2.3 Biochemistry

Biochemistry is the molecular language of pharmacotherapy. Most drugs act on proteins — enzymes, receptors, ion channels, transporters — and many act on the metabolic and signaling pathways that biochemistry describes. This section covers the macromolecules, enzyme kinetics, central metabolism, molecular biology, and signal transduction that the FPGEE expects you to integrate with pharmacology.

Macromolecules

Proteins and the Four Levels of Structure

Proteins are polymers of 20 amino acids linked by peptide bonds. Their function depends on shape, and shape is described in four levels:

• Primary structure — the linear sequence of amino acids, encoded by DNA.
• Secondary structure — local folding into alpha-helices and beta-sheets stabilized by backbone hydrogen bonds.
• Tertiary structure — the overall 3-D shape of a single polypeptide, stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges (covalent).
• Quaternary structure — the assembly of multiple polypeptide subunits (e.g., hemoglobin is a tetramer of two alpha and two beta chains).

Misfolded proteins cause disease (prion diseases, Alzheimer's amyloid plaques). Many drugs stabilize or destabilize specific conformations — allosteric modulators of GPCRs are a major modern drug class.

Carbohydrates, Lipids, and Nucleic Acids

Carbohydrates are sugars and polymers (glycogen, starch, cellulose). Glycogen is the body's glucose store; glycogen phosphorylase releases glucose-1-phosphate, the target of inhibition in McArdle disease. Lipids include triglycerides (energy storage), phospholipids (membranes), cholesterol (membrane fluidity and steroid precursor), and eicosanoids (prostaglandins, leukotrienes — targets of NSAIDs and leukotriene antagonists). Nucleic acids (DNA, RNA) store and express genetic information; purines and pyrimidines are the bases, and their synthesis is the target of antimetabolites like methotrexate and 5-fluorouracil.

Enzymes and Kinetics

Enzymes are protein catalysts that lower activation energy. The Michaelis-Menten equation describes their rate:

v = (Vmax × [S]) / (Km + [S])

where Vmax is the maximum velocity at saturating substrate and Km is the substrate concentration at half-maximal velocity. A low Km means high affinity (the enzyme reaches half-Vmax at low substrate). At low [S], the reaction is first-order in substrate; at high [S], it is zero-order (saturated, at Vmax). Phenytoin and ethanol display nonlinear (zero-order at therapeutic doses) kinetics — small dose increases cause disproportionate concentration rises.

Inhibition Patterns

• Competitive inhibition — inhibitor resembles substrate and binds the active site; Km increases, Vmax unchanged; overcome by raising substrate. Example: methotrexate competes with folate at dihydrofolate reductase.
• Noncompetitive inhibition — inhibitor binds an allosteric site; Vmax decreases, Km unchanged; not overcome by substrate. Example: heavy metals binding sulfhydryl groups.
• Irreversible inhibition — covalent modification; both Vmax and apparent Km change permanently. Examples: aspirin acetylates COX-1, omeprazole covalently binds the H⁺/K⁺ ATPase, clopidogrel covalently modifies the P2Y12 platelet receptor.
• Allosteric regulation — effector molecules bind regulatory sites and change enzyme activity; can be positive (feed-forward) or negative (feedback). PFK-1 is allosterically activated by fructose-2,6-bisphosphate and inhibited by ATP.

Metabolic Pathways

Glycolysis converts glucose to pyruvate; in the absence of oxygen, pyruvate becomes lactate (anaerobic glycolysis). In the presence of oxygen, pyruvate enters mitochondria, is converted to acetyl-CoA by pyruvate dehydrogenase, and enters the TCA cycle. NADH and FADH2 then deliver electrons to the electron transport chain (Complexes I-IV), which pumps protons to drive ATP synthase — about 30-32 ATP per glucose.

Gluconeogenesis reverses glycolysis using four bypass enzymes; it is the metabolic target of metformin, the most prescribed antidiabetic. Fatty acid metabolism uses carnitine shuttle to move fatty acyl-CoA into mitochondria; the absence of carnitine or CPT-1 prevents ketone formation in fasting. Cholesterol synthesis is anchored by HMG-CoA reductase, the statin target.

Molecular Biology — The Central Dogma

DNA → RNA → protein. Replication is performed by DNA polymerase (target of acyclovir, which is selective for viral DNA polymerase after phosphorylation by viral thymidine kinase). Transcription is performed by RNA polymerase (target of rifampin, which inhibits bacterial RNA polymerase). Translation occurs at the ribosome (target of aminoglycosides, tetracyclines, macrolides, chloramphenicol — each binding a different ribosomal site).

Gene expression regulation occurs at multiple levels: transcription factors bind promoter and enhancer elements; epigenetic modifications (DNA methylation, histone acetylation) open or close chromatin; mRNA splicing produces isoforms; microRNAs degrade or silence transcripts. Many anticancer drugs target these mechanisms (e.g., DNA methyltransferase inhibitors like azacitidine, HDAC inhibitors like vorinostat).

Signal Transduction and Drug Targets

Cells communicate through receptors that translate extracellular signals into intracellular responses. The two receptor superfamilies most relevant to pharmacy:

G-Protein-Coupled Receptors (GPCRs)

Seven-transmembrane receptors coupled to heterotrimeric G proteins (α, β, γ). The α subunit determines signaling:

• Gs → activates adenylyl cyclase → ↑ cAMP → activates protein kinase A. Receptors: beta-1, beta-2, beta-3, D1, H2.
• Gi → inhibits adenylyl cyclase → ↓ cAMP. Receptors: alpha-2, M2, D2.
• Gq → activates phospholipase C → generates IP3 (releases Ca²⁺ from ER) and DAG (activates protein kinase C). Receptors: alpha-1, M3, H1, V1.

Roughly one-third of marketed drugs act on GPCRs — beta-blockers, antihistamines, opioids, anticholinergics, dopamine agonists, serotonin modulators.

Receptor Tyrosine Kinases

Single-transmembrane receptors with intracellular kinase domains. Ligand binding induces dimerization and autophosphorylation, recruiting downstream effectors (RAS-RAF-MEK-ERK, PI3K-AKT-mTOR). Examples: insulin receptor, EGFR, HER2, VEGFR. Cancer therapies targeting these include imatinib (BCR-ABL), trastuzumab (HER2), erlotinib (EGFR), and sunitinib (VEGFR).

Relevance to Pharmacotherapy

• Statins inhibit HMG-CoA reductase (cholesterol synthesis).
• ACE inhibitors block angiotensin-converting enzyme (RAAS).
• Methotrexate inhibits dihydrofolate reductase (folate pathway, used in cancer, rheumatoid arthritis, psoriasis).
• Proton pump inhibitors irreversibly inhibit the H⁺/K⁺ ATPase (gastric acid).
• Aspirin irreversibly acetylates COX-1/2 (prostaglandin synthesis).
• Metformin inhibits Complex I of the electron transport chain and gluconeogenesis.
• Sulfonylureas close beta-cell K-ATP channels; GLP-1 agonists activate beta-cell GLP-1 GPCRs.

Biochemistry is therefore not a stand-alone science on the FPGEE — it is the molecular explanation for almost every drug mechanism you will study in later chapters.