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🧬 BIOCHEMISTRY CRASH COURSE — EXAM READY

Reference: Vasudevan/Satyanarayan | Lippincott | Harper's

Your exam is tomorrow. We go chapter by chapter, deep and fast. Read each section fully before moving on.

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CHAPTER 1: CHEMISTRY OF PROTEINS AND METABOLISM

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1.1 Amino Acids - The Building Blocks

• An amino group (-NH₂)
• A carboxyl group (-COOH)
• A hydrogen atom
• A side chain (R group) - this determines the type

Classification of Amino Acids (LAQ-worthy)

• Essential (must be taken in diet - 9): Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginine (semi), Leucine, Lysine
• Mnemonic: PVT TIM HaLL (Private Tim Hall)
• Non-essential: Synthesized by body (Alanine, Glycine, Serine, etc.)
• Conditionally essential: Arginine, Histidine (essential during growth/disease)

• Purely ketogenic: Leucine, Lysine (LL - only ketone bodies)
• Both: Isoleucine, Phenylalanine, Tryptophan, Tyrosine, Threonine
• Glucogenic: All others

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1.2 Properties of Amino Acids

• pI = (pKa1 + pKa2) / 2
• At pI: amino acid is least soluble, migrates least in electric field

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1.3 Peptide Bond

• Partial double bond character (resonance) - makes it rigid and planar
• Trans configuration (usually)
• No free rotation around C-N bond
• Bond length: 1.33 Å (between single and double bond)

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1.4 Levels of Protein Structure (LAQ)

Primary Structure

• Sequence of amino acids linked by peptide bonds
• Determined by genetic code
• Determines all higher-order structures
• Example: Insulin - 51 amino acids in 2 chains (A=21, B=30) linked by 2 disulfide bonds

Secondary Structure

• Right-handed helix (usually)
• 3.6 amino acids per turn
• Pitch: 5.4 Å (rise per turn)
• Stabilized by intramolecular H-bonds between C=O of residue n and N-H of residue n+4
• Disrupted by: Proline (introduces kink), Glycine (too flexible), charged amino acids

• Antiparallel (more stable) or parallel arrangement
• Stabilized by inter-strand H-bonds
• Extended zigzag conformation

Tertiary Structure

• 3D folding of entire polypeptide chain
• Stabilized by:
  • Hydrophobic interactions (most important - nonpolar R groups cluster)
  • Hydrogen bonds
  • Ionic bonds (salt bridges)
  • Disulfide bonds (-S-S- between cysteines) - strongest covalent bonds in proteins
  • Van der Waals forces

Quaternary Structure

• Association of 2+ polypeptide subunits
• Example: Hemoglobin (α₂β₂), Collagen (triple helix)

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1.5 Denaturation of Proteins

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1.6 Classification of Proteins

• Simple proteins: Only amino acids (albumin, globulin, keratin, collagen)
• Conjugated proteins: Protein + non-protein prosthetic group
  • Glycoproteins (carbohydrate) - IgG, mucin
  • Lipoproteins (lipid) - LDL, HDL
  • Hemoproteins (heme) - hemoglobin, cytochromes
  • Nucleoproteins (nucleic acid) - ribosomes
  • Metalloproteins (metal) - ferritin (Fe), ceruloplasmin (Cu)
  • Phosphoproteins (phosphate) - casein (milk)

• Structural (collagen, keratin, elastin)
• Enzymatic (all enzymes)
• Transport (hemoglobin, albumin, transferrin)
• Regulatory (hormones - insulin)
• Defense (immunoglobulins)
• Contractile (actin, myosin)

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1.7 Important Structural Proteins (LAQ)

Collagen

• Most abundant protein in humans (~30% total body protein)
• Found in skin, bone, tendons, cartilage, blood vessels
• Rich in Glycine (every 3rd residue), Proline, Hydroxyproline, Hydroxylysine
• Structure: Three left-handed alpha chains wound into a right-handed triple helix
• Hydroxylation of proline and lysine requires Vitamin C (ascorbic acid) - Deficiency causes Scurvy (defective collagen)
• Cross-linking by Lysyl oxidase (requires Copper) - gives tensile strength

Keratin

• Fibrous protein in hair, nails, skin
• Rich in cysteine (disulfide bonds give hardness to nails)

Elastin

• Found in elastic tissues (lungs, large blood vessels)
• Contains desmosine and isodesmosine (unusual cross-links)

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1.8 Plasma Proteins (LAQ)

• Maintains colloid osmotic pressure (oncotic pressure)
• Transports bilirubin, fatty acids, Ca²⁺, drugs (warfarin, aspirin), hormones
• Buffer (weak acid)
• Hypoalbuminemia → edema (decreased oncotic pressure)

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1.9 Amino Acid Metabolism (LAQ)

Transamination

• Transfer of amino group from amino acid to alpha-keto acid
• Enzyme: Transaminase (aminotransferase)
• Coenzyme: Pyridoxal phosphate (PLP) - Vitamin B6
• Key reactions:
  • ALT (SGPT): Alanine + α-ketoglutarate ⇌ Pyruvate + Glutamate (liver specific)
  • AST (SGOT): Aspartate + α-ketoglutarate ⇌ Oxaloacetate + Glutamate

Deamination

• Enzyme: Glutamate dehydrogenase (mitochondrial)
• Coenzyme: NAD⁺ or NADP⁺
• Allosteric regulation: Activated by ADP/GDP, Inhibited by ATP/GTP

Urea Cycle (LAQ - HIGH PRIORITY)

1. NH₃ + CO₂ + 2ATP → Carbamoyl phosphate (mitochondria)
   • Enzyme: Carbamoyl phosphate synthetase I (CPS-I)
   • Activator: N-acetylglutamate (NAG)
2. Carbamoyl phosphate + Ornithine → Citrulline (mitochondria)
   • Enzyme: Ornithine transcarbamylase (OTC)
3. Citrulline transported to cytoplasm
4. Citrulline + Aspartate → Argininosuccinate (cytoplasm)
   • Enzyme: Argininosuccinate synthetase
   • ATP consumed
5. Argininosuccinate → Arginine + Fumarate
   • Enzyme: Argininosuccinase
6. Arginine → Ornithine + Urea
   • Enzyme: Arginase (liver specific)
   • Ornithine re-enters cycle

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1.10 Special Amino Acid Metabolism

Phenylalanine and Tyrosine

• Phenylalanine → Tyrosine (by phenylalanine hydroxylase, requires tetrahydrobiopterin)
• Phenylketonuria (PKU): Deficiency of phenylalanine hydroxylase → accumulation of phenylpyruvate → intellectual disability, mousy odor, fair skin/hair. Treat with phenylalanine-restricted diet.
• Tyrosine → DOPA → Dopamine → Norepinephrine → Epinephrine (catecholamines)
• Tyrosine → Melanin (by tyrosinase). Deficiency → Albinism
• Tyrosine → Thyroxine (T3, T4)

Tryptophan

• Tryptophan → Serotonin (5-HT) → Melatonin
• Tryptophan → Niacin (Vitamin B3) - requires B6, B2, iron
• Hartnup disease: Defective tryptophan transport → pellagra-like symptoms

Methionine

• Source of methyl groups via SAM (S-adenosylmethionine)
• SAM is universal methyl donor
• Methionine → Homocysteine → Cysteine (transsulfuration)
• Homocystinuria: Defective cystathionine beta-synthase → elevated homocysteine → atherosclerosis, thrombosis, intellectual disability

Glycine

• Conjugates with bile acids (glycocholic acid)
• Component of heme (with succinyl-CoA)
• Neurotransmitter (inhibitory)

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CHAPTER 2: VITAMINS AND NUTRITION

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

Vitamin A (Retinol) - LAQ

1. Vision: Retinal + Opsin → Rhodopsin (visual pigment in rods). 11-cis retinal → all-trans retinal (photoisomerization) → nerve impulse
2. Epithelial differentiation: Retinoic acid acts via nuclear receptors (RAR/RXR) → gene expression
3. Growth and reproduction
4. Immune function
5. Antioxidant (beta-carotene)

• Night blindness (nyctalopia) - first sign
• Xerophthalmia - dry eyes
• Bitot's spots - foamy white patches on conjunctiva
• Keratomalacia - corneal ulceration (leads to blindness)
• Follicular hyperkeratosis (skin)
• Increased susceptibility to infections

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Vitamin D (Calciferol) - LAQ

• D₂ = Ergocalciferol (plant/fungi)
• D₃ = Cholecalciferol (animal, skin synthesis)

• 1-alpha hydroxylase in kidney is stimulated by PTH, low Ca²⁺, low phosphate

1. Stimulates intestinal absorption of Ca²⁺ and phosphate
2. Stimulates bone mineralization (at normal levels) and resorption (at high levels)
3. Stimulates renal reabsorption of Ca²⁺
4. Acts via nuclear receptors → gene transcription

• Rickets (children): Bow legs, knock knees, rachitic rosary, Harrison's sulcus, delayed dentition, craniotabes
• Osteomalacia (adults): Bone pain, muscle weakness, fractures
• Lab: Low Ca, Low P, High ALP, High PTH

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Vitamin E (Tocopherols) - LAQ

• Major antioxidant - protects cell membranes from lipid peroxidation by scavenging free radicals (especially ROS)
• Protects RBCs from hemolysis
• Prevents oxidation of LDL (anti-atherogenic)
• Important for normal neurological function and reproduction

• Hemolytic anemia (premature infants)
• Peripheral neuropathy
• Ataxia
• Retinopathy

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Vitamin K (Phylloquinone/Menaquinone)

• K₁ = Phylloquinone (green leafy vegetables)
• K₂ = Menaquinone (gut bacteria)
• K₃ = Menadione (synthetic)

• Essential cofactor for gamma-carboxylation of glutamate residues in clotting factors II (prothrombin), VII, IX, X, Protein C, Protein S
• Also involved in bone protein (osteocalcin) carboxylation

• Prolonged PT (prothrombin time), prolonged APTT
• Bleeding tendency
• Hemorrhagic disease of newborn - newborns have low gut bacteria → prophylactic Vitamin K injection at birth

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2.2 Water-Soluble Vitamins (B-complex, C)

Vitamin B1 (Thiamine) - LAQ

• Pyruvate dehydrogenase (Pyruvate → Acetyl-CoA)
• Alpha-ketoglutarate dehydrogenase (in TCA)
• Branched-chain ketoacid dehydrogenase
• Transketolase (pentose phosphate pathway) - used in RBC test for B1 deficiency

• Beriberi:
  • Dry beriberi: Peripheral neuropathy (symmetric, ascending)
  • Wet beriberi: High-output cardiac failure, edema
  • Wernicke's encephalopathy: Ophthalmoplegia, ataxia, confusion (3 Cs: Confusion, Ataxia, Ophthalmoplegia) - seen in alcoholics
  • Korsakoff's psychosis: Anterograde amnesia, confabulation (chronic Wernicke's)
• Lab test: Reduced RBC transketolase activity

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Vitamin B2 (Riboflavin)

• Ariboflavinosis: Angular cheilitis, glossitis (magenta tongue), corneal vascularization, seborrheic dermatitis, photophobia

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Vitamin B3 (Niacin/Nicotinic acid)

• Dermatitis (photosensitive, Casal's necklace)
• Diarrhea
• Dementia
• Death (if untreated)
• Causes: Poor corn diet (corn is low in tryptophan, niacin in bound form), Isoniazid (B6 antagonist → less tryptophan → niacin conversion), Carcinoid tumor (tryptophan diverted to serotonin), Hartnup disease

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Vitamin B5 (Pantothenic acid)

• Fatty acid synthesis and oxidation
• Acetyl-CoA metabolism (TCA, cholesterol synthesis)

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Vitamin B6 (Pyridoxine) - LAQ

1. Transamination (AST, ALT)
2. Decarboxylation reactions - synthesis of neurotransmitters:
   • DOPA → Dopamine
   • Histidine → Histamine
   • Glutamate → GABA
   • Tryptophan → Serotonin
3. Glycogen phosphorylase
4. Sphingolipid synthesis
5. Heme synthesis (ALA synthase)
6. Tryptophan → Niacin conversion

• Peripheral neuropathy
• Sideroblastic anemia (ring sideroblasts)
• Convulsions (decreased GABA)
• Pellagra-like symptoms
• Drug interaction: Isoniazid (INH) is a B6 antagonist → give B6 with INH

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Vitamin B7 (Biotin)

• Pyruvate carboxylase (Pyruvate → OAA)
• Acetyl-CoA carboxylase (Acetyl-CoA → Malonyl-CoA - rate-limiting step of FA synthesis)
• Propionyl-CoA carboxylase

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Vitamin B9 (Folic acid/Folate) - LAQ

• Purine synthesis (steps requiring N10-formyl-THF)
• dTMP synthesis (thymidylate synthase uses N5,N10-methylene-THF)
• Serine-glycine interconversion
• Methionine synthesis from homocysteine (requires B12 as cofactor → methyl trap)

• Megaloblastic anemia (macrocytic, hyperlobulated neutrophils)
• Neural tube defects (NTDs) if deficient in early pregnancy - Spina bifida, anencephaly
• Glossitis, diarrhea
• Prevention: 400 mcg folic acid daily periconceptionally

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Vitamin B12 (Cobalamin) - LAQ

1. Methylcobalamin: Cofactor for methionine synthase (Homocysteine → Methionine), also regenerates THF from methyl-THF (methyl trap)
2. Adenosylcobalamin: Cofactor for methylmalonyl-CoA mutase (Methylmalonyl-CoA → Succinyl-CoA) - essential for odd-chain fatty acid metabolism and myelin synthesis

• Megaloblastic anemia (same as folate - due to methyl trap)
• Subacute combined degeneration of spinal cord (SCDS) - demyelination of posterior and lateral columns → ataxia, loss of vibration/proprioception, upper motor neuron signs (NOT seen in folate deficiency)
• Glossitis, hyperhomocysteinemia, elevated methylmalonic acid

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Vitamin C (Ascorbic acid) - LAQ

1. Hydroxylation of proline and lysine in collagen synthesis (requires Vitamin C as cofactor for prolyl and lysyl hydroxylase)
2. Antioxidant - scavenges ROS, regenerates Vitamin E
3. Iron absorption - reduces Fe³⁺ → Fe²⁺ (more absorbable)
4. Immune function
5. Adrenal cortex steroid synthesis

• Perifollicular hemorrhage - hemorrhages around hair follicles
• Corkscrew hairs
• Gingival bleeding - swollen, bleeding gums
• Impaired wound healing
• Subperiosteal hemorrhages (bone pain in children)
• Anemia (iron deficiency due to poor absorption)

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2.3 Minerals in Nutrition

Iron (Fe) - LAQ

• Hepcidin blocks Ferroportin → prevents iron export from enterocytes
• Low iron stores/hypoxia → low hepcidin → increased absorption

• Serum iron: 60-160 mcg/dL
• TIBC (Total Iron Binding Capacity): 250-370 mcg/dL
• Serum ferritin: 12-300 ng/mL (best indicator of stores)

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CHAPTER 3: ENZYMES

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3.1 Introduction

1. Speed up reactions (increase rate by 10⁶ to 10¹² times)
2. Not consumed in reaction
3. Highly specific (substrate specificity)
4. Work at mild conditions (37°C, pH 7.4)
5. Regulated (allosteric, covalent modification, etc.)

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3.2 Enzyme Nomenclature and Classification

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3.3 Active Site and Enzyme-Substrate Complex

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3.4 Enzyme Kinetics - Michaelis-Menten (LAQ)

• Vmax: Maximum velocity (when all enzyme molecules saturated with substrate)
• Km (Michaelis constant): [S] at which V = Vmax/2. Measure of affinity - LOW Km = HIGH affinity
• When [S] << Km: V ≈ Vmax[S]/Km (first-order kinetics)
• When [S] >> Km: V ≈ Vmax (zero-order kinetics)

• Y-intercept = 1/Vmax
• X-intercept = -1/Km
• Slope = Km/Vmax
• Useful to determine type of inhibition

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3.5 Enzyme Inhibition (LAQ)

Competitive Inhibition

• Inhibitor resembles substrate, binds to active site
• Reversible - can be overcome by increasing [S]
• Km increases, Vmax unchanged
• Lineweaver-Burk: Lines intersect on Y-axis (same Y-intercept)
• Example: Succinate dehydrogenase inhibited by malonate; Statins inhibit HMG-CoA reductase; Methotrexate inhibits dihydrofolate reductase

Non-competitive Inhibition

• Inhibitor binds to allosteric site (NOT active site)
• Binds both E and ES complex equally
• Km unchanged, Vmax decreases
• Lineweaver-Burk: Lines intersect on X-axis (same X-intercept)
• Example: Heavy metals (Pb, Hg) inhibiting enzymes

Uncompetitive Inhibition

• Inhibitor binds only to ES complex
• Both Km and Vmax decrease
• Lineweaver-Burk: Parallel lines

Irreversible Inhibition

• Covalent binding to active site
• Organophosphates (e.g., DFP, nerve gases, malathion) irreversibly inhibit acetylcholinesterase
• Aspirin irreversibly inhibits COX-1 and COX-2

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3.6 Allosteric Enzymes

• Multi-subunit proteins with cooperative kinetics
• Sigmoidal (S-shaped) curve instead of hyperbolic Michaelis-Menten curve
• Regulatory sites separate from active sites
• Allosteric activators: Increase enzyme activity, shift curve left
• Allosteric inhibitors: Decrease activity, shift curve right
• Regulated by feedback inhibition (end product inhibits first/committed step enzyme)

• ATCase (aspartate transcarbamylase) - inhibited by CTP, activated by ATP
• Phosphofructokinase-1 (PFK-1) - activated by AMP/ADP/F-2,6-BP, inhibited by ATP/citrate

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3.7 Regulation of Enzymes

• Phosphorylation/dephosphorylation - by kinases/phosphatases
  • Activates glycogen phosphorylase, inhibits glycogen synthase
  • Phosphorylase b (inactive) → Phosphorylase a (active) by phosphorylation

• Inactive precursors activated by proteolytic cleavage
• Examples: Pepsinogen → Pepsin; Trypsinogen → Trypsin (by enterokinase); Prothrombin → Thrombin

• LDH (Lactate dehydrogenase):
  • LDH-1 (H₄): Heart muscle, RBCs - elevated in MI
  • LDH-5 (M₄): Liver, skeletal muscle - elevated in hepatitis
  • Electrophoresis separates 5 bands
• CK (Creatine Kinase):
  • CK-MM: Skeletal muscle
  • CK-MB: Cardiac muscle (elevated in MI)
  • CK-BB: Brain

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3.8 Clinically Important Enzymes (LAQ)

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CHAPTER 4: ELECTRON TRANSPORT CHAIN (ETC) AND BIOENERGETICS

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4.1 Bioenergetics - Key Concepts

• Substrate-level phosphorylation: ATP produced directly (glycolysis, TCA)
• Oxidative phosphorylation: ATP produced by ETC (mitochondria) - accounts for 90% of cellular ATP

• ΔG < 0: Exergonic (spontaneous)
• ΔG > 0: Endergonic (requires energy)
• Hydrolysis of ATP: ΔG = -7.3 kcal/mol

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4.2 Glycolysis (LAQ - Very Important)

1. Glucose + ATP → Glucose-6-phosphate (Hexokinase/Glucokinase) - irreversible
2. G6P ⇌ Fructose-6-phosphate (Phosphoglucose isomerase)
3. F6P + ATP → Fructose-1,6-bisphosphate (PFK-1) - Rate-limiting step - irreversible
4. F1,6-BP → DHAP + Glyceraldehyde-3-phosphate (Aldolase)
5. DHAP ⇌ G3P (Triose phosphate isomerase) - effectively 2 G3P continue

• PFK-1 (rate-limiting): Activated by AMP, ADP, Fructose-2,6-bisphosphate, Pi; Inhibited by ATP, citrate
• Pyruvate kinase: Activated by fructose-1,6-BP (feed-forward); Inhibited by ATP, acetyl-CoA

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4.3 Pyruvate Dehydrogenase Complex (PDC) - LAQ

• Activated by: ADP, CoA, NAD⁺, Ca²⁺
• Inhibited by: ATP, Acetyl-CoA, NADH, Fatty acids

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4.4 TCA Cycle (Krebs Cycle) - LAQ

• Isocitrate dehydrogenase (rate-limiting): Activated by ADP, Ca²⁺; Inhibited by ATP, NADH
• Alpha-KG dehydrogenase: Activated by Ca²⁺; Inhibited by NADH, succinyl-CoA

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4.5 Electron Transport Chain (ETC) - LAQ (High Priority)

• Complex I pumps 4H⁺
• Complex III pumps 4H⁺
• Complex IV pumps 2H⁺

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4.6 Oxidative Phosphorylation (Chemiosmotic Theory - Mitchell) - LAQ

• Electron transport creates a proton gradient across inner mitochondrial membrane (high H⁺ in intermembrane space, low in matrix)
• Protons flow back through ATP synthase (Complex V / F₀F₁-ATPase) → drives ATP synthesis
• ATP synthase: F₀ subunit (in membrane, proton channel), F₁ subunit (catalytic site, in matrix)

• NADH → ~2.5 ATP
• FADH₂ → ~1.5 ATP

• 2 ATP from glycolysis
• 2 GTP from TCA
• 10 NADH × 2.5 = 25 ATP
• 2 FADH₂ × 1.5 = 3 ATP
• Total ≈ 30-32 ATP per glucose

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4.7 Uncouplers and Inhibitors of Oxidative Phosphorylation

• 2,4-DNP (dinitrophenol) - old weight loss drug; lipophilic weak acid that carries H⁺ across membrane
• Thermogenin (UCP-1): Natural uncoupler in brown adipose tissue → generates heat (non-shivering thermogenesis) - activated by norepinephrine, fatty acids
• Aspirin (salicylate) in toxic doses

• Rotenone (insecticide), Amytal (barbiturate) → Complex I
• Antimycin A → Complex III
• Cyanide (CN⁻), Carbon monoxide (CO), Azide (N₃⁻) → Complex IV (block oxygen binding to Cyt a3)

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CHAPTER 5: CHEMISTRY AND METABOLISM OF HEMOGLOBIN

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5.1 Structure of Hemoglobin - LAQ

• Porphyrin ring (4 pyrrole rings) + Fe²⁺ at center
• Fe²⁺ can form 6 coordinate bonds:
  • 4 bonds to pyrrole nitrogens
  • 1 bond to proximal histidine (F8) of globin
  • 1 bond to O₂ (or other ligands)

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5.2 Oxygen Dissociation Curve - LAQ (Very Important)

• T state (tense/deoxy) - low O₂ affinity
• R state (relaxed/oxy) - high O₂ affinity
• Binding of O₂ to one subunit increases affinity of remaining subunits (positive cooperativity)

• Increased CO₂ (increased H⁺ - Bohr effect)
• Increased temperature
• Increased 2,3-BPG (2,3-bisphosphoglycerate)
• Decreased pH (acidosis)

• Decreased CO₂, decreased H⁺
• Decreased temperature
• Decreased 2,3-BPG
• Increased pH (alkalosis)
• Carbon monoxide (CO) - CO binds Hb with 200x greater affinity than O₂

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5.3 Heme Synthesis - LAQ

1. Glycine + Succinyl-CoA → ALA (delta-aminolevulinic acid)
   • Enzyme: ALA synthase (rate-limiting)
   • Location: Mitochondria
   • Coenzyme: Pyridoxal phosphate (B6)
   • Inhibited by heme (feedback)
   • Induced by: Drugs (barbiturates), steroids (AIP trigger)
2. 2 ALA → Porphobilinogen (PBG)
   • Enzyme: ALA dehydratase (PBG synthase)
   • Inhibited by Lead (Pb) - important!
3. 4 PBG → Hydroxymethylbilane
4. Hydroxymethylbilane → Uroporphyrinogen III
5. Uroporphyrinogen III → Coproporphyrinogen III
6. Coproporphyrinogen III → Protoporphyrinogen IX
7. Protoporphyrinogen IX → Protoporphyrin IX
   • Enzyme: Protoporphyrinogen oxidase
   • Inhibited by Lead
8. Protoporphyrin IX + Fe²⁺ → Heme
   • Enzyme: Ferrochelatase
   • Inhibited by Lead

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5.4 Porphyrias (LAQ)

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5.5 Hemoglobin Catabolism - LAQ

1. RBCs phagocytosed by macrophages of reticuloendothelial system (spleen, liver, bone marrow)
2. Hemoglobin → Globin + Heme
   • Globin → amino acids (recycled)
3. Heme → Fe + Biliverdin (green)
   • Enzyme: Heme oxygenase (requires O₂, NADPH)
   • Fe²⁺ stored as ferritin or exported
4. Biliverdin → Bilirubin (yellow-orange)
   • Enzyme: Biliverdin reductase (requires NADPH)
   • Unconjugated bilirubin (indirect): Insoluble, lipid soluble, bound to albumin, cannot be filtered by kidney, toxic to brain (kernicterus)
5. Unconjugated bilirubin → Liver (transported bound to albumin)
6. In liver: Bilirubin + 2 Glucuronic acid → Bilirubin diglucuronide (conjugated/direct bilirubin)
   • Enzyme: UDP-glucuronyltransferase
   • Water soluble, excreted in bile
7. In intestine: Conjugated bilirubin → Urobilinogen (by gut bacteria)
   • Urobilinogen → Urobilin (yellow - urine color) - absorbed, excreted in urine
   • Urobilinogen → Stercobilin (brown - feces color)

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5.6 Abnormal Hemoglobins - LAQ

Sickle Cell Anemia (HbS)

• Mutation: Glutamic acid → Valine at position 6 of beta chain (single point mutation, GAG→GTG)
• Mechanism: Deoxy-HbS polymerizes → long fibers → distorts RBC into sickle shape
• Sickle precipitated by: Low O₂, acidosis, dehydration, infection, cold
• Clinical features: Chronic hemolytic anemia, vaso-occlusive crises (pain crises), acute chest syndrome, stroke, avascular necrosis, splenic infarction/autosplenectomy, "H-vertebrae", dactylitis, aplastic crisis (Parvovirus B19)
• HbAS (sickle trait): Protective against malaria
• Treatment: Hydroxyurea (increases HbF), bone marrow transplant

HbC

• Glutamic acid → Lysine at position 6 of beta chain
• Mild hemolytic anemia, target cells

Methemoglobin

• Fe²⁺ oxidized to Fe³⁺ - cannot carry O₂
• Causes: Nitrites (well water), dapsone, primaquine, benzocaine
• Appearance: Chocolate brown blood
• Treatment: Methylene blue (reduces met-Hb back to Hb; requires NADPH → requires G6PD)
• G6PD deficiency: Methylene blue ineffective → use ascorbic acid
• Fetal Hb more susceptible → infant methemoglobinemia

Thalassemias (LAQ)

• β-thal minor (trait): β/β⁺ or β/β⁰ - mild microcytic hypochromic anemia, ↑HbA₂
• β-thal major (Cooley's anemia): β⁰/β⁰ - severe anemia requiring transfusions, skull X-ray shows "hair on end" (crew-cut) appearance due to extramedullary hematopoiesis, hepatosplenomegaly, iron overload
• Treatment: Blood transfusions + iron chelation (desferrioxamine), bone marrow transplant

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CHAPTER 6: CELL AND IMMUNOLOGY

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6.1 Cell Structure and Organelles - LAQ

The Nucleus

• Double membrane (nuclear envelope with nuclear pores)
• Contains DNA (genome) and nucleolus (rRNA synthesis)
• Site of DNA replication and transcription

Mitochondria

• Double membrane: Outer (permeable) and inner (cristae - site of ETC)
• Matrix: TCA cycle, beta-oxidation, PDC
• Own circular DNA (mtDNA), 37 genes
• Maternally inherited
• ~500-2000 per cell depending on energy demand

Endoplasmic Reticulum (ER)

• Rough ER (RER): Ribosomes on surface → protein synthesis and folding, glycosylation
• Smooth ER (SER): No ribosomes → lipid synthesis, steroid synthesis, drug detoxification (CYP450 enzymes), calcium storage

Golgi Apparatus

• "Post office of cell" - modifies, sorts, packages proteins from RER
• Site of final glycosylation
• Products: Secretory vesicles, lysosomes

Lysosomes

• Contain 50+ hydrolytic enzymes (acid hydrolases - active at pH 5)
• Digest cellular debris, engulfed bacteria, worn organelles
• Lysosomal storage diseases: Enzyme deficiencies → accumulation of substrates
  • Gaucher's: Glucocerebrosidase deficiency → glucocerebroside in macrophages
  • Niemann-Pick: Sphingomyelinase deficiency
  • Tay-Sachs: Hexosaminidase A deficiency → GM₂ ganglioside
  • Hurler/Hunter: Mucopolysaccharidoses

Ribosomes

• 80S in eukaryotes (60S + 40S subunits)
• 70S in prokaryotes (50S + 30S) - target of many antibiotics

Cell Membrane

• Fluid mosaic model (Singer-Nicolson)
• Phospholipid bilayer with proteins (integral and peripheral)
• Cholesterol: Maintains membrane fluidity (stiffens at high temp, fluidizes at low temp)

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6.2 Immunology - LAQ

Overview of Immune System

• Physical barriers (skin, mucosa)
• Phagocytes: Neutrophils, macrophages
• NK cells
• Complement system
• Interferons
• Pattern recognition receptors (PRRs) - recognize PAMPs (pathogen-associated molecular patterns) via Toll-like receptors (TLRs)

• Humoral immunity: B cells → plasma cells → antibodies
• Cell-mediated immunity: T cells

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Immunoglobulins (Antibodies) - LAQ

• Fc region (constant): Complement activation, Fc receptor binding, placental transfer
• Fab region (variable): Antigen binding (2 Fab per antibody)

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T Lymphocytes - LAQ

• CD4+ Helper T cells (Th):
  • Th1: Activates macrophages and CTLs via IFN-γ, IL-2 → cell-mediated immunity
  • Th2: Activates B cells, promotes IgE via IL-4, IL-5, IL-13 → humoral/allergic immunity
  • Th17: IL-17 → inflammation, mucosal immunity
• CD8+ Cytotoxic T cells (CTL/Tc): Kill virus-infected and tumor cells via perforin/granzyme and Fas-FasL. Recognize antigen on MHC I.
• Regulatory T cells (Treg): CD4+CD25+FoxP3+ → suppress immune response, prevent autoimmunity. Secrete IL-10, TGF-β.

1. TCR recognizes antigen-MHC complex
2. Co-stimulatory signal (CD28 on T cell + B7 on APC)

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MHC (Major Histocompatibility Complex) / HLA - LAQ

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Complement System - LAQ

• Classical pathway: Antigen-antibody complex activates C1 → C4 → C2 → C3 (IgG or IgM required)
• Alternative pathway: Spontaneous C3 hydrolysis, amplified by microbial surfaces (no antibody needed)
• Lectin pathway: MBL (mannose-binding lectin) + MASPs → C4 → C2 → C3

• C3b: Opsonization (enhances phagocytosis)
• C3a, C5a: Anaphylatoxins - mast cell degranulation, vasodilation, increased permeability
• C5a: Chemotaxis of neutrophils (most potent)
• C5b-9: Membrane Attack Complex (MAC) - kills gram-negative bacteria

• C1-C4 deficiency → recurrent bacterial infections, SLE (clearance of immune complexes impaired)
• C3 deficiency → most severe (recurrent encapsulated bacteria)
• C5-C9 (MAC) deficiency → recurrent Neisseria infections

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Hypersensitivity Reactions - LAQ (Important)

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Important Cytokines

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CHAPTER 7: CHEMISTRY AND METABOLISM OF NUCLEIC ACIDS

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7.1 Chemistry of Nucleic Acids - LAQ

Purines and Pyrimidines

Nucleoside vs Nucleotide

• Nucleoside = Base + Sugar (ribose or deoxyribose) - N-glycosidic bond
• Nucleotide = Base + Sugar + Phosphate group(s)
  • Mono (NMP), Di (NDP), Tri (NTP)

Watson-Crick Base Pairing

• A = T (2 hydrogen bonds) in DNA; A = U in RNA
• G ≡ C (3 hydrogen bonds)
• Higher G+C content → higher melting temperature of DNA

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7.2 DNA Structure - LAQ

• Right-handed double helix
• Two antiparallel strands
• Base pairs on inside, sugar-phosphate backbone on outside
• Pitch: 34 Å (3.4 nm) per turn
• Rise per base pair: 3.4 Å
• 10 base pairs per turn
• Major groove (wider, deeper - protein-DNA interactions) and minor groove
• Stabilized by: H-bonds between base pairs + hydrophobic stacking interactions

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7.3 DNA Replication - LAQ

• Each daughter cell gets one parental strand and one newly synthesized strand

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7.4 Transcription - LAQ

• Prokaryotes: Single RNA pol (core: α₂ββ'ω; holoenzyme: + sigma factor)
  • Sigma factor recognizes promoter (Pribnow box -10, -35 regions)
  • Inhibited by Rifampicin (blocks initiation - used in TB)
• Eukaryotes:
  • RNA Pol I: rRNA (large - 28S, 18S, 5.8S) - in nucleolus
  • RNA Pol II: mRNA precursors (hnRNA) - Inhibited by alpha-amanitin (Amanita mushroom toxin)
  • RNA Pol III: tRNA, 5S rRNA, snRNA

1. Initiation: RNA Pol binds promoter (TATA box in eukaryotes - Hogness box)
2. Elongation: RNA synthesized 5'→3' using 3'→5' template strand (antisense strand)
3. Termination:
   • Prokaryotes: Rho-dependent or intrinsic (hairpin structure)
   • Eukaryotes: Poly-A signal (AAUAAA)

• 5' Cap: 7-methylguanosine cap → protects from degradation, ribosome recognition
• 3' Poly-A tail: ~200 A residues → stability, export
• RNA splicing: Introns removed, exons joined. Spliceosome (snRNPs) catalyze. Splicing requires GU...AG rule (introns start with GU and end with AG).

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7.5 Types of RNA

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7.6 Genetic Code - LAQ

1. Triplet code: 3 nucleotides (codon) = 1 amino acid
2. Non-overlapping: Each nucleotide read only once
3. Degenerate/Redundant: More than one codon for same amino acid (64 codons for 20 amino acids)
4. Universal: Same code used by all organisms (with minor exceptions)
5. Commaless: No punctuation between codons (read continuously)

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7.7 Translation (Protein Synthesis) - LAQ

• Small subunit + mRNA + initiator tRNA (Met-tRNA) + initiation factors (eIF in eukaryotes)
• AUG start codon recognized
• Large subunit joins → complete ribosome

• A site (Aminoacyl site): New aminoacyl-tRNA enters
• P site (Peptidyl site): Growing peptide chain
• E site (Exit site): tRNA leaves
• Peptide bond formation: Peptidyl transferase (23S rRNA - ribozyme) transfers growing chain to amino acid in A site
• Translocation: Ribosome moves 3 nucleotides (1 codon) in 5'→3' direction

• Stop codon reaches A site → release factors bind → polypeptide released

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7.8 Purine Synthesis and Salvage - LAQ

De Novo Purine Synthesis

• Built on ribose-5-phosphate backbone (from pentose phosphate pathway)
• Requires: Glutamine (N), Aspartate (N), Glycine (C2,N3,C4,C5), CO₂, Folate, N10-formyl-THF
• End products: IMP → AMP and GMP
• Rate-limiting enzyme: PRPP amidotransferase - inhibited by AMP and GMP (feedback)
• Requires folate - methotrexate inhibits → impairs purine synthesis → antiproliferative

Purine Salvage Pathway

• Reuses free purines (from nucleic acid breakdown)
• HGPRT (hypoxanthine-guanine phosphoribosyltransferase): Hypoxanthine + PRPP → IMP; Guanine + PRPP → GMP
• APRT: Adenine → AMP
• Lesch-Nyhan syndrome: HGPRT deficiency (X-linked) → uric acid overproduction → gout + neurological symptoms (self-mutilation, choreoathetosis, intellectual disability)

Purine Catabolism

• AMP → Inosine → Hypoxanthine → Xanthine → Uric acid
• GMP → Guanosine → Guanine → Xanthine → Uric acid
• Enzyme: Xanthine oxidase (final step - inhibited by Allopurinol)
• Gout: Uric acid crystals in joints. Allopurinol (xanthine oxidase inhibitor) or febuxostat used.

Pyrimidine Synthesis

• Synthesized as free base first (unlike purines)
• Carbamoyl phosphate (cytoplasm - CPS-II, uses glutamine) → reacts with Aspartate → UMP → UDP → UTP → CTP
• Rate-limiting enzyme: CPS-II (in cytoplasm for pyrimidines; CPS-I in mitochondria for urea cycle)
• Feedback: UTP inhibits CPS-II

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7.9 Nucleic Acid Degradation

Pyrimidine Catabolism

• Cytosine → Uracil → Beta-alanine + NH₃ + CO₂ (water-soluble products → easily excreted)
• Thymine → Beta-aminoisobutyrate → excreted in urine

Clinically Relevant Nucleotide Drugs

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📋 QUICK REVISION SUMMARY - HIGH-YIELD FOR EXAM

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TOP LAQ-LIKELY TOPICS (Prepare these first)

1. Urea Cycle - all 6 steps, enzymes, locations, clinical aspects (hyperammonemia)
2. Heme Synthesis + Porphyrias - ALA synthase (rate-limiting), Lead inhibits 3 enzymes, AIP vs PCT
3. Oxygen Dissociation Curve - Bohr effect, 2,3-BPG, right vs left shift factors
4. ETC + Oxidative Phosphorylation - 4 complexes + inhibitors, Mitchell's chemiosmosis, uncouplers
5. Vitamin B12 and Folate - megaloblastic anemia, methyl trap, SCDS for B12 only
6. Enzyme Kinetics - Km, Vmax, competitive vs non-competitive inhibition, Lineweaver-Burk
7. DNA Replication - enzymes (helicase, primase, DNA pol, ligase), semiconservative
8. Sickle Cell Anemia - mutation, mechanism, complications
9. TCA Cycle - all 8 steps, 2 CO₂ and 3 NADH released
10. Immunoglobulins - 5 types, structure, functions, IgM is pentamer

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MUST-REMEMBER NUMBERS

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KEY MNEMONICS

• Essential AAs: PVT TIM HaLL
• Ketogenic only: Leucine, Lysine (LL)
• PDC cofactors: The Lovely Cat Finds Nice (TPP, Lipoate, CoA, FAD, NAD)
• AIP triggers: 4 Ss - Starvation, Steroids, Sulfonamides, Stress
• Pellagra (3 Ds+1): Dermatitis, Diarrhea, Dementia, Death
• Scurvy: Perifollicular hemorrhages, Corkscrew hairs, Gum bleeding
• Right shift ODC: ACAT (Acidosis, CO₂↑, Altitude = 2,3-BPG↑, Temperature↑)
• Stop codons: UAA, UAG, UGA = "U Are Annoying, U Are Gone, U Go Away"

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CLINICAL CORRELATIONS THAT ALWAYS COME IN EXAMS

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