Biochemistry

01 Overview & Scope of Medical Biochemistry

Biochemistry is the study of chemical processes within and relating to living organisms. In medical education, it serves as the molecular foundation for understanding physiology, pharmacology, pathology, and genetics. Virtually every clinical discipline relies on biochemical principles—from diabetic ketoacidosis in the emergency department to enzyme replacement therapy for lysosomal storage diseases, from pharmacokinetics in anesthesia to tumor metabolism in oncology.

Core Domains of Medical Biochemistry

02 Water, pH & Buffer Systems

Water constitutes approximately 60% of body mass and serves as the universal solvent for biochemical reactions. Its unique properties—high heat capacity, high heat of vaporization, and ability to form hydrogen bonds—make it indispensable for life. The Henderson-Hasselbalch equation (pH = pKa + log [A⁻]/[HA]) is the central relationship for understanding buffer chemistry and acid-base physiology.

Physiological Buffer Systems

Amino Acid Titration & pI

Each amino acid has characteristic pKa values for its α-amino group (~9.0), α-carboxyl group (~2.0), and side chain (if ionizable). The isoelectric point (pI) is the pH at which the net charge is zero. For amino acids without ionizable side chains, pI = (pKa1 + pKa2)/2. For acidic AAs (Asp, Glu), pI = average of the two lowest pKa values; for basic AAs (Lys, Arg, His), pI = average of the two highest pKa values.

Acid-Base Disorders at a Glance

Anion Gap

The anion gap (AG) = Na⁺ − (Cl⁻ + HCO₃⁻); normal = 8–12 mEq/L. Elevated AG metabolic acidosis indicates accumulation of unmeasured anions. Mnemonic for causes: MUDPILES — Methanol, Uremia, DKA, Propylene glycol, Iron/Isoniazid, Lactic acidosis, Ethylene glycol, Salicylates. Normal AG (hyperchloremic) acidosis: diarrhea, RTA types I & II, acetazolamide, normal saline infusion.

03 Thermodynamics & Bioenergetics

Biochemical reactions obey the laws of thermodynamics. The Gibbs free energy change (ΔG) determines whether a reaction proceeds spontaneously. ΔG < 0 indicates an exergonic (spontaneous) reaction; ΔG > 0 indicates an endergonic (nonspontaneous) reaction. ΔG depends on ΔG°′ (standard free energy change at pH 7) and the actual concentrations of reactants/products: ΔG = ΔG°′ + RT ln Q.

High-Energy Compounds

ATP coupling allows endergonic reactions to proceed by pairing them with ATP hydrolysis so that the net ΔG is negative. Enzymes do not alter ΔG; they lower the activation energy (Ea), increasing reaction rate without shifting equilibrium.

Oxidation-Reduction Reactions

Biological oxidation-reduction (redox) reactions involve electron transfer mediated by coenzymes. NAD⁺/NADH and FAD/FADH₂ are the major electron carriers feeding the ETC. NAD⁺ accepts two electrons plus a proton (as a hydride ion) to become NADH. FAD accepts two hydrogen atoms to become FADH₂. The standard reduction potential (E°′) determines the direction of electron flow: electrons flow from carriers with more negative E°′ (NADH, −0.32 V) toward those with more positive E°′ (O₂, +0.82 V), releasing energy captured as the proton gradient.

Shuttle Systems for Cytoplasmic NADH

The inner mitochondrial membrane is impermeable to NADH. Two shuttle systems transfer reducing equivalents from cytoplasmic NADH into the mitochondria. The malate-aspartate shuttle (liver, heart, kidney) regenerates mitochondrial NADH → 2.5 ATP/NADH. The glycerol-3-phosphate shuttle (brain, skeletal muscle) generates mitochondrial FADH₂ → 1.5 ATP/NADH. This difference explains why total ATP yield from glucose is quoted as a range (30–32).

04 Amino Acid Classification & Properties

There are 20 standard amino acids encoded by the genetic code, each with a central α-carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R-group (side chain). All standard amino acids except glycine are L-enantiomers. Amino acids are classified by the chemical properties of their side chains.

Essential Amino Acids

Nine amino acids cannot be synthesized by the human body and must be obtained from the diet: Phe, Val, Thr, Trp, Ile, Met, His, Leu, Lys (mnemonic: PVT TIM HaLL). Histidine is considered conditionally essential (essential in infants, marginally so in adults). Arginine is conditionally essential during growth, pregnancy, and critical illness.

Side Chain Classification

Special Amino Acids

Glycine: smallest AA, achiral, flexible; component of collagen (every 3rd residue), porphyrin synthesis, conjugation reactions. Proline: imino acid with cyclic side chain, disrupts α-helices, introduces rigid kinks; hydroxylated in collagen (requires vitamin C). Selenocysteine: the "21st amino acid," encoded by UGA with a SECIS element; found in glutathione peroxidase and thioredoxin reductase.

Amino Acid Derivatives of Clinical Importance

05 Protein Structure & Folding

Protein function depends entirely on three-dimensional structure. There are four hierarchical levels of protein structure, each stabilized by distinct forces.

Levels of Protein Structure

Chaperones & Protein Folding

Chaperones assist in proper protein folding without becoming part of the final structure. Hsp70 binds hydrophobic regions of nascent polypeptides, preventing aggregation. Hsp60 (chaperonins) provide an isolated chamber for folding. Protein disulfide isomerase (PDI) catalyzes correct disulfide bond formation in the ER. Misfolded proteins are tagged with ubiquitin and degraded by the proteasome (ubiquitin-proteasome pathway).

Post-Translational Modifications

06 Hemoglobin & Oxygen Transport

Hemoglobin (Hb) is a tetrameric protein (α₂β₂ in HbA) that binds up to four O₂ molecules with cooperative binding, producing a sigmoidal oxygen-dissociation curve. This cooperativity arises from conformational changes between the tense (T, deoxy, low O₂ affinity) and relaxed (R, oxy, high O₂ affinity) states. By contrast, myoglobin is a monomer with a hyperbolic binding curve and higher O₂ affinity, serving as an intracellular O₂ reservoir in muscle.

Oxygen-Dissociation Curve Shifts

Hemoglobin Variants

HbA (α₂β₂): 97% of adult Hb. HbA₂ (α₂δ₂): 2–3%; elevated in β-thalassemia trait. HbF (α₂γ₂): predominant in fetal life; higher O₂ affinity; elevated in sickle cell treated with hydroxyurea. HbS: Glu6Val in β-globin → polymerization when deoxygenated → sickle cells. HbC: Glu6Lys → target cells. HbH (β₄): 3-gene deletion α-thalassemia.

Hemoglobin Pathology Summary

07 Collagen & Connective Tissue Disorders

Collagen is the most abundant protein in the body (~25–35% of total protein). Its hallmark is the triple helix: three left-handed polypeptide chains (each a polyproline II helix) wind around each other in a right-handed super-helix. The repeating sequence is Gly-X-Y, where X is often proline and Y is often hydroxyproline.

Collagen Types

Collagen Synthesis Steps

Collagen synthesis is a multi-step process spanning multiple cellular compartments:

Elastin & Marfan Syndrome

Elastin is an extracellular matrix protein that provides elastic recoil to tissues such as large arteries, lungs, and ligaments. It is rich in glycine, proline, and hydrophobic amino acids but (unlike collagen) is not glycosylated and has minimal hydroxyproline. Elastin monomers (tropoelastin) are cross-linked by lysyl oxidase (same enzyme as collagen cross-linking, requiring Cu²⁺) to form desmosine and isodesmosine cross-links unique to elastin. Marfan syndrome (AD, fibrillin-1 gene FBN1 on chromosome 15) affects the microfibrillar scaffold for elastin: tall stature, arachnodactyly, pectus deformities, upward lens subluxation, mitral valve prolapse, aortic root dilation (risk of dissection). α-1-Antitrypsin deficiency leads to unopposed elastase activity in the lungs → panacinar emphysema (lower lobes); associated with liver disease (PAS-positive, diastase-resistant globules in hepatocytes).

08 Enzyme Kinetics & Inhibition

Enzymes are biological catalysts that increase reaction rates by lowering activation energy without being consumed. Most are proteins; some are RNA (ribozymes). The active site binds substrate with specificity described by the lock-and-key model (Fischer) or the induced-fit model (Koshland). Enzyme kinetics follows the Michaelis-Menten equation: V = V_max[S] / (K_m + [S]).

Key Kinetic Parameters

Types of Enzyme Inhibition

Cooperative Kinetics & Allosteric Enzymes

Allosteric enzymes do not follow Michaelis-Menten kinetics. They display a sigmoidal (S-shaped) velocity curve rather than a hyperbolic one, reflecting cooperative substrate binding among multiple subunits. The Hill coefficient (n_H) quantifies cooperativity: n_H > 1 = positive cooperativity (e.g., hemoglobin, n_H ≈ 2.8); n_H = 1 = no cooperativity (Michaelis-Menten); n_H < 1 = negative cooperativity.

Allosteric activators stabilize the R (relaxed) state, shifting the curve left (lower K_0.5, increased apparent affinity). Allosteric inhibitors stabilize the T (tense) state, shifting the curve right (higher K_0.5, decreased apparent affinity). The classic example is PFK-1: ATP acts as both a substrate and an allosteric inhibitor at a separate regulatory site, while AMP and fructose-2,6-bisphosphate are potent allosteric activators.

Enzyme Classification (EC Numbers)

09 Enzyme Regulation & Clinical Enzymology

Enzyme activity is regulated at multiple levels to maintain metabolic homeostasis.

Mechanisms of Enzyme Regulation

Clinically Important Serum Enzymes

Isoenzymes & Isozymes

Isozymes (isoenzymes) are different molecular forms of the same enzyme that catalyze the same reaction but differ in kinetic properties, tissue distribution, and electrophoretic mobility. Clinically important examples:

Enzyme Defects & Drug Metabolism

The cytochrome P450 family (particularly CYP3A4, CYP2D6, CYP2C19, CYP2C9) is responsible for phase I drug metabolism in the liver. Genetic polymorphisms cause variable drug metabolism: poor metabolizers (e.g., CYP2D6 poor metabolizers cannot activate codeine to morphine) and ultra-rapid metabolizers (excessive activation → toxicity). CYP inducers (rifampin, carbamazepine, phenobarbital, phenytoin, St. John's wort) increase drug clearance. CYP inhibitors (azole antifungals, macrolides, grapefruit juice, cimetidine, ritonavir) decrease drug clearance → toxicity risk.

10 Glycolysis & Pyruvate Metabolism

Glycolysis is the 10-step cytoplasmic pathway that converts one molecule of glucose into two molecules of pyruvate, generating 2 net ATP (by substrate-level phosphorylation) and 2 NADH. It is the central metabolic pathway used by all cells and the only source of ATP in cells lacking mitochondria (e.g., mature RBCs).

Key Regulatory Steps of Glycolysis

Fates of Pyruvate

Aerobic: Pyruvate enters mitochondria → pyruvate dehydrogenase complex (PDH) converts it to acetyl-CoA + CO₂ + NADH. PDH requires 5 cofactors: thiamine (B1), lipoic acid, CoA (from B5), FAD (from B2), NAD⁺ (from B3) (mnemonic: Tender Loving Care For Nancy). Anaerobic: Lactate dehydrogenase (LDH) converts pyruvate to lactate, regenerating NAD⁺ to sustain glycolysis. Transamination: Pyruvate → alanine (ALT reaction). Carboxylation: Pyruvate carboxylase converts pyruvate to oxaloacetate (gluconeogenesis entry, TCA anaplerosis).

Glucokinase vs. Hexokinase

Warburg Effect

Cancer cells preferentially utilize glycolysis even in the presence of adequate O₂ (aerobic glycolysis). This metabolic reprogramming supports rapid biosynthesis of nucleotides, amino acids, and lipids needed for proliferation. The Warburg effect is the basis for FDG-PET scanning in oncology: tumor cells have increased glucose uptake (via GLUT1 upregulation), and ¹⁸F-fluorodeoxyglucose accumulates because it is phosphorylated by hexokinase but cannot proceed further through glycolysis.

11 TCA Cycle & Oxidative Phosphorylation

The tricarboxylic acid (TCA/Krebs/citric acid) cycle occurs in the mitochondrial matrix. Acetyl-CoA condenses with oxaloacetate to form citrate, and through 8 enzymatic steps regenerates oxaloacetate while producing 3 NADH, 1 FADH₂, and 1 GTP per turn. Two turns occur per glucose molecule.

TCA Cycle: Key Enzymes & Products

Electron Transport Chain & Oxidative Phosphorylation

The ETC comprises four complexes (I–IV) embedded in the inner mitochondrial membrane, plus mobile carriers (ubiquinone/CoQ, cytochrome c). NADH donates electrons at Complex I (NADH dehydrogenase); FADH₂ donates at Complex II (succinate dehydrogenase). Electrons flow through Complex III (cytochrome bc1) and Complex IV (cytochrome c oxidase) to O₂, reducing it to H₂O. Proton pumping at Complexes I, III, and IV creates the electrochemical gradient. ATP synthase (Complex V) uses this gradient to synthesize ATP from ADP + Pi.

ETC Inhibitors & Uncouplers

Anaplerotic Reactions

TCA cycle intermediates are drained off for biosynthesis (e.g., citrate for fatty acid synthesis, α-KG for amino acid synthesis, succinyl-CoA for heme synthesis, OAA for gluconeogenesis). Anaplerotic reactions replenish these intermediates: the most important is pyruvate carboxylase (pyruvate + CO₂ → OAA; activated by acetyl-CoA, requires biotin). Others include glutamate dehydrogenase (α-KG ↔ glutamate) and propionyl-CoA pathway (odd-chain fatty acids and some amino acids → succinyl-CoA via methylmalonyl-CoA mutase, requiring B12).

12 Gluconeogenesis & Glycogen Metabolism

Gluconeogenesis generates glucose from non-carbohydrate precursors (lactate, glycerol, glucogenic amino acids, propionyl-CoA) primarily in the liver and to a lesser extent the kidney cortex. It is essentially the reverse of glycolysis except at three irreversible steps, which are bypassed by different enzymes.

Gluconeogenesis Bypass Enzymes

Glycogen Metabolism

Glycogen Structure & Enzymes

Glycogen is a highly branched polymer of glucose with α-1,4 glycosidic bonds (linear chains) and α-1,6 glycosidic bonds (branch points, every 8–12 residues). The extensive branching creates many non-reducing ends, allowing rapid simultaneous glucose release by multiple glycogen phosphorylase molecules—critical for the rapid mobilization of glucose during exercise or the fight-or-flight response.

Glycogenesis (synthesis): Glycogenin serves as a primer (auto-glucosylating protein). Glycogen synthase (rate-limiting) adds UDP-glucose to the non-reducing end in α-1,4 linkages. Branching enzyme transfers a block of ~7 residues to create α-1,6 branch points. Glycogenolysis (breakdown): Glycogen phosphorylase (rate-limiting) cleaves α-1,4 bonds from non-reducing ends, releasing glucose-1-phosphate. Debranching enzyme has dual activity: transferase (moves 3 residues) + α-1,6-glucosidase (cleaves the branch point, releasing free glucose). In liver, G1P → G6P → free glucose (via glucose-6-phosphatase) for blood glucose maintenance; in muscle, G6P enters glycolysis directly (muscle lacks G6Pase and therefore cannot export glucose).

Fructose-2,6-Bisphosphate: The Master Metabolic Switch

Fructose-2,6-bisphosphate (F2,6BP) is the most potent allosteric activator of PFK-1 (glycolysis) and inhibitor of fructose-1,6-bisphosphatase (gluconeogenesis). It is produced by phosphofructokinase-2 (PFK-2) and degraded by fructose-bisphosphatase-2 (FBPase-2)—both activities reside on the same bifunctional enzyme. In the fed state, insulin activates a phosphatase that dephosphorylates PFK-2/FBPase-2, promoting PFK-2 activity → ↑F2,6BP → glycolysis favored. In the fasted state, glucagon activates PKA which phosphorylates the enzyme, promoting FBPase-2 activity → ↓F2,6BP → gluconeogenesis favored.

Cori Cycle & Alanine Cycle

The Cori cycle transfers the metabolic burden of lactate recycling from muscle to liver: muscle glycolysis produces lactate → lactate travels to liver → liver converts lactate back to glucose via gluconeogenesis → glucose returns to muscle. The alanine (glucose-alanine) cycle is analogous: muscle transamination produces alanine from pyruvate → alanine travels to liver → liver converts alanine to pyruvate (then to glucose) and channels the amino group into the urea cycle. Both cycles are critical during exercise and fasting.

13 Glycogen Storage Diseases

The glycogen storage diseases (GSDs) are inherited enzyme deficiencies that lead to abnormal glycogen accumulation or impaired glycogen mobilization. They classically present with hepatomegaly, hypoglycemia, or myopathy depending on the tissue affected.

Additional Glycogen Storage Diseases

14 Pentose Phosphate Pathway & G6PD Deficiency

The pentose phosphate pathway (PPP/HMP shunt) occurs in the cytoplasm and has two phases. The oxidative phase is irreversible and generates NADPH (for reductive biosynthesis and glutathione reduction) and ribulose-5-phosphate. The non-oxidative phase is reversible, interconverting sugars and connecting to glycolysis (via fructose-6-phosphate and glyceraldehyde-3-phosphate). The rate-limiting enzyme is glucose-6-phosphate dehydrogenase (G6PD).

Pentose Phosphate Pathway — Two Phases

The oxidative phase is irreversible and consists of three reactions: (1) G6PD oxidizes G6P to 6-phosphoglucono-δ-lactone (producing the first NADPH). (2) Lactonase hydrolyzes the lactone to 6-phosphogluconate. (3) 6-Phosphogluconate dehydrogenase oxidizes and decarboxylates to ribulose-5-phosphate (producing the second NADPH + CO₂). Net per G6P entering: 2 NADPH + 1 ribulose-5-phosphate + 1 CO₂.

The non-oxidative phase is reversible and uses transketolase (requires TPP/B1) and transaldolase to interconvert C3, C4, C5, C6, and C7 sugars. This connects the PPP to glycolysis: it can generate ribose-5-phosphate for nucleotide synthesis when needed, or funnel excess pentose phosphates back into glycolysis (as F6P and G3P) when NADPH demand exceeds ribose demand. Tissues with high NADPH demand (liver, adrenal cortex, RBCs, lactating mammary gland, adipose) have particularly active PPP.

Functions of NADPH

G6PD Deficiency

G6PD deficiency is the most common enzyme deficiency worldwide (X-linked recessive, protective against P. falciparum malaria). Reduced NADPH production leads to inability to maintain reduced glutathione in RBCs → oxidative damage to hemoglobin → Heinz bodies (denatured Hb precipitates) and bite cells (splenic macrophage removal of Heinz bodies). Episodes are triggered by oxidant stresses: fava beans, infections, sulfonamides, primaquine, dapsone, nitrofurantoin.

G6PD Deficiency Variants

Oxidant Stressors Triggering G6PD Hemolysis

Common triggers include: Infections (most common precipitant overall), fava beans (contain vicine/divicine), medications (primaquine, dapsone, sulfonamides, nitrofurantoin, rasburicase, methylene blue), and metabolic acidosis (DKA). Methylene blue is both a cause (oxidant in excess) and a treatment for methemoglobinemia (requires NADPH from G6PD to reduce MetHb), meaning methylene blue is contraindicated in G6PD-deficient patients with methemoglobinemia—use ascorbic acid instead.

15 Fructose & Galactose Metabolism

Fructose and galactose are dietary sugars that enter glycolysis after conversion to glycolytic intermediates. Defects in these pathways cause distinct clinical syndromes.

Fructose Metabolism Disorders

Galactose Metabolism Disorders

Sorbitol (Polyol) Pathway

In tissues that do not require insulin for glucose uptake (lens, retina, kidneys, Schwann cells), chronically elevated glucose is converted to sorbitol by aldose reductase (using NADPH) and then to fructose by sorbitol dehydrogenase (using NAD⁺). Because sorbitol cannot cross cell membranes, it accumulates intracellularly, causing osmotic damage. This mechanism contributes to diabetic complications: cataracts (lens), retinopathy (retina), peripheral neuropathy (Schwann cells), and nephropathy (kidney). Aldose reductase inhibitors have been explored therapeutically but have limited clinical success to date.

Lactose Intolerance

Lactase is a brush border enzyme in small intestinal villi that cleaves lactose into glucose + galactose. Lactase deficiency (primary: age-related downregulation, most common worldwide; secondary: mucosal injury from celiac disease, infectious enteritis, etc.) leads to undigested lactose reaching the colon → bacterial fermentation → bloating, flatulence, osmotic diarrhea, abdominal cramps. Diagnosis: hydrogen breath test (colonic bacteria metabolize lactose producing H₂). Treatment: dietary lactose restriction, oral lactase supplements.

Other Disaccharidase Deficiencies

In addition to lactase, the brush border contains sucrase-isomaltase (cleaves sucrose into glucose + fructose, and isomaltose at α-1,6 branch points) and trehalase (cleaves trehalose from mushrooms). Congenital sucrase-isomaltase deficiency presents in infancy with osmotic diarrhea upon introduction of sucrose-containing foods (fruits, juice, table sugar). Secondary disaccharidase deficiency can accompany any condition damaging the intestinal brush border (viral gastroenteritis, celiac disease, Crohn disease, tropical sprue). After mucosal recovery, disaccharidase activity typically returns, but lactase is the slowest to recover and may remain persistently low.

16 Fatty Acid Synthesis & Beta-Oxidation

Fatty acid synthesis and β-oxidation are reciprocally regulated pathways that occur in different cellular compartments.

Fatty Acid Synthesis vs. Beta-Oxidation

Carnitine Shuttle

Long-chain fatty acids cannot cross the inner mitochondrial membrane directly. The carnitine shuttle is a three-step process:

CPT-I is the rate-limiting step and the key regulatory point: it is allosterically inhibited by malonyl-CoA (the first committed intermediate in fatty acid synthesis). This ensures that synthesis and oxidation do not occur simultaneously. Medium-chain fatty acids (C6–C12) bypass the carnitine shuttle entirely, entering the mitochondrial matrix by diffusion.

Fatty Acid Oxidation Disorders

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is the most common fatty acid oxidation defect. Presents in infancy with hypoketotic hypoglycemia, vomiting, lethargy, and liver dysfunction after fasting. Elevated medium-chain acylcarnitines on newborn screen. Avoid fasting; frequent feeding. Systemic carnitine deficiency presents similarly; treatment: oral carnitine supplementation.

Odd-Chain & Very-Long-Chain Fatty Acid Oxidation

Odd-chain fatty acids (e.g., C15, C17, found in dairy and ruminant fat) undergo β-oxidation normally until the final 3-carbon unit, propionyl-CoA. Propionyl-CoA carboxylase (requires biotin) converts it to D-methylmalonyl-CoA, which is racemized and then converted to succinyl-CoA by methylmalonyl-CoA mutase (requires B12). Succinyl-CoA enters the TCA cycle. B12 deficiency thus causes elevated methylmalonic acid.

Very-long-chain fatty acids (VLCFAs, ≥C22) are first shortened in peroxisomes (via peroxisomal β-oxidation), then transferred to mitochondria for completion. Zellweger syndrome: absent peroxisomes (peroxisome biogenesis disorder) → VLCFA accumulation, hypotonia, seizures, hepatomegaly, characteristic facies; fatal in infancy. X-linked adrenoleukodystrophy: defective peroxisomal VLCFA transporter (ABCD1) → VLCFA accumulation in adrenal cortex and CNS white matter → adrenal insufficiency, progressive demyelination.

17 Ketogenesis & Ketolysis

Ketogenesis occurs in liver mitochondria during prolonged fasting, starvation, or uncontrolled diabetes when acetyl-CoA production (from β-oxidation) exceeds TCA cycle capacity. The three ketone bodies are acetoacetate, β-hydroxybutyrate (the predominant circulating form), and acetone (volatile, exhaled → fruity breath).

Ketogenesis Pathway

2 Acetyl-CoA → acetoacetyl-CoA (thiolase) → HMG-CoA (HMG-CoA synthase, rate-limiting) → acetoacetate + acetyl-CoA (HMG-CoA lyase). Acetoacetate is reduced to β-hydroxybutyrate by β-hydroxybutyrate dehydrogenase (using NADH), or spontaneously decarboxylated to acetone.

Ketolysis (Peripheral Utilization)

Extrahepatic tissues (brain, heart, skeletal muscle, kidney) convert β-hydroxybutyrate back to acetoacetate, then to acetoacetyl-CoA via succinyl-CoA-acetoacetate CoA transferase (thiophorase), and finally to 2 acetyl-CoA for the TCA cycle. The liver cannot use ketone bodies because it lacks thiophorase.

Alcoholic Ketoacidosis (AKA)

Chronic alcohol use combined with poor nutrition and recent binge → depleted glycogen stores + ↑NADH/NAD⁺ ratio (from ethanol metabolism) → impaired gluconeogenesis + enhanced lipolysis and ketogenesis. Unlike DKA, glucose is typically low or normal (not elevated). Labs show high anion gap metabolic acidosis with positive ketones. β-Hydroxybutyrate predominates (high NADH shifts acetoacetate → β-HB), so the nitroprusside test (detects only acetoacetate) may be falsely negative initially. Treatment: IV fluids with dextrose (D5NS), thiamine before glucose (to prevent Wernicke encephalopathy), electrolyte replacement.

Starvation Ketosis

During prolonged fasting (>48–72 hours), hepatic glycogen is exhausted and gluconeogenesis alone cannot meet glucose demands. The liver increases ketogenesis from fatty acids. Ketone bodies (particularly β-hydroxybutyrate) become the brain's major fuel source, reducing the need for gluconeogenesis and thereby sparing muscle protein. In simple starvation, the degree of ketoacidosis is milder than in DKA because basal insulin secretion is preserved, limiting lipolysis to a controlled rate.

18 Lipoproteins & Cholesterol Metabolism

Lipids are transported in blood as lipoproteins—spherical particles with a hydrophobic core (triglycerides, cholesterol esters) and an amphipathic shell (phospholipids, free cholesterol, apolipoproteins).

Lipoprotein Classes

Key Enzymes & Receptors

Lipoprotein lipase (LPL): on capillary endothelium; activated by ApoC-II; hydrolyzes TGs in chylomicrons and VLDL. Hepatic lipase: converts IDL to LDL. LCAT (lecithin-cholesterol acyltransferase): esterifies cholesterol on HDL; activated by ApoA-I. CETP (cholesterol ester transfer protein): transfers cholesterol esters from HDL to LDL/VLDL in exchange for TGs. LDL receptor: hepatic uptake of LDL; recognizes ApoB-100 and ApoE.

Dyslipidemias

Cholesterol Synthesis & Bile Acid Metabolism

Cholesterol is synthesized from acetyl-CoA in the liver. The rate-limiting enzyme is HMG-CoA reductase (converts HMG-CoA to mevalonate). This enzyme is the target of statins. Cholesterol is the precursor for bile acids (7α-hydroxylase is rate-limiting), steroid hormones (all classes), and vitamin D. Bile acids (cholic, chenodeoxycholic) are conjugated with glycine or taurine, secreted into bile, and recycled via the enterohepatic circulation (terminal ileum reabsorption). Bile acid sequestrants (cholestyramine) interrupt this cycle and are used to lower LDL cholesterol and treat bile acid diarrhea.

Eicosanoid Synthesis

Eicosanoids (prostaglandins, thromboxanes, leukotrienes) are derived from arachidonic acid (a 20-carbon polyunsaturated fatty acid released from membrane phospholipids by phospholipase A₂). COX-1/COX-2 produce prostaglandins and thromboxanes (NSAIDs and aspirin inhibit COX). 5-Lipoxygenase produces leukotrienes (zileuton inhibits; montelukast blocks leukotriene receptors). Corticosteroids inhibit phospholipase A₂ (via lipocortin), blocking both pathways.

19 Lysosomal Storage Diseases

Lysosomal storage diseases are inherited deficiencies of lysosomal enzymes, leading to accumulation of undigested substrates within lysosomes. Most are autosomal recessive (except Fabry and Hunter, which are X-linked).

Sphingolipid Metabolism Overview

Sphingolipids are membrane lipids derived from ceramide (sphingosine + fatty acid). Ceramide synthesis begins with condensation of palmitoyl-CoA + serine by serine palmitoyltransferase. Adding phosphocholine yields sphingomyelin; adding sugars yields cerebrosides (one sugar) or gangliosides (oligosaccharide with sialic acid). Degradation occurs stepwise in lysosomes by specific hydrolases. Deficiency of any hydrolase causes accumulation of its substrate—the molecular basis of the sphingolipidoses listed above.

Sphingolipid Degradation Pathway

I-Cell Disease (Mucolipidosis Type II)

I-cell disease results from deficiency of GlcNAc phosphotransferase, the enzyme that adds mannose-6-phosphate (M6P) tags to lysosomal enzymes in the Golgi. Without M6P, lysosomal enzymes are secreted extracellularly instead of being directed to lysosomes. Result: intracellular lysosomes lack enzymes and fill with undigested substrates (dense "inclusion bodies" → "I-cell"). Clinically resembles severe Hurler syndrome: coarse facies, skeletal abnormalities, restricted joint mobility, psychomotor retardation. Serum lysosomal enzyme levels are elevated (misdirected into blood).

20 Amino Acid Metabolism & Inborn Errors

Amino acid catabolism involves removal of the α-amino group (via transamination to α-ketoglutarate forming glutamate, then oxidative deamination by glutamate dehydrogenase releasing NH₄⁺) and disposal of the carbon skeleton. Ammonia is detoxified by the urea cycle in the liver.

Urea Cycle

The urea cycle converts two nitrogen atoms (one from NH₄⁺ via carbamoyl phosphate, one from aspartate) and CO₂ into urea for renal excretion. The cycle spans two compartments: the first two steps (CPS I and OTC) occur in the mitochondrial matrix; the remaining three steps (argininosuccinate synthetase, argininosuccinate lyase, arginase) occur in the cytoplasm.

Defects in any urea cycle enzyme cause hyperammonemia with lethargy, vomiting, cerebral edema, and respiratory alkalosis (NH₃ stimulates respiratory center). Treatment: low-protein diet, nitrogen scavengers (sodium benzoate conjugates glycine, sodium phenylbutyrate conjugates glutamine), lactulose (promotes NH₃ excretion by colonic bacteria), dialysis in acute crisis.

Inborn Errors of Amino Acid Metabolism

Heme Synthesis & Porphyrias

Heme synthesis begins in the mitochondria (ALA synthase: rate-limiting, requires B6, inhibited by heme) and continues in the cytoplasm before returning to mitochondria for the final step (ferrochelatase inserts Fe²⁺ into protoporphyrin IX). The porphyrias are enzyme deficiencies in the heme synthesis pathway.

21 Purine & Pyrimidine Metabolism

Purines (adenine, guanine) are synthesized de novo on a ribose-5-phosphate scaffold (from the PPP) using amino acids (Gly, Asp, Gln), CO₂, and THF derivatives. IMP is the first purine nucleotide formed. Pyrimidines (cytosine, uracil, thymine) are built as a free base first (orotate), then attached to ribose-5-phosphate.

Key Enzymes & Pharmacological Targets

Gout & Lesch-Nyhan Syndrome

Gout: hyperuricemia → monosodium urate crystal deposition in joints, causing acute inflammatory arthritis. Negatively birefringent, needle-shaped crystals under polarized light. Treatment: acute (NSAIDs, colchicine, steroids); chronic (allopurinol [xanthine oxidase inhibitor], febuxostat, probenecid [uricosuric]).

Lesch-Nyhan syndrome: X-linked deficiency of HGPRT → excess purine synthesis (cannot salvage) → severe hyperuricemia, gout, intellectual disability, self-mutilating behavior (lip and finger biting), choreoathetosis. Mnemonic: "HGPRT—He's Got Purine Recovery Trouble."

Adenosine Deaminase (ADA) Deficiency

ADA deficiency causes severe combined immunodeficiency (SCID). ADA normally converts adenosine and deoxyadenosine to inosine and deoxyinosine. When ADA is absent, deoxyadenosine accumulates and is phosphorylated to dATP, which inhibits ribonucleotide reductase. This prevents DNA synthesis, particularly devastating to lymphocytes (which rely heavily on de novo nucleotide synthesis). Result: absent T cells and B cells → life-threatening infections from infancy. Treatment: enzyme replacement (PEG-ADA), hematopoietic stem cell transplant, or gene therapy (one of the first successful gene therapy targets).

Pseudogout vs. Gout

Purine vs. Pyrimidine Synthesis Comparison

Chemotherapy Targeting Nucleotide Metabolism

22 Fat-Soluble Vitamins (A, D, E, K)

Fat-soluble vitamins are absorbed with dietary fat via micelles, transported in chylomicrons, and stored in liver and adipose tissue. Deficiency may result from fat malabsorption (e.g., cystic fibrosis, celiac disease, cholestasis, short bowel syndrome, pancreatic insufficiency).

Fat-Soluble Vitamin Absorption

Fat-soluble vitamins (A, D, E, K) require bile salts for micelle formation and intestinal absorption. Any condition causing fat malabsorption will lead to deficiency of all four vitamins: cystic fibrosis (pancreatic insufficiency), celiac disease (villous atrophy), Crohn disease (terminal ileum), cholestatic liver disease (bile flow obstruction), short bowel syndrome, and chronic pancreatitis. Patients with these conditions require supplementation and monitoring of fat-soluble vitamin levels.

Vitamin A & Retinoid Signaling

Vitamin A exists in three active forms: retinal (component of rhodopsin in rod cells, essential for dark adaptation), retinoic acid (binds nuclear receptors RAR/RXR to regulate gene expression, cell differentiation, and immune function), and retinol (transport and storage form). Retinoic acid is critical for epithelial integrity and immune function. Its role in cell differentiation is exploited therapeutically: all-trans retinoic acid (ATRA) is used to treat acute promyelocytic leukemia (APL; PML-RARa fusion), inducing differentiation of promyelocytes. Isotretinoin (13-cis-retinoic acid) is used for severe acne but is a potent teratogen (iPLEDGE program required).

Vitamin D Metabolism in Detail

The vitamin D pathway: (1) 7-dehydrocholesterol in skin is converted to cholecalciferol (D3) by UV-B radiation. (2) Liver 25-hydroxylase produces 25-OH-D3 (calcidiol)—the best clinical measure of vitamin D status. (3) Kidney 1α-hydroxylase produces 1,25-(OH)₂D3 (calcitriol)—the most active form. 1α-Hydroxylase is stimulated by PTH and low phosphate, and inhibited by FGF-23 and high calcium/phosphate. Calcitriol acts on intestine (↑Ca²⁺ and PO₄ absorption), bone (mobilization of Ca²⁺/PO₄), and kidney (↑Ca²⁺ reabsorption). Vitamin D₂ (ergocalciferol) is plant-derived and undergoes the same hydroxylation steps.

23 Water-Soluble Vitamins (B Complex & C)

Water-soluble vitamins generally serve as enzyme cofactors. They are not stored extensively (except B12 in liver, lasting 3–5 years), so deficiencies develop more rapidly than fat-soluble vitamin deficiencies.

Thiamine (B1) Deficiency in Detail

Thiamine pyrophosphate (TPP) is the cofactor for four critical enzyme complexes: pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, branched-chain α-ketoacid dehydrogenase, and transketolase (PPP). Alcoholism is the most common cause of B1 deficiency in developed countries (poor intake, impaired absorption, increased demand). Wernicke encephalopathy is a medical emergency: classic triad of confusion, ophthalmoplegia (CN VI palsy), and ataxia (cerebellar). If untreated, it progresses to Korsakoff syndrome: irreversible anterograde amnesia with confabulation (mammillary body and dorsomedial thalamic nuclei damage). Treatment: IV thiamine BEFORE glucose administration (glucose metabolism consumes B1 and can precipitate Wernicke in a thiamine-depleted patient).

Niacin (B3) Pharmacology

At pharmacological doses, niacin lowers triglycerides and LDL while raising HDL (most effective HDL-raising agent). It inhibits lipolysis in adipose tissue (reducing hepatic VLDL production). Major side effect: flushing (prostaglandin-mediated cutaneous vasodilation); reduced by aspirin pretreatment or extended-release formulation. Other adverse effects: hyperglycemia, hyperuricemia, hepatotoxicity.

Folate & Neural Tube Defects

Folate supplementation (400 μg/day) beginning at least one month before conception and continuing through the first trimester dramatically reduces the incidence of neural tube defects (anencephaly, spina bifida). Women with a prior NTD-affected pregnancy should take 4 mg/day. Folate fortification of grain products (mandatory in the US since 1998) has reduced NTD incidence by ~25–30%. Methotrexate and other antifolates are teratogenic and absolutely contraindicated in pregnancy.

Vitamin Toxicity Quick-Reference

24 Minerals, Trace Elements & Nutrition

Minerals and trace elements serve as enzyme cofactors, structural components, and electrolytes essential for physiological function.

Key Minerals & Trace Elements

Nutrition Disorders

Kwashiorkor: protein malnutrition with adequate caloric intake. Features: edema (low albumin → low oncotic pressure), fatty liver, skin lesions, flag sign (alternating pigmented/depigmented hair bands), preserved fat stores. Marasmus: total calorie deficiency. Features: muscle wasting, loss of subcutaneous fat, emaciation, no edema. Refeeding syndrome: occurs when malnourished patients are fed too quickly. Insulin surge drives PO₄³⁻, K⁺, and Mg²⁺ into cells → dangerous hypophosphatemia → cardiac arrhythmias, respiratory failure, rhabdomyolysis.

Iron Metabolism

Dietary iron is absorbed in the duodenum as heme iron (from meat, directly absorbed) or non-heme ferric iron (Fe³⁺, reduced to Fe²⁺ by duodenal cytochrome B, then transported by DMT-1). Inside enterocytes, iron is either stored as ferritin or exported by ferroportin (the only known iron exporter). In blood, iron is bound to transferrin and delivered to cells via transferrin receptor. Hepcidin, produced by the liver, is the master regulator: it degrades ferroportin, reducing iron absorption and release from macrophages. Hepcidin is upregulated by iron excess and inflammation (explaining anemia of chronic disease) and downregulated by iron deficiency, erythropoietic activity, and hypoxia.

Wilson Disease vs. Hemochromatosis

25 Molecular Biology & DNA Repair

The central dogma of molecular biology describes the flow of genetic information: DNA → RNA (transcription) → Protein (translation). Understanding these processes is essential for interpreting molecular diagnostics and understanding antibiotic and chemotherapeutic mechanisms.

DNA Replication

Replication is semiconservative, bidirectional, and proceeds 5′ → 3′. Helicase unwinds the double helix. Topoisomerase relieves supercoiling (fluoroquinolones inhibit bacterial topoisomerase II/DNA gyrase). Primase synthesizes RNA primers. DNA polymerase III (prokaryotes) / Pol δ and Pol ε (eukaryotes) elongate the new strand. Leading strand is synthesized continuously; lagging strand is synthesized as Okazaki fragments, joined by DNA ligase. Telomerase (a reverse transcriptase) maintains telomere length in germ cells, stem cells, and most cancer cells.

DNA Repair Mechanisms

Key Antibiotics & Their Molecular Targets

Transcription

RNA polymerase synthesizes RNA 5′ → 3′ from a DNA template (read 3′ → 5′). Eukaryotes have three RNA polymerases: Pol I (rRNA, except 5S), Pol II (mRNA, snRNA, miRNA), Pol III (tRNA, 5S rRNA). α-Amanitin (Amanita phalloides mushroom toxin) inhibits RNA Pol II → hepatotoxicity. Eukaryotic mRNA is processed: 5′ cap (7-methylguanosine, added by guanylyltransferase), 3′ poly-A tail (added by poly-A polymerase), and splicing (introns removed by the spliceosome). The 5′ cap is critical for ribosome recognition and mRNA stability.

Translation

Translation occurs on ribosomes (80S in eukaryotes = 40S + 60S; 70S in prokaryotes = 30S + 50S). The process involves three stages: Initiation (small subunit binds mRNA, start codon AUG recognized, Met-tRNA loaded), Elongation (aminoacyl-tRNA binds A site, peptidyl transferase forms peptide bond, ribosome translocates), and Termination (stop codons UAA, UAG, UGA; release factors). Diphtheria toxin inactivates EF-2 (elongation factor 2) via ADP-ribosylation. Pseudomonas exotoxin A has the same mechanism.

Genetic Code Features

Types of Mutations

Cell Signaling Pathways

26 Clinical Correlates & Metabolic Integration

Metabolic pathways do not operate in isolation; they are interconnected, hormonally regulated, and tissue-specific. Understanding the fed vs. fasted metabolic states and the integration of major pathways is essential for clinical reasoning.

Fed vs. Fasted State

Rate-Limiting Enzymes of Major Pathways

Metabolic Fuel Sources by Duration of Fasting

0–4 hours: dietary glucose, hepatic glycogenolysis. 4–16 hours: hepatic glycogenolysis, gluconeogenesis begins. 16–48 hours: hepatic glycogen depleted; gluconeogenesis (from amino acids, glycerol, lactate) is primary glucose source; fatty acid oxidation increases. >2–3 days: ketogenesis accelerates; brain switches to ketone bodies (sparing glucose and muscle protein). Weeks of starvation: ketones supply ~75% of brain fuel; muscle proteolysis slows to preserve lean mass.

Tissue-Specific Metabolism

Insulin & Glucagon Signaling Integration

GLUT Transporters

Diabetes Mellitus: Biochemical Basis

Non-Enzymatic Glycation

In hyperglycemia, glucose non-enzymatically attaches to proteins (Maillard reaction), forming advanced glycation end products (AGEs). AGEs cross-link collagen in vessel walls, trap LDL (accelerating atherosclerosis), activate RAGE receptors (inducing inflammation and oxidative stress), and thicken basement membranes. This underlies diabetic microvascular complications: retinopathy, nephropathy, and neuropathy. HbA1c is a glycated hemoglobin that reflects average blood glucose over 2–3 months (RBC lifespan ~120 days). Target HbA1c <7% in most diabetic patients.

Four Pathways of Diabetic Damage

Chronic hyperglycemia damages tissues through four major biochemical mechanisms:

27 High-Yield Review & Reference Tables

This section consolidates the most frequently tested biochemistry concepts for rapid board review.

Inborn Errors Quick-Reference

Vitamin Deficiency Quick-Reference

Key Cofactor Associations

Metabolic Pathway Locations

X-Linked Metabolic Disorders

Inheritance Patterns in Metabolic Disease

The vast majority of inborn errors of metabolism follow autosomal recessive inheritance: both parents are carriers, and each offspring has a 25% chance of being affected. Notable X-linked exceptions are listed above. Autosomal dominant metabolic disorders are rare but include familial hypercholesterolemia (LDL receptor), acute intermittent porphyria (PBG deaminase), and some forms of hereditary spherocytosis.

Laboratory Values & Metabolic Panels

Tumor Metabolism