Difficulty: Intermediate | Prerequisites: Chapter 2 (biomolecules, organelles)
Chapter 3 covers how the body builds and breaks down molecules (anabolism and catabolism), how energy is transferred in chemical reactions (exergonic vs. endergonic, oxidation vs. reduction), and how enzymes lower activation energy through the induced-fit model. It then walks through ATP production from glucose: glycolysis, the linking step (pyruvate oxidation), the TCA cycle, and the electron transport chain. The chapter finishes with energy storage (glycogen, triglycerides), the named metabolic processes (glycolysis, glycogenesis, glycogenolysis, gluconeogenesis), protein metabolism, and lactate production.
Anabolism (anabolic pathway)
The set of metabolic reactions that build larger molecules from smaller ones. Energy is consumed. Example: linking amino acids to form contractile proteins during muscle hypertrophy.
In simple terms, anabolism is building up.
Catabolism (catabolic pathway)
The set of metabolic reactions that break larger molecules into smaller ones. Energy is released. Example: breaking down glucose into pyruvate during glycolysis.
In simple terms, catabolism is breaking down.
Oxidation
The loss of electrons (or hydrogen atoms). When FADH2 donates two hydrogen atoms and becomes FAD, it has been oxidised. Its electron count decreases.
Remember: OIL RIG (Oxidation Is Loss, Reduction Is Gain).
Reduction
The gain of electrons (or hydrogen atoms). When NAD+ accepts electrons and becomes NADH, it has been reduced.
Exergonic reaction
A reaction that releases energy. The products have less free energy than the reactants (negative delta G). Example: ATP hydrolysis, the power stroke of muscle contraction.
Endergonic reaction
A reaction that absorbs energy. The products have more free energy than the reactants (positive delta G). Example: converting glucose monosaccharides into glycogen polysaccharides.
Activation energy (Ea)
The minimum energy required for a reaction to proceed. On a reaction energy diagram, it is the energy gap between the reactants and the transition state (the peak of the curve).
Induced-fit model
The model of enzyme action where the enzyme undergoes a conformational change upon substrate binding. This dynamic structural shift aligns specific functional groups to stabilise the high-energy transition state, lowering the activation energy.
Think of it as a foot stretching a sock: the enzyme moulds around the substrate rather than being a rigid lock-and-key.
ATP (adenosine triphosphate)
The cell's primary energy currency. ATP releases usable energy when its terminal phosphate group is removed by hydrolysis (dephosphorylation), producing ADP + Pi.
Substrate-level phosphorylation
A method of ATP production where a phosphate group is transferred directly from a metabolic intermediate to ADP. Occurs during glycolysis and the TCA cycle.
Oxidative phosphorylation
A method of ATP production using the electron transport chain and chemiosmotic coupling. NADH and FADH2 donate electrons, creating a proton gradient that drives ATP synthase. Produces the majority of ATP from glucose.
Glycolysis
The metabolic pathway that breaks glucose into two molecules of pyruvate. Occurs in the cytoplasm. Produces a small amount of ATP via substrate-level phosphorylation.
Pyruvate oxidation (the linking step)
The conversion of pyruvate to acetyl-CoA inside the mitochondrion. Produces NADH and releases CO2. This step links glycolysis to the TCA cycle. No ATP is directly produced.
Acetyl-CoA
The two-carbon molecule that enters the TCA cycle after pyruvate oxidation. It is the gateway between glycolysis and the citric acid cycle.
TCA cycle (citric acid cycle, Krebs cycle)
A cycle of reactions in the mitochondrial matrix that processes acetyl-CoA. Per turn: 1 GTP, 3 NADH, 1 FADH2, 2 CO2. Since one glucose produces two acetyl-CoA, the cycle runs twice per glucose.
Electron transport chain (ETC)
A series of protein complexes in the inner mitochondrial membrane. NADH and FADH2 donate electrons, creating a proton gradient that drives ATP synthase. This is where the bulk of ATP is produced.
Glycogenesis
The conversion of glucose into glycogen for storage.
Glycogenolysis
The breakdown of glycogen back into glucose.
Gluconeogenesis
The synthesis of glucose from non-carbohydrate substrates (amino acids, lactate, glycerol).
Proteolysis
The breakdown of proteins into individual amino acids. This is the first step in protein metabolism.
Deamination
The removal of the amino group from an amino acid, producing a keto acid and ammonia. Occurs after proteolysis.
Lactate
Produced from pyruvate when oxygen availability or mitochondrial capacity is insufficient. The purpose is to regenerate NAD+, allowing glycolysis to continue producing ATP via substrate-level phosphorylation.
Anabolism builds polymers from monomers. It requires energy input. Example: amino acids linked into contractile proteins during muscle hypertrophy.
Catabolism breaks polymers into monomers. It releases energy. Example: glucose broken into pyruvate during glycolysis.
If the question says "monomers are linked together to form a polymer," the answer is anabolic.
Oxidation = loss of electrons (or hydrogen atoms). FADH2 donating 2 H atoms to become FAD is oxidation; the electron count decreases.
Reduction = gain of electrons. NAD+ gaining electrons to become NADH is reduction.
OIL RIG: Oxidation Is Loss, Reduction Is Gain.
Exergonic reactions release energy. Products have less free energy than reactants (delta G is negative). The muscle power stroke (charged myosin head converting potential energy to kinetic energy) is exergonic.
Endergonic reactions absorb energy. Products have more free energy than reactants (delta G is positive). Glucose to glycogen is endergonic.
On a reaction energy diagram: if products sit higher than reactants, the reaction is endergonic. If lower, exergonic.
Activation energy (Ea) is the height of the peak above the reactants. Enzymes lower Ea but do not change the overall delta G.
The induced-fit model: the enzyme changes shape upon substrate binding (conformational change). This aligns specific functional groups to stabilise the transition state, lowering the activation energy.
This is distinct from the lock-and-key model, which treats the active site as rigid.
Enzymes stabilise the transition state, making it less reactive and more stable. This lowers Ea.
Enzymes are not consumed; they are reusable catalysts.
Substrate-level phosphorylation: a phosphate group is transferred directly from a metabolic intermediate to ADP. Occurs in glycolysis and the TCA cycle.
Oxidative phosphorylation: NADH and FADH2 donate electrons to the ETC, creating a proton gradient that drives ATP synthase. Produces the majority of cellular ATP.
ATP releases energy through hydrolysis (dephosphorylation): ATP to ADP + Pi.
ATP also regulates metabolic pathways through feedback inhibition.
Glycolysis: glucose to 2 pyruvate. Occurs in the cytoplasm. Small ATP yield via substrate-level phosphorylation.
Linking step (pyruvate oxidation): pyruvate to acetyl-CoA. Produces NADH, releases CO2. No direct ATP. Connects glycolysis to the TCA cycle.
TCA cycle: processes acetyl-CoA in the mitochondrial matrix. Per turn: 1 GTP, 3 NADH, 1 FADH2, 2 CO2. Runs twice per glucose (2 acetyl-CoA), so totals per glucose: 2 GTP, 6 NADH, 2 FADH2, 4 CO2.
ETC: NADH and FADH2 donate electrons. The proton gradient drives ATP synthase. This is where most ATP comes from.
The body stores excess energy in two main forms: glycogen (shorter-term, in liver and skeletal muscle) and triglycerides (long-term, in adipose tissue).
ATP is an immediate energy currency, not a storage molecule. Glucose itself is not the primary storage form.
Glycolysis = glucose to pyruvate
Glycogenesis = glucose to glycogen (storage)
Glycogenolysis = glycogen to glucose (mobilisation)
Gluconeogenesis = non-carbohydrate molecules to glucose
Step 1: Proteolysis (proteins broken into amino acids)
Step 2: Deamination (amino group removed, producing a keto acid + ammonia)
Later steps: keto acid enters the TCA cycle; ammonia is carried to the liver for processing
When oxygen is limited or mitochondrial capacity is exceeded, pyruvate is converted to lactate.
The purpose is to regenerate NAD+, which allows glycolysis to continue producing ATP via substrate-level phosphorylation.
Lactate production is reversible. It does not permanently remove pyruvate from metabolism. Lactate can be transported and metabolised later.
Pyruvate oxidation (the linking step)
Pyruvate to Acetyl-CoA + NADH + CO2
TCA cycle products per glucose (2 turns)
2 GTP + 6 NADH + 2 FADH2 + 4 CO2
(Per single turn: 1 GTP, 3 NADH, 1 FADH2, 2 CO2)
Lactate production
Pyruvate + NADH to Lactate + NAD+
ATP hydrolysis
ATP to ADP + Pi + energy
Students confuse anabolism and catabolism. If monomers are being joined into a polymer, it is anabolic. If a polymer is being broken into monomers, it is catabolic.
Students swap the definitions of substrate-level phosphorylation and oxidative phosphorylation. Substrate-level is the direct transfer of a phosphate from a metabolic intermediate. Oxidative uses the ETC and a proton gradient.
Students often think the TCA cycle directly produces large amounts of ATP. It does not. Most of the energy is captured in NADH and FADH2, which feed the ETC.
Students mix up the four metabolic process names. Glycogenolysis is the breakdown of glycogen (not its storage). Gluconeogenesis makes glucose from non-carbohydrate sources (not the breakdown of glucose).
Students sometimes think lactate production is a dead end. It is not. Lactate can be transported to the liver and converted back to glucose (Cori cycle).
⚠️ The induced-fit model appears in multiple questions. Know: conformational change upon substrate binding, stabilises the transition state, lowers Ea. Distinguish it from the lock-and-key model (rigid, no conformational change).
⚠️ TCA cycle products per glucose is a favourite calculation question. Memorise: 2 GTP, 6 NADH, 2 FADH2, 4 CO2. Remember it runs twice per glucose.
⚠️ The exam swaps the definitions of substrate-level and oxidative phosphorylation in the answer choices. Read each option carefully.
⚠️ Know the four metabolic process names cold: glycolysis, glycogenesis, glycogenolysis, gluconeogenesis. The exam tests whether you can match each name to its correct direction.
⚠️ Lactate metabolism: know that the purpose of converting pyruvate to lactate is to regenerate NAD+, not to produce ATP directly.
⚠️ Proteolysis is the first step of protein metabolism, not deamination. Deamination comes after the protein has already been broken into amino acids.
Fill in the blank: Building polymers from monomers is called __________. (Anabolism.)
True or False: When FADH2 donates hydrogen atoms and becomes FAD, it has been reduced. (False. It has been oxidised, because it lost electrons.)
Fill in the blank: The TCA cycle runs __________ times per molecule of glucose. (Twice.)
True or False: Glycogenolysis is the conversion of glucose into glycogen for storage. (False. That is glycogenesis. Glycogenolysis is the breakdown of glycogen into glucose.)
Fill in the blank: The first step of protein metabolism is __________. (Proteolysis.)
Q: During muscle hypertrophy, amino acid monomers are linked to form contractile proteins. Is this anabolic or catabolic?
A: Anabolic. Anabolism builds larger molecules from smaller ones (polymers from monomers). Catabolism does the reverse.
Q: FADH2 donates two hydrogen atoms and becomes FAD. Has it been oxidised or reduced, and what happened to its electron count?
A: Oxidised. Each hydrogen atom carries one electron, so donating two hydrogen atoms means losing two electrons. The electron count decreased.
Q: A charged myosin head binds to actin, contracts, and enters a low-energy state (rigor). Describe the energy dynamics.
A: Potential energy (stored in the charged myosin head) was converted into kinetic energy (the mechanical movement of contraction) through an exergonic reaction. Energy was released as the myosin moved from high-energy to low-energy state.
Q: The body converts glucose into glycogen for storage. Is this exergonic or endergonic?
A: Endergonic. It absorbs energy to form the complex chemical bonds of glycogen. The products (glycogen) have more free energy than the reactants (glucose).
Q: What does the induced-fit model of enzyme action describe?
A: The enzyme undergoes a conformational change when the substrate binds. This structural shift aligns functional groups that stabilise the high-energy transition state, lowering the activation energy required for the reaction.
Q: From one molecule of glucose, what are the total products of the TCA cycle?
A: 2 GTP, 6 NADH, 2 FADH2, and 4 CO2. Each turn produces 1 GTP, 3 NADH, 1 FADH2, and 2 CO2, and the cycle runs twice per glucose.
Q: Which pairing is correct: glycolysis/glucose to pyruvate, glycogenesis/glycogen to glucose, glycogenolysis/glucose to glycogen, gluconeogenesis/glucose to pyruvate?
A: Glycolysis/glucose to pyruvate. The others are swapped: glycogenesis is glucose to glycogen, glycogenolysis is glycogen to glucose, and gluconeogenesis is non-carbohydrate molecules to glucose.
Q: What is the role of lactate production during anaerobic conditions?
A: Lactate is produced from pyruvate to regenerate NAD+, which allows glycolysis to continue producing ATP via substrate-level phosphorylation. It is not a dead end; lactate can be transported and metabolised later.
Q: What is the first step in protein metabolism?
A: Proteolysis, the breakdown of proteins into individual amino acids. Deamination (removal of the amino group) comes later, after the protein has been broken down.
The metabolic pathways here connect directly to exercise physiology and the muscular system: ATP supply determines how long and how hard a muscle can contract, and lactate metabolism explains what happens during intense exercise. Enzyme kinetics and the induced-fit model reappear whenever the course discusses hormones and receptor binding.
The energy storage material (glycogen and triglycerides) links to endocrine regulation later in the course, particularly insulin and glucagon signalling, which control when the body stores and mobilises energy.
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