Clinical Biochemistry

Comprehensive study resource covering molecular biology, metabolism, and biochemical pathways. Every pathway, every enzyme, every clinical correlation you need to know.

1. Cellular Biochemistry and Water

Cell Structure Water and pH Buffers Amino Acids Protein Structure Folding and Chaperones

Cell Structure and Organelles
  • The eukaryotic cell is compartmentalized into membrane-bound organelles that enable specialized biochemical functions.
  • The plasma membrane is a phospholipid bilayer with embedded proteins, cholesterol, and glycocalyx following the fluid mosaic model proposed by Singer and Nicolson.
  • The nucleus contains chromatin (DNA + histones), nucleolus (rRNA synthesis), and nuclear pores regulating macromolecular transport.
  • Mitochondria are the powerhouses featuring double membranes, cristae (ETC complexes), and matrix (TCA cycle, β-oxidation) with their own circular DNA and ribosomes.
  • The endoplasmic reticulum exists as rough (ribosome-studded for protein synthesis and modification) and smooth (lipid synthesis, detoxification, Ca^2 +/- storage).
  • The Golgi apparatus modifies, sorts, and packages proteins into vesicles.
  • Lysosomes contain hydrolytic enzymes (acid hydrolases, pH ~5) for intracellular digestion; defects cause storage diseases (Tay-Sachs, Gaucher, Niemann-Pick).
  • Peroxisomes house oxidative enzymes (catalase, D-amino acid oxidase, β-oxidation of very-long-chain fatty acids); defects cause Zellweger syndrome and adrenoleukodystrophy.
  • The cytosol is the aqueous milieu for glycolysis, fatty acid synthesis, and protein translation.
Water, pH and the Henderson-Hasselbalch Equation
  • Water is the universal biological solvent with unique properties: high dielectric constant, hydrogen bonding, cohesion, and high specific heat.
  • The ionization of water produces H+ and OH− (Kw = 1. 0 x 10−^1&sup4; at 25 degrees C). pH is defined as −log[H+]; normal blood pH is 7. 35 - 7. 45, tightly regulated by buffers, respiration, and renal function.
  • The Henderson-Hasselbalch equation pH = pKa + log([A−]/[HA]), is fundamental to understanding acid-base physiology.
  • For a weak acid, when pH = pKa, the species are 50% ionized.
  • The bicarbonate buffer system (H&bdq;CO^3/HCO^3−) is the major extracellular buffer with pKa ~6. 1; despite being an open system (CO&bdq; cleared by lungs), it operates effectively at physiological pH.
  • Other buffers: phosphate (pKa 6. 86, intracellular/urinary), proteins (histidine imidazole groups, pKa ~6. 0), and hemoglobin (Bohr effect - deoxyhemoglobin binds H+ better, facilitating CO&bdq; transport).
  • The body defends pH through chemical buffers (instantaneous), respiratory compensation (minutes), and renal compensation (hours to days).
Amino Acids: Classification and Properties
  • The 20 standard amino acids are classified by side-chain properties.
  • Nonpolar aliphatic: glycine (simplest, no chiral center), alanine, valine (branching), leucine, isoleucine, methionine (sulfur-containing, start codon), proline (secondary amine, rigid ring).
  • Aromatic: phenylalanine (precursor to tyrosine), tyrosine (thyroid hormones, catecholamines), tryptophan (serotonin, melatonin, niacin precursors).
  • Polar uncharged: serine (active site of serine proteases), threonine, cysteine (disulfide bonds), asparagine, glutamine (nitrogen donor).
  • Positively charged (basic): lysine (histone acetylation sites), arginine (urea cycle, NO precursor), histidine (imidazole, pKa ~6. 0, crucial buffer in proteins).
  • Negatively charged (acidic): aspartate, glutamate (excitatory neurotransmitter, GABA precursor). pKa values: α-carboxyl (~2. 2), α-amino (~9. 5), side chains (Asp 3. 9, Glu 4. 1, His 6. 0, Cys 8. 3, Tyr 10. 1, Lys 10. 5, Arg 12. 5).
  • The isoelectric point (pI) is the pH where net charge = 0.
  • Titration curves reveal buffering regions near each pKa.
  • At pH pI, negatively charged.
Protein Structure: Primary to Quaternary
  • Proteins exhibit four levels of structural organization.
  • Primary structure is the linear sequence of amino acids linked by peptide bonds via condensation - the peptide bond has partial double-bond character (planar, restricted rotation), rendering it rigid and trans-configured.
  • Secondary structure involves local hydrogen-bonding patterns: the α-helix is a right-handed coil with 3. 6 residues per turn, stabilized by H-bonds between C=O of residue n and NH of residue n+4 (destabilized by proline and bulky/branched chains); the β-sheet consists of parallel or antiparallel strands with inter-strand H-bonds.
  • Tertiary structure is the global 3D fold of a single polypeptide, stabilized by hydrophobic interactions (major driving force), hydrogen bonds, ionic interactions, disulfide bonds (covalent, formed in ER), and van der Waals forces.
  • Domains are independently folding units (50 - 200 residues).
  • Quaternary structure refers to subunit assembly: homodimers (creatine kinase), heterotetramers (hemoglobin α&bdq;β&bdq;), and large complexes (proteasome, RNA polymerase).
  • The Anfinsen principle states that all information for tertiary structure is contained in the primary sequence.
Protein Folding and Chaperones
  • Protein folding is a thermodynamically driven process seeking the lowest free-energy conformation via the folding funnel energy landscape.
  • Chaperones facilitate proper folding without becoming part of the final structure.
  • Heat shock proteins (Hsp70, Hsp90) are stress-induced chaperones: Hsp70 binds exposed hydrophobic patches, uses ATP hydrolysis for release and refolding.
  • Chaperonins (GroEL/GroES in E. coli; TRiC in eukaryotes) are barrel-shaped complexes providing an isolated folding chamber.
  • Disulfide isomerase (PDI) catalyzes correct disulfide bond formation in the ER.
  • Prolyl isomerases catalyze cis-trans isomerization.
  • Misfolded proteins are targeted for degradation via ubiquitin-proteasome pathway (cytosolic) or ER-associated degradation (ERAD).
  • Heat shock response activates HSF1 -> transcription of chaperone genes.
Clinical: pH Disorders and Protein Misfolding
  • Acid-base disorders: metabolic acidosis (↓ HCO^3−) from DKA, lactic acidosis, renal failure, diarrhea; metabolic alkalosis (↑ HCO^3−) from vomiting, diuretics; respiratory acidosis (↑ PaCO&bdq;) from COPD, opioid overdose; respiratory alkalosis (↓ PaCO&bdq;) from hyperventilation, PE, liver disease.
  • Anion gap (AG = Na − Cl − HCO^3) distinguishes AG vs non-AG metabolic acidosis (MUDPILES).
  • Delta ratio identifies mixed disorders.
  • Protein misfolding diseases: Alzheimer's (Aβ plaques + tau tangles), Parkinson's (α-synuclein Lewy bodies), Huntington's (polyglutamine expansions), prion diseases (CJD, kuru - PrP&supSc; conversion), transthyretin amyloidosis (ATTR), light chain (AL) amyloidosis.
  • Congo red stain gives apple-green birefringence under polarized light.
High-Yield Pearls
  • Isoelectric focusing separates proteins by pI; 2D-PAGE combines IEF + SDS-PAGE.
  • Peptide bond is planar and trans (except proline - cis possible).
  • Glycine is achiral; proline induces kinks in α-helices.
  • Edman degradation: N-terminal residue sequenced one at a time.
  • Congo red: apple-green birefringence = amyloid.
  • Chaperonin mutations: Hsp60 -> hereditary spastic paraplegia.
  • Anion gap = Na − (Cl + HCO^3); normal 8 - 12; MUDPILES mnemonic.
Red Flags and Complications
  • High AG metabolic acidosis + osmolar gap = methanol/ethylene glycol poisoning.
  • Delta gap < 1 = concurrent non-AG acidosis; > 2 = concurrent metabolic alkalosis.
  • AL amyloidosis: nephrotic syndrome, hepatomegaly, cardiomyopathy, macroglossia.
  • Prion diseases: always fatal; iatrogenic transmission from contaminated instruments.
  • Temperature-sensitive folding mutants: function at permissive but not body temperature.

2. Carbohydrate Metabolism

Glycolysis Gluconeogenesis Glycogen PPP TCA Cycle ETC Clinical Disorders

Glycolysis: Reactions, Regulation and Energetics
  • Glycolysis is the 10-step cytosolic pathway converting one glucose (6C) to two pyruvate (3C) with net 2 ATP and 2 NADH.
  • Energy investment phase (steps 1 - 5, consumes 2 ATP) and energy payoff phase (steps 6 - 10, produces 4 ATP + 2 NADH).
  • Key irreversible regulatory steps: hexokinase/glucokinase (step 1: glucose -> glucose-6-P, inhibited by G6P), phosphofructokinase-1 (PFK-1, step 3: fructose-6-P -> fructose-1,6-bisP, committed step, activated by AMP and fructose-2,6-BP, inhibited by ATP and citrate), and pyruvate kinase (step 10: PEP -> pyruvate, activated by F-1,6-BP, inhibited by ATP and alanine).
  • Substrate-level phosphorylation at steps 7 (1,3-BPG -> 3-PG via phosphoglycerate kinase) and 10.
  • In anaerobic conditions, lactate dehydrogenase (LDH) converts pyruvate to lactate, regenerating NAD+.
  • The Warburg effect: cancer cells prefer aerobic glycolysis. Overall: Glucose + 2 NAD+ + 2 ADP + 2 Pi -> 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H&bdq;O.
Gluconeogenesis and the Cori Cycle
  • Gluconeogenesis is glucose synthesis from non-carbohydrate precursors (lactate, glycerol, amino acids) in liver and renal cortex.
  • Three bypass reactions circumvent irreversible glycolysis steps.
  • Bypass 1: pyruvate carboxylase (pyruvate -> oxaloacetate, mitochondrial) + PEP carboxykinase (OAA -> PEP).
  • Pyruvate carboxylase is activated by acetyl-CoA (allosteric).
  • Bypass 2: fructose-1,6-bisphosphatase (F-1,6-BP -> F-6-P), inhibited by AMP and fructose-2,6-BP.
  • Bypass 3: glucose-6-phosphatase (G6P -> glucose) - only in liver/kidney (absent in muscle).
  • The Cori cycle: muscle produces lactate (anaerobic glycolysis) -> liver converts it to glucose via gluconeogenesis -> glucose returned to muscle.
  • Substrates: glucogenic amino acids (all except Leu, Lys), glycerol, lactate/pyruvate, propionate.
  • Regulation: insulin inhibits gluconeogenesis; glucagon, cortisol, and epinephrine stimulate it.
  • The reciprocal regulation of PFK-1 and F-1,6-BPase via fructose-2,6-BP balances glycolysis and gluconeogenesis.
Glycogen Metabolism and Storage Diseases
  • Glycogen is a branched polymer of glucose (α-1,4 linear, α-1,6 branches).
  • Glycogenesis: glucose -> G6P -> G1P -> UDP-glucose -> glycogenin (primer) -> glycogen synthase (elongation) + branching enzyme.
  • Glycogenolysis: glycogen phosphorylase (rate-limiting) cleaves α-1,4 linkages -> G1P -> G6P; debranching enzyme handles branches (transferase + α-1,6 glucosidase).
  • Liver has G6Pase (releases free glucose); muscle lacks it.
  • Regulation: phosphorylase activated by phosphorylation (PKA cascade via glucagon/epinephrine); glycogen synthase inactivated by phosphorylation.
  • Glycogen storage diseases: von Gierke (GSD I, G6Pase deficiency) -> severe fasting hypoglycemia, hepatomegaly, lactic acidosis; Pompe (GSD II, acid maltase deficiency) -> cardiomyopathy, muscle weakness; Cori (GSD III, debranching enzyme deficiency) -> milder hypoglycemia; McArdle (GSD V, muscle phosphorylase deficiency) -> exercise intolerance, myoglobinuria, second-wind phenomenon; Hers (GSD VI, liver phosphorylase) -> mild hypoglycemia; Tarui (GSD VII, PFK deficiency) -> hemolytic anemia + exercise intolerance.
Pentose Phosphate Pathway and G6PD Deficiency
  • The PPP is an alternative glucose oxidation pathway in cytosol of RBCs, liver, adrenal, gonads, and lactating mammary gland. Oxidative phase: G6PD produces 6-phosphogluconolactone + NADPH; then 6-phosphogluconate DH produces ribulose-5-P + NADPH + CO&bdq;.
  • Non-oxidative phase: transketolase and transaldolase rearrange pentoses to F-6-P and G-3-P. Products: NADPH (reductive biosynthesis, glutathione reduction, cytochrome P450) and ribose-5-P (nucleotide synthesis).
  • G6PD deficiency is X-linked, the most common enzyme deficiency worldwide ( > 400M).
  • Oxidative stress (fava beans, sulfonamides, primaquine) -> hemolytic anemia, Heinz bodies, bite cells.
  • Protects against malaria. Diagnosis: G6PD assay (false normal during acute hemolysis due to high G6PD in reticulocytes).
TCA Cycle and Anaplerosis
  • The TCA cycle in the mitochondrial matrix oxidizes acetyl-CoA to CO&bdq;, generating NADH, FADH&bdq;, and GTP.
  • Pyruvate dehydrogenase complex (PDC, 3 enzymes + 5 cofactors: TPP, lipoic acid, CoA, FAD, NAD+) decarboxylates pyruvate to acetyl-CoA irreversibly.
  • PDC inactivated by phosphorylation (PDK) and activated by dephosphorylation (PDP).
  • TCA steps: citrate synthase (OAA + acetyl-CoA -> citrate), aconitase (citrate -> isocitrate), isocitrate dehydrogenase (isocitrate -> α-KG, rate-limiting, NADH), α-ketoglutarate dehydrogenase complex (α-KG -> succinyl-CoA, NADH), succinyl-CoA synthetase (substrate-level GTP), succinate dehydrogenase (succinate -> fumarate, FADH&bdq;, also Complex II), fumarase (fumarate -> malate), malate dehydrogenase (malate -> OAA, NADH).
  • Net: 3 NADH, 1 FADH&bdq;, 1 GTP per acetyl-CoA.
  • Anaplerotic reactions: pyruvate carboxylase (pyruvate -> OAA), transamination of aspartate/glutamate.
  • Regulation: substrate availability, NADH inhibition of isocitrate DH and α-KG DH, Ca^2 +/- activation.
Electron Transport Chain and ATP Synthesis
  • The ETC (inner mitochondrial membrane) transfers electrons from NADH/FADH&bdq; to O&bdq;.
  • Complex I (NADH -> CoQ, pumps 4 H+).
  • Complex II (succinate -> CoQ, no pumping).
  • Complex III (CoQ -> cyt c via Q cycle, pumps 4 H+).
  • Complex IV (cyt c -> O&bdq;, pumps 2 H+, reduces O&bdq; to H&bdq;O).
  • The proton gradient drives ATP synthase (Complex V, F&sub1;F&sub0;ATPase) via Boyer's binding-change mechanism (rotational catalysis).
  • P/O ratio: ~2. 5 for NADH, ~1. 5 for FADH&bdq;.
  • Inhibitors: rotenone (I), antimycin A (III), cyanide/CO/azide (IV), oligomycin (ATP synthase).
  • Uncouplers (UCP1 in brown fat, DNP) dissipate gradient -> heat.
  • ATP exported via ANT (adenine nucleotide translocase) in exchange for ADP.
High-Yield Pearls
  • Pyruvate dehydrogenase deficiency: lactic acidosis + neurological issues; treat with thiamine.
  • Von Gierke: severe fasting hypoglycemia, hepatomegaly; give cornstarch feeds.
  • McArdle: second wind phenomenon; no lactate rise on ischemic forearm test.
  • G6PD deficiency: X-linked, hemolysis with oxidative stress, Heinz bodies, bite cells.
  • Fluoroacetate -> fluorocitrate -> inhibits aconitase (lethal synthesis).
  • Brown fat UCP1 uncouples ETC for thermogenesis in neonates.
  • Cyanide: binds cytochrome a^3 in Complex IV; treat with amyl nitrite + thiosulfate.
Red Flags and Complications
  • Lactic acidosis (Type A): tissue hypoxia -> sepsis, shock; mortality > 50% if pH < 7.2.
  • Mitochondrial encephalomyopathies: MELAS (A3243G), MERRF (A8344G) - heteroplasmic mtDNA mutations.
  • Thiamine deficiency inhibits PDC, α-KGDH, transketolase -> lactic acidosis + Wernicke.
  • Arsenate: replaces phosphate in glycolysis -> arsensolysis, uncouples substrate-level phosphorylation.
  • DNP uncoupling: catastrophic hyperthermia, death.

3. Lipid Metabolism

Fatty Acid Metabolism Ketone Bodies Cholesterol Lipoproteins Eicosanoids Clinical

Fatty Acid Synthesis and β-Oxidation
  • Fatty acid synthesis occurs in cytosol using acetyl-CoA (from citrate shuttle) and NADPH (from PPP).
  • Acetyl-CoA carboxylase (ACC) catalyzes the committed step: acetyl-CoA -> malonyl-CoA (biotin-dependent).
  • ACC is activated by citrate and insulin, inactivated by palmitoyl-CoA and AMPK phosphorylation.
  • Fatty acid synthase (FAS, multifunctional homodimer) sequentially adds 2C from malonyl-CoA via condensation, reduction, dehydration, reduction cycles, producing palmitate (16:0).
  • Essential fatty acids: linoleate (ω-6) and linolenate (ω-3) must be dietary. β-Oxidation in mitochondria: carnitine shuttle (CPT1, translocase, CPT2) transports long-chain fatty acids across inner membrane.
  • CPT1 is inhibited by malonyl-CoA.
  • Each cycle: oxidation (FADH&bdq;), hydration, oxidation (NADH), thiolysis (acetyl-CoA).
  • Medium/short chains enter directly.
  • Palmitate yields ~106 ATP.
  • MCAD deficiency: most common β-oxidation defect -> hypoketotic hypoglycemia, Reye-like syndrome.
Ketone Body Metabolism and DKA
  • Ketone bodies (acetoacetate, β-hydroxybutyrate, acetone) produced in liver mitochondria when acetyl-CoA exceeds TCA capacity.
  • Ketogenesis: 2 acetyl-CoA -> acetoacetyl-CoA -> HMG-CoA (HMG-CoA synthase, rate-limiting) -> acetoacetate -> β-hydroxybutyrate (via NADH).
  • Acetone forms spontaneously.
  • Peripheral tissues (muscle, brain during starvation) use ketones via SCOT (succinyl-CoA:3-ketoacid-CoA transferase, absent in liver).
  • In DKA: insulin deficiency + glucagon excess -> massive lipolysis + ketogenesis + decreased utilization -> elevated anion gap metabolic acidosis. β-Hydroxybutyrate:acetoacetate ratio > 3:1 in DKA.
  • Treatment: insulin, IV fluids, K+ repletion.
Cholesterol Synthesis and Regulation
  • Cholesterol is essential for membranes, myelin, steroid hormones, bile acids, and vitamin D.
  • Synthesis (cytosol/ER): acetyl-CoA -> HMG-CoA -> mevalonate (HMG-CoA reductase, rate-limiting, target of statins) -> isopentenyl-PP -> farnesyl-PP -> squalene -> lanosterol -> cholesterol ( > 20 steps).
  • HMG-CoA reductase is regulated by SREBP-2 (transcriptional), phosphorylation (AMPK inactivates), and sterol-mediated degradation.
  • Statins competitively inhibit HMG-CoA reductase -> decrease hepatic cholesterol -> upregulate LDL receptors -> reduce plasma LDL.
  • Bile acids synthesized via CYP7A1 (7α-hydroxylase), conjugated with glycine/taurine, undergo enterohepatic circulation.
  • Bile acid sequestrants interrupt circulation -> promote cholesterol excretion.
Lipoprotein Metabolism
  • Lipoproteins transport hydrophobic lipids.
  • Chylomicrons (apo B-48) carry dietary TG; LPL hydrolyzes TG (activated by apo C-II) -> remnants cleared by liver via apo E/LRP.
  • VLDL (apo B-100) carries hepatic TG -> LPL -> IDL -> LDL (cholesterol-rich).
  • LDL delivers cholesterol to cells via LDL receptor (LDLR); FH results from LDLR mutations.
  • HDL mediates reverse cholesterol transport: nascent HDL (apo A-I) accepts cholesterol from cells via ABCA1 (Tangier disease), esterified by LCAT, delivered to liver via SR-BI.
  • CETP exchanges CE for TG between HDL and VLDL/LDL.
  • High HDL ( > 60 mg/dL) is cardioprotective; low HDL ( < 40 mg/dL) is a risk factor.
  • Atherogenic dyslipidemia (metabolic syndrome): elevated TG, low HDL, small dense LDL.
  • Lipoprotein(a) is a genetically determined independent CVD risk factor.
Eicosanoids: Prostaglandins, Leukotrienes and NSAIDs
  • Eicosanoids derive from arachidonic acid via phospholipase A&bdq;. COX pathway: COX-1 (constitutive, gastric protection, platelet TXA&bdq;) and COX-2 (inducible, inflammation, pain, fever) convert arachidonate to PGH&bdq;.
  • Tissue synthases produce PGE&bdq; (pain/fever), PGI&bdq; (vasodilation, anti-platelet), TXA&bdq; (vasoconstriction, platelet aggregation).
  • NSAIDs inhibit COX-1/2 (aspirin irreversibly).
  • Selective COX-2 inhibitors (celecoxib) spare GI but increase cardiovascular risk (decreased PGI&bdq;). 5-LOX pathway produces leukotrienes: LTB&acr; (chemotaxis), LTC&acr;/D&acr;/E&acr; (SRS-A, bronchoconstriction).
  • Zileuton (5-LOX inhibitor) and montelukast (cysLT1 antagonist) for asthma.
  • Aspirin-exacerbated respiratory disease (AERD): asthma + nasal polyps + NSAID sensitivity due to shunting to 5-LOX pathway.
Clinical Lipid Disorders
  • Familial hypercholesterolemia (FH): LDLR mutation -> high LDL, tendon xanthomas, premature CAD; homozygous FH -> LDL > 500 mg/dL, CAD by age 20.
  • Familial combined hyperlipidemia: elevated cholesterol + TG (VLDL overproduction).
  • Dysbetalipoproteinemia (type III): IDL accumulation, apo E2/E2, palmar/tuberoeruptive xanthomas.
  • Tangier disease: ABCA1 mutation -> very low HDL, orange tonsils, neuropathy.
  • LCAT deficiency: fish-eye disease, corneal opacities, low HDL.
  • Abetalipoproteinemia: absent chylomicrons/VLDL/LDL, acanthocytes, fat malabsorption.
  • Refsum disease: phytanic acid accumulation -> retinitis pigmentosa, neuropathy, ataxia; dietary restriction of dairy and ruminant fats.
High-Yield Pearls
  • MCAD deficiency: hypoketotic hypoglycemia + (C6-C10) acylcarnitines on newborn screen.
  • Statin side effects: myopathy (CK elevation), transaminitis; increased with CYP3A4 inhibitors.
  • PCSK9 inhibitors (evolocumab, alirocumab) ↓ LDL > 50% by increasing LDLR recycling.
  • MCT oil bypasses CPT1; used in ketogenic diet and CPT1 deficiency.
  • HMG-CoA lyase deficiency: hypoketotic hypoglycemia + organic aciduria.
  • LPL deficiency (type I): creamy plasma, TG > 1000, pancreatitis risk.
  • Fish odor syndrome: trimethylaminuria (FMO3 deficiency), avoid choline-rich foods.
Red Flags and Complications
  • DKA: cerebral edema in children; monitor mental status closely.
  • Pancreatitis from TG > 1000 -> plasmapheresis if severe.
  • Reye syndrome: aspirin + viral infection -> fatty liver + encephalopathy.
  • NASH: lipotoxicity -> cirrhosis -> HCC; leading liver transplant cause in young adults.
  • Homozygous FH: LDL apheresis needed; CVD events before age 20.

4. Protein and Amino Acid Metabolism

Transamination Urea Cycle Amino Acid Disorders One-Carbon Heme Porphyrias

Transamination and Nitrogen Disposal
  • Amino acid catabolism begins with transamination: the amino group is transferred to α-ketoglutarate to form glutamate, using PLP (B6) as cofactor.
  • ALT (alanine transaminase) converts alanine + α-KG -> pyruvate + glutamate.
  • AST (aspartate transaminase) converts aspartate + α-KG -> OAA + glutamate.
  • ALT is more liver-specific; AST also in heart, muscle, RBCs.
  • Glutamate enters mitochondria where glutamate dehydrogenase (GDH) releases NH&acr;+ (oxidative deamination).
  • Glutamine synthetase fixes ammonia into glutamine (nontoxic transport form).
  • In kidney glutaminase releases NH&acr; for acid-base regulation.
  • The α-ketoacids become metabolic intermediates: glucogenic (to pyruvate/TCA), ketogenic (to acetyl-CoA/acetoacetate), or both.
  • Leucine and lysine are purely ketogenic; the rest are glucogenic or mixed.
The Urea Cycle and Hyperammonemia
  • The urea cycle converts toxic ammonia to urea in liver (periportal hepatocytes).
  • CPS-I (mitochondrial, rate-limiting, activated by N-acetylglutamate) condenses NH&acr;+ + CO&bdq; + 2 ATP -> carbamoyl phosphate.
  • OTC (X-linked, most common deficiency) -> citrulline.
  • ASS -> argininosuccinate.
  • ASL -> arginine + fumarate.
  • ARG1 -> urea + ornithine.
  • Ornithine returns via ORNT1 transporter. Deficiencies: CPS-I -> hyperammonemia; OTC deficiency -> severe neonatal hyperammonemia + orotic aciduria; ASS -> citrullinemia; ASL -> argininosuccinic aciduria; ARG1 -> argininemia (milder).
  • Treatment: ammonia scavengers (sodium benzoate, phenylacetate), arginine supplementation, hemodialysis, protein restriction.
Amino Acid Disorders: PKU, MSUD, Homocystinuria
  • Phenylketonuria (PKU): phenylalanine hydroxylase (PAH) deficiency -> Phe accumulation -> intellectual disability, microcephaly, seizures, fair skin, musty odor; newborn screen (tandem MS); treat with Phe-restricted diet + sapropterin.
  • Maternal PKU: high Phe in pregnancy -> microcephaly, IUGR, CHD.
  • Maple syrup urine disease (MSUD): BCKDH deficiency -> branched-chain amino acids accumulate -> maple syrup odor, neonatal encephalopathy, hypoglycemia, acidosis; treat with dietary restriction + thiamine (some responsive).
  • Homocystinuria: cystathionine β-synthase (CBS) deficiency -> homocysteine + methionine elevated; features: ectopia lentis (downward), marfanoid habitus, thromboembolism, intellectual disability; 50% respond to pyridoxine.
  • Alkaptonuria: homogentisate dioxygenase deficiency -> homogentisic acid -> ochronosis, dark urine (black on standing), degenerative arthritis; treat with nitisinone. Tyrosinemia type I: FAH deficiency -> liver failure, renal tubular dysfunction; treat with nitisinone.
One-Carbon Metabolism and the SAM Cycle
  • One-carbon metabolism involves THF (from folate) carrying formyl, methylene, or methyl groups for nucleotide and amino acid metabolism. 10-Formyl-THF: purine synthesis. 5,10-Methylene-THF: thymidine synthesis (via thymidylate synthase, target of 5-FU). 5-Methyl-THF: homocysteine remethylation (methionine synthase, B12-dependent).
  • DHFR converts folate to THF (inhibited by methotrexate).
  • The methionine cycle: methionine -> SAM (universal methyl donor) -> SAH -> homocysteine.
  • Homocysteine is either remethylated (B12/folate) or transsulfurated (CBS, B6-dependent) to cysteine.
  • Elevated homocysteine is an independent CVD risk factor.
  • MTHFR deficiency (C677T variant) causes mild hyperhomocysteinemia; folate supplementation lowers homocysteine.
  • Severe MTHFR deficiency -> homocystinuria without ectopia lentis.
Heme Synthesis and Porphyrias
  • Heme synthesis spans mitochondria and cytosol.
  • ALAS (rate-limiting, PLP-dependent) condenses glycine + succinyl-CoA -> ALA.
  • ALAS1 (liver, feedback-regulated by heme); ALAS2 (erythroid, regulated by iron).
  • Subsequent steps: ALA dehydratase (inhibited by lead) -> PBG -> hydroxymethylbilane (PBG deaminase, deficient in AIP) -> uroporphyrinogen III -> coproporphyrinogen III -> protoporphyrin IX + Fe^2 +/- (ferrochelatase, inhibited by lead) -> heme.
  • Acute intermittent porphyria (AIP): PBG deaminase deficiency -> acute attacks (abdominal pain, neuropsychiatric, autonomic instability), triggered by drugs (barbiturates, sulfa), fasting; diagnose by elevated PBG/ALA; treat with hemin + glucose.
  • Porphyria cutanea tarda (PCT): uroporphyrinogen decarboxylase deficiency -> photosensitivity, bullae, hypertrichosis; associated with HCV, alcohol, Fe overload; treat with phlebotomy.
  • Lead poisoning: inhibits ALA-D and ferrochelatase -> elevated ALA + FEP, microcytic anemia, basophilic stippling, encephalopathy; treat with chelation.
Clinical: Neonatal Screening and Ammonia Toxicity
  • Newborn screening via tandem MS detects PKU, MSUD, homocystinuria, tyrosinemia, MCAD, and many organic acidemias.
  • Early treatment prevents irreversible damage (PKU diet before 3 weeks prevents intellectual disability).
  • Hyperammonemia in adults: progressive confusion, lethargy, vomiting, cerebral edema.
  • Acquired causes: liver failure, valproate, portosystemic shunts, parenteral nutrition.
  • Hepatic encephalopathy grades I - IV: from personality changes to coma.
  • Ammonia causes astrocyte swelling via glutamine accumulation.
  • Treatment: lactulose (acidifies colon, traps NH&acr;+), rifaximin, protein restriction (avoid catabolism), zinc.
  • Acute severe hyperammonemia ( > 150 - 200 μmol/L with encephalopathy) -> hemodialysis + ammonia scavengers.
High-Yield Pearls
  • OTC deficiency: X-linked, hyperammonemia + orotic aciduria + low citrulline.
  • PKU: elevated Phe > 120 μmol/L on newborn screen; Phe/Tyr ratio diagnostic.
  • Homocystinuria: downward lens dislocation + thromboembolism; differentiate from Marfan (no lens issues).
  • Alkaptonuria: dark urine with NaOH; adult-onset ochronotic arthropathy.
  • AIP: abdominal pain + neuropsychiatric + reddish urine (Watson-Schwartz positive).
  • Lead poisoning: basophilic stippling, elevated FEP, microcytic anemia.
  • Nitrogen balance: positive in growth/pregnancy; negative in starvation/stress.
Red Flags and Complications
  • Neonatal hyperammonemia > 200 μM -> hemodialysis + scavengers urgently.
  • AIP: avoid barbiturates, sulfonamides, estrogens, starvation; give hemin.
  • Methotrexate toxicity: leucovorin rescue; renal impairment increases toxicity.
  • Tyrosinemia type I: high HCC risk; treat with nitisinone.
  • PCT: avoid alcohol, estrogens, iron; screen for HCV.

5. Enzymology

Classification Kinetics Inhibition Regulation Isoenzymes Clinical Diagnostics

Enzyme Classification and Active Sites
  • Enzymes accelerate reactions by lowering activation energy (G^1†).
  • IUBMB classifies into 6 EC classes: Oxidoreductases (EC 1), Transferases (EC 2), Hydrolases (EC 3), Lyases (EC 4), Isomerases (EC 5), Ligases (EC 6).
  • Many require cofactors: coenzymes (organic, e. g. , NAD+, FAD, PLP, biotin, THF) and metal ions (Zn^2 +/-, Mg^2 +/-, Fe^2 +/-).
  • Apoenzyme + cofactor = holoenzyme.
  • The active site is a 3D cleft with catalytic residues and binding determinants, exhibiting specificity (lock-and-key vs induced fit).
  • Catalytic efficiency = kcat/Km; diffusion-controlled limit ~10&sup8; - 10&sup9; M−^1s−^1.
Michaelis-Menten Kinetics and Lineweaver-Burk
  • Michaelis-Menten: v = Vmax [S] / (Km + [S]).
  • Vmax = kcat[E]total at saturation.
  • Km = [S] at half-Vmax, inversely related to binding affinity.
  • Turnover number kcat = Vmax/[E]total.
  • Catalytic efficiency kcat/Km defines substrate specificity.
  • Lineweaver-Burk plot: 1/v = (Km/Vmax)(1/[S]) + 1/Vmax; y-intercept = 1/Vmax, x-intercept = −1/Km.
  • Factors affecting activity: temperature (Q&sub1;&sub0; ~2 per 10 degrees C), pH (optimum varies: pepsin ~2, ALP ~10), ionic strength.
  • Multi-substrate kinetics: sequential (ordered Bi-Bi, e. g. , LDH) and ping-pong (e. g. , ALT).
Enzyme Inhibition: Types and Clinical Relevance
  • Competitive: resembles substrate, binds active site; Vmax unchanged, Km increases; overcome by high [S]; drugs: statins, methotrexate, ACE inhibitors, ethanol for methanol poisoning.
  • Noncompetitive: binds distinct site; Vmax decreases, Km unchanged.
  • Uncompetitive: binds ES complex only; both Vmax and Km decrease.
  • Mixed: binds free E and ES differently.
  • Irreversible: covalent modification; examples: aspirin (acetylates COX), organophosphates (AChE, treat with atropine + pralidoxime), penicillin (transpeptidase), omeprazole (proton pump), MAO inhibitors.
  • Suicide inhibition: mechanism-based; examples: 5-FU (thymidylate synthase), isoniazid (InhA), clavulanic acid.
Enzyme Regulation Mechanisms
  • Allosteric regulation: effectors bind at regulatory sites distinct from active site.
  • Homotropic (substrate as effector, e. g. , O&bdq; binding to hemoglobin is cooperative, sigmoidal kinetics) vs heterotropic (different molecule). ATCase: CTP inhibits, ATP activates (sigmoidal kinetics).
  • Concerted (MWC) and sequential (KNF) models explain cooperativity.
  • Covalent modification: phosphorylation (kinases/phosphatases), e. g. , glycogen phosphorylase (phosphorylation activates), glycogen synthase (phosphorylation inactivates), PDC (phosphorylation inactivates).
  • Other modifications: acetylation, ubiquitination, palmitoylation, ADP-ribosylation.
  • Zymogen activation: limited proteolysis converts inactive precursors, e. g. , trypsinogen -> trypsin, prothrombin -> thrombin.
  • Compartmentation: separates pathways (glycolysis cytosol, TCA mitochondria).
  • Rate-limiting enzymes: early irreversible steps (PFK-1, HMG-CoA reductase, CPS-I).
Isoenzymes: CK, LDH, ALP
  • Creatine kinase (CK): dimer of M and B subunits.
  • CK-MM (skeletal muscle, > 95%), CK-MB (myocardium, best MI marker, rises 4 - 6h, peaks 12 - 24h), CK-BB (brain).
  • Relative index (CK-MB/total CK) > 2. 5 - 3 suggests cardiac origin.
  • Lactate dehydrogenase (LDH): tetramer of H and M subunits.
  • LDH1 (heart/RBC), LDH2, LDH3 (lung), LDH4, LDH5 (liver/skeletal muscle).
  • LDH1 > LDH2 (flipped) in MI, hemolysis, renal infarct.
  • Alkaline phosphatase (ALP): bone (osteoblast activity, elevated in Paget disease, fractures), liver (cholestasis), intestine, placental.
  • Heat stability: placental > liver > bone > intestine.
  • ALP + GGT elevation confirms liver origin.
  • Prostate ACP replaced by PSA.
  • Amylase (P-type pancreatic, S-type salivary) and lipase: lipase more specific for pancreatitis.
Clinical Enzyme Diagnostics
  • MI: troponin (gold standard), CK-MB, LDH (LDH1 > LDH2). Liver disease: ALT (hepatocyte injury, highest in acute viral hepatitis), AST (AST > ALT with ratio >= 2 suggests alcoholic liver disease), ALP + GGT (cholestasis). Bone disease: ALP, TRACP (osteoclast activity).
  • Pancreatitis: lipase > amylase.
  • Muscle: CK-MM (massive in Duchenne dystrophy).
  • Inborn errors: enzyme assays in leukocytes/fibroblasts.
  • CYP450 genetic variants (CYP2D6, CYP2C19, CYP3A4) affect drug metabolism.
  • Therapeutic drug monitoring ensures safe drug levels.
High-Yield Pearls
  • LDH1 > LDH2 (flipped): MI, hemolysis, renal infarct.
  • CK-MB rises 4 - 6h post-MI, peaks 12 - 24h; relative index > 2.5 - 3 suggests cardiac.
  • GGT induced by alcohol, phenytoin, rifampin; confirms liver origin of elevated ALP.
  • ALT > AST: acute viral hepatitis; AST > ALT ratio >= 2: alcoholic liver disease.
  • Km approximates physiological [substrate] for many enzymes.
  • Competitive inhibition: same Vmax, higher apparent Km; overcome by increasing [S].
  • Zymogen activation provides rapid amplification in coagulation/digestion.
Red Flags and Complications
  • Macro-CK: CK bound to IgG, persistently elevated CK without disease.
  • CK-MM > 100,000 U/L in rhabdomyolysis -> AKI risk; aggressive IVF.
  • Troponin elevates in PE, HF, myocarditis, renal failure - not specific for MI.
  • Organophosphate: AChE inhibition -> SLUDGE + paralysis; atropine + pralidoxime.
  • Malignant hyperthermia: RYR1 mutation, volatile anesthetics -> dantrolene.

6. Vitamins and Coenzymes

Fat-Soluble Water-Soluble Deficiencies Toxicity Clinical Syndromes

Vitamin A and Vitamin D
  • Vitamin A (retinol, retinal, retinoic acid): sources (liver, carrots, leafy greens, β-carotene).
  • Functions: vision (11-cis-retinal in rhodopsin for phototransduction), gene expression (RAR/RXR), immunity, epithelial integrity.
  • RDA: 900 μg (men), 700 μg (women).
  • Deficiency: night blindness, xerophthalmia (Bitot spots, keratomalacia -> blindness), follicular hyperkeratosis, impaired immunity.
  • Toxicity (hypervitaminosis A): pseudotumor cerebri, hepatotoxicity, teratogenicity.
  • Vitamin D (D^3 cholecalciferol, D&bdq; ergocalciferol): sources (sunlight, fatty fish, fortified milk).
  • Functions: Ca/PO´ homeostasis via 25-OH-D (liver) -> 1,25-(OH)&bdq;D (kidney, stimulated by PTH). Receptor: VDR (nuclear). RDA: 600 IU ( 70).
  • Deficiency: rickets (children -> bowed legs, rachitic rosary, craniotabes), osteomalacia (adults -> bone pain, Looser zones, proximal weakness).
  • Labs: low 25-OH-D, low Ca/PO´, elevated ALP, elevated PTH.
  • Toxicity: hypercalcemia, nephrolithiasis (only from supplements).
Vitamin E and Vitamin K
  • Vitamin E (α-tocopherol): antioxidant, protects membranes from lipid peroxidation. RDA: 15 mg.
  • Deficiency: hemolytic anemia (neonates), peripheral neuropathy, ataxia (in abetalipoproteinemia, cholestatic liver disease).
  • Vitamin K (K&sub1; phylloquinone from greens, K&bdq; menaquinone from bacteria): cofactor for γ-glutamyl carboxylase -> activates factors II, VII, IX, X and proteins C, S, Z (carboxylates Glu -> Gla for Ca^2 +/- binding).
  • Also bone osteocalcin.
  • RDA: 120 μg (men), 90 μg (women).
  • Deficiency: elevated PT/INR, bleeding (neonatal hemorrhagic disease, malabsorption, warfarin).
  • Warfarin inhibits vitamin K epoxide reductase.
  • Neonatal IM vitamin K is routine prophylaxis.
  • Treatment: vitamin K supplementation.
Vitamin B&sub1; (Thiamine), B&bdq; (Riboflavin), B^3 (Niacin)
  • Thiamine (B&sub1;) as TPP cofactor: PDC, α-KGDH, transketolase, BCKDH.
  • Sources: whole grains, pork, legumes.
  • RDA: 1. 2 mg (men), 1. 1 mg (women).
  • Deficiency (beriberi): dry -> peripheral neuropathy; wet -> high-output heart failure.
  • Wernicke-Korsakoff: acute confusion + ataxia + ophthalmoplegia -> amnestic-confabulatory syndrome.
  • Give IV thiamine BEFORE glucose.
  • Riboflavin (B&bdq;) as FMN/FAD for redox reactions.
  • Sources: dairy, eggs, organ meats.
  • RDA: 1. 3 mg (men), 1. 1 mg (women).
  • Deficiency: angular stomatitis, glossitis, seborrheic dermatitis, corneal vascularization.
  • Niacin (B^3) as NAD+/NADP+ for dehydrogenases.
  • Can be synthesized from tryptophan (60 mg Trp -> 1 mg niacin).
  • RDA: 16 mg NE (men), 14 mg (women).
  • Pellagra: 4 Ds - dermatitis (photosensitive, Casal necklace), diarrhea, dementia, death.
  • Treatment: niacin 50 - 100 mg TID.
  • High-dose niacin lowers TG/ LDL and raises HDL but causes flushing (prostaglandin-mediated, reduced by aspirin), hepatotoxicity, hyperglycemia.
Vitamin B&sub5;, B&sub6;, B&sub7;, B&sub9;, B&sub1;&sub2;
  • Pantothenic acid (B&sub5;): component of CoA and ACP; deficiency rare (burning feet syndrome). RDA: 5 mg.
  • Pyridoxine (B&sub6;) as PLP cofactor: transaminases, decarboxylases, heme synthesis (ALAS), homocysteine metabolism (CBS).
  • Sources: meat, fish, potatoes.
  • RDA: 1. 3 - 2. 0 mg.
  • Deficiency: microcytic anemia, peripheral neuropathy, seizures (infants), homocystinemia.
  • Isoniazid causes B6 deficiency -> give 25 - 50 mg/d prophylaxis.
  • Toxicity ( > 200 mg/day): irreversible sensory neuropathy.
  • Biotin (B&sub7;): carboxylase cofactor (ACC, pyruvate carboxylase, PCC, MCC).
  • Egg white avidin binds biotin. RDA: 30 μg.
  • Deficiency: periorificial dermatitis, alopecia, lactic acidosis.
  • Folate (B&sub9;): THF for one-carbon metabolism (nucleotide synthesis, homocysteine remethylation).
  • Sources: leafy greens, fortified grains.
  • RDA: 400 μg (600 μg pregnancy).
  • Deficiency: megaloblastic anemia, glossitis, NTDs (spina bifida, anencephaly), elevated homocysteine.
  • Periconceptional folate 400 μg/day reduces NTD risk by > 50%.
  • Vitamin B12 (cobalamin): absorption requires IF (parietal cells), absorbed in terminal ileum.
  • Functions: methionine synthase (homocysteine -> methionine) and methylmalonyl-CoA mutase (MMA -> succinyl-CoA).
  • Sources: animal products only. RDA: 2. 4 μg.
  • Deficiency: megaloblastic anemia + subacute combined degeneration (dorsal columns -> vibration/proprioception loss, corticospinal tracts -> spasticity).
  • Causes: pernicious anemia (autoimmune, anti-IF antibodies), atrophic gastritis, vegan diet, metformin.
  • Diagnosis: low B12, elevated MMA and homocysteine. Treat: IM B12.
  • Correct B12 before folate to avoid masking B12 deficiency and precipitating neurologic damage.
Vitamin C (Ascorbic Acid)
  • Vitamin C is a water-soluble antioxidant and cofactor for hydroxylation reactions: collagen synthesis (proline/lysine hydroxylation, Fe^2 +/- + α-KG dependent), carnitine synthesis, dopamine -> norepinephrine, tyrosine metabolism.
  • Enhances non-heme iron absorption.
  • Sources: citrus, strawberries, bell peppers.
  • RDA: 90 mg (men), 75 mg (women), +35 mg smokers.
  • Scurvy: defective collagen -> perifollicular hemorrhages, petechiae, ecchymoses, gingival swelling/bleeding, coiled hairs, poor wound healing, bone pain (subperiosteal hemorrhage), pseudoparalysis in infants.
  • Treatment: ascorbic acid 100 - 200 mg/day.
  • Labs: low plasma/leukocyte vitamin C.
  • Other micronutrients: choline, carnitine, α-lipoic acid, CoQ10, molybdenum.
Clinical Deficiency Syndromes
  • Wernicke-Korsakoff (B&sub1;): emergency IV thiamine 500 mg TID before glucose.
  • Beriberi: wet (cardiac) and dry (neurological).
  • Megaloblastic anemia (B9/B12): macrocytic (MCV > 100), hypersegmented neutrophils, LDH elevated.
  • Pernicious anemia: autoimmune gastritis, anti-parietal cell/IF antibodies, associated with other autoimmune disorders; increased gastric carcinoma risk.
  • Pellagra (B^3): 4 Ds + Casal necklace.
  • Osteomalacia/rickets (D): Looser zones, pseudofractures; treat with 50,000 IU/week vitamin D x 8 weeks.
  • Scurvy (C): perifollicular hemorrhages, corkscrew hairs, gum hypertrophy.
  • Biotin deficiency: periorificial rash + alopecia; biotinidase deficiency on newborn screen, treat with oral biotin 5 - 20 mg/day.
  • Vitamin K deficiency: prolonged PT/INR; treat with vitamin K.
High-Yield Pearls
  • Wernicke: confusion + ataxia + ophthalmoplegia; Korsakoff: amnestic-confabulatory.
  • Pellagra: 4 Ds + Casal necklace; think corn-based diets.
  • Correct B12 BEFORE folate to avoid precipitating neurologic damage.
  • Subacute combined degeneration: dorsal columns + corticospinal tracts.
  • Rickets: frontal bossing, rachitic rosary, Harrison groove, bowed legs.
  • Megaloblastic anemia: oval macrocytes + hypersegmented neutrophils + elevated LDH.
  • Isoniazid causes B6 deficiency -> give pyridoxine 25 - 50 mg/day prophylaxis.
Red Flags and Complications
  • Thiamine before glucose: giving glucose first in thiamine deficiency can precipitate Wernicke.
  • Vitamin A toxicity: pseudotumor cerebri; avoid > 10,000 IU/day in pregnancy (teratogenic).
  • Niacin flushing: give aspirin 30 min before; hepatotoxicity at > 2 g/day.
  • Nitrous oxide oxidizes B12, can precipitate acute neurological damage with subclinical B12 deficiency.
  • Warfarin reversal: vitamin K; fresh frozen plasma/PCC for life-threatening bleeding.

7. Molecular Biology

DNA Structure Replication Transcription Translation DNA Repair Clinical Genetics

DNA Structure, Supercoiling and Topoisomerases
  • DNA is a double helix (Watson-Crick, 1953): antiparallel strands, right-handed B-form helix (10 bp/turn, 3. 4 nm pitch, 2 nm diameter), complementary base pairing (A=T via 2 H-bonds, G≡C via 3 H-bonds).
  • Major groove (wider, more available for protein interactions) and minor groove. Alternative forms: A-DNA (short, wide, dehydrated) and Z-DNA (left-handed, zigzag, alternating purine-pyrimidine).
  • Supercoiling: negative supercoiling in vivo facilitates strand separation. Topoisomerases: Topo I (relaxes negative supercoils via single-strand break), Topo II (DNA gyrase in bacteria introduces negative supercoils; Topo IIα in eukaryotes relieves supercoils via double-strand break).
  • Inhibitors: quinolones (gyrase), etoposide/doxorubicin (Topo II, anticancer).
  • Histones package DNA into nucleosomes (147 bp around histone octamer: 2 x H2A, H2B, H3, H4), linked by H1.
  • Higher-order chromatin: 30 nm fiber -> loops -> territories.
  • Heterochromatin (condensed, inactive) vs euchromatin (open, active). Telomeres: TTAGGG repeats protected by shelterin; shorten with division.
  • Telomerase (TERT + TR RNA template) active in germ/stem cells and most cancers.
DNA Replication
  • Semi-conservative replication (Meselson-Stahl).
  • Initiation at origins (oriC in E. coli).
  • Replication fork: helicase (DnaB, MCM complex) unwinds; SSB/RPA stabilize single strands; topoisomerase relieves supercoils.
  • Primase (DnaG) synthesizes RNA primers.
  • DNA Pol III (E. coli, high processivity via β-clamp) adds dNTPs 5′ -> 3′.
  • Leading strand: continuous.
  • Lagging strand: Okazaki fragments.
  • Pol I removes RNA primers, fills gaps. Ligase seals nicks.
  • Eukaryotic: multiple origins (ARS), Pol α/primase (initiation), Pol δ (lagging), Pol ε (leading).
  • PCNA = sliding clamp, RFC loads it. Licensing: ORC, Cdc6, Cdt1 load MCM in G1; geminin and CDK prevent re-replication.
  • Fidelity: 3′ -> 5′ proofreading (Pol III ε, Pol δ, Pol ε) reduces errors to ~10−&sup7;; MMR further improves to ~10−&sup9;.
  • Telomerase adds TTAGGG repeats to prevent end-replication problem.
Transcription and RNA Processing
  • Transcription produces RNA 5′ -> 3′. RNA polymerases: Pol I (rRNA, nucleolus), Pol II (mRNA, snRNA, nucleoplasm), Pol III (tRNA, 5S rRNA, U6 snRNA).
  • E. coli: core enzyme (α&bdq;ββ′ω) + σ factor (e. g. , σ&sup7;&sub0; for most genes, binds −10 Pribnow and −35 boxes). Pol II promoters: TATA box (−30, bound by TBP/TFIID), Inr, DPE.
  • Enhancers (distal, orientation-independent) interact via looping with mediators/cohesins.
  • GTFs (TFIIA, B, D, E, F, H) assemble Pol II; TFIIH has helicase (XPB/XPD) and CTD kinase (CDK7). Elongation: CTD Ser5-P (initiation), Ser2-P (elongation).
  • Termination: poly-A signal (AAUAAA) -> cleavage + poly-A polymerase adds ~200 A residues. 5′ Capping: 7-methylguanosine, protects from exonucleases, enhances translation.
  • Splicing: spliceosome (snRNPs U1, U2, U4, U5, U6) removes introns via lariat intermediate.
  • Alternative splicing > 90% of human genes. RNA editing: APOBEC1 (C -> U in apoB), ADAR (A -> I).
Translation and Protein Synthesis
  • Translation on ribosomes: 70S (prokaryotes, 50S+30S) vs 80S (eukaryotes, 60S+40S). tRNA: cloverleaf structure, anticodon, 3′ CCA.
  • Aminoacyl-tRNA synthetases charge tRNAs (one per aa).
  • Wobble hypothesis: 5′ anticodon base pairs non-standardly with 3′ codon base.
  • Initiation: prokaryotes -> Shine-Dalgarno + fMet-tRNA; eukaryotes -> Kozak consensus + Met-tRNA, eIF4E cap binding, eIF2-GTP-Met-tRNA ternary complex (key regulation).
  • Elongation: A-site entry (EF-Tu/eEF1A), peptide bond (peptidyl transferase = ribozyme), translocation (EF-G/eEF2).
  • Termination: stop codons (UAA, UAG, UGA) -> release factors (RF1/2, eRF1).
  • Polysomes: multiple ribosomes on one mRNA. Signal hypothesis: SRP binds signal peptide -> SRP receptor on ER -> Sec61 translocon -> co-translational translocation.
  • Post-translational modifications: phosphorylation, glycosylation, acetylation, ubiquitination, proteolysis, disulfide bonds.
DNA Repair Pathways
  • Direct reversal: MGMT (O&sup6;-methylguanine repair). BER: DNA glycosylase detects damaged base -> AP endonuclease -> Pol β fills -> ligase (uracil, 8-oxoguanine). NER: XPC recognizes distortion -> TFIIH unwinds -> XPA verifies -> XPF/ERCC1 + XPG cut 24 - 32 nt lesion -> Pol δ/ε fills (pyrimidine dimers, bulky adducts). MMR: MSH2/MSH6 recognizes mismatch -> MLH1/PMS2 recruits EXO1 -> excision -> resynthesis (replication errors). DSB repair: HR (error-free, S/G2, BRCA1/2, RAD51) vs NHEJ (error-prone, G1, Ku70/80, DNA-PKcs, XRCC4, ligase IV).
  • Defects: xeroderma pigmentosum (NER -> UV sensitivity, skin cancer), Cockayne syndrome (TC-NER -> progeroid), BRCA1/2 (HR -> breast/ovarian cancer, PARP inhibitor sensitivity), Lynch syndrome (MMR -> MSI, colon cancer), Ataxia telangiectasia (ATM -> radiosensitivity, neurodegeneration, cancer).
Clinical: PCR, Blotting and Cancer Genetics
  • PCR: denature (94 degrees C) -> anneal (50 - 65 degrees C) -> extend (72 degrees C); 30 - 40 cycles amplify DNA exponentially. qPCR/RT-PCR: quantify RNA.
  • Sanger sequencing: ddNTPs terminate chains, 4-color capillary electrophoresis.
  • NGS: massively parallel sequencing. Southern blot: DNA -> restriction -> gel -> membrane -> probe. Northern: RNA.
  • Western: protein (SDS-PAGE -> antibody).
  • CRISPR-Cas9: gene editing via gRNA + Cas9.
  • Cancer genetics: oncogenes (Ras, Myc, EGFR, BRAF), tumor suppressors (p53, Rb, APC, PTEN), DNA repair (BRCA, MSH).
  • Knudson two-hit hypothesis. p53: guardian of genome, mutated in > 50% cancers.
  • EGFR in NSCLC -> gefitinib/erlotinib.
  • BRAF V600E in melanoma -> vemurafenib.
  • BCR-ABL in CML -> imatinib.
  • PARP inhibitors: synthetic lethality in BRCA-deficient cancers.
High-Yield Pearls
  • Xeroderma pigmentosum: NER defect -> skin cancer > 1000-fold increased risk.
  • BRCA1/2: HR repair defect -> PARP inhibitor synthetic lethality.
  • Lynch syndrome: MMR defect -> microsatellite instability, colon cancer.
  • Wobble hypothesis: 3′ base of codon less specific; 5′ anticodon base wobbles.
  • Telomerase: active in germ/stem cells and ~85% of cancers.
  • Shine-Dalgarno (prokaryotic) vs Kozak (eukaryotic) translation initiation sequences.
  • p53 most commonly mutated gene in human cancer.
Red Flags and Complications
  • Ataxia telangiectasia: ATM mutation -> cerebellar degeneration, telangiectasias, lymphoma.
  • Cockayne syndrome: TC-NER defect -> progeroid features, severe neuro impairment.
  • Fanconi anemia: DNA crosslink repair defect -> bone marrow failure, cancer.
  • Ribosomopathies: Diamond-Blackfan anemia, Shwachman-Diamond -> bone marrow failure.
  • mtDNA mutations: heteroplasmy, maternal inheritance, threshold effect.

8. Genetics and Gene Regulation

Mendelian Inheritance Mutations Epigenetics Gene Expression Genetic Counseling

Mendelian Inheritance Patterns
  • Autosomal dominant: single allele sufficient (NF1, Huntington, Marfan, FH); vertical transmission, 50% offspring risk, variable expressivity, incomplete penetrance.
  • Autosomal recessive: two alleles (CF, sickle cell, PKU, Tay-Sachs, Wilson); horizontal transmission, 25% risk, consanguinity increases risk.
  • X-linked recessive: affected males (Duchenne, hemophilia A/B, G6PD, OTC, color blindness); no male-to-male transmission, 50% sons of carriers affected. X-linked dominant: Rett, X-linked hypophosphatemic rickets; more severe in males. Y-linked: SRY, male infertility.
  • Mitochondrial: maternal inheritance, heteroplasmy, threshold (MELAS, MERRF, LHON).
  • Anticipation: trinucleotide repeat expansions (Huntington, myotonic dystrophy, fragile X).
  • Genetic heterogeneity: same phenotype from different genes.
  • Pleiotropy: one gene, multiple effects.
Chromosomes, Cell Cycle and Mutations
  • Human genome: 3. 2 Gb, ~20,000 protein-coding genes.
  • Karyotype: 46,XX or 46,XY. Cell cycle: G1-S-G2-M.
  • CDK-cyclin complexes: CDK4/6-cyclin D (G1), CDK2-cyclin E (G1/S), CDK2-cyclin A (S), CDK1-cyclin B (G2/M).
  • Checkpoints: G1/S (Rb-p53 pathway), G2/M (DNA damage), M (spindle). p53 -> p21 -> inhibits CDKs -> Rb binds E2F -> blocks S-phase.
  • Mutation types: synonymous, missense (conservative/non-conservative), nonsense, frameshift, splice site, promoter.
  • Trinucleotide repeats: CAG (Huntington), CGG (fragile X), CTG (myotonic dystrophy).
  • Chromosomal: deletions (Cri-du-chat 5p), translocations (Philadelphia t(9;22)), aneuploidy (trisomies 21/18/13, Turner 45,X, Klinefelter 47,XXY).
  • Uniparental disomy: both copies from one parent -> Prader-Willi/Angelman.
Epigenetics: Methylation, Imprinting and Histone Modification
  • Epigenetics: heritable changes without DNA sequence alteration. DNA methylation: CpG islands methylated by DNMTs (DNMT1 maintenance, DNMT3A/3B de novo) at cytosine -> 5-methylcytosine.
  • Hypermethylation silences genes; hypomethylation activates.
  • Histone modifications: acetylation (HAT -> open chromatin/active, HDAC -> closed/repressed), methylation (H3K4me3 active, H3K9me3/H3K27me3 repressive), phosphorylation, SUMOylation.
  • Histone code hypothesis: combinatorial marks determine state.
  • Imprinting: parent-of-origin expression.
  • Prader-Willi: paternal 15q deletion -> hypotonia, obesity, ID.
  • Angelman: maternal 15q deletion -> severe ID, ataxia, happy demeanor.
  • Beckwith-Wiedemann (11p15. 5): paternal -> overgrowth, Wilms tumor.
  • Silver-Russell: maternal -> IUGR. X-inactivation: XIST RNA random inactivates one X -> Barr body; skewed inactivation unmasks X-linked disorders.
Gene Expression Regulation and the lac Operon
  • Prokaryotic regulation: lac operon (Jacob-Monod). lacZ (β-galactosidase), lacY (permease), lacA (transacetylase).
  • Repressor (lacI) binds operator -> blocks transcription in absence of lactose.
  • Allolactose binds repressor -> releases -> transcription.
  • Catabolite repression: glucose ↓ -> ↑ cAMP -> CAP-cAMP binds -> stimulates transcription.
  • Trp operon: attenuation via ribosome stalling alters mRNA structure.
  • Eukaryotic: TFs bind specific sequences; combinatorial control.
  • Enhancers interact with promoters via looping (cohesin, mediator).
  • Chromatin remodeling: SWI/SNF, ISWI, CHD complexes.
  • Non-coding RNAs: miRNA (DROSHA/DICER -> RISC -> mRNA degradation/translational repression), siRNA (RNAi), lncRNA (XIST, HOTAIR).
  • Alternative splicing polyadenylation, RNA editing.
  • RNA-binding proteins regulate stability and translation (ARE-mediated decay, IRES).
Inborn Errors and Hardy-Weinberg
  • Inborn errors of metabolism (Garrod): enzyme defects cause substrate accumulation/product deficiency.
  • Categories: amino acidopathies (PKU, MSUD), organic acidemias, FAO defects, lysosomal storage diseases (Tay-Sachs, Gaucher, Niemann-Pick, Fabry, Hurler), peroxisomal (Zellweger, X-ALD), mitochondrial.
  • Newborn screening via tandem MS enables early detection.
  • Hardy-Weinberg: p^2 + 2pq + q^2 = 1.
  • Assumptions: large population, random mating, no mutation/selection/migration.
  • For AR disease (incidence = q^2), carrier frequency = 2pq approx 2q.
  • For AD disease: incidence approx 2pq.
  • For X-linked: q = male incidence, 2q = carrier frequency.
  • HW deviations indicate selection, inbreeding, stratification.
  • Consanguinity ↑ AR risk (first cousins share 1/8 alleles).
Clinical: Genetic Counseling and Testing
  • Genetic counseling: nondirective communication of risks, diagnostic options, management. Indications: AMA, family history, multiple miscarriages, abnormal prenatal screen, carrier status, consanguinity, ethnicity (CF Caucasian, Tay-Sachs Jewish, sickle cell African, thalassemia Mediterranean). Prenatal: NIPT (cfDNA), CVS (10 - 12 wk), amniocentesis (15 - 20 wk). PGD: IVF + embryo biopsy.
  • Predictive: presymptomatic (Huntington), predisposition (BRCA).
  • Testing: karyotype, FISH, CMA, Sanger, NGS panels, WES/WGS.
  • GWAS: common variants for complex traits. Pharmacogenomics: CYP variants, TPMT (thiopurine), UGT1A1 (irinotecan), HLA-B*5701 (abacavir HSR), VKORC1/CYP2C9 (warfarin), DPYD (5-FU toxicity).
  • Ethical: consent, confidentiality, discrimination, psychological impact.
High-Yield Pearls
  • Prader-Willi: paternal deletion 15q; Angelman: maternal deletion 15q (same region, imprinting).
  • Huntington: CAG repeat, anticipation, AD; onset inversely with repeat length.
  • Fragile X: CGG repeat (FMR1), methylation silences, X-linked, macroorchidism, long face.
  • Lysosomal storage: Niemann-Pick (cherry red spot), Gaucher (Gaucher cells), Fabry (angiokeratomas).
  • HW: carrier freq = 2q for AR; q = sqrt incidence for rare diseases.
  • Tay-Sachs: Hex A deficiency, GM&bdq;, cherry red spot, Ashkenazi Jewish.
  • Pharmacogenomics: HLA-B*5701 -> abacavir HSR; TPMT -> 6-MP toxicity.
Red Flags and Complications
  • Triple repeat diseases: anticipation -> earlier onset in generations.
  • Uniparental disomy: imprinting disorders or recessive disease manifestation.
  • Mosaicism: somatic/gonadal -> variable expressivity, underestimated recurrence.
  • CF: ΔF508 most common; PI, recurrent infections, CBAVD in males.
  • Mitochondrial disease: heteroplasmy, threshold, wide variability.

9. Hormonal Biochemistry

Hormone Classes Receptors Insulin Glucagon Steroids Second Messengers

Hormone Classification and Receptor Families
  • Hormones are chemical messengers via specific receptors.
  • Three classes: peptide (insulin, glucagon, GH, PTH, ADH - water-soluble, surface receptors), steroid (cortisol, aldosterone, estradiol, testosterone, vitamin D - lipid-soluble, diffuse, nuclear receptors), and amino acid-derived (catecholamines: epinephrine/norepinephrine/dopamine; T^3/T&acr;; histamine; serotonin). Receptor families: GPCRs (7TM, > 800 in humans) -> Gs (↑cAMP), Gi (↓cAMP), Gq (↑IP^3/DAG), G&sub1;&sub2;/13 (Rho).
  • Enzyme-linked: RTKs (insulin, EGF, PDGF, FGF -> dimerize, autophosphorylate, Ras-MAPK, PI3K-Akt, PLCγ), receptor guanylyl cyclase (ANP), Ser/Thr kinase receptors (TGFβ -> Smads), JAK-STAT (cytokines, GH, prolactin, EPO, IFNs -> JAK phosphorylates STAT -> dimerize -> nucleus).
  • Nuclear receptors: ligand-activated TFs (steroid, TR, RAR, VDR, PPAR). Structure: N-terminal AF-1, DBD (zinc fingers), hinge, LBD (AF-2).
  • Ligand -> conformational change -> dimerize (homodimers for steroids, heterodimers with RXR for TR/RAR/VDR) -> bind HRE -> recruit coactivators/corepressors.
Insulin Signaling and Glucose Homeostasis
  • Insulin from β-cells: preproinsulin -> proinsulin -> insulin + C-peptide.
  • Secretion stimulated by glucose (GLUT2, glucokinase sensor, ATP-sensitive K+ channel closes -> depolarization -> Ca^2 +/- influx), amino acids, incretins (GLP-1, GIP). Insulin receptor: RTK (α&bdq;β&bdq;).
  • Binding -> autophosphorylation -> IRS phosphorylation -> PI3K-Akt (GLUT4 translocation, glycogen synthase via GSK-3 inhibition, mTOR protein synthesis) and Ras-MAPK (growth, gene expression).
  • Metabolic: ↑ glucose uptake, glycolysis, glycogenesis, lipogenesis, protein synthesis; ↓ gluconeogenesis.
  • T1DM: autoimmune β-cell destruction, absolute deficiency, ketosis.
  • T2DM: insulin resistance + β-cell dysfunction, obesity. MODY: GCK, HNF1A, HNF4A mutations. Insulin resistance: IRS serine phosphorylation (PKC, JNK, IKKβ), SOCS, inflammation (TNFα, IL-6), lipotoxicity (ceramides).
Glucagon, Catecholamines and Second Messengers
  • Glucagon from α-cells, hypoglycemia -> GPCR (Gs) -> ↑cAMP -> PKA -> phosphorylates phosphorylase kinase (glycogenolysis), PFK-2 (inhibits glycolysis, stimulates gluconeogenesis), CREB (PEPCK/G6Pase).
  • Net: ↑ blood glucose.
  • Catecholamines via adrenergic receptors: β&sub1;/β&sub2; (Gs -> ↑cAMP -> ↑ inotropy, bronchodilation, glycogenolysis, lipolysis). α&sub1; (Gq -> PLCβ -> IP^3 + DAG -> Ca^2 +/- release, PKC activation). α&sub2; (Gi -> ↓cAMP). cAMP signaling: PKA targets; cAMP degraded by PDE (caffeine, theophylline, milrinone inhibit -> ↑cAMP).
  • Ca^2 +/- signaling: CaM activates CaMKII, calcineurin, MLCK.
  • IP^3R and RyR release Ca^2 +/- from ER/SR.
  • PI3K -> PIP^3 -> Akt.
  • PLC -> IP^3 + DAG -> PKC. cGMP: GC-A (ANP/BNP), sGC (NO) -> PKG -> vasodilation.
  • Sildenafil inhibits PDE5 -> ↑cGMP.
Steroid Hormone Synthesis and Mechanism
  • Synthesized from cholesterol in adrenal/gonads/placenta.
  • StAR transports cholesterol to mitochondria (rate-limiting).
  • CYP11A1 (P450scc) -> pregnenolone.
  • Pathways: 17α-OH (CYP17) -> DHEA -> androstenedione -> testosterone (17β-HSD) -> estradiol (aromatase).
  • Alternatively: pregnenolone -> progesterone -> 11-deoxycorticosterone (21-OHase) -> corticosterone -> aldosterone.
  • Progesterone -> 17-OH-P -> 11-deoxycortisol (21-OHase) -> cortisol (11β-OHase).
  • CAH: 21-OHase deficiency (95%) -> ↑17-OH-P, ↑ androgens, ↓ cortisol/aldosterone, virilization; newborn screen for 17-OH-P.
  • Transport: carrier proteins (CBG, SHBG, albumin).
  • Mechanism: diffuse -> bind receptor -> Hsp dissociate -> dimerize -> nucleus -> HRE -> coactivators -> transcription (genomic, hours).
  • Non-genomic rapid effects also exist.
Thyroid Hormone Biochemistry
  • T&acr;/T^3 synthesized in thyroid: I− transported via NIS, oxidized by TPO, organified on Tg -> MIT/DIT.
  • TPO couples MIT+DIT -> T^3; 2 DIT -> T&acr;.
  • Tg proteolyzed -> release.
  • T&acr; converted to T^3 (active) by deiodinases (D1 liver/kidney, D2 brain/pituitary).
  • D3 inactivates T&acr; -> rT^3.
  • Transport: TBG (~70%), TTR (~10%), albumin (~15%).
  • Free T&acr;/T^3 biologically active. Mechanism: T^3 binds TR (heterodimer with RXR) -> TRE -> coactivators.
  • Effects: ↑ metabolic rate, ↑ β-adrenergic sensitivity, ↑ heart rate, growth, brain development.
  • TRα and TRβ isoforms.
  • Thyroid hormone resistance: TRβ mutation -> elevated T&acr;/T^3, non-suppressed TSH, goiter.
Hormone Resistance Syndromes
  • Target tissue fails to respond to normal/elevated hormone due to receptor or post-receptor defects. Insulin resistance: T2DM, metabolic syndrome, lipodystrophies, type A (INSR mutation), Rabson-Mendenhall (severe INSR), Donohue syndrome (leprechaunism). Laron syndrome: GH receptor defect -> low IGF-1, short stature, high GH; treat with IGF-1. Nephrogenic DI: V&bdq;R or aquaporin-2 mutation -> polyuria, hypernatremia.
  • ACTH resistance (FGD): MC&bdq;R mutation -> hyperpigmentation, low cortisol. FSH/LH resistance: FSH/LH-R mutations -> ovarian/testicular failure. TSH resistance: TSH-R mutation -> high TSH with normal T&acr;/T^3. AIS: AR mutation -> complete (46,XY female phenotype) or partial (ambiguous). McCune-Albright: GNAS activating mutation (Gsα) -> polyostotic fibrous dysplasia, caf�-au-lait, endocrine overactivity.
High-Yield Pearls
  • C-peptide distinguishes endogenous vs exogenous insulin (low in factitious/T1DM).
  • GLUT4 insulin-responsive (muscle, adipose); GLUT2 (β-cells, liver); GLUT1 ubiquitous.
  • CAH (21-OHase deficiency): ↑ 17-OH-P, ↑ androgens, ↓ cortisol/aldosterone.
  • Laron syndrome: GH receptor defect -> treat with IGF-1, not GH.
  • Androgen insensitivity: 46,XY, female external, absent uterus, testes.
  • McCune-Albright: GNAS mutation -> precocious puberty, fibrous dysplasia, CAL spots.
  • Thyroid hormone resistance: ↑ T&acr;/T^3 with non-suppressed TSH; TRβ mutation.
Red Flags and Complications
  • DKA: cerebral edema in children; avoid rapid osmotic shifts, monitor neuro status.
  • Congenital adrenal hyperplasia: salt-wasting crisis -> hyponatremia, hyperkalemia, shock.
  • Insulin overdose: severe hypoglycemia; glucagon IM, dextrose IV.
  • Thyroid storm: β-blocker + PTU + SSKI + steroids; mortality > 20% untreated.
  • Myxedema coma: hypothermia, bradycardia, coma -> IV levothyroxine + stress steroids.

10. Clinical Biochemistry and Organ Function Tests

LFTs RFTs Cardiac Markers Lipid Panel Electrolytes Test Interpretation

Liver Function Tests
  • LFTs evaluate hepatocellular injury, cholestasis, and synthetic function.
  • ALT (cytosolic, most specific for hepatocytes) and AST (cytosolic + mitochondrial, also in heart/muscle/RBC).
  • ALT > AST: acute viral hepatitis, NAFLD.
  • AST > ALT (ratio >= 2): alcoholic hepatitis (AST rarely > 300, alcohol induces mitochondrial AST).
  • Massive elevation ( > 10,000): ischemic hepatitis, acetaminophen OD, acute viral hepatitis.
  • ALP (canalicular, elevated in cholestasis, obstruction, infiltrative disease, also bone).
  • GGT (induced by alcohol/phenytoin, confirms liver ALP origin). 5′-Nucleotidase: liver-specific cholestasis marker.
  • Bilirubin: total, direct (conjugated, water-soluble, urine), indirect (unconjugated, albumin-bound).
  • Pre-hepatic: indirect ↑ (hemolysis).
  • Hepatic: both ↑.
  • Post-hepatic: direct ↑.
  • Urine bilirubin = conjugated only.
  • Urobilinogen: ↑ in hemolysis, ↓ in obstruction.
  • Albumin (↓ in chronic liver disease, half-life 20d).
  • PT/INR (factor VII half-life 6h, sensitive acute dysfunction marker; INR > 1. 5 in acute liver failure indicates severe dysfunction).
  • Ammonia in hepatic encephalopathy.
Renal Function Tests and Electrolytes
  • BUN (7 - 20 mg/dL): ↑ in prerenal azotemia (↑ BUN:Cr > 20:1), postrenal, intrinsic, GI bleed, catabolism.
  • Creatinine (0. 6 - 1. 2): freely filtered, not reabsorbed.
  • BUN: Cr > 20:1 (prerenal), 10 - 20:1 (normal), 3. 5 g/d. Electrolytes: Na (135 - 145, water balance, ADH/thirst), K (3. 5 - 5. 0, insulin/aldosterone), Cl (98 - 106), HCO^3 (22 - 28), Ca (8. 5 - 10. 5 total/4. 5 - 5. 5 ionized), Mg (1. 7 - 2. 2), PO&acr; (2. 5 - 4. 5).
  • Anion gap = Na − (Cl + HCO^3) = 8 - 12; corrected for albumin: +2. 5 per ↓1 g/dL albumin.
Cardiac Markers and Lipid Panel
  • Cardiac biomarkers: troponin I/T (gold standard, cardiac-specific, rise 3 - 6h, peak 12 - 24h, elevated 7 - 14d). hs-cTn: sex-specific 99th percentile URLs; rise/fall pattern distinguishes MI.
  • CK-MB: rises 4 - 6h, peaks 12 - 24h, normalizes 48 - 72h (useful for reinfarction).
  • Myoglobin: early (1 - 4h) but non-specific.
  • BNP ( 60 protective/ < 40 risk), TG ( < 150).
  • Friedewald: LDL = TC − HDL − (TG/5) [valid TG < 400].
  • Non-HDL = TC − HDL.
  • Apo B and Lp(a) emerging markers.
  • ASCVD risk estimator guides statin therapy.
Electrolyte Disorders: Na, K, Ca, Mg, PO&acr;
  • Hyponatremia ( 145): DI, insensible losses. Correct 5. 0): AKI, CKD, ACEi/ARB, K-sparing diuretics, rhabdomyolysis, acidosis, tumor lysis.
  • ECG: peaked T, wide QRS.
  • Emergency: Ca gluconate IV, insulin+glucose, albuterol, loop diuretic, binders/dialysis.
  • Hypocalcemia ( 10. 5): primary hyperparathyroidism, malignancy (PTHrP), granulomatous.
  • Corrected Ca = measured + 0. 8(4 − alb). Mild: IVF; severe: calcitonin + bisphosphonate.
  • Hypomagnesemia ( 4. 5): CKD, hypoparathyroidism, tumor lysis; phosphate binders (sevelamer).
Acid-Base Disorders and ABG Interpretation
  • ABG: pH (7. 35 - 7. 45), PaCO&bdq; (35 - 45), PaO&bdq; (80 - 100), HCO^3 (22 - 28).
  • Approach: (1) Acidemia or alkalemia? (2) Primary: PaCO&bdq; ↑ (resp acidosis) or ↓ (resp alkalosis); HCO^3 ↓ (met acidosis) or ↑ (met alkalosis). (3) Compensation appropriate? Winter's formula: PaCO&bdq; = 1. 5(HCO^3) + 8 +/- 2.
  • Met alkalosis: PaCO&bdq; = 0. 7(HCO^3) + 21 +/- 2.
  • Resp: ΔpH ~0. 1/10 mmHg acute, ~0. 03/10 chronic. (4) Anion gap: if elevated, delta ratio = (ΔAG)/(ΔHCO^3). 2 = concurrent met alkalosis. AG acidosis: MUDPILES (methanol, uremia, DKA, propylene glycol/propofol, isoniazid/iron/infection, lactic acidosis, ethylene glycol, salicylates).
  • Non-AG: diarrhea, RTA, pancreatic/biliary fistula, ureteral diversion, acetazolamide.
Clinical Test Interpretation and Quality
  • Sensitivity = TP/(TP+FN), Specificity = TN/(TN+FP), PPV = TP/(TP+FP), NPV = TN/(TN+FN).
  • LR+ = sens/(1−spec); LR− = (1−sens)/spec. ROC curves: AUC measures discrimination ( > 0. 9 excellent).
  • Bayes theorem: post-test probability from pre-test and LR.
  • Reference ranges: mean +/- 2SD (~95% of healthy), 5% false positive.
  • Pre-analytical: hemolysis (↑K, LDH, AST), lipemia (falsely low electrolytes), icterus, fasting, tourniquet, posture, diurnal variation, drug interference (biotin in supplements affects immunoassays).
  • Critical values requiring urgent action: K 6. 5, Na 160, glucose 500, troponin > 99th%ile, INR > 5. 0, pH 7. 6.
High-Yield Pearls
  • ALT > AST = viral/NAFLD; AST > ALT (ratio >= 2) = alcoholic liver disease.
  • Bilirubin: only conjugated (direct) in urine; urobilinogen ↑ in hemolysis, ↓ in obstruction.
  • Winter's formula: expected PaCO&bdq; = 1.5(HCO^3) + 8 +/- 2.
  • Delta ratio: < 1 = add non-AG; 1 - 2 = pure AG; > 2 = add met alkalosis.
  • Corrected Ca = measured + 0.8(4 − albumin); always check Mg with hypocalcemia.
  • Troponin gold standard for MI; BNP for HF; LR+ > 10 rules in, LR− < 0.1 rules out.
  • Reference range = mean +/- 2SD; 1 in 20 healthy individuals will be "abnormal."
Red Flags and Complications
  • Hyperkalemia + ECG changes -> IV Ca gluconate IMMEDIATELY.
  • Hyponatremia correction > 8 - 10 mEq/L/24h -> osmotic demyelination (CPM).
  • Acute liver failure: ALT/AST > 10,000 + INR > 1.5 + encephalopathy -> transplant eval.
  • Tumor lysis: ↑K, ↑PO&acr;, ↓Ca, ↑UA, AKI -> allopurinol/rasburicase + hydration.
  • Critical lab values require immediate verbal confirmation and clinical action.

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