mass, signals to the hypothalamus that energy stores are adequate and suppresses appetite; ghrelin, secreted by the empty stomach, stimulates it. Gut hormones such as cholecystokinin, peptide YY and glucagon-like peptide-1 reduce appetite after a meal and, in the case of glucagon-like peptide-1, enhance insulin secretion.
Hormonal state before slaughter has direct consequences for meat quality. Stress in the hours or days before slaughter, from transport, mixing of unfamiliar animals, fasting or rough handling, releases adrenaline and cortisol that deplete muscle glycogen. With little glycogen left, post-mortem glycolysis produces little lactic acid, the ultimate pH stays high and the meat is dark, firm and dry; acute stress immediately before slaughter, by contrast, can accelerate post-mortem glycolysis while the carcass is still hot, contributing to pale, soft, exudative pork. Good animal handling is therefore both a welfare and a quality requirement.
A harvested fruit or vegetable is still alive. Cut off from the plant, it respires its stored sugars, organic acids and sometimes fats through glycolysis, the TCA cycle and oxidative phosphorylation, consuming oxygen, releasing carbon dioxide, water and heat, and slowly using up the reserves that give it flavour and texture. The respiration rate, measured as oxygen uptake or carbon dioxide output per kilogram per hour, roughly predicts perishability: asparagus, broccoli and mushrooms respire fast and deteriorate quickly, while potatoes, onions and nuts respire slowly. Respiration rises steeply with temperature, typically two- to threefold for each 10 °C rise in the storage range, which is why rapid cooling after harvest is the first rule of post-harvest handling. The respiratory quotient, RQ = CO₂ produced/O₂ consumed, indicates the substrate: about 1.0 for sugars, about 0.7 for fats and above 1 for organic acids (about 1.33 for malic acid). When oxygen falls too low, as in an over-sealed pack or a badly controlled atmosphere store, respiration becomes anaerobic: CO₂ output rises relative to O₂ uptake (RQ climbs well above 1), and ethanol and acetaldehyde accumulate, causing off-flavours.
Fruits are classed by their ripening behaviour. Climacteric fruits, such as apple, banana, mango, tomato, avocado and pear, show a burst of respiration and of ethylene production at the onset of ripening and can be harvested mature but unripe and ripened later. Non-climacteric fruits, such as citrus, grape, strawberry, pineapple and cherry, show no such burst and do not improve after harvest. Ethylene, the ripening hormone, is synthesised from methionine via S-adenosylmethionine and 1-aminocyclopropane-1-carboxylic acid (ACC); ACC synthase is usually the rate-limiting enzyme, and ACC oxidase, which needs oxygen, makes ethylene. Ripening involves cell-wall softening by pectin-degrading enzymes, conversion of starch to sugars, loss of acids and chlorophyll, and synthesis of carotenoids, anthocyanins and aroma volatiles. Storage technologies act on these processes: low temperature; controlled or modified atmospheres with less oxygen and more carbon dioxide, which slow respiration and ethylene action; ethylene scrubbing; and 1-methylcyclopropene, which blocks ethylene receptors. Not all post-harvest changes are ripening: sweet corn and peas lose sweetness as sugars are converted to starch, and potatoes stored too cold accumulate reducing sugars (cold sweetening), which darken and form acrylamide when fried.
In living muscle, oxygen delivered by the blood lets mitochondria regenerate ATP efficiently. At slaughter, circulation stops, oxygen in the muscle is quickly used up, and the cells continue to make ATP anaerobically, first from phosphocreatine and then by glycolysis of muscle glycogen to lactic acid. Because the lactate cannot be removed, the muscle pH falls, typically from about 7.0 to an ultimate pH of about 5.4 to 5.8 in well-rested cattle, sheep and pigs, over several hours to a day. As ATP runs out, the myosin heads bind actin permanently, and the muscle becomes stiff and inextensible: rigor mortis. Over the following days, endogenous proteases, chiefly the calcium-activated calpains (with cathepsins playing a smaller part), degrade structural proteins of the myofibril such as desmin and titin, and the meat becomes more tender; this is the basis of ageing (conditioning) of beef.
The rate and extent of pH fall decide much of meat quality. A low ultimate pH near the isoelectric point of myofibrillar proteins (about 5.0 to 5.5) gives lower water-holding capacity than a higher pH. If glycolysis is too fast while the carcass is still warm, as in pigs carrying a mutation of the ryanodine receptor (the halothane gene) or stressed just before slaughter, the combination of low pH and high temperature denatures proteins, giving pale, soft, exudative (PSE) meat. If glycogen was depleted before slaughter, the pH stays high (above about 6.0) and the meat is dark, firm and dry (DFD), with good water-holding but poor keeping quality, because bacteria grow faster at high pH. If muscle is chilled below about 10 to 15 °C before rigor, while ATP is still present, calcium released from the sarcoplasmic reticulum makes it contract strongly (cold shortening), making it tough; electrical stimulation of carcasses speeds glycolysis so that rapid chilling can be used safely. Fish muscle has less glycogen and a higher ultimate pH (often 6.2 to 6.6) and spoils faster. The breakdown of ATP in fish continues after death, ATP → ADP → AMP → IMP → inosine → hypoxanthine, and the K value, (inosine + hypoxanthine) as a percentage of all these compounds, is a freshness index: IMP contributes pleasant savoury taste, hypoxanthine a bitter one.
Centrifugation separates particles by their rate of sedimentation in a centrifugal field. The force is expressed as relative centrifugal force (RCF), in multiples of gravity: RCF = 1.118 × 10⁻⁵ × r × N², with r the radius in centimetres and N the speed in revolutions per minute. A rotor of 10 cm radius at 10 000 rpm gives about 11 200 × g. Because RCF depends on the radius, methods should state × g rather than rpm. Differential centrifugation spins a homogenate at increasing forces to pellet nuclei, then mitochondria, then microsomes. Density-gradient centrifugation separates particles in a gradient of sucrose (rate-zonal, by size and shape) or caesium chloride (isopycnic, by buoyant density, as used to separate DNA strands of different density in the Meselson-Stahl experiment). Sedimentation coefficients are given in Svedberg units (S), which are not additive, so the 70S ribosome has 50S and 30S subunits. In the food industry the same physics separates cream from skim milk, clarifies juices and removes yeast from beer.
Electrophoresis separates charged molecules in an electric field. In sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), proteins are denatured and coated with the anionic detergent SDS, which gives them a roughly uniform charge-to-mass ratio, and a reducing agent such as 2-mercaptoethanol or dithiothreitol breaks disulphide bonds; the polyacrylamide gel then sieves them by size, so mobility depends on molecular mass, which is estimated from standards. Native PAGE keeps proteins folded and separates by charge, size and shape. Isoelectric focusing separates proteins by their isoelectric point in a pH gradient; combining it with SDS-PAGE gives two-dimensional electrophoresis, the original tool of proteomics. Agarose gels separate DNA fragments by size. Electrophoresis is used in food science to identify species in meat and fish, to detect adulteration of milk from different species, to study proteolysis during cheese ripening, and, followed by antibody detection (Western blotting), to identify allergens.
Spectrophotometry measures how much light of a chosen wavelength a solution absorbs. The Beer-Lambert law states that absorbance is proportional to concentration and path length: A = εcl, where ε is the molar absorption coefficient, c the concentration and l the path length, usually 1 cm. Absorbance is related to transmittance T by A = −log₁₀T, so a solution transmitting 10 per cent of the light has A = 1. The law holds best at low absorbance, and readings are kept within the instrument's linear range by dilution. Proteins absorb at 280 nm, mainly because of tryptophan and tyrosine, and nucleic acids at 260 nm; the ratio A260/A280 is about 1.8 for pure DNA and about 2.0 for pure RNA, and lower values indicate protein contamination. NADH absorbs at 340 nm (ε = 6220 L mol⁻¹ cm⁻¹) while NAD⁺ does not, so many enzyme assays, including enzymatic kits for glucose, lactate, ethanol and other food constituents, follow the change in absorbance at 340 nm. For example, a rise of 0.311 in absorbance at 340 nm in a 1 cm cuvette corresponds to 0.311/6220 = 5.0 × 10⁻⁵ mol/L of NADH formed.
Colorimetric protein assays convert protein into a coloured product read against a standard curve, usually of bovine serum albumin: the biuret method (copper complexes of peptide bonds), the Lowry method (biuret plus the Folin reagent reacting with tyrosine and tryptophan), the bicinchoninic acid method, and the Bradford method, in which Coomassie Brilliant Blue G-250 binds protein and shifts its absorbance maximum to 595 nm. Each responds differently to different proteins and interfering substances, so the method must be stated. Total protein in foods for labelling is usually measured as nitrogen (Kjeldahl or Dumas) times a conversion factor, as covered in food analysis. Chromatography completes the biochemist's toolkit: gel filtration separates by size, ion exchange by charge, and affinity chromatography by specific binding, and these are used to purify enzymes and proteins in the steps of biochemical research.
A student uses biochemistry to understand why the later subjects work: why lactic acid bacteria acidify milk, why blanching is checked by a peroxidase test, why a cereal-legume blend has better protein quality, why apples are stored in low oxygen and why carcasses are not chilled too fast. Laboratory classes add practical skills: running enzyme assays at 340 nm, preparing standard curves, reading SDS-PAGE gels and calculating relative centrifugal force. In examinations, the pathway diagrams, ATP yields, inhibition patterns and BV/PER formulas carry many marks.
Five years in, a technologist uses this knowledge on real problems: choosing an enzyme preparation and its dose from Km and optimum data; validating blanching by enzyme tests; diagnosing PSE or DFD meat from pH records; setting controlled-atmosphere conditions from respiration and RQ data; interpreting a supplier's protein-quality claims; and using enzymatic kits and electrophoresis in quality control and species identification.
A senior technical manager with twenty-five years' experience applies biochemistry to strategy: approving handling standards that protect meat quality and animal welfare, deciding on cold-chain and ripening-room investment for fresh produce, judging protein-quality and health claims for new products, and evaluating enzyme and fermentation technologies offered by suppliers. They also explain the biochemical basis of quality problems to non-specialist managers.
A researcher at this level works on the biochemistry of food raw materials and human metabolism: regulation of ripening and senescence, proteolysis and tenderisation, enzyme engineering for processing aids, metabolomic responses to diets, and amino-acid digestibility for protein-quality scoring. They design experiments with appropriate enzyme kinetics and controls and critically assess models of nutrient metabolism.
This manual covers general biochemistry for food scientists. It does not cover photosynthesis, nitrogen fixation, membrane transport in detail, signal-transduction networks beyond the hormones named, immunology, or the molecular genetics of gene regulation in eukaryotes; recombinant DNA methods are in fermentation-food-biotechnology. Nutrient requirements and deficiency are in human-nutrition, and food enzymes as ingredients in food-chemistry-minor-constituents-enzymes. ATP yields are given with modern P/O ratios and the older values noted; ultimate pH and other meat values are typical ranges and differ by species, muscle and handling.
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