Difficulty: Intermediate | Prerequisites: Energy and chemical bonds (Doc 2), basic organic chemistry
This material covers how cells build and break down molecules, and how enzymes control the speed of those reactions. You will need a grasp of energy types and chemical bonds (Doc 2) before this makes full sense. The topics here, from protein folding to the TCA cycle to oxidative phosphorylation, form the metabolic core of the entire course. Every organ system you study later depends on the pathways and regulatory principles introduced here.
Enzymes are biological catalysts regulated by cofactors, inhibitors, and allosteric modulators. Proteins, carbohydrates, and lipids each have distinct structures and metabolic roles. The central metabolic pathways (glycolysis, TCA cycle, oxidative phosphorylation) extract energy from nutrients and store it as ATP, with the electron transport chain and proton motive force doing the heavy lifting.
Primary structure
The linear sequence of amino acids in a protein. Think of it as the spelling of the protein's "word."
Secondary structure
Local folding patterns: alpha-helices and beta-sheets, stabilised by hydrogen bonds along the backbone.
Tertiary structure
The overall three-dimensional shape of a single polypeptide chain, stabilised by numerous weak bonds (and sometimes disulphide bridges).
Molecular chaperones
Proteins that assist other proteins in folding into their correct shape. Not all proteins can fold on their own.
Heat shock proteins
Chaperones whose production increases during heat stress, helping the cell cope with a surge of denatured proteins.
Metabolic flux
The flow rate through a metabolic pathway. Think of it as metabolic throughput: how fast substrates are being converted to products.
Amphibolic
A metabolic pathway that can be both synthetic (anabolic) and degradative (catabolic). The TCA cycle is the classic amphibolic pathway.
Cofactors
Non-protein helpers of enzymes, including metal ions (zinc, iron, magnesium).
Prosthetic group
A cofactor that is covalently and permanently bonded into the enzyme.
Coenzymes
Organic cofactors derived from vitamins. NAD+ and FAD are key examples.
Active site
The specific location on an enzyme where the substrate binds and the reaction takes place.
Equilibrium
The state in which forward and reverse reaction rates are equal. No net change in concentrations.
Michaelis-Menten equation
v = Vmax x [S] / ([S] + Km). Describes the relationship between substrate concentration and reaction velocity for many enzymes.
Near-equilibrium reaction
A reaction where in vivo concentrations of products and substrates are close to what equilibrium would produce. Regulated by substrate and product levels, not by enzyme activity.
Conservation of Km
The observation that enzymes from different species share a similar Km when assayed under conditions that approximate those in the animal. In simple terms, evolution conserves the enzyme's affinity for its substrate.
Competitive inhibitors
Molecules that bind to the active site, blocking the substrate from entering. Overcome by increasing substrate concentration.
Allosteric regulators
Molecules that alter enzyme activity by binding at a site other than the active site. They change the enzyme's shape and therefore its function.
Protein kinase
An enzyme that transfers a phosphate group from ATP to a target protein (phosphorylation), often switching the target on or off.
Protein phosphatases
Enzymes that remove phosphate groups from phosphorylated proteins, reversing the effect of kinases.
Reducing equivalents
NAD+ and NADP+ (and their reduced forms NADH and NADPH). They carry electrons between metabolic reactions.
Redox status
The relative levels of reduced to oxidised molecules in a cell. A key indicator of metabolic state.
Phosphorylation potential
An expression of energy status: the mass action ratio for ATPase, [ATP]/[ADP][Pi]. Higher values mean more available energy.
Monosaccharides
Simple sugars with three to seven carbons. Glucose is the most physiologically important.
Disaccharides
Two monosaccharides joined by a covalent bond (e.g., sucrose, lactose).
Polysaccharides
Larger polymers of sugars that serve in energy storage (glycogen, starch) and structure (cellulose, chitin).
Glycogen
The main carbohydrate energy store in animals. A glucose polymer stored primarily in liver and muscle.
Glycosylation
The addition of carbohydrate groups to other macromolecules, producing glycolipids and glycoproteins found in the plasma membrane.
Chitin
A polymer of N-acetyl glucosamine used by arthropods to build their exoskeleton.
Glycosaminoglycans (GAGs)
Non-protein components of the extracellular matrix.
Lipogenesis
Triglyceride synthesis.
Lipolysis
Triglyceride breakdown by lipases.
Phosphoglycerides
The major class of membrane phospholipids: a glycerol backbone, two fatty acids, and a polar head group linked via phosphate.
Sphingolipid
A phospholipid based on a sphingosine backbone rather than glycerol.
Steroids
Lipid molecules sharing a basic four-ring hydrocarbon structure (e.g., cholesterol, testosterone, cortisol).
Tricarboxylic acid cycle (TCA cycle)
The cyclical mitochondrial pathway that oxidises acetyl CoA to produce 3 NADH, 1 FADH2, and 1 GTP per turn. Also called the Krebs cycle or citric acid cycle. Produces most of the CO2 from metabolism.
Substrate-level phosphorylation
Direct transfer of a phosphate group from a substrate to ADP, producing ATP without the electron transport chain.
Anaplerotic pathways
Reactions that replenish TCA cycle intermediates when they are siphoned off for biosynthesis.
Oxidative phosphorylation
ATP production driven by the oxidation of NADH and FADH2. The electron transport chain pumps protons, creating a proton motive force that the F1F0 ATPase uses to make ATP.
Electron transport system (ETS)
A series of protein complexes in the inner mitochondrial membrane that pass electrons from reducing equivalents to oxygen, pumping protons and building the gradient.
Proton motive force
The electrochemical gradient of protons across the inner mitochondrial membrane, created by the ETS. This is the energy that drives ATP synthesis.
Reactive oxygen species (ROS)
Free radicals with an unpaired electron on oxygen. Byproducts of the ETS that can damage cells if not neutralised.
Turnover rate
The number of catalytic events per unit time for an enzyme (synonymous with kcat). Also used for the rate of synthesis and degradation of a metabolite.
Futile cycle
A pair of opposing enzymatic reactions that run simultaneously, consuming ATP and releasing heat without net change in substrates. Sometimes used deliberately for thermogenesis.
Respiratory quotient (RQ)
CO2 produced / O2 consumed. An RQ of 1.0 indicates carbohydrate oxidation; 0.7 indicates fat oxidation. Useful for determining which fuel an animal is burning.
Redox shuttle
A multi-enzyme pathway that transfers reducing equivalents from cytoplasmic NADH into the mitochondria for oxidation (e.g., the malate-aspartate shuttle).
Ketogenesis
Synthesis of ketone bodies, used when tissues cannot use fatty acids directly (e.g., the brain during prolonged fasting).
Ketolysis
Conversion of ketone bodies (beta-hydroxybutyrate, acetoacetate) back to acetyl CoA for energy.
Primary (sequence) determines secondary (alpha-helix, beta-sheet) determines tertiary (3D shape). Each level depends on the one before it.
Molecular chaperones and heat shock proteins assist folding. Without them, many proteins misfold, aggregate, and lose function.
Enzymes lower activation energy without being consumed. They do not change the equilibrium, only how fast it is reached.
The Michaelis-Menten equation (v = Vmax [S] / ([S] + Km)) describes the hyperbolic relationship between substrate concentration and reaction velocity.
Km is the substrate concentration at which velocity is half of Vmax. A low Km means high affinity.
Vmax is the maximum velocity when the enzyme is fully saturated.
Competitive inhibitors bind the active site and raise the apparent Km (the enzyme appears to have lower affinity) without changing Vmax.
Allosteric regulators bind elsewhere and can change both Km and Vmax by altering the enzyme's conformation.
Protein kinases (add phosphate) and phosphatases (remove phosphate) act as on/off switches for enzyme activity.
Monosaccharides (3-7 carbons) are the building blocks. Glucose is the central fuel.
Disaccharides (two monosaccharides) and polysaccharides (many) serve storage (glycogen) and structural (chitin, cellulose) roles.
Glycosylation attaches sugars to lipids (glycolipids) and proteins (glycoproteins) in the plasma membrane, affecting cell recognition and signalling.
Phosphoglycerides and sphingolipids are the main structural lipids of membranes.
Steroids (four-ring structure) include cholesterol, sex hormones, and corticosteroids.
Lipogenesis (synthesis) and lipolysis (breakdown) of triglycerides are tightly regulated by hormonal signals.
The TCA cycle is amphibolic: it both degrades acetyl CoA (catabolism) and provides intermediates for biosynthesis (anabolism). Each turn produces 3 NADH, 1 FADH2, 1 GTP, and 2 CO2.
Anaplerotic pathways replenish TCA intermediates when they are diverted to biosynthesis.
Oxidative phosphorylation is where most ATP is made. The electron transport system passes electrons from NADH and FADH2 to O2, pumping protons to create the proton motive force. The F1F0 ATPase then uses that gradient to synthesise ATP.
Substrate-level phosphorylation (direct phosphate transfer) produces smaller amounts of ATP during glycolysis and the TCA cycle.
ROS are unavoidable byproducts of the ETS. Cells have antioxidant defences (superoxide dismutase, catalase, glutathione) to neutralise them.
The respiratory quotient (RQ) reveals what fuel is being burned: 1.0 for carbohydrates, 0.7 for fats, roughly 0.8 for protein.
Redox status (NADH/NAD+ ratio) and phosphorylation potential ([ATP]/[ADP][Pi]) are cellular energy gauges.
Futile cycles waste ATP by running opposing reactions simultaneously, but some organisms use them deliberately for heat production.
Michaelis-Menten equation
v = Vmax x [S] / ([S] + Km)
When [S] = Km, v = Vmax/2. This is how Km is experimentally determined. On a Michaelis-Menten plot, the curve is hyperbolic, approaching Vmax asymptotically.
Respiratory quotient (RQ)
RQ = CO2 produced / O2 consumed
RQ of 1.0 = carbohydrate oxidation. RQ of 0.7 = fat oxidation. Values between indicate mixed fuel use.
Phosphorylation potential
[ATP] / [ADP][Pi]
A high ratio means the cell has abundant usable energy. A falling ratio signals energy depletion.
The respiratory quotient is used clinically in metabolic testing and sports science to determine what mix of fuels a patient or athlete is burning at a given exercise intensity.
Enzyme inhibitors are the basis of many drugs. Statins are competitive inhibitors of HMG-CoA reductase, the rate-limiting enzyme in cholesterol synthesis.
Students think enzymes "give" energy to reactions. They do not. Enzymes lower the activation energy barrier; they do not change the overall energy balance of the reaction.
Students assume that a higher Km means better enzyme function. The opposite: a low Km means the enzyme reaches half-maximal velocity at a lower substrate concentration, indicating higher affinity.
Students confuse substrate-level phosphorylation with oxidative phosphorylation. Substrate-level is a direct phosphate transfer (happens in glycolysis and the TCA cycle). Oxidative phosphorylation requires the electron transport chain and the proton motive force.
Students forget that the TCA cycle is amphibolic. It is not purely catabolic: its intermediates are siphoned off for amino acid synthesis, gluconeogenesis, and other biosynthetic pathways.
⚠️ Be able to interpret a Michaelis-Menten plot: identify Km, Vmax, and the effect of competitive vs. allosteric inhibition.
⚠️ Know the products of one turn of the TCA cycle (3 NADH, 1 FADH2, 1 GTP, 2 CO2).
⚠️ Understand the logic of oxidative phosphorylation: ETS builds the gradient, ATPase uses it.
⚠️ Be able to calculate or interpret RQ values and state which fuel is being oxidised.
⚠️ Know the difference between cofactors, prosthetic groups, and coenzymes.
Fill in the blank: Km is the substrate concentration at which reaction velocity is ______ of Vmax. (half / 50%)
True or False: Competitive inhibitors change the Vmax of an enzyme. (False. They raise the apparent Km but Vmax remains the same if enough substrate is added.)
Fill in the blank: An RQ of 1.0 indicates the animal is primarily oxidising ______. (carbohydrates)
True or False: The TCA cycle is purely catabolic. (False. It is amphibolic, serving both catabolic and anabolic functions.)
Fill in the blank: The proton motive force is generated by the ______ and used by the ______ to synthesise ATP. (electron transport system; F1F0 ATPase)
Q: An enzyme has a Km of 2 mM. A competitive inhibitor is added. What happens to the apparent Km and to Vmax?
A: The apparent Km increases (the enzyme appears to need more substrate to reach half-maximal velocity), but Vmax remains unchanged because the inhibitor can be outcompeted by adding enough substrate.
Q: Why are anaplerotic pathways necessary?
A: Because TCA cycle intermediates are constantly being diverted for biosynthesis (amino acids, glucose, haem). Without anaplerotic reactions to replenish them, the cycle would slow or stall.
Q: A hibernating animal has an RQ of 0.71. What fuel is it primarily using, and why does this make physiological sense?
A: An RQ of 0.71 indicates fat oxidation. This makes sense because hibernating animals rely on stored fat reserves, which provide more energy per gram than carbohydrates and last longer during prolonged fasting.
Q: Explain why reactive oxygen species are considered both a normal byproduct and a potential danger.
A: ROS are inevitably produced by the electron transport chain during normal metabolism: electrons occasionally escape and react with oxygen. At low levels, cells handle them with antioxidant enzymes. At high levels (oxidative stress), ROS damage DNA, proteins, and lipids, contributing to ageing and disease.
Enzyme kinetics connects to pharmacology: most drug design targets enzyme active sites or allosteric sites.
Oxidative phosphorylation and the proton motive force connect directly to the electrochemical gradient concepts in Doc 2 and to membrane transport in Doc 4.
The RQ and metabolic fuel selection connect to exercise physiology, fasting metabolism, and clinical nutrition.
primary structure, secondary structure, tertiary structure, alpha helix, beta sheet, molecular chaperone, heat shock protein, metabolic flux, amphibolic, cofactor, prosthetic group, coenzyme, NAD, NADP, FAD, active site, Michaelis-Menten, Km, Vmax, competitive inhibitor, allosteric regulator, protein kinase, protein phosphatase, phosphorylation, reducing equivalent, redox status, phosphorylation potential, monosaccharide, disaccharide, polysaccharide, glycogen, glycosylation, glycolipid, glycoprotein, chitin, GAG, lipogenesis, lipolysis, phosphoglyceride, sphingolipid, steroid, cholesterol, TCA cycle, Krebs cycle, citric acid cycle, substrate-level phosphorylation, anaplerotic, oxidative phosphorylation, electron transport chain, ETS, proton motive force, ROS, turnover rate, kcat, futile cycle, respiratory quotient, RQ, redox shuttle, ketogenesis, ketolysis, BIO 225, University of Michigan