IMAT Biology · Bioenergetics and Metabolism

Fats and Proteins as Fuel, and Where Each Pathway Runs

Fatty acids are cut two carbons at a time into acetyl CoA, amino acids lose their nitrogen as urea in the liver, and every pathway has its own place in the cell and the body.

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Why this matters

The 2025 paper asked which process happens mainly in the liver (the urea cycle) and why the body stores energy as fat rather than protein, and used β-oxidation and amino group removal as options in other items. The 2024 and 2026 papers asked where respiration and its stages take place.

Concept 1 of 3: Fat as fuel: lipolysis and β-oxidation

Fat is the body's long-term energy store. A triglyceride is split into glycerol and three fatty acids, and each fatty acid is then cut two carbons at a time into acetyl CoA, which enters the Krebs cycle. Fatty acid carbons carry more hydrogen than sugar carbons, so fat releases about twice as much energy per gram.

Definition

Lipolysis: lipase hydrolyses a triglyceride into glycerol + 3 fatty acids. In adipose tissue this is switched on by glucagon and adrenaline.
Glycerol goes to the liver and joins glycolysis as a triose phosphate, or is used to make glucose.
Fatty acids are activated with coenzyme A in the cytoplasm (this costs ATP) and carried into the mitochondrial matrix by carnitine.
β-oxidation (mitochondrial matrix): each round removes 2 carbons as acetyl CoA and makes 1 $\mathrm{FADH_2}$ and 1 NADH. The acetyl CoA enters the Krebs cycle; the reduced carriers go to the respiratory chain.
Energy density: about 37 kJ/g (9 kcal/g) for fat, against about 17 kJ/g (4 kcal/g) for carbohydrate or protein. Fat is also stored almost without water, while glycogen is stored with about 2 to 3 g of water per gram. So, gram for gram, a fat store holds several times more energy.
Fatty acid synthesis is a separate anabolic pathway in the cytoplasm that uses NADPH; it is not β-oxidation run backwards.

β-oxidation of a saturated fatty acid with n carbons

\text{acetyl CoA} = \frac{n}{2} \qquad \text{rounds} = \frac{n}{2} - 1

$n$ number of carbon atoms in the fatty acid (an even number)
roundseach round gives 1 NADH and 1 $\mathrm{FADH_2}$ ; the last round leaves two acetyl CoA, so there is one round fewer than acetyl CoA

Worked example

Palmitic acid has 16 carbon atoms. How many acetyl CoA, NADH and

\mathrm{FADH_2}

does its β-oxidation give? Using 10 ATP per acetyl CoA through the Krebs cycle and chain, 2.5 per NADH and 1.5 per

\mathrm{FADH_2}

, and 2 ATP spent to activate it, estimate its total ATP yield.

Practice this conceptself-check · 4 quick reps

Fat beats protein as a store on two counts

Triglycerides release about twice the energy per gram of protein or carbohydrate, and they are stored with very little water. Protein in muscle is not an energy store at all: it is working tissue, used as fuel only in prolonged fasting.

β-oxidation is not oxidative phosphorylation

β-oxidation breaks fatty acids into acetyl CoA and makes NADH and

\mathrm{FADH_2}

; it makes no ATP itself. The ATP comes later, when those carriers are reoxidised by the respiratory chain.

Concept 2 of 3: Protein breakdown: transamination, deamination and the urea cycle

Amino acids are not stored, so any extra is broken down. The nitrogen-containing amino group has to come off first, and its ammonia is toxic. The liver turns that ammonia into urea for the kidneys to excrete, and the carbon skeleton left over is burned in the Krebs cycle or turned into glucose or fat.

Definition

Proteases hydrolyse proteins into amino acids. The body has no protein store; muscle protein is broken down for fuel only in prolonged fasting.
Transamination (many tissues, especially liver and muscle): an aminotransferase moves the amino group from an amino acid onto a keto acid such as α-ketoglutarate, making glutamate. No ammonia is released. Vitamin B6 is the coenzyme.
Oxidative deamination (mainly liver): glutamate loses its amino group as ammonia ( $\mathrm{NH_3}$ ), reducing $\mathrm{NAD^+}$ .
Urea cycle (liver only, partly in the mitochondria and partly in the cytoplasm): ammonia and $\mathrm{CO_2}$ are combined into urea, at a cost of ATP. Urea travels in the blood to the kidneys and leaves in urine.
Carbon skeletons enter metabolism as pyruvate, acetyl CoA or Krebs cycle intermediates. Glucogenic amino acids can be made into glucose; ketogenic ones only into fat or ketone bodies.
Protein releases about 17 kJ/g, like carbohydrate.

Process	What happens	Where
Proteolysis	Proteins hydrolysed to amino acids	Gut (digestion) and inside cells
Transamination	Amino group moved from an amino acid to a keto acid	Many tissues, especially liver and muscle
Deamination	Amino group removed as ammonia	Mainly the liver
Urea cycle	Ammonia and CO₂ combined into urea, using ATP	Liver cells only
Excretion of urea	Urea filtered from the blood into urine	Kidneys
Use of the carbon skeleton	Burned in the Krebs cycle, or made into glucose or fat	Mainly the liver

Practice this conceptself-check · 4 quick reps

Transamination moves the amino group; deamination removes it

Transamination passes the amino group to another molecule and frees no ammonia. Deamination takes the amino group off as ammonia, which then enters the urea cycle in the liver.

Concept 3 of 3: Where each metabolic pathway takes place: organelle and organ

Many questions on this chapter are answered once you know where each pathway runs. The pathways that need oxygen to finish run in mitochondria; glycolysis, which needs no oxygen, runs in the cytoplasm of every cell. A few pathways belong mainly to one organ, usually the liver.

Definition

Cytoplasm: glycolysis, both fermentations, fatty acid synthesis, most of gluconeogenesis.
Mitochondrial matrix: link reaction, Krebs cycle, β-oxidation, the first steps of the urea cycle.
Inner mitochondrial membrane: respiratory chain and ATP synthase. So the mitochondrion is the main site of cellular respiration, but not of all of it: glycolysis is outside.
Chloroplast: light-dependent reactions on the thylakoid membranes, Calvin cycle in the stroma.
Gluconeogenesis is the making of new glucose from non-carbohydrates (lactate, glycerol, glucogenic amino acids). It runs mainly in the liver, and in the kidney during long fasting.
Mainly liver: urea cycle, gluconeogenesis, ketone body formation, glycogen stored to keep blood glucose steady. Muscles store glycogen too, but only for their own use.

Pathway	Site in the cell	Main tissues
Glycolysis	Cytoplasm	Every cell, including red blood cells
Lactic fermentation	Cytoplasm	Working muscle, red blood cells
Link reaction and Krebs cycle	Mitochondrial matrix	Every cell with mitochondria
Respiratory chain and ATP synthase	Inner mitochondrial membrane	Every cell with mitochondria
β-oxidation	Mitochondrial matrix	Muscle, heart and liver (the brain uses little fat)
Fatty acid synthesis	Cytoplasm	Liver and adipose tissue
Urea cycle	Mitochondrial matrix and cytoplasm	Liver only
Gluconeogenesis	Mostly cytoplasm (starts in mitochondria)	Liver, and kidney in long fasting
Light-dependent reactions	Thylakoid membranes	Green plant cells and algae
Calvin cycle	Chloroplast stroma	Green plant cells and algae

Practice this conceptself-check · 4 quick reps

Respiration starts outside the mitochondrion

Mitochondria are the main site of cellular respiration, but its first stage, glycolysis, runs in the cytoplasm. An option placing glycolysis in mitochondria is wrong; an option naming mitochondria as the site of the Krebs cycle or of respiration as a whole is right.

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (1)

Fat as fuel: lipolysis and β-oxidation
β-oxidation of a saturated fatty acid with n carbons
$\text{acetyl CoA} = \frac{n}{2} \qquad \text{rounds} = \frac{n}{2} - 1$

Reference tables (2)

Protein breakdown: transamination, deamination and the urea cycle6 rows

Process	What happens	Where
Proteolysis	Proteins hydrolysed to amino acids	Gut (digestion) and inside cells
Transamination	Amino group moved from an amino acid to a keto acid	Many tissues, especially liver and muscle
Deamination	Amino group removed as ammonia	Mainly the liver
Urea cycle	Ammonia and CO₂ combined into urea, using ATP	Liver cells only
Excretion of urea	Urea filtered from the blood into urine	Kidneys
Use of the carbon skeleton	Burned in the Krebs cycle, or made into glucose or fat	Mainly the liver

Where each metabolic pathway takes place: organelle and organ10 rows

Pathway	Site in the cell	Main tissues
Glycolysis	Cytoplasm	Every cell, including red blood cells
Lactic fermentation	Cytoplasm	Working muscle, red blood cells
Link reaction and Krebs cycle	Mitochondrial matrix	Every cell with mitochondria
Respiratory chain and ATP synthase	Inner mitochondrial membrane	Every cell with mitochondria
β-oxidation	Mitochondrial matrix	Muscle, heart and liver (the brain uses little fat)
Fatty acid synthesis	Cytoplasm	Liver and adipose tissue
Urea cycle	Mitochondrial matrix and cytoplasm	Liver only
Gluconeogenesis	Mostly cytoplasm (starts in mitochondria)	Liver, and kidney in long fasting
Light-dependent reactions	Thylakoid membranes	Green plant cells and algae
Calvin cycle	Chloroplast stroma	Green plant cells and algae

Watch out for (4)

Fat beats protein as a store on two counts
→ Fat as fuel: lipolysis and β-oxidation
β-oxidation is not oxidative phosphorylation
→ Fat as fuel: lipolysis and β-oxidation
Transamination moves the amino group; deamination removes it
→ Protein breakdown: transamination, deamination and the urea cycle
Respiration starts outside the mitochondrion
→ Where each metabolic pathway takes place: organelle and organ

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