Tamil Nadu HSE First Year Biochemistry cheat sheet

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.

Nucleotides consist of a nitrogenous base, a pentose sugar (ribose in RNA, deoxyribose in DNA) and one or more phosphate groups; nucleoside = base + sugar.

Bases: purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine in DNA, uracil in RNA) are single-ringed; base pairing is A=T (two hydrogen bonds) and G≡C (three hydrogen bonds).

DNA is a double helix with antiparallel strands, sugar-phosphate backbones outside and bases inside; the two strands are complementary and the helix shows major and minor grooves (Watson-Crick model).

Chargaff's rules: in double-stranded DNA, A = T and G = C, so (A+G) = (T+C); the GC content correlates with helix stability and melting temperature.

RNA types: messenger RNA (carries the code), transfer RNA (adapter delivering amino acids; has anticodon and CCA end), ribosomal RNA (part of the ribosome) and heterogeneous/ncRNA.

DNA replication is semi-conservative: helicase unwinds, DNA polymerase synthesises 5' to 3' with a primer, leading strand is continuous and lagging strand forms Okazaki fragments joined by ligase.

Transcription makes RNA from a DNA template using RNA polymerase; in eukaryotes introns are spliced out and exons joined; translation at the ribosome uses codons read 5' to 3' against tRNA anticodons.

The genetic code is triplet, degenerate, non-overlapping and nearly universal; AUG codes methionine and is the start codon; UAA, UAG and UGA are stop codons.

Mutations: substitution (missense, nonsense, silent), insertion or deletion causing frameshift; the central dogma is DNA to RNA to protein, with reverse transcription as an exception in retroviruses.

Vitamins are organic micronutrients required in small amounts that the body cannot synthesise adequately; they are classified as fat-soluble (A, D, E, K) and water-soluble (B-complex and C).

Fat-soluble vitamins are absorbed with dietary fat and stored in the liver; excess intake can cause toxicity (hypervitaminosis A and D), whereas water-soluble vitamins are excreted in urine and rarely toxic.

Coenzyme forms: thiamine (B1) gives thiamine pyrophosphate (TPP) for decarboxylation; riboflavin (B2) gives FAD and FMN; niacin (B3) gives NAD+ and NADP+; pantothenic acid (B5) gives coenzyme A.

Pyridoxal phosphate from vitamin B6 is the coenzyme for transamination and decarboxylation of amino acids; biotin (B7) is the coenzyme for carboxylation reactions; cobalamin (B12) is needed for methylmalonyl-CoA mutase and methionine synthase.

Deficiency diseases: beriberi (B1), cheilosis and ariboflavinosis (B2), pellagra - dermatitis, diarrhoea, dementia (niacin), pernicious anaemia (B12), megaloblastic anaemia (folate), scurvy (vitamin C), rickets (vitamin D), night blindness (vitamin A).

Vitamin C (ascorbic acid) is a water-soluble antioxidant and cofactor for prolyl and lysyl hydroxylases in collagen synthesis; deficiency causes bleeding gums, poor wound healing and scurvy.

Vitamin A as retinal is required for the visual cycle in rhodopsin; vitamin K is required for gamma-carboxylation of glutamate residues in clotting factors II, VII, IX and X; vitamin E is a lipid-soluble antioxidant.

Minerals: macrominerals (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, Cu, I, Se, Mn, F); iron is in haemoglobin and cytochromes, iodine in thyroid hormones, zinc in carbonic anhydrase and DNA-binding proteins, selenium in glutathione peroxidase.

Calcium and phosphorus are stored in bone; parathyroid hormone raises plasma calcium, calcitonin lowers it, and vitamin D (calcitriol) increases intestinal calcium absorption.

Bioenergetics studies energy transformations in cells; ATP is the universal energy currency, hydrolysis of its terminal phosphate releasing about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions.

Free energy change: delta-G = delta-H - T delta-S; a reaction is spontaneous when delta-G is negative; reactions with positive delta-G are coupled to ATP hydrolysis to proceed.

Glycolysis (cytoplasm): glucose to 2 pyruvate, net gain 2 ATP and 2 NADH; key regulated enzymes are hexokinase, phosphofructokinase-1 and pyruvate kinase; anaerobic pyruvate is reduced to lactate.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA (yielding NADH and CO2); the citric acid cycle oxidises acetyl-CoA to 2 CO2, 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxidative phosphorylation: electrons pass from NADH and FADH2 through the respiratory chain to oxygen, pumping protons and generating a gradient used by ATP synthase; about 2.5 ATP per NADH and 1.5 ATP per FADH2.

Gluconeogenesis (mainly liver and kidney) makes glucose from lactate, glycerol and amino acids; it uses pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to bypass irreversible glycolytic steps.

Glycogen metabolism: glycogenesis uses glycogen synthase and branching enzyme; glycogenolysis uses glycogen phosphorylase and debranching enzyme; blood glucose is maintained by glycogenolysis and gluconeogenesis under glucagon and adrenaline.

Beta-oxidation of fatty acids in mitochondria removes two carbons per cycle as acetyl-CoA, generating NADH and FADH2; ketone bodies (acetoacetate, beta-hydroxybutyrate, acetone) form during fasting or uncontrolled diabetes.

Reference (normal) ranges are age- and method-dependent; typical adult values: fasting plasma glucose 70-110 mg/dL, total cholesterol below 200 mg/dL, serum creatinine about 0.6-1.2 mg/dL, total protein 6-8 g/dL.

Diabetes mellitus diagnosis relies on fasting glucose at or above 126 mg/dL on two occasions, random glucose at or above 200 mg/dL with symptoms, or an abnormal oral glucose tolerance test; glycated haemoglobin reflects 2-3 months of glycaemic control.

Liver function tests: serum bilirubin, ALT and AST (raised in hepatocellular damage), alkaline phosphatase and gamma-glutamyl transferase (raised in biliary obstruction), albumin and total protein for synthetic capacity.

Kidney function: blood urea and serum creatinine rise in renal impairment; creatinine clearance estimates glomerular filtration rate; urine analysis for protein, glucose, ketones, blood and pH is a basic screen.

Lipid profile: total cholesterol, HDL and LDL cholesterol and triglycerides; LDL is calculated by the Friedewald formula (LDL = total - HDL - triglycerides/5) when triglycerides are below 400 mg/dL.

Colorimetry is based on Beer-Lambert law, A = epsilon times c times l: absorbance is proportional to concentration and path length; a standard curve converts absorbance to concentration.

Chromatography separates by differential distribution between mobile and stationary phases (paper, thin-layer, column, ion-exchange, gel filtration, affinity); electrophoresis separates charged molecules by charge-to-mass ratio.

Centrifugation separates by density and size; spectrophotometry, flame photometry (Na, K, Li) and immunoassays (ELISA, radioimmunoassay) are standard clinical measurement techniques.

Quality control uses normal and abnormal control sera to monitor precision and accuracy; pre-analytical errors such as haemolysis, delayed separation or wrong anticoagulant are common causes of invalid results.

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.

Nucleotides consist of a nitrogenous base, a pentose sugar (ribose in RNA, deoxyribose in DNA) and one or more phosphate groups; nucleoside = base + sugar.

Bases: purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine in DNA, uracil in RNA) are single-ringed; base pairing is A=T (two hydrogen bonds) and G≡C (three hydrogen bonds).

DNA is a double helix with antiparallel strands, sugar-phosphate backbones outside and bases inside; the two strands are complementary and the helix shows major and minor grooves (Watson-Crick model).

Chargaff's rules: in double-stranded DNA, A = T and G = C, so (A+G) = (T+C); the GC content correlates with helix stability and melting temperature.

RNA types: messenger RNA (carries the code), transfer RNA (adapter delivering amino acids; has anticodon and CCA end), ribosomal RNA (part of the ribosome) and heterogeneous/ncRNA.

DNA replication is semi-conservative: helicase unwinds, DNA polymerase synthesises 5' to 3' with a primer, leading strand is continuous and lagging strand forms Okazaki fragments joined by ligase.

Transcription makes RNA from a DNA template using RNA polymerase; in eukaryotes introns are spliced out and exons joined; translation at the ribosome uses codons read 5' to 3' against tRNA anticodons.

The genetic code is triplet, degenerate, non-overlapping and nearly universal; AUG codes methionine and is the start codon; UAA, UAG and UGA are stop codons.

Mutations: substitution (missense, nonsense, silent), insertion or deletion causing frameshift; the central dogma is DNA to RNA to protein, with reverse transcription as an exception in retroviruses.

Vitamins are organic micronutrients required in small amounts that the body cannot synthesise adequately; they are classified as fat-soluble (A, D, E, K) and water-soluble (B-complex and C).

Fat-soluble vitamins are absorbed with dietary fat and stored in the liver; excess intake can cause toxicity (hypervitaminosis A and D), whereas water-soluble vitamins are excreted in urine and rarely toxic.

Coenzyme forms: thiamine (B1) gives thiamine pyrophosphate (TPP) for decarboxylation; riboflavin (B2) gives FAD and FMN; niacin (B3) gives NAD+ and NADP+; pantothenic acid (B5) gives coenzyme A.

Pyridoxal phosphate from vitamin B6 is the coenzyme for transamination and decarboxylation of amino acids; biotin (B7) is the coenzyme for carboxylation reactions; cobalamin (B12) is needed for methylmalonyl-CoA mutase and methionine synthase.

Deficiency diseases: beriberi (B1), cheilosis and ariboflavinosis (B2), pellagra - dermatitis, diarrhoea, dementia (niacin), pernicious anaemia (B12), megaloblastic anaemia (folate), scurvy (vitamin C), rickets (vitamin D), night blindness (vitamin A).

Vitamin C (ascorbic acid) is a water-soluble antioxidant and cofactor for prolyl and lysyl hydroxylases in collagen synthesis; deficiency causes bleeding gums, poor wound healing and scurvy.

Vitamin A as retinal is required for the visual cycle in rhodopsin; vitamin K is required for gamma-carboxylation of glutamate residues in clotting factors II, VII, IX and X; vitamin E is a lipid-soluble antioxidant.

Minerals: macrominerals (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, Cu, I, Se, Mn, F); iron is in haemoglobin and cytochromes, iodine in thyroid hormones, zinc in carbonic anhydrase and DNA-binding proteins, selenium in glutathione peroxidase.

Calcium and phosphorus are stored in bone; parathyroid hormone raises plasma calcium, calcitonin lowers it, and vitamin D (calcitriol) increases intestinal calcium absorption.

Bioenergetics studies energy transformations in cells; ATP is the universal energy currency, hydrolysis of its terminal phosphate releasing about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions.

Free energy change: delta-G = delta-H - T delta-S; a reaction is spontaneous when delta-G is negative; reactions with positive delta-G are coupled to ATP hydrolysis to proceed.

Glycolysis (cytoplasm): glucose to 2 pyruvate, net gain 2 ATP and 2 NADH; key regulated enzymes are hexokinase, phosphofructokinase-1 and pyruvate kinase; anaerobic pyruvate is reduced to lactate.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA (yielding NADH and CO2); the citric acid cycle oxidises acetyl-CoA to 2 CO2, 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxidative phosphorylation: electrons pass from NADH and FADH2 through the respiratory chain to oxygen, pumping protons and generating a gradient used by ATP synthase; about 2.5 ATP per NADH and 1.5 ATP per FADH2.

Gluconeogenesis (mainly liver and kidney) makes glucose from lactate, glycerol and amino acids; it uses pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to bypass irreversible glycolytic steps.

Glycogen metabolism: glycogenesis uses glycogen synthase and branching enzyme; glycogenolysis uses glycogen phosphorylase and debranching enzyme; blood glucose is maintained by glycogenolysis and gluconeogenesis under glucagon and adrenaline.

Beta-oxidation of fatty acids in mitochondria removes two carbons per cycle as acetyl-CoA, generating NADH and FADH2; ketone bodies (acetoacetate, beta-hydroxybutyrate, acetone) form during fasting or uncontrolled diabetes.

Reference (normal) ranges are age- and method-dependent; typical adult values: fasting plasma glucose 70-110 mg/dL, total cholesterol below 200 mg/dL, serum creatinine about 0.6-1.2 mg/dL, total protein 6-8 g/dL.

Diabetes mellitus diagnosis relies on fasting glucose at or above 126 mg/dL on two occasions, random glucose at or above 200 mg/dL with symptoms, or an abnormal oral glucose tolerance test; glycated haemoglobin reflects 2-3 months of glycaemic control.

Liver function tests: serum bilirubin, ALT and AST (raised in hepatocellular damage), alkaline phosphatase and gamma-glutamyl transferase (raised in biliary obstruction), albumin and total protein for synthetic capacity.

Kidney function: blood urea and serum creatinine rise in renal impairment; creatinine clearance estimates glomerular filtration rate; urine analysis for protein, glucose, ketones, blood and pH is a basic screen.

Lipid profile: total cholesterol, HDL and LDL cholesterol and triglycerides; LDL is calculated by the Friedewald formula (LDL = total - HDL - triglycerides/5) when triglycerides are below 400 mg/dL.

Colorimetry is based on Beer-Lambert law, A = epsilon times c times l: absorbance is proportional to concentration and path length; a standard curve converts absorbance to concentration.

Chromatography separates by differential distribution between mobile and stationary phases (paper, thin-layer, column, ion-exchange, gel filtration, affinity); electrophoresis separates charged molecules by charge-to-mass ratio.

Centrifugation separates by density and size; spectrophotometry, flame photometry (Na, K, Li) and immunoassays (ELISA, radioimmunoassay) are standard clinical measurement techniques.

Quality control uses normal and abnormal control sera to monitor precision and accuracy; pre-analytical errors such as haemolysis, delayed separation or wrong anticoagulant are common causes of invalid results.

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.

Nucleotides consist of a nitrogenous base, a pentose sugar (ribose in RNA, deoxyribose in DNA) and one or more phosphate groups; nucleoside = base + sugar.

Bases: purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine in DNA, uracil in RNA) are single-ringed; base pairing is A=T (two hydrogen bonds) and G≡C (three hydrogen bonds).

DNA is a double helix with antiparallel strands, sugar-phosphate backbones outside and bases inside; the two strands are complementary and the helix shows major and minor grooves (Watson-Crick model).

Chargaff's rules: in double-stranded DNA, A = T and G = C, so (A+G) = (T+C); the GC content correlates with helix stability and melting temperature.

RNA types: messenger RNA (carries the code), transfer RNA (adapter delivering amino acids; has anticodon and CCA end), ribosomal RNA (part of the ribosome) and heterogeneous/ncRNA.

DNA replication is semi-conservative: helicase unwinds, DNA polymerase synthesises 5' to 3' with a primer, leading strand is continuous and lagging strand forms Okazaki fragments joined by ligase.

Transcription makes RNA from a DNA template using RNA polymerase; in eukaryotes introns are spliced out and exons joined; translation at the ribosome uses codons read 5' to 3' against tRNA anticodons.

The genetic code is triplet, degenerate, non-overlapping and nearly universal; AUG codes methionine and is the start codon; UAA, UAG and UGA are stop codons.

Mutations: substitution (missense, nonsense, silent), insertion or deletion causing frameshift; the central dogma is DNA to RNA to protein, with reverse transcription as an exception in retroviruses.

Vitamins are organic micronutrients required in small amounts that the body cannot synthesise adequately; they are classified as fat-soluble (A, D, E, K) and water-soluble (B-complex and C).

Fat-soluble vitamins are absorbed with dietary fat and stored in the liver; excess intake can cause toxicity (hypervitaminosis A and D), whereas water-soluble vitamins are excreted in urine and rarely toxic.

Coenzyme forms: thiamine (B1) gives thiamine pyrophosphate (TPP) for decarboxylation; riboflavin (B2) gives FAD and FMN; niacin (B3) gives NAD+ and NADP+; pantothenic acid (B5) gives coenzyme A.

Pyridoxal phosphate from vitamin B6 is the coenzyme for transamination and decarboxylation of amino acids; biotin (B7) is the coenzyme for carboxylation reactions; cobalamin (B12) is needed for methylmalonyl-CoA mutase and methionine synthase.

Deficiency diseases: beriberi (B1), cheilosis and ariboflavinosis (B2), pellagra - dermatitis, diarrhoea, dementia (niacin), pernicious anaemia (B12), megaloblastic anaemia (folate), scurvy (vitamin C), rickets (vitamin D), night blindness (vitamin A).

Vitamin C (ascorbic acid) is a water-soluble antioxidant and cofactor for prolyl and lysyl hydroxylases in collagen synthesis; deficiency causes bleeding gums, poor wound healing and scurvy.

Vitamin A as retinal is required for the visual cycle in rhodopsin; vitamin K is required for gamma-carboxylation of glutamate residues in clotting factors II, VII, IX and X; vitamin E is a lipid-soluble antioxidant.

Minerals: macrominerals (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, Cu, I, Se, Mn, F); iron is in haemoglobin and cytochromes, iodine in thyroid hormones, zinc in carbonic anhydrase and DNA-binding proteins, selenium in glutathione peroxidase.

Calcium and phosphorus are stored in bone; parathyroid hormone raises plasma calcium, calcitonin lowers it, and vitamin D (calcitriol) increases intestinal calcium absorption.

Bioenergetics studies energy transformations in cells; ATP is the universal energy currency, hydrolysis of its terminal phosphate releasing about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions.

Free energy change: delta-G = delta-H - T delta-S; a reaction is spontaneous when delta-G is negative; reactions with positive delta-G are coupled to ATP hydrolysis to proceed.

Glycolysis (cytoplasm): glucose to 2 pyruvate, net gain 2 ATP and 2 NADH; key regulated enzymes are hexokinase, phosphofructokinase-1 and pyruvate kinase; anaerobic pyruvate is reduced to lactate.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA (yielding NADH and CO2); the citric acid cycle oxidises acetyl-CoA to 2 CO2, 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxidative phosphorylation: electrons pass from NADH and FADH2 through the respiratory chain to oxygen, pumping protons and generating a gradient used by ATP synthase; about 2.5 ATP per NADH and 1.5 ATP per FADH2.

Gluconeogenesis (mainly liver and kidney) makes glucose from lactate, glycerol and amino acids; it uses pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to bypass irreversible glycolytic steps.

Glycogen metabolism: glycogenesis uses glycogen synthase and branching enzyme; glycogenolysis uses glycogen phosphorylase and debranching enzyme; blood glucose is maintained by glycogenolysis and gluconeogenesis under glucagon and adrenaline.

Beta-oxidation of fatty acids in mitochondria removes two carbons per cycle as acetyl-CoA, generating NADH and FADH2; ketone bodies (acetoacetate, beta-hydroxybutyrate, acetone) form during fasting or uncontrolled diabetes.

Reference (normal) ranges are age- and method-dependent; typical adult values: fasting plasma glucose 70-110 mg/dL, total cholesterol below 200 mg/dL, serum creatinine about 0.6-1.2 mg/dL, total protein 6-8 g/dL.

Diabetes mellitus diagnosis relies on fasting glucose at or above 126 mg/dL on two occasions, random glucose at or above 200 mg/dL with symptoms, or an abnormal oral glucose tolerance test; glycated haemoglobin reflects 2-3 months of glycaemic control.

Liver function tests: serum bilirubin, ALT and AST (raised in hepatocellular damage), alkaline phosphatase and gamma-glutamyl transferase (raised in biliary obstruction), albumin and total protein for synthetic capacity.

Kidney function: blood urea and serum creatinine rise in renal impairment; creatinine clearance estimates glomerular filtration rate; urine analysis for protein, glucose, ketones, blood and pH is a basic screen.

Lipid profile: total cholesterol, HDL and LDL cholesterol and triglycerides; LDL is calculated by the Friedewald formula (LDL = total - HDL - triglycerides/5) when triglycerides are below 400 mg/dL.

Colorimetry is based on Beer-Lambert law, A = epsilon times c times l: absorbance is proportional to concentration and path length; a standard curve converts absorbance to concentration.

Chromatography separates by differential distribution between mobile and stationary phases (paper, thin-layer, column, ion-exchange, gel filtration, affinity); electrophoresis separates charged molecules by charge-to-mass ratio.

Centrifugation separates by density and size; spectrophotometry, flame photometry (Na, K, Li) and immunoassays (ELISA, radioimmunoassay) are standard clinical measurement techniques.

Quality control uses normal and abnormal control sera to monitor precision and accuracy; pre-analytical errors such as haemolysis, delayed separation or wrong anticoagulant are common causes of invalid results.

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.

Nucleotides consist of a nitrogenous base, a pentose sugar (ribose in RNA, deoxyribose in DNA) and one or more phosphate groups; nucleoside = base + sugar.

Bases: purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine in DNA, uracil in RNA) are single-ringed; base pairing is A=T (two hydrogen bonds) and G≡C (three hydrogen bonds).

DNA is a double helix with antiparallel strands, sugar-phosphate backbones outside and bases inside; the two strands are complementary and the helix shows major and minor grooves (Watson-Crick model).

Chargaff's rules: in double-stranded DNA, A = T and G = C, so (A+G) = (T+C); the GC content correlates with helix stability and melting temperature.

RNA types: messenger RNA (carries the code), transfer RNA (adapter delivering amino acids; has anticodon and CCA end), ribosomal RNA (part of the ribosome) and heterogeneous/ncRNA.

DNA replication is semi-conservative: helicase unwinds, DNA polymerase synthesises 5' to 3' with a primer, leading strand is continuous and lagging strand forms Okazaki fragments joined by ligase.

Transcription makes RNA from a DNA template using RNA polymerase; in eukaryotes introns are spliced out and exons joined; translation at the ribosome uses codons read 5' to 3' against tRNA anticodons.

The genetic code is triplet, degenerate, non-overlapping and nearly universal; AUG codes methionine and is the start codon; UAA, UAG and UGA are stop codons.

Mutations: substitution (missense, nonsense, silent), insertion or deletion causing frameshift; the central dogma is DNA to RNA to protein, with reverse transcription as an exception in retroviruses.

Vitamins are organic micronutrients required in small amounts that the body cannot synthesise adequately; they are classified as fat-soluble (A, D, E, K) and water-soluble (B-complex and C).

Fat-soluble vitamins are absorbed with dietary fat and stored in the liver; excess intake can cause toxicity (hypervitaminosis A and D), whereas water-soluble vitamins are excreted in urine and rarely toxic.

Coenzyme forms: thiamine (B1) gives thiamine pyrophosphate (TPP) for decarboxylation; riboflavin (B2) gives FAD and FMN; niacin (B3) gives NAD+ and NADP+; pantothenic acid (B5) gives coenzyme A.

Pyridoxal phosphate from vitamin B6 is the coenzyme for transamination and decarboxylation of amino acids; biotin (B7) is the coenzyme for carboxylation reactions; cobalamin (B12) is needed for methylmalonyl-CoA mutase and methionine synthase.

Deficiency diseases: beriberi (B1), cheilosis and ariboflavinosis (B2), pellagra - dermatitis, diarrhoea, dementia (niacin), pernicious anaemia (B12), megaloblastic anaemia (folate), scurvy (vitamin C), rickets (vitamin D), night blindness (vitamin A).

Vitamin C (ascorbic acid) is a water-soluble antioxidant and cofactor for prolyl and lysyl hydroxylases in collagen synthesis; deficiency causes bleeding gums, poor wound healing and scurvy.

Vitamin A as retinal is required for the visual cycle in rhodopsin; vitamin K is required for gamma-carboxylation of glutamate residues in clotting factors II, VII, IX and X; vitamin E is a lipid-soluble antioxidant.

Minerals: macrominerals (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, Cu, I, Se, Mn, F); iron is in haemoglobin and cytochromes, iodine in thyroid hormones, zinc in carbonic anhydrase and DNA-binding proteins, selenium in glutathione peroxidase.

Calcium and phosphorus are stored in bone; parathyroid hormone raises plasma calcium, calcitonin lowers it, and vitamin D (calcitriol) increases intestinal calcium absorption.

Bioenergetics studies energy transformations in cells; ATP is the universal energy currency, hydrolysis of its terminal phosphate releasing about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions.

Free energy change: delta-G = delta-H - T delta-S; a reaction is spontaneous when delta-G is negative; reactions with positive delta-G are coupled to ATP hydrolysis to proceed.

Glycolysis (cytoplasm): glucose to 2 pyruvate, net gain 2 ATP and 2 NADH; key regulated enzymes are hexokinase, phosphofructokinase-1 and pyruvate kinase; anaerobic pyruvate is reduced to lactate.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA (yielding NADH and CO2); the citric acid cycle oxidises acetyl-CoA to 2 CO2, 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxidative phosphorylation: electrons pass from NADH and FADH2 through the respiratory chain to oxygen, pumping protons and generating a gradient used by ATP synthase; about 2.5 ATP per NADH and 1.5 ATP per FADH2.

Gluconeogenesis (mainly liver and kidney) makes glucose from lactate, glycerol and amino acids; it uses pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to bypass irreversible glycolytic steps.

Glycogen metabolism: glycogenesis uses glycogen synthase and branching enzyme; glycogenolysis uses glycogen phosphorylase and debranching enzyme; blood glucose is maintained by glycogenolysis and gluconeogenesis under glucagon and adrenaline.

Beta-oxidation of fatty acids in mitochondria removes two carbons per cycle as acetyl-CoA, generating NADH and FADH2; ketone bodies (acetoacetate, beta-hydroxybutyrate, acetone) form during fasting or uncontrolled diabetes.

Reference (normal) ranges are age- and method-dependent; typical adult values: fasting plasma glucose 70-110 mg/dL, total cholesterol below 200 mg/dL, serum creatinine about 0.6-1.2 mg/dL, total protein 6-8 g/dL.

Diabetes mellitus diagnosis relies on fasting glucose at or above 126 mg/dL on two occasions, random glucose at or above 200 mg/dL with symptoms, or an abnormal oral glucose tolerance test; glycated haemoglobin reflects 2-3 months of glycaemic control.

Liver function tests: serum bilirubin, ALT and AST (raised in hepatocellular damage), alkaline phosphatase and gamma-glutamyl transferase (raised in biliary obstruction), albumin and total protein for synthetic capacity.

Kidney function: blood urea and serum creatinine rise in renal impairment; creatinine clearance estimates glomerular filtration rate; urine analysis for protein, glucose, ketones, blood and pH is a basic screen.

Lipid profile: total cholesterol, HDL and LDL cholesterol and triglycerides; LDL is calculated by the Friedewald formula (LDL = total - HDL - triglycerides/5) when triglycerides are below 400 mg/dL.

Colorimetry is based on Beer-Lambert law, A = epsilon times c times l: absorbance is proportional to concentration and path length; a standard curve converts absorbance to concentration.

Chromatography separates by differential distribution between mobile and stationary phases (paper, thin-layer, column, ion-exchange, gel filtration, affinity); electrophoresis separates charged molecules by charge-to-mass ratio.

Centrifugation separates by density and size; spectrophotometry, flame photometry (Na, K, Li) and immunoassays (ELISA, radioimmunoassay) are standard clinical measurement techniques.

Quality control uses normal and abnormal control sera to monitor precision and accuracy; pre-analytical errors such as haemolysis, delayed separation or wrong anticoagulant are common causes of invalid results.

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.

Nucleotides consist of a nitrogenous base, a pentose sugar (ribose in RNA, deoxyribose in DNA) and one or more phosphate groups; nucleoside = base + sugar.

Bases: purines (adenine, guanine) are double-ringed; pyrimidines (cytosine, thymine in DNA, uracil in RNA) are single-ringed; base pairing is A=T (two hydrogen bonds) and G≡C (three hydrogen bonds).

DNA is a double helix with antiparallel strands, sugar-phosphate backbones outside and bases inside; the two strands are complementary and the helix shows major and minor grooves (Watson-Crick model).

Chargaff's rules: in double-stranded DNA, A = T and G = C, so (A+G) = (T+C); the GC content correlates with helix stability and melting temperature.

RNA types: messenger RNA (carries the code), transfer RNA (adapter delivering amino acids; has anticodon and CCA end), ribosomal RNA (part of the ribosome) and heterogeneous/ncRNA.

DNA replication is semi-conservative: helicase unwinds, DNA polymerase synthesises 5' to 3' with a primer, leading strand is continuous and lagging strand forms Okazaki fragments joined by ligase.

Transcription makes RNA from a DNA template using RNA polymerase; in eukaryotes introns are spliced out and exons joined; translation at the ribosome uses codons read 5' to 3' against tRNA anticodons.

The genetic code is triplet, degenerate, non-overlapping and nearly universal; AUG codes methionine and is the start codon; UAA, UAG and UGA are stop codons.

Mutations: substitution (missense, nonsense, silent), insertion or deletion causing frameshift; the central dogma is DNA to RNA to protein, with reverse transcription as an exception in retroviruses.

Vitamins are organic micronutrients required in small amounts that the body cannot synthesise adequately; they are classified as fat-soluble (A, D, E, K) and water-soluble (B-complex and C).

Fat-soluble vitamins are absorbed with dietary fat and stored in the liver; excess intake can cause toxicity (hypervitaminosis A and D), whereas water-soluble vitamins are excreted in urine and rarely toxic.

Coenzyme forms: thiamine (B1) gives thiamine pyrophosphate (TPP) for decarboxylation; riboflavin (B2) gives FAD and FMN; niacin (B3) gives NAD+ and NADP+; pantothenic acid (B5) gives coenzyme A.

Pyridoxal phosphate from vitamin B6 is the coenzyme for transamination and decarboxylation of amino acids; biotin (B7) is the coenzyme for carboxylation reactions; cobalamin (B12) is needed for methylmalonyl-CoA mutase and methionine synthase.

Deficiency diseases: beriberi (B1), cheilosis and ariboflavinosis (B2), pellagra - dermatitis, diarrhoea, dementia (niacin), pernicious anaemia (B12), megaloblastic anaemia (folate), scurvy (vitamin C), rickets (vitamin D), night blindness (vitamin A).

Vitamin C (ascorbic acid) is a water-soluble antioxidant and cofactor for prolyl and lysyl hydroxylases in collagen synthesis; deficiency causes bleeding gums, poor wound healing and scurvy.

Vitamin A as retinal is required for the visual cycle in rhodopsin; vitamin K is required for gamma-carboxylation of glutamate residues in clotting factors II, VII, IX and X; vitamin E is a lipid-soluble antioxidant.

Minerals: macrominerals (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, Cu, I, Se, Mn, F); iron is in haemoglobin and cytochromes, iodine in thyroid hormones, zinc in carbonic anhydrase and DNA-binding proteins, selenium in glutathione peroxidase.

Calcium and phosphorus are stored in bone; parathyroid hormone raises plasma calcium, calcitonin lowers it, and vitamin D (calcitriol) increases intestinal calcium absorption.

Bioenergetics studies energy transformations in cells; ATP is the universal energy currency, hydrolysis of its terminal phosphate releasing about 7.3 kcal/mol (30.5 kJ/mol) under standard conditions.

Free energy change: delta-G = delta-H - T delta-S; a reaction is spontaneous when delta-G is negative; reactions with positive delta-G are coupled to ATP hydrolysis to proceed.

Glycolysis (cytoplasm): glucose to 2 pyruvate, net gain 2 ATP and 2 NADH; key regulated enzymes are hexokinase, phosphofructokinase-1 and pyruvate kinase; anaerobic pyruvate is reduced to lactate.

Pyruvate dehydrogenase converts pyruvate to acetyl-CoA (yielding NADH and CO2); the citric acid cycle oxidises acetyl-CoA to 2 CO2, 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxidative phosphorylation: electrons pass from NADH and FADH2 through the respiratory chain to oxygen, pumping protons and generating a gradient used by ATP synthase; about 2.5 ATP per NADH and 1.5 ATP per FADH2.

Gluconeogenesis (mainly liver and kidney) makes glucose from lactate, glycerol and amino acids; it uses pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase and glucose-6-phosphatase to bypass irreversible glycolytic steps.

Glycogen metabolism: glycogenesis uses glycogen synthase and branching enzyme; glycogenolysis uses glycogen phosphorylase and debranching enzyme; blood glucose is maintained by glycogenolysis and gluconeogenesis under glucagon and adrenaline.

Beta-oxidation of fatty acids in mitochondria removes two carbons per cycle as acetyl-CoA, generating NADH and FADH2; ketone bodies (acetoacetate, beta-hydroxybutyrate, acetone) form during fasting or uncontrolled diabetes.

Reference (normal) ranges are age- and method-dependent; typical adult values: fasting plasma glucose 70-110 mg/dL, total cholesterol below 200 mg/dL, serum creatinine about 0.6-1.2 mg/dL, total protein 6-8 g/dL.

Diabetes mellitus diagnosis relies on fasting glucose at or above 126 mg/dL on two occasions, random glucose at or above 200 mg/dL with symptoms, or an abnormal oral glucose tolerance test; glycated haemoglobin reflects 2-3 months of glycaemic control.

Liver function tests: serum bilirubin, ALT and AST (raised in hepatocellular damage), alkaline phosphatase and gamma-glutamyl transferase (raised in biliary obstruction), albumin and total protein for synthetic capacity.

Kidney function: blood urea and serum creatinine rise in renal impairment; creatinine clearance estimates glomerular filtration rate; urine analysis for protein, glucose, ketones, blood and pH is a basic screen.

Lipid profile: total cholesterol, HDL and LDL cholesterol and triglycerides; LDL is calculated by the Friedewald formula (LDL = total - HDL - triglycerides/5) when triglycerides are below 400 mg/dL.

Colorimetry is based on Beer-Lambert law, A = epsilon times c times l: absorbance is proportional to concentration and path length; a standard curve converts absorbance to concentration.

Chromatography separates by differential distribution between mobile and stationary phases (paper, thin-layer, column, ion-exchange, gel filtration, affinity); electrophoresis separates charged molecules by charge-to-mass ratio.

Centrifugation separates by density and size; spectrophotometry, flame photometry (Na, K, Li) and immunoassays (ELISA, radioimmunoassay) are standard clinical measurement techniques.

Quality control uses normal and abnormal control sera to monitor precision and accuracy; pre-analytical errors such as haemolysis, delayed separation or wrong anticoagulant are common causes of invalid results.

Biochemistry studies the chemical basis of life: the structure, properties and reactions of biomolecules in living cells, and the energy changes that accompany them.

Four major classes of biomolecules: carbohydrates, lipids, proteins (with amino acids and peptides) and nucleic acids; water is the most abundant molecule in cells (about 70% of cell mass).

Carbon forms the backbone of biomolecules because it has a valence of 4 and forms stable single, double and triple bonds, giving rise to the huge diversity of organic compounds.

Functional groups to recognise: hydroxyl (-OH), carbonyl (aldehyde -CHO, ketone -C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-PO4) and methyl (-CH3).

Biopolymers are built by condensation (loss of water) and broken by hydrolysis (addition of water); monomers are joined by covalent bonds such as glycosidic, ester, peptide and phosphodiester bonds.

Biological importance of water: high polarity, high specific heat, high latent heat of vaporisation, high surface tension and its role as a solvent for ions and polar molecules, and as a reactant in hydrolysis.

Weak interactions: hydrogen bonds, ionic bonds, hydrophobic interactions and van der Waals forces stabilise protein structure, DNA double helices and membranes.

Isomerism in biomolecules: structural isomers, stereoisomers (geometric cis/trans and optical D/L forms) - most natural sugars and amino acids are optically active.

pH and buffers: pH = -log[H+]; a buffer resists pH change on adding small amounts of acid or base; the bicarbonate system (H2CO3/HCO3-) is the main extracellular buffer of blood.

Carbohydrates are polyhydroxy aldehydes or ketones; general formula (CH2O)n, e.g. glucose C6H12O6; they are classified as monosaccharides, oligosaccharides and polysaccharides.

Monosaccharide classification by carbon number: triose (3C, glyceraldehyde), tetrose (4C, erythrose), pentose (5C, ribose, xylose), hexose (6C, glucose, fructose, galactose).

Glucose is an aldohexose; fructose is a ketohexose; both are reducing sugars. In aqueous solution glucose exists mainly as the pyranose ring (alpha and beta anomers) with a small open-chain fraction.

Reducing sugars reduce Cu2+ in Fehling's or Benedict's solution to red Cu2O and reduce Tollens' reagent to silver; sucrose (non-reducing) gives a negative test unless hydrolysed first.

Disaccharides: maltose = glucose + glucose (alpha-1,4); lactose = galactose + glucose (beta-1,4); sucrose = glucose + fructose (alpha-1,2) - sucrose is non-reducing.

Polysaccharides: starch (amylose alpha-1,4 chains plus amylopectin with alpha-1,6 branches), glycogen (more branched storage form in animals), cellulose (beta-1,4 glucose, structural, not digested by humans), chitin (N-acetylglucosamine).

Glycosidic bond forms between the anomeric carbon of one sugar and a hydroxyl of another with loss of water; the number and position of such bonds determine polymer structure and digestibility.

Mutarotation is the change in optical rotation when alpha- and beta-anomers equilibrate through the open-chain form; osazone formation, oxidation to aldonic/uronic acids and reduction to sugar alcohols are typical sugar reactions.

Biological roles: immediate energy (glucose), storage (glycogen, starch), structural support (cellulose, chitin) and cell-surface recognition (glycoproteins and glycolipids).

Lipids are a heterogeneous group of hydrophobic or amphipathic molecules soluble in organic solvents and poorly soluble in water; they include fats, oils, waxes, phospholipids, sphingolipids, steroids and terpenes.

Fatty acids: saturated (no double bonds, e.g. palmitic C16:0, stearic C18:0) and unsaturated (one or more double bonds, e.g. oleic C18:1, linoleic C18:2); double bonds in natural fatty acids are usually cis, causing kinks.

Essential fatty acids cannot be synthesised by humans: linoleic acid (omega-6) and alpha-linolenic acid (omega-3) must be obtained from the diet.

Triacylglycerols (triglycerides) are esters of glycerol with three fatty acids; they are the most concentrated energy store (~9 kcal/g) and are hydrolysed by lipases; saponification with alkali gives soap plus glycerol.

Iodine value measures unsaturation (g iodine absorbed per 100 g fat); saponification number measures average fatty acid chain length; acid value indicates free fatty acid content from hydrolysis or rancidity.

Phospholipids: glycerol-based (phosphatidylcholine, phosphatidylethanolamine) and sphingomyelin; they are amphipathic, forming bilayers with polar heads outwards and hydrophobic tails inwards - the basis of membranes.

Cholesterol is a steroid with a four-ring nucleus; it is a precursor of bile acids, steroid hormones (cortisol, aldosterone, testosterone, estrogens) and vitamin D, and is carried in plasma lipoproteins (LDL and HDL).

Waxes are esters of long-chain fatty acids with long-chain alcohols; they provide waterproofing. Rancidity results from hydrolysis or oxidation of unsaturated fatty acids.

An alpha-amino acid has an amino group and a carboxyl group attached to the same carbon; general formula NH2-CHR-COOH; the 20 standard amino acids are coded by DNA.

Classification by side chain: nonpolar/aliphatic (Gly, Ala, Val, Leu, Ile, Pro), aromatic (Phe, Tyr, Trp), sulfur-containing (Cys, Met), hydroxyl (Ser, Thr, Tyr), acidic (Asp, Glu), basic (Lys, Arg, His) and amide-containing (Asn, Gln).

Glycine is the only achiral standard amino acid; cysteine can form disulfide bonds (Cys-S-S-Cys); proline is an imino acid that introduces kinks in chains; histidine's imidazole ring buffers near pH 6.

At low pH amino acids are cationic (NH3+); at high pH anionic (COO-); at the isoelectric point (pI) the net charge is zero and the molecule does not migrate in an electric field; pI = (pK1 + pK2)/2 for a neutral amino acid.

The peptide bond forms between the alpha-carboxyl of one amino acid and the alpha-amino of another with loss of water; it is a partial double bond, planar and rigid, and is cleaved by proteases or strong acid hydrolysis.

Protein structure levels: primary (amino acid sequence), secondary (alpha-helix and beta-pleated sheet stabilised by hydrogen bonds), tertiary (3D folding with disulfide, hydrophobic and ionic interactions) and quaternary (association of subunits, e.g. haemoglobin).

Denaturation disrupts secondary, tertiary and quaternary structure (heat, extremes of pH, urea, detergents) without breaking peptide bonds, usually abolishing biological activity; primary structure is retained.

Protein functions: enzymes (catalysis), transport (haemoglobin, albumin), structural (collagen, keratin), hormones (insulin), defence (immunoglobulins), contraction (actin, myosin) and storage (ferritin).

Enzymes are biological catalysts, mostly proteins (some are RNA ribozymes); they lower activation energy and increase reaction rate without being consumed or changing the equilibrium constant.

Active site: a specific cleft where substrate binds by weak interactions; the lock-and-key model assumes rigid complementarity, the induced-fit model assumes conformational change on binding.

Enzyme specificity is absolute or relative; cofactors (metal ions) and coenzymes (organic, often vitamin-derived, e.g. NAD+, FAD, TPP) are needed by many enzymes; a holoenzyme = apoenzyme + cofactor.

Michaelis-Menten equation: v = Vmax[S]/(Km + [S]); Km is the substrate concentration at half Vmax, an inverse measure of affinity; Vmax = kcat[E]total.

Lineweaver-Burk plot (1/v versus 1/[S]) is linear: y-intercept = 1/Vmax, x-intercept = -1/Km; useful for diagnosing inhibition type.

Competitive inhibition raises apparent Km but leaves Vmax unchanged (reversed by more substrate); non-competitive inhibition lowers Vmax with unchanged Km; uncompetitive inhibition lowers both Km and Vmax.

Factors affecting enzyme activity: substrate concentration, enzyme concentration, temperature (optimum near 37 degrees C in humans, denaturation above), pH (optimum is characteristic, e.g. pepsin ~2, trypsin ~8) and inhibitors.

Allosteric enzymes show a sigmoid v-versus-[S] curve and are regulated by effectors; covalent modification such as phosphorylation and zymogen activation (trypsinogen to trypsin) also control activity.

Enzyme units: one international unit (IU) converts 1 micromole of substrate per minute; specific activity is units per milligram of protein; turnover number is substrate molecules converted per enzyme molecule per unit time.