Cellular energetics · AP Biology

Chapter 3 · Cellular energetics

enzymes, light and respiration

A cell is a highly ordered system, and order costs energy. Every living thing needs a steady supply of it, and gets it through reactions that enzymes run.

On the left, a chloroplast captures light energy and stores it in glucose, releasing O₂. On the right, a mitochondrion breaks glucose down with that O₂, back to CO₂ and H₂O, and keeps the released energy in ATP, the molecule the cell spends.

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O

Photosynthesis runs this equation backwards, driven by light. Matter goes round the loop; energy does not. It enters as light and leaves as heat.

This chapter takes apart the enzymes that make each step fast, the coupling that lets ATP pay for work, and the two pathways: photosynthesis and cellular respiration.

3.1 · Enzymes

a pocket shaped for one substrate

An enzyme is a catalyst, nearly always a protein, that speeds up one reaction without being used up.

The molecule it acts on is its substrate. The substrate binds in the active site, a pocket in the folded protein lined by amino acid side chains. For the reaction to happen, the substrate’s shape and charge must be compatible with the active site: a positively charged side chain attracts a negatively charged region of the substrate, a nonpolar patch holds a nonpolar one.

That is why an enzyme is specific. In the figure the blue molecule has the wrong shape; it drifts past and nothing happens.

When the substrate binds, the enzyme changes shape slightly and closes around it: induced fit. The enzyme–substrate complex strains the bond to be broken, the products are released, and the enzyme is free to take another substrate, unchanged.

The active site’s shape comes from the protein’s 3-D folding, so anything that changes the folding changes what the enzyme can do (3.2).

3.1 · Lowering the barrier

activation energy

Even a reaction that releases energy has to be pushed over a hill first. The height of that hill is the activation energy, E_a.

The figure plots free energy G along the reaction. Without the enzyme (ink), E_a = 80 kJ/mol; few molecules have enough energy to cross, so the reaction is slow. The enzyme (red) gives a path with E_a = 40 kJ/mol, and far more molecules make it over.

	without enzyme	with enzyme
activation energy (kJ/mol)	80	40
ΔG of the reaction (kJ/mol)	−30	−30

For these barriers, at body temperature the catalysed reaction runs about 5.5 × 10⁶ times faster.

What the enzyme does not change: the energy of the reactants and products, so ΔG is the same, and the direction the reaction goes. An enzyme speeds a reaction that would happen anyway; it cannot make an energy-requiring reaction go on its own.

3.2 · Temperature and pH

each enzyme has its best conditions

An enzyme works fastest at an optimum temperature and pH. Away from it, the rate falls.

Temperature. Warming speeds molecules, so they collide more often and with more energy: below the optimum the rate rises, often about 2× for every 10 °C. Above it, the heat breaks the hydrogen bonds and other weak interactions that hold the protein’s shape, the active site loses its shape, and the rate drops steeply. This is denaturation. In the figure the optimum is about 37 °C, typical of a human enzyme.

Q₁₀. The factor by which a rate changes over 10 °C. If a reaction runs at 3.2 μmol/min at 15 °C and 6.4 μmol/min at 25 °C:

Q_{10} = \left(\frac{R_2}{R_1}\right)^{10/(T_2 - T_1)} = \left(\frac{6.4}{3.2}\right)^{10/10} = 2.0

pH. H⁺ concentration changes the charges on side chains, which changes the protein’s folding and the charges in the active site. Pepsin works in the stomach (optimum pH 2); trypsin in the small intestine (optimum pH 8).

Denaturation is sometimes reversible: if the shape returns when conditions do, so does the activity.

3.2 · Concentration and inhibitors

what fills the active sites

With more substrate, more active sites are occupied at any moment, so the rate rises, until nearly every site is busy and the rate levels off at V_max (here 10 μmol/min).

At that point only more enzyme makes it faster: with substrate in excess, the rate is proportional to the enzyme concentration. Products piling up slow the net reaction too.

An inhibitor lowers the rate.

	binds	more substrate
competitive	the active site	outcompetes it: same V_max
noncompetitive	another site (allosteric)	does not help: lower V_max

A competitive inhibitor resembles the substrate and takes the active site; at high [S] the substrate wins most sites, so the blue curve still climbs toward 10. A noncompetitive inhibitor binds an allosteric site and changes the enzyme’s shape so the active site no longer works; the red curve tops out at 5, however much substrate is added.

Cells use this: the end product of a pathway often inhibits its first enzyme allosterically (feedback inhibition). Many enzymes also need a cofactor (a metal ion such as Mg²⁺) or coenzyme (an organic molecule, often from a vitamin) to take their working shape.

3.3 · Cellular energy

ATP pays for what will not go alone

Life is ordered, and order does not keep itself. Living systems need a constant input of energy; it is passed along in sequential pathways and some is lost as heat at every step.

This does not break the second law of thermodynamics: the cell becomes more ordered while its surroundings become more disordered, with heat and simpler molecules (CO₂, H₂O) released. When energy input stops, order is lost and the organism dies.

A reaction with ΔG < 0 releases energy (exergonic) and can go by itself. One with ΔG > 0 needs energy (endergonic). The cell runs an endergonic reaction by coupling it to an exergonic one, usually the hydrolysis of ATP.

Example. Making glutamine from glutamate and ammonia:

reaction	ΔG (kJ/mol)
glutamate + NH₃ → glutamine	+14.2
ATP + H₂O → ADP + P_i	−30.5
coupled	14.2 + (−30.5) = −16.3

The coupling is chemical: ATP hands its last phosphate to glutamate, the phosphorylated glutamate is less stable and reacts with NH₃, and the phosphate leaves. The pair has ΔG < 0, so it goes.

3.4 · The light reactions

light, an electron chain and a proton gradient

In the thylakoid membranes of the chloroplast, light energy is turned into the chemical energy of ATP and NADPH.

Capturing light. Chlorophylls in photosystem II and photosystem I absorb light, which excites electrons to a higher energy level. Other pigments (chlorophyll b, carotenoids) absorb other wavelengths and pass the energy on; this variety of molecules widens the range of light a plant can use.

The electron transport chain. Excited electrons leave PS II and pass along carriers to PS I, which re-excites them, and then to NADP⁺, making NADPH. PS II replaces its electrons by splitting water: 2 H₂O → 4 H⁺ + 4 e⁻ + O₂. That is where the O₂ comes from.

Chemiosmosis. The electrons’ energy pumps H⁺ into the thylakoid space, and water splitting adds more there. The lumen reaches about pH 5, the stroma about pH 8: 1,000 times more H⁺ inside. H⁺ can only flow back out through ATP synthase; the flow turns its rotor, and the turning makes ATP from ADP and P_i on the stroma side.

Photosynthesis first evolved in prokaryotes (cyanobacteria), whose O₂ changed Earth’s atmosphere; chloroplasts descend from such a cell.

3.4 · The Calvin cycle

carbon fixed into sugar

In the stroma, the ATP and NADPH from the light reactions power the Calvin cycle, which builds sugar from CO₂.

Fixation. The enzyme rubisco attaches each CO₂ to a 5-carbon acceptor (RuBP); the product splits into two 3-carbon molecules.

Reduction. ATP and the electrons of NADPH turn those into the 3-carbon sugar G3P.

Regeneration. Most of the G3P, with more ATP, is rearranged back into the acceptor, so the cycle can continue. The rest leaves to make glucose and other molecules.

The count. Carbon is conserved, so to export one 3-carbon G3P the cycle must fix 3 CO₂:

	CO₂	ATP	NADPH
per G3P	3	6 + 3 = 9	6
per glucose (2 G3P)	6	18	12

The light reactions and the Calvin cycle depend on each other: the cycle returns ADP and NADP⁺ for the membrane to recharge. In the dark, ATP and NADPH run out and the cycle stops. The names of the intermediates are here only to follow the carbon; the exam does not ask for them.

3.5 · Glycolysis and the Krebs cycle

taking glucose apart

Cellular respiration releases the energy in glucose step by step. The first stages strip off its carbon as CO₂ and load its electrons onto carriers.

Glycolysis, in the cytosol, splits glucose into two 3-carbon pyruvate. It invests 2 ATP and makes 4, a net 2 ATP, and loads 2 NAD⁺ to NADH. It needs no O₂.

Pyruvate oxidation. Pyruvate is carried into the mitochondrial matrix and converted to acetyl-CoA, releasing a CO₂ and making an NADH.

The Krebs cycle, in the matrix, oxidises the acetyl group to 2 CO₂, making ATP, NADH and FADH₂. It turns twice per glucose.

per glucose	ATP	NADH	FADH₂	CO₂
glycolysis	2	2	0	0
pyruvate oxidation	0	2	0	2
Krebs cycle	2	6	2	4
total	4	10	2	6

All six carbons of glucose leave as the 6 CO₂ of the overall equation. Only 4 ATP have been made so far; most of the energy is in the 12 loaded carriers.

3.5 · Oxidative phosphorylation

the chain, the gradient and ATP synthase

NADH and FADH₂ deliver their electrons to the electron transport chain in the inner mitochondrial membrane. In prokaryotes, the chain sits in the plasma membrane.

The electrons pass from carrier to carrier, each holding them more tightly, and the energy they release pumps H⁺ from the matrix into the intermembrane space. At the end, O₂ is the final electron acceptor: it takes the electrons and H⁺ and becomes water. Some prokaryotes use another final acceptor, such as sulfate or nitrate.

The gradient drives H⁺ back through ATP synthase, which turns and makes ATP: chemiosmosis, as in the chloroplast. The folding of the inner membrane into cristae gives room for many chains.

The yield. About 2.5 ATP per NADH and 1.5 per FADH₂:

10(2.5) + 2(1.5) + 4 = 32\ \text{ATP}

That is about 34% of glucose’s 2870 kJ/mol kept as ATP (32 × 30.5 kJ/mol); the rest is heat. Without O₂, the chain backs up and stops.

Uncoupling. If H⁺ leak back across the membrane without passing through ATP synthase, the electron transport goes on but the gradient’s energy is released as heat. Brown fat does this deliberately, to keep endotherms warm.

3.5 · Fermentation

ATP without oxygen

Without O₂, glycolysis can still make 2 ATP per glucose, if it has NAD⁺.

Glycolysis turns NAD⁺ into NADH. With no O₂ to empty the chain, the NADH cannot unload there, and the cell would soon run out of NAD⁺. Fermentation regenerates it: pyruvate (or a product of it) takes NADH’s electrons.

	pyruvate becomes	where
lactic acid fermentation	lactate	muscle cells, some bacteria
alcohol fermentation	ethanol + CO₂	yeast, some bacteria

Fermentation itself makes no ATP; it keeps glycolysis going. With O₂, the same glucose gives about 32 ATP, 16 times as much. A fermenting cell must burn glucose far faster for the same ATP.

Glycolysis is found in nearly every organism and needs no O₂ or membrane-bound organelle, evidence that it evolved early, before O₂ was in the atmosphere.