IMAT Biology · Formula sheet

Bioenergetics and Metabolism formulas

3 formulas, 15 reference tables and 29 common traps for IMAT Biology Bioenergetics and Metabolism, grouped by subtopic.

Metabolism, ATP and the Electron Carriers

Metabolism: catabolism and anabolism, exergonic and endergonic

Feature	Catabolism	Anabolism
What happens	Large molecules are broken into smaller ones	Small molecules are built into larger ones
Energy overall	Released (exergonic)	Required (endergonic)
Typical chemistry	Oxidation, hydrolysis	Reduction, condensation
Link with ATP	The energy released is used to make ATP from ADP	ATP hydrolysis supplies the energy
Electron carriers	NAD⁺ and FAD are reduced	NADPH is oxidised (it gives up its electrons)
Examples	Glycolysis, Krebs cycle, β-oxidation of fat, digestion	Protein synthesis, DNA replication, Calvin cycle, glycogen synthesis

How fast a spontaneous reaction actually goes depends on enzymes, which the Biomolecules and Enzymes chapter covers.

ATP: structure, hydrolysis and the cell's energy currency

Molecule	What it is	Role
ATP	Adenine + ribose + 3 phosphates	Universal energy currency: its hydrolysis powers muscle contraction, active transport and biosynthesis
ADP	Adenine + ribose + 2 phosphates	Product of ATP hydrolysis; recharged to ATP by phosphorylation
AMP	Adenine + ribose + 1 phosphate	Signals that the cell is low on energy; also a nucleotide of RNA
Creatine phosphate	Creatine carrying a phosphate group	Muscle reserve that regenerates ATP from ADP for a few seconds
NADH, FADH₂	Reduced electron carriers	Carry energy as electrons to the respiratory chain; not spent directly like ATP

Redox reactions and the carriers NAD⁺, FAD and NADP⁺

Carrier (oxidised → reduced)	Main pathways	Where its electrons go	Vitamin source
NAD⁺ → NADH	Glycolysis, link reaction, Krebs cycle, β-oxidation	Complex I of the respiratory chain	Niacin (vitamin B3)
FAD → FADH₂	Krebs cycle (succinate step), β-oxidation	Complex II, then the rest of the chain	Riboflavin (vitamin B2)
NADP⁺ → NADPH	Made in the light-dependent reactions; used in the Calvin cycle and fat synthesis	Onto carbon compounds being built (biosynthesis)	Niacin (vitamin B3)
Coenzyme A	Link reaction, Krebs cycle, β-oxidation	Carries acetyl groups, not electrons	Pantothenic acid (vitamin B5)

Common traps

Spontaneous does not mean fast

An exergonic reaction is spontaneous: it releases energy and needs no energy input to proceed. That says nothing about its speed. Many exergonic reactions are extremely slow until an enzyme lowers the activation energy.

Metabolism is both breaking down and building up

Options that limit metabolism to synthesis, to animal cells, or to reactions in light are wrong. Metabolism is all the reactions of a cell, catabolic and anabolic together.

NADH and FADH₂ are not the energy currency

ATP is the currency that cell processes spend. NADH, FADH₂ and NADPH are electron carriers: their energy becomes usable only after they pass their electrons on, for example to the respiratory chain that makes ATP.

Creatine phosphate, creatinine and carnitine are different molecules

Creatine phosphate is the phosphate reserve in muscle. Creatinine is its waste product, excreted in urine. Carnitine carries fatty acids into mitochondria. The names look alike, and options use that.

Coenzymes are not enzymes

\mathrm{NAD^+}

, NADH, FAD, coenzyme A and acetyl coenzyme A are carriers, not enzymes. The enzymes in these steps are the dehydrogenases and synthases. An option calling any of these carriers a respiratory enzyme is wrong.

A redox reaction is defined by moving electrons

To spot a redox reaction, ask whether electrons pass from one molecule to another. Hydrolysis, condensation (such as joining two sugars) and base pairing move no electrons between molecules, so they are not redox reactions; reducing NAD⁺ to NADH is.

Glycolysis and the Link Reaction

Learn this subtopic in the notes

Glycolysis: the ten steps from glucose to pyruvate

Step	Change	Enzyme	ATP or NADH
1	Glucose → glucose 6-phosphate	Hexokinase	1 ATP used
2	Glucose 6-phosphate → fructose 6-phosphate	Phosphoglucose isomerase	None
3	Fructose 6-phosphate → fructose 1,6-bisphosphate	Phosphofructokinase	1 ATP used
4	Fructose 1,6-bisphosphate → dihydroxyacetone phosphate + glyceraldehyde 3-phosphate	Aldolase	None
5	Dihydroxyacetone phosphate → glyceraldehyde 3-phosphate	Triose phosphate isomerase	None
6	Glyceraldehyde 3-phosphate → 1,3-bisphosphoglycerate	Glyceraldehyde 3-phosphate dehydrogenase	1 NADH made
7	1,3-bisphosphoglycerate → 3-phosphoglycerate	Phosphoglycerate kinase	1 ATP made
8	3-phosphoglycerate → 2-phosphoglycerate	Phosphoglycerate mutase	None
9	2-phosphoglycerate → phosphoenolpyruvate (water removed)	Enolase	None
10	Phosphoenolpyruvate → pyruvate	Pyruvate kinase	1 ATP made

Steps 6 to 10 happen twice per glucose, once for each triose phosphate: 2 NADH and 4 ATP made, minus 2 ATP used in steps 1 and 3.

The link reaction: pyruvate to acetyl coenzyme A

Product	Per pyruvate	Per glucose	What happens to it
Acetyl CoA	1	2	Enters the Krebs cycle
CO₂	1	2	Diffuses out; the first CO₂ of aerobic respiration
NADH	1	2	Reoxidised by the respiratory chain
ATP	0	0	No ATP is made in this step

Common traps

Gross is not net

Glycolysis makes 4 ATP per glucose but spends 2 in the investment phase, so the net yield is 2 ATP. Options with 4 ATP give the gross figure.

Glycolysis releases no CO₂

Glucose has 6 carbons and the two pyruvates have 3 each, so no carbon is lost. In aerobic respiration the first

\mathrm{CO_2}

is released in the link reaction; in yeast, the fermentation step after glycolysis releases it.

Isomerases rearrange; kinases phosphorylate

The isomerase steps change one sugar phosphate into another with the same atoms: glucose 6-phosphate to fructose 6-phosphate, and dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. Adding a phosphate from ATP is done by a kinase, and splitting the 6-carbon sugar by aldolase.

Decarboxylation releases CO₂ but uses no oxygen

In the link reaction the

\mathrm{CO_2}

comes from pyruvate's own carboxyl group, not from oxygen gas. Oxygen gas is used only at the end of the respiratory chain, where it accepts electrons and forms water.

The Krebs Cycle, the Respiratory Chain and the ATP Total

Learn this subtopic in the notes

Counting the ATP from one glucose, and the efficiency of respiration

ATP yield and efficiency

\text{ATP} \approx 2.5\,n_{\text{NADH}} + 1.5\,n_{\text{FADH}_2} + n_{\text{sub}} \qquad \text{efficiency} = \frac{n_{\text{ATP}} \times E_{\text{ATP}}}{E_{\text{released}}} \times 100\%

$n_{\text{NADH}}, n_{\text{FADH}_2}$ number of reduced carriers sent to the respiratory chain
$n_{\text{sub}}$ ATP (or GTP) made by substrate-level phosphorylation
$E_{\text{ATP}}$ energy stored per mole of ATP, about 30.5 kJ/mol
$E_{\text{released}}$ energy released by burning the same fuel completely

The Krebs cycle: products per turn and per glucose

Step	Carbon atoms	Product made
Acetyl CoA + oxaloacetate → citrate	2 + 4 → 6	Coenzyme A released
Citrate → isocitrate	6 → 6	Rearrangement only
Isocitrate → α-ketoglutarate	6 → 5	1 CO₂ and 1 NADH
α-ketoglutarate → succinyl CoA	5 → 4	1 CO₂ and 1 NADH
Succinyl CoA → succinate	4 → 4	1 GTP (or ATP), by substrate-level phosphorylation
Succinate → fumarate	4 → 4	1 FADH₂ (succinate dehydrogenase)
Fumarate → malate	4 → 4	Water added
Malate → oxaloacetate	4 → 4	1 NADH; the acceptor is ready again

The respiratory chain: complexes, mobile carriers and oxygen

Component	Type	Takes electrons from	Passes them to	Pumps protons?
Complex I	Integral membrane protein	NADH	Ubiquinone	Yes
Complex II	Integral membrane protein (also a Krebs enzyme)	FADH₂ (from succinate)	Ubiquinone	No
Ubiquinone (coenzyme Q)	Mobile, lipid-soluble	Complexes I and II	Complex III	No
Complex III	Integral membrane protein	Ubiquinone	Cytochrome c	Yes
Cytochrome c	Mobile peripheral protein	Complex III	Complex IV	No
Complex IV	Integral membrane protein	Cytochrome c	Oxygen, which forms water	Yes

Chemiosmosis: the proton gradient drives ATP synthase

Part of the mitochondrion	Location	Role
Complexes I, III and IV	Inner membrane	Pump H⁺ from the matrix into the intermembrane space
Intermembrane space	Between the outer and inner membranes	Holds the high H⁺ concentration (low pH)
Inner membrane	Folded into cristae	Impermeable to H⁺, so the gradient is kept
ATP synthase	Inner membrane, its head facing the matrix	Lets H⁺ flow back and uses the flow to make ATP
Matrix	Inside the inner membrane	Low H⁺ concentration; ATP is made here, and the Krebs cycle runs here

Common traps

Per turn or per glucose?

The cycle turns twice for each glucose. Per turn: 3 NADH, 1

\mathrm{FADH_2}

, 1 GTP, 2

\mathrm{CO_2}

. Per glucose, double everything. Read the question for which one it wants.

Oxygen does not oxidise NADH directly

Reduced coenzymes are reoxidised through the respiratory chain, step by step; oxygen meets the electrons only at complex IV, the very end. Options saying oxygen acts directly on NADH, at complex III, or inside the Krebs cycle are wrong.

FADH₂ enters the chain later than NADH

\mathrm{FADH_2}

passes its electrons to complex II, skipping complex I. Fewer protons are pumped for its electrons, so it yields less ATP than NADH (about 1.5 against 2.5).

ATP synthase is driven by protons, not by electrons

No electrons pass through ATP synthase. The electron carriers pump protons; ATP synthase uses the flow of those protons back into the matrix. An option saying ATP is made by electrons passing through ATP synthase is wrong.

ATP totals are approximate

Books quote 30, 32, 36 or 38 ATP per glucose, depending on the values used per carrier and on how glycolytic NADH enters the mitochondrion. All are estimates. Use the convention the options use; what never changes is that the respiratory chain gives most of the ATP and fermentation gives 2.

Fermentation: Respiration Without Oxygen

Learn this subtopic in the notes

Comparing ATP yields: fermentation against aerobic respiration

Total ATP from a pathway

\text{total ATP} = (\text{number of glucose}) \times (\text{ATP per glucose for that pathway})

$2$ ATP per glucose for glycolysis alone, or glycolysis + fermentation
$30 \text{ to } 32$ ATP per glucose for complete aerobic respiration (approximate)

Lactic and alcoholic fermentation compared

Feature	Lactic fermentation	Alcoholic fermentation
Where it occurs	Animal muscle, red blood cells, lactic acid bacteria	Yeast, some plant cells
Site in the cell	Cytoplasm	Cytoplasm
End products	Lactate	Ethanol and CO₂
CO₂ released	No	Yes, one per pyruvate
What happens to pyruvate	Reduced directly to lactate	Decarboxylated to ethanal, which is then reduced
ATP per glucose	2	2
Everyday use	Yoghurt and cheese making	Bread rising, beer and wine

Common traps

Fermentation regenerates NAD⁺; it makes no extra ATP

All the ATP of fermentation, 2 per glucose, comes from glycolysis. The step from pyruvate to lactate or ethanol makes no ATP; it only reoxidises NADH so that glycolysis can continue.

Only alcoholic fermentation releases CO₂

Lactic fermentation keeps all 3 carbons of pyruvate in lactate. Alcoholic fermentation removes one as

\mathrm{CO_2}

. Exercising muscle does still release

\mathrm{CO_2}

, but that comes from its aerobic respiration running at the same time, not from lactic fermentation.

Both fermentations happen in the cytoplasm

Neither kind uses mitochondria. Options placing fermentation in the matrix or on the cristae are wrong for yeast and for muscle alike.

Compare totals, not yields per glucose

Per glucose, aerobic respiration always beats fermentation. But a ranking question may give different numbers of glucose for each pathway; then multiply first. Many fermented glucose molecules can out-produce one glucose respired aerobically.

Photosynthesis: Light Reactions and the Calvin Cycle

Learn this subtopic in the notes

Photosynthesis: the overall equation and the chloroplast

Part	Structure	What happens there
Envelope	Two membranes, outer and inner	Controls exchange with the cytoplasm; holds no chlorophyll
Thylakoid membrane	Membrane of the flattened sacs	Light absorbed by chlorophyll, water split, electron transport, ATP synthase
Granum	A stack of thylakoids	Gives a large membrane area for the light-dependent reactions
Thylakoid lumen	The space inside each thylakoid	Protons collect here; oxygen from water is released here
Stroma	Fluid around the thylakoids	Calvin cycle: CO₂ fixed by RuBisCO and sugar made; starch stored

The light-dependent reactions: photolysis, NADPH and ATP

Feature	Mitochondrion	Chloroplast
Membrane holding the chain and ATP synthase	Inner membrane (cristae)	Thylakoid membrane
Source of the electrons	NADH and FADH₂ from food	Water, split using light energy
Protons pumped into	Intermembrane space	Thylakoid lumen
ATP made in	Matrix	Stroma
Final electron acceptor	Oxygen, forming water	NADP⁺, forming NADPH
Name of the ATP synthesis	Oxidative phosphorylation	Photophosphorylation

Both organelles make ATP by chemiosmosis, so ATP is made in both photosynthesis and respiration.

The Calvin cycle: fixing carbon dioxide in the stroma

Stage	What happens	Uses	Carbon atoms
Fixation	CO₂ joins RuBP, catalysed by RuBisCO	No ATP or NADPH	1 + 5 → 6, which splits into 2 × 3
Reduction	GP is reduced to triose phosphate	ATP and NADPH	3 → 3
Regeneration	Five triose phosphates are rearranged into three RuBP	ATP	5 × 3 → 3 × 5
Export	One triose phosphate in six leaves the cycle	Nothing more	2 × 3 → 6 (two make one glucose)

Limiting factors, the compensation point and respiration in plants

Condition	Photosynthesis	Respiration	Net gas exchange with the air
Darkness	Stopped	Running	CO₂ released, O₂ taken in
Dim light, below the compensation point	Slower than respiration	Running	Small net release of CO₂
At the compensation point	Equal to respiration	Running	None
Bright light	Faster than respiration	Running	O₂ released, CO₂ taken in

Common traps

The oxygen comes from water

In the equation, the 6

\mathrm{O_2}

all come from the split water molecules. The oxygen atoms of

\mathrm{CO_2}

end up in the sugar and in new water.

Proton pumps are in membranes, not in spaces

A pump has to sit in a membrane to move protons across it. In the chloroplast the pumping complex and ATP synthase are in the thylakoid (granum) membrane. The stroma and the lumen are spaces: they hold protons but contain no pumps.

Photosynthesis reduces NADP⁺, not NAD⁺

The carrier reduced in the light-dependent reactions is

\mathrm{NADP^+}

, and it ends up reduced (NADPH). NAD⁺ and FAD are the carriers of respiration.

Light-independent does not mean it runs at night

The Calvin cycle needs a constant supply of ATP and NADPH, which only the light-dependent reactions make. In the dark it stops within a minute or so.

Light splits water, not carbon dioxide

\mathrm{CO_2}

is never split by light. It is joined whole to RuBP by RuBisCO, and the product is then reduced with hydrogen that came from water.

Plants respire all the time

Photosynthesis does not replace respiration. A plant releases

\mathrm{CO_2}

from respiration in the light as well as in the dark; in bright light the release is simply hidden, because photosynthesis takes in more than respiration gives out.

Fats and Proteins as Fuel, and Where Each Pathway Runs

Learn this subtopic in the notes

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

$n$ 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

Protein breakdown: transamination, deamination and the urea cycle

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 organ

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

Common traps

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.

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.

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.

Bioenergetics and Metabolism formulas

Metabolism, ATP and the Electron Carriers

Metabolism: catabolism and anabolism, exergonic and endergonic

ATP: structure, hydrolysis and the cell's energy currency

Redox reactions and the carriers NAD⁺, FAD and NADP⁺

Common traps

Glycolysis and the Link Reaction

Glycolysis: the ten steps from glucose to pyruvate

The link reaction: pyruvate to acetyl coenzyme A

Common traps

The Krebs Cycle, the Respiratory Chain and the ATP Total

Counting the ATP from one glucose, and the efficiency of respiration

The Krebs cycle: products per turn and per glucose

The respiratory chain: complexes, mobile carriers and oxygen

Chemiosmosis: the proton gradient drives ATP synthase

Common traps

Fermentation: Respiration Without Oxygen

Comparing ATP yields: fermentation against aerobic respiration

Lactic and alcoholic fermentation compared

Common traps

Photosynthesis: Light Reactions and the Calvin Cycle

Photosynthesis: the overall equation and the chloroplast

The light-dependent reactions: photolysis, NADPH and ATP

The Calvin cycle: fixing carbon dioxide in the stroma

Limiting factors, the compensation point and respiration in plants

Common traps

Fats and Proteins as Fuel, and Where Each Pathway Runs

Fat as fuel: lipolysis and β-oxidation

Protein breakdown: transamination, deamination and the urea cycle

Where each metabolic pathway takes place: organelle and organ

Common traps

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