Cellular Energetics

Cyanide kills in minutes, yet a person poisoned by it is still breathing normally and their blood is full of oxygen. Cyanide binds to one protein at the very end of the electron transport chain in their mitochondria. Oxygen can no longer accept electrons, the chain stops, and the cells run out of ATP. One blocked step in a long pathway is enough. This unit is about those pathways: the enzymes that run each step, and how cells capture energy from light and release it from food.

An enzyme 酶 is a protein catalyst 催化剂 that speeds a reaction by lowering its activation energy 活化能, without being used up. Each enzyme has an active site 活性位点 that binds a specific substrate 底物 (the "lock and key" or induced fit), so enzymes are highly specific. They do not change whether a reaction is favorable – only how fast it goes.

Fit means both shape and charge. The active site's shape matches the substrate, and the R groups lining it carry charges or polar groups that attract opposite charges on the substrate. A substrate with the right shape but the wrong charge pattern will not bind well. When the substrate binds, it forms an enzyme-substrate complex; the enzyme then releases the products and can be used again.

Enzyme activity depends on conditions. Each enzyme has an optimal temperature and pH; beyond it, the protein denatures 变性 (loses shape) and stops working. Substrate concentration raises the rate until the enzyme saturates. Inhibitors 抑制剂 slow enzymes – competitive ones block the active site, noncompetitive ones bind elsewhere and change the shape.

At low substrate concentration, adding substrate speeds the reaction because more collisions fill more active sites. At high concentration every active site is busy, so the rate levels off. The graph shows how to tell the two kinds of inhibitor apart: adding lots of substrate overcomes a competitive inhibitor, but not a noncompetitive one. Product concentration matters too: if products build up, the reaction slows, and in many pathways the final product itself switches off an early enzyme (feedback inhibition). Denaturation is sometimes reversible: if the temperature or pH returns to normal before the protein has been badly damaged, it can fold back and work again.

Worked example (a blocked pathway). A cell makes amino acid B in three steps: substrate $\xrightarrow{\text{enzyme 1}}$ X $\xrightarrow{\text{enzyme 2}}$ Y $\xrightarrow{\text{enzyme 3}}$ B. The product of enzyme 2 is Y. If the pH changes so that enzyme 3 denatures, it can no longer bind Y: B is not made, and Y builds up. The pH change breaks the hydrogen and ionic bonds that hold enzyme 3's shape, so its active site no longer fits Y in shape and charge.

ATP (adenosine triphosphate) is the cell's energy currency. Hydrolysing its last phosphate (ATP + H₂O → ADP + Pᵢ) releases free energy to power cellular work, and making ATP from ADP + Pᵢ takes energy in. The energy comes from the products being far more stable than ATP, not from "breaking a bond": breaking any bond takes energy. Cells constantly recycle ATP, coupling energy-releasing reactions to energy-requiring ones.

Life and the laws of thermodynamics

A living cell is highly ordered, and that order is often mistaken for a violation of physics. It is not.

• The first law 热力学第一定律 says energy is conserved: it changes form but is never created or destroyed. A cell does not make energy — it transforms the chemical energy of glucose, or the light energy of the Sun, into the chemical energy of ATP.
• The second law 热力学第二定律 says that in any energy transfer, some energy is lost as heat and the entropy 熵 of the universe increases. A cell builds order inside itself, but only by releasing more disorder to its surroundings, mostly as heat.

Living systems need a constant input of free energy 自由能 to maintain organised processes over time. That energy can come from current intake or stored resources. An organism does not necessarily die when external intake stops, but cannot maintain these processes indefinitely without replenishing its energy supply.

Photosynthesis 光合作用 captures light energy to build sugar from $\text{CO}_2$ and water, releasing $\text{O}_2$. It has two stages:

• The light reactions (in the thylakoid membranes) use light to make ATP and NADPH and split water, releasing oxygen.
• The Calvin cycle 卡尔文循环 (in the stroma) uses that ATP and NADPH to fix $\text{CO}_2$ into sugar.

So light energy becomes chemical energy stored in glucose.

The light reactions, step by step

The light reactions happen in the thylakoid 类囊体 membrane. Thylakoids are flattened sacs stacked into piles called grana, which pack a large membrane area into each chloroplast; the fluid around them is the stroma. Two groups of pigments and proteins, photosystem 光系统 II (PSII) and photosystem I (PSI), absorb light. Between them is a chain of electron carriers. Follow the numbers in the figure:

1. Light energy excites electrons in the chlorophyll of PSII to a higher energy level, and they leave PSII.
2. PSII replaces them by splitting water in the thylakoid space: $\text{H}_2\text{O} \rightarrow \tfrac{1}{2}\text{O}_2 + 2\text{H}^+ + 2e^-$. This is where the oxygen comes from: it comes from water, not from $\text{CO}_2$.
3. The electrons pass along the chain. Their energy is used to pump $\text{H}^+$ from the stroma into the thylakoid space, so a proton gradient 质子梯度 builds up.
4. Light excites the electrons again at PSI. They then reduce $\text{NADP}^+$ to NADPH in the stroma.
5. $\text{H}^+$ flow back into the stroma, down their gradient, through ATP synthase ATP合酶, which uses that flow to make ATP from ADP and $\text{P}_\text{i}$.

Cyclic electron flow. Electrons from PSI can also be passed back to the carriers between the two photosystems instead of to $\text{NADP}^+$. They pump more $\text{H}^+$ on the way, so the cell makes ATP but no NADPH and splits no water. The Calvin cycle uses ATP and NADPH in a ratio of 3 : 2, more ATP than the linear pathway alone gives, and cyclic flow tops up the ATP. When NADPH builds up and $\text{NADP}^+$ runs short, electrons from PSI have nowhere else to go, so more of them take the cyclic route.

Making ATP using the energy of a proton gradient is called chemiosmosis 化学渗透. The same mechanism makes most of the ATP in mitochondria (see below). Only the location differs.

The Calvin cycle in numbers

The Calvin cycle runs in the stroma 基质. It needs no light directly, but it stops in the dark because it runs out of ATP and NADPH. It has three phases:

• Carbon fixation 碳固定: the enzyme rubisco 核酮糖二磷酸羧化酶 joins $\text{CO}_2$ to a 5-carbon sugar, RuBP. The 6-carbon product splits at once into two 3-carbon molecules.
• Reduction 还原: ATP and NADPH turn these into the 3-carbon sugar G3P.
• Regeneration 再生: most of the G3P is rearranged, using more ATP, to make RuBP again.

Three turns fix 3 $\text{CO}_2$ and give one spare G3P. Making one glucose (6 carbons) takes 6 turns, which use 18 ATP and 12 NADPH.

Where the oxygen in the air came from

Photosynthesis did not only feed the first organisms; it changed the planet. Scientific evidence supports the claim that photosynthesis by prokaryotes 原核生物 — specifically cyanobacteria 蓝细菌 — produced the oxygen that built Earth's oxygenated atmosphere 含氧大气.

The evidence is physical: banded iron formations 条带状铁建造 in rocks about 2.4 billion years old record iron dissolved in the ocean being oxidised and precipitating out, which needs free oxygen. Before that event, called the Great Oxidation Event, the atmosphere held almost none.

Two consequences matter for the rest of the course. Free oxygen made aerobic respiration possible, which releases far more ATP per glucose than anaerobic pathways do. And it was lethal to much of the anaerobic life already present, so it counts as one of the largest extinction events in Earth's history — an early example of organisms changing their own environment.

Cellular respiration 细胞呼吸 releases the energy in glucose to make ATP, mostly using oxygen. Its stages:

• Glycolysis 糖酵解 (in the cytoplasm) splits glucose, making a little ATP.
• The Krebs cycle 克雷布斯循环 (mitochondrial matrix) releases $\text{CO}_2$ and loads electron carriers.
• The electron transport chain 电子传递链 (inner membrane) uses those electrons to pump protons and make most of the ATP, with oxygen as the final electron acceptor.

Without oxygen, cells use fermentation 发酵 to keep glycolysis running, making far less ATP. Photosynthesis and respiration are complementary – the products of one are the reactants of the other.

Following the electrons

Glucose is oxidised in steps. At each step, electrons (with $\text{H}^+$) are loaded onto the carriers $\text{NAD}^+$ and FAD, which become NADH and $\text{FADH}_2$.

• Glycolysis: glucose (6C) → 2 pyruvate 丙酮酸 (3C), giving a net 2 ATP and 2 NADH.
• Pyruvate oxidation 丙酮酸氧化: in the matrix, each pyruvate loses one $\text{CO}_2$ and becomes acetyl-CoA (2C), giving 1 NADH.
• Krebs cycle: each acetyl-CoA is oxidised to 2 $\text{CO}_2$. Per glucose (two turns) this gives 2 ATP, 6 NADH and 2 $\text{FADH}_2$.

So the six carbons of glucose all leave as $\text{CO}_2$ before the electron transport chain is reached. The chain then gets the electrons, not the carbon.

Compare the two membranes:

Why fermentation is needed. Glycolysis needs $\text{NAD}^+$. Without oxygen, the chain stops, NADH is not turned back into $\text{NAD}^+$, and glycolysis would stop as well. Fermentation passes the electrons from NADH to pyruvate (or to a molecule made from it). In animals this makes lactate; in yeast it makes ethanol and $\text{CO}_2$. This regenerates $\text{NAD}^+$ so that glycolysis can keep making its 2 ATP. Fermentation itself makes no extra ATP.

What happens if the gradient leaks. A substance that lets $\text{H}^+$ cross the membrane without passing through ATP synthase is an uncoupler 解偶联剂. The chain keeps running and oxygen is still used, but little ATP is made: the energy is released as heat. Brown fat in newborn babies and hibernating mammals does this on purpose, using a channel protein, to keep the body warm.

Common mistakes.

• "Photosynthesis releases the oxygen from $\text{CO}_2$." The $\text{O}_2$ comes from water, split at PSII.
• "The electron transport chain makes ATP." The chain pumps $\text{H}^+$; it is ATP synthase that makes the ATP, powered by the $\text{H}^+$ flowing back.
• Mixing up the compartments. In the chloroplast, $\text{H}^+$ build up inside the thylakoid. In the mitochondrion, they build up in the intermembrane space, not in the matrix.
• "Fermentation makes ATP." Only its glycolysis step does; the extra step only regenerates $\text{NAD}^+$.
• "The Calvin cycle is the dark reaction, so it happens at night." It runs in the light, when ATP and NADPH are being made.
• "Oxygen is used in the Krebs cycle." Oxygen is used only at the end of the chain. The Krebs cycle stops without it because $\text{NAD}^+$ and FAD are not regenerated.
• "Blocking ATP synthase makes the proton gradient disappear." The opposite: with no way back, $\text{H}^+$ pile up and the gradient gets steeper.
• "A competitive inhibitor lowers the maximum rate." Enough substrate outcompetes it, so the maximum rate is unchanged; a noncompetitive inhibitor lowers it.
• Describing an active site by shape alone. It fits its substrate in shape and charge.

Worked example. Aerobic respiration of one glucose nets about 2 ATP from glycolysis, 2 ATP from the Krebs cycle, and about 28 ATP from oxidative phosphorylation, for $\approx$ 32 ATP total. With no oxygen only glycolysis runs, so fermentation nets just 2 ATP per glucose — roughly 16 times less energy, which is why aerobic pathways dominate in oxygen-rich cells.

Fermentation comes in two common forms. In muscle cells short of oxygen, and in the bacteria that cause tooth decay, pyruvate takes the electrons from NADH and becomes lactic acid 乳酸, which lowers the pH. In yeast, pyruvate is turned into ethanol and $\text{CO}_2$, which makes bread rise.

Exam skill (predict the effect of a block). Free-response questions often name one step that is blocked and ask what changes. Work along the pathway in both directions.

• ATP synthase blocked (for example by oligomycin): $\text{H}^+$ cannot flow back, so the proton gradient becomes steeper, ATP production falls, and the chain slows because pumping against an ever-steeper gradient gets harder; oxygen use falls.
• The end of the chain blocked (cyanide, or an enzyme deficiency): electrons cannot reach oxygen, NADH is not turned back into $\text{NAD}^+$, and the Krebs cycle stops. Glycolysis can continue only through fermentation, so lactic acid production rises and ATP falls to 2 per glucose.
• Pyruvate cannot enter the mitochondrion or cannot be oxidised: glycolysis still makes its NADH, but the Krebs cycle gets no acetyl-CoA, so Krebs-cycle NADH and $\text{FADH}_2$ fall, and the cell turns to fermentation.
• An uncoupler lets $\text{H}^+$ leak back without ATP synthase: the chain speeds up and oxygen use rises, but the energy is released as heat. Brown fat in newborn babies and hibernating mammals does this on purpose to keep warm.

Exam skill (hypotheses and graphs). The null hypothesis 零假设 says the factor being tested has no effect, for example "temperature has no effect on the rate of ATP synthesis". Use a line graph when the independent variable is continuous, such as time or temperature, and a bar graph when it is in separate categories, such as treatment groups. Label both axes with units, and add error bars when the data give a spread or confidence interval.

• An enzyme lowers the activation energy and is not used up; its active site is specific to one substrate (lock and key).
• Rate rises with temperature only up to the optimum — beyond it the enzyme denatures and the rate falls (unlike an ordinary reaction).
• Know the ATP↔ADP cycle: hydrolysis of ATP to ADP + Pᵢ releases energy to power the cell (never write "breaking the bond releases energy").
• Write the overall equations: photosynthesis stores energy (builds glucose); respiration releases it (breaks glucose down) — they are opposites.
• Match each stage to its location and whether it needs oxygen.