Free MCAT study guide — Biological and Biochemical Foundations of Living Systems
Metabolism is arguably the most tested biochemistry topic on the MCAT. You must understand the three main stages of aerobic glucose oxidation: glycolysis (cytoplasm), the citric acid cycle/TCA cycle (mitochondrial matrix), and oxidative phosphorylation (inner mitochondrial membrane). For each pathway, know the key enzymes, substrates, products, regulation points, and energy yields. Glycolysis converts one glucose into two pyruvate molecules, yielding 2 ATP and 2 NADH per glucose. Pyruvate enters the mitochondria and is converted to acetyl-CoA by pyruvate dehydrogenase. The TCA cycle generates 3 NADH, 1 FADH2, and 1 GTP per turn (two turns per glucose). Oxidative phosphorylation uses the electron transport chain to create a proton gradient that drives ATP synthase, producing the bulk of ATP (approximately 30-32 per glucose). You also need to understand gluconeogenesis, glycogenesis, glycogenolysis, the pentose phosphate pathway, beta-oxidation of fatty acids, ketogenesis, and the regulation of all these pathways by hormones (insulin, glucagon, epinephrine) and allosteric effectors.
Glycolysis occurs in the cytoplasm and converts one molecule of glucose (6C) into two molecules of pyruvate (3C) through ten enzymatic steps. The pathway has two phases: the energy investment phase (steps 1-5, consuming 2 ATP) and the energy payoff phase (steps 6-10, producing 4 ATP and 2 NADH). The net yield is 2 ATP, 2 NADH, and 2 pyruvate per glucose. Three irreversible, regulated steps are catalyzed by hexokinase/glucokinase (step 1, phosphorylates glucose to glucose-6-phosphate), phosphofructokinase-1/PFK-1 (step 3, the committed and rate-limiting step, phosphorylates fructose-6-phosphate to fructose-1,6-bisphosphate), and pyruvate kinase (step 10, converts PEP to pyruvate). PFK-1 is activated by AMP, fructose-2,6-bisphosphate, and ADP, and inhibited by ATP and citrate. Under anaerobic conditions, pyruvate is reduced to lactate by lactate dehydrogenase (LDH), regenerating NAD+ to allow glycolysis to continue. In yeast, anaerobic fermentation produces ethanol and CO2 instead.
Pyruvate enters the mitochondrial matrix and is oxidatively decarboxylated by the pyruvate dehydrogenase complex (PDC) to produce acetyl-CoA, CO2, and NADH. PDC requires five coenzymes derived from vitamins: thiamine pyrophosphate (B1), lipoic acid, CoA (from pantothenic acid, B5), FAD (from riboflavin, B2), and NAD+ (from niacin, B3). PDC is inhibited by its products (acetyl-CoA and NADH) and activated by CoA and NAD+. The TCA cycle (Krebs cycle) begins when acetyl-CoA (2C) condenses with oxaloacetate (4C) to form citrate (6C), catalyzed by citrate synthase. Per turn: 3 NADH (at isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase, and malate dehydrogenase), 1 FADH2 (at succinate dehydrogenase, which is also Complex II of the ETC), and 1 GTP (at succinyl-CoA synthetase). Two CO2 are released per turn. Since one glucose yields two acetyl-CoA, the cycle turns twice per glucose, producing 6 NADH, 2 FADH2, and 2 GTP total.
The electron transport chain (ETC) is located on the inner mitochondrial membrane and consists of four complexes plus two mobile carriers. Complex I (NADH dehydrogenase) accepts electrons from NADH and pumps 4 H+. Coenzyme Q (ubiquinone) carries electrons to Complex III (cytochrome bc1), which pumps 4 H+. Cytochrome c carries electrons to Complex IV (cytochrome c oxidase), which pumps 2 H+ and transfers electrons to O2, forming H2O. Complex II (succinate dehydrogenase) accepts electrons from FADH2 and passes them to CoQ without pumping protons. The proton gradient across the inner membrane (proton-motive force) drives ATP synthase (Complex V), which uses the flow of H+ back into the matrix to catalyze ADP + Pi -> ATP (chemiosmotic coupling, as proposed by Peter Mitchell). Each NADH yields approximately 2.5 ATP; each FADH2 yields approximately 1.5 ATP. Total ATP from one glucose: approximately 30-32 (2 from glycolysis + 2 GTP from TCA + approximately 26-28 from oxidative phosphorylation).
Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors (lactate, amino acids, glycerol) and occurs primarily in the liver and kidney cortex. It is essentially the reverse of glycolysis but uses four unique enzymes to bypass the three irreversible steps: pyruvate carboxylase (pyruvate to oxaloacetate, requires biotin), PEP carboxykinase (PEPCK, oxaloacetate to PEP), fructose-1,6-bisphosphatase (F1,6BP to F6P), and glucose-6-phosphatase (G6P to glucose, only in liver and kidney, not muscle). Gluconeogenesis is stimulated by glucagon and cortisol during fasting. Glycogenesis (glycogen synthesis) uses glycogen synthase to add glucose residues to glycogen via alpha-1,4 linkages, with branching enzyme creating alpha-1,6 branches. Glycogenolysis (glycogen breakdown) uses glycogen phosphorylase to release glucose-1-phosphate. Epinephrine activates glycogenolysis in muscle (via cAMP/PKA), while glucagon does so in the liver. Insulin promotes glycogenesis and inhibits glycogenolysis.
Beta-oxidation of fatty acids occurs in the mitochondrial matrix and sequentially removes two-carbon units as acetyl-CoA. Long-chain fatty acids must be transported across the inner mitochondrial membrane via the carnitine shuttle (carnitine palmitoyltransferase I/CPT-I on the outer membrane is the rate-limiting step, inhibited by malonyl-CoA). Each round of beta-oxidation produces 1 NADH, 1 FADH2, and 1 acetyl-CoA. A 16-carbon fatty acid (palmitate) undergoes 7 rounds of beta-oxidation, yielding 8 acetyl-CoA, 7 NADH, and 7 FADH2, for a total of approximately 106 ATP (minus 2 for activation). This demonstrates why fats are a much more energy-dense fuel than carbohydrates. During prolonged fasting or uncontrolled diabetes, excess acetyl-CoA in the liver is converted to ketone bodies (acetoacetate, beta-hydroxybutyrate, and acetone) through ketogenesis. Ketone bodies are water-soluble fuels used by the brain, heart, and skeletal muscle when glucose is scarce. Excessive ketone production causes metabolic acidosis (diabetic ketoacidosis/DKA).
The pentose phosphate pathway (PPP) branches from glycolysis at glucose-6-phosphate and has two phases. The oxidative phase produces NADPH (used for reductive biosynthesis and glutathione reduction to combat oxidative stress) and CO2. The rate-limiting enzyme is glucose-6-phosphate dehydrogenase (G6PD). The non-oxidative phase produces ribose-5-phosphate (for nucleotide synthesis) and can regenerate glycolytic intermediates. G6PD deficiency (X-linked) reduces NADPH production, making red blood cells vulnerable to oxidative damage (Heinz bodies, hemolytic anemia triggered by oxidant stressors like fava beans or certain drugs). Metabolic integration is controlled by energy status: high ATP/NADH inhibits catabolic pathways (glycolysis, TCA, ETC) and stimulates anabolic pathways (gluconeogenesis, fatty acid synthesis). Insulin promotes anabolism (fed state), while glucagon and epinephrine promote catabolism (fasted/fight-or-flight state). The liver is the central metabolic hub, uniquely capable of gluconeogenesis, ketogenesis, and urea cycle function.
Net glycolysis yield: 2 ATP, 2 NADH, 2 pyruvate per glucose.
PFK-1 is the rate-limiting enzyme of glycolysis, activated by AMP and F-2,6-BP, inhibited by ATP and citrate.
Pyruvate dehydrogenase requires 5 coenzymes: TPP (B1), lipoic acid, CoA (B5), FAD (B2), NAD+ (B3).
TCA cycle yield per glucose: 6 NADH, 2 FADH2, 2 GTP, 4 CO2.
Total ATP from complete glucose oxidation: approximately 30-32 ATP.
NADH yields ~2.5 ATP; FADH2 yields ~1.5 ATP via oxidative phosphorylation.
Cyanide and CO inhibit Complex IV; rotenone inhibits Complex I; antimycin A inhibits Complex III.
Oligomycin inhibits ATP synthase; 2,4-DNP is an uncoupler (dissipates proton gradient as heat).
Gluconeogenesis occurs in liver and kidney; muscle lacks glucose-6-phosphatase.
CPT-I is the rate-limiting step of fatty acid oxidation, inhibited by malonyl-CoA.
Palmitate (C16) yields approximately 106 ATP (minus 2 for activation = 104 net).
Ketone bodies are produced in the liver but consumed by peripheral tissues and brain during fasting.
G6PD deficiency is the most common enzyme deficiency worldwide, causing hemolytic anemia.
The Cori cycle: lactate from muscle goes to liver for gluconeogenesis, glucose returns to muscle.
Confusing net ATP from glycolysis (2 ATP) with gross ATP (4 ATP) -- 2 ATP are consumed in the investment phase.
Forgetting that anaerobic conditions do not stop glycolysis -- they redirect pyruvate to lactate/ethanol to regenerate NAD+.
Mixing up the location: glycolysis in cytoplasm, PDC and TCA in mitochondrial matrix, ETC on inner mitochondrial membrane.
Assuming oxygen is consumed in glycolysis or the TCA cycle -- O2 is only the final electron acceptor in the ETC.
Confusing uncouplers (like DNP, which dissipate the gradient and increase O2 consumption but decrease ATP) with ETC inhibitors (which block electron flow and decrease O2 consumption).
Forgetting that Complex II does NOT pump protons, which is why FADH2 yields fewer ATP than NADH.
Mixing up gluconeogenesis (making new glucose) with glycogenolysis (breaking down glycogen).
Create a master table listing each metabolic pathway with its location, key enzymes, inputs, outputs, regulators, and associated diseases. The MCAT expects you to trace carbons, hydrogens, and energy carriers through each pathway. Practice calculating total ATP yield from different substrates (glucose, palmitate, odd-chain fatty acids) and be able to explain how inhibitors and uncouplers affect ATP production, oxygen consumption, and the proton gradient.
Focus on metabolic regulation: understand how insulin, glucagon, and epinephrine shift the balance between anabolic and catabolic pathways. The MCAT loves scenarios describing a patient in a specific metabolic state (fed, fasted, exercising, diabetic ketoacidosis) and asking which pathways are active or inhibited. Practice identifying enzyme deficiencies from clinical presentations -- for example, G6PD deficiency from hemolytic anemia after oxidant exposure, or McArdle disease from exercise intolerance due to muscle glycogen phosphorylase deficiency.
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