Week 5 · Chapter

Chapter 5 — Energy, Enzymes & Metabolism

Introduction to Biology Free sample edition

The module's primary reading · ~35–45 minutes · Objective 4 (explain how cells obtain and transform energy — the laws of thermodynamics, ATP, and enzyme action with its temperature and pH limits — and trace cellular respiration and photosynthesis as ordered, located overviews, including fermentation and the relationship between the two processes), with Objective 2 (explain the chemistry of life — atoms and the three kinds of chemical bonds, water's polarity and the properties it produces, and the logarithmic pH scale with buffers — and relate the structure of each of the four classes of biological macromolecules (carbohydrates, lipids, proteins, nucleic acids) to its function) and Objective 1 (describe the practice of science in biology — the characteristics of life as a set, the levels of biological organization, the scientific method and a controlled experiment's variables and control, and the difference between a hypothesis and a theory — and explain evolution by natural selection as the unifying framework of biology) carried forward · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Every living thing runs on energy, and this week you learn where a cell's energy comes from and how it gets spent. You will meet energy (the capacity to do work) in its two forms, moving and stored, and two rules about it that no cell can break. You will meet ATP (the small molecule a cell spends to pay for its work), the cell's everyday cash. You will meet enzymes (proteins that speed up the cell's chemistry without being used up), and you will find out why heat, acid, and too little fuel change how fast they work. Finally, you will read a potato-and-peroxide experiment from start to finish and see why a boiled enzyme stops working for good.

Why you already care about this

Think about the last time you had a fever. Your body ran only a few degrees warmer than its usual set point of about 37 °C, yet you may have felt weak, achy, and foggy. A few degrees sounds small. So why does it matter so much?

This week gives you one way to read it, through the proteins that run your chemistry. Reaction after reaction inside you depends on an enzyme. Each enzyme has a temperature at which it works best, and for human enzymes that best temperature sits near 37 °C. Push the temperature too far and the enzyme's shape starts to fail. In one illustrative kitchen experiment made for this course, potato catalase made an average of 10 cm of foam at body temperature, only 2 cm when cold, and 0 cm after the potato was boiled.

You already live this week's ideas. You eat a sandwich and later climb a flight of stairs. You drink milk, and lactase in your gut goes to work on it. You crack an egg into a hot pan and watch the clear part turn solid and white, never to turn clear again. This chapter explains each of these in the language of energy and enzymes.

By the end of this chapter you will be able to:

sort an example as kinetic or potential energy, and state the two laws of thermodynamics in plain words;
explain why a cell captures and transfers energy and never makes it;
sort a reaction as catabolic and exergonic, or anabolic and endergonic;
write the ATP and ADP cycle and keep ATP apart from DNA;
explain how an enzyme lowers activation energy and why it is reused;
compare the lock-and-key and induced fit models of an enzyme;
predict how temperature, pH, and substrate concentration change an enzyme's rate, and tell a slowed enzyme from a denatured one;
compute the four averages and ranges of the catalase experiment, with every step shown.

Carry this line with you: a cell spends energy; it never makes it.

Where we are

Already covered: Week 1 taught you to read a controlled experiment; Week 2 covered water and the pH scale; Week 3 covered proteins, their four levels of shape, and denaturation; Week 4 toured the cell and met the pump that spends ATP.
This week: energy and its two laws, metabolism, ATP, enzymes, and what changes an enzyme's rate.
How they connect: an enzyme is one of Week 3's proteins, so its shape is its job; pH from Week 2 tells you where each enzyme works; and the lab is read with Week 1's experiment habits.
Where we're going next: Week 6, Cellular Respiration, follows a glucose molecule through the pathways that recharge ATP, and every step of those pathways is run by an enzyme.

Week 1 gave you the controlled experiment: change one thing, measure one thing, and hold the rest steady. You will use it on the catalase lab in Section 9. Week 2 gave you the pH scale, where a lower number means more hydrogen ions and each whole step is a tenfold change. Week 3 gave you proteins and denaturation, the loss of a protein's shape and, with it, its job. That one idea carries half of this chapter. Week 4 introduced ATP as the cell's energy currency, spent by the sodium-potassium pump. This week you learn what ATP is and how the cell keeps it charged.

1. Define energy: kinetic versus potential

Picture an archer drawing a bow. While the string is pulled back and held still, nothing moves, yet the bow is loaded with something. Let go, and the arrow flies. That "something" is energy.

Energy is the capacity to do work, such as moving something, building something, or warming something. It comes in two broad forms:

Kinetic energy is the energy of motion, including heat, which is the motion of molecules. A sprinter crossing the finish line has kinetic energy.
Potential energy is stored energy that can do work later, such as the energy in a stretched bowstring or in the chemical bonds of food.

For a cell, the most important store is the chemical bond. The bonds in a sugar molecule hold potential energy. When a cell breaks those bonds in a controlled way, some of that energy is captured to do the cell's work, and some escapes as heat.

Worked example — sort the energy. Label each case kinetic or potential.

A drawn bowstring, held still: potential. The energy is stored in the bent bow, waiting.
The arrow in flight: kinetic. The stored energy has become motion.
A granola bar in your backpack: potential. The energy is stored in the chemical bonds of its sugars and fats.
Your warm skin after a run: kinetic. Heat is the motion of molecules.

In words: stored energy is potential; energy in motion, including heat, is kinetic, and one form keeps turning into the other.

Misconception check. Students often think only moving things have energy. The idea is tempting because motion is the energy we can see. But a still bowstring and a granola bar both hold energy, stored and waiting. Food is a store of potential energy in its chemical bonds, which is why it can power you hours after you eat it.

Memory hook: stored is potential; moving is kinetic.

2. Follow the two laws of thermodynamics

Think about a phone that has been charging on a desk. It feels warm. Not all of the electricity went into the battery; some became heat in the charger and the phone. Every energy change you have ever seen works this way, and two laws describe it.

The first law of thermodynamics is the rule that energy can be transferred from place to place and transformed from one form to another, but is never created or destroyed.

The second law of thermodynamics is the rule that every energy transfer or transformation loses some energy as heat that can no longer do work, which raises the entropy of the surroundings, so no energy conversion is completely efficient.

Entropy is a measure of disorder. When energy escapes as heat, it spreads out into the surroundings and becomes less useful, and that spreading raises entropy.

Put the two laws together and you get the first rule of this week: a cell captures and transfers energy; it never makes energy. Your cells capture the energy stored in food, move it into a form they can spend, and lose some as heat along the way.

Worked example — follow the energy in a sandwich. Trace where the energy goes when you eat a sandwich and then climb the stairs.

Stored: the sandwich holds potential energy in the chemical bonds of its sugars, fats, and proteins.
Transferred: your cells break those bonds and move part of the energy into ATP (Section 4).
Transformed: your muscle cells spend ATP to contract, turning stored energy into the kinetic energy of your legs moving.
Lost as heat: at every step, some energy escapes as heat, and you feel warmer at the top of the stairs.

In words: no energy was created and none was destroyed; it was moved and changed, and some became heat at every step, exactly as the two laws say.

Misconception check. Students often say, "The cell makes energy." It is an easy phrase to pick up, because ads say a drink "gives you energy" and textbooks say a structure "makes ATP." But the first law forbids making energy. A cell captures energy from food, or a plant from light, and transfers it. Say "captures and transfers," and you will never break the first law.

Memory hook: energy is moved and changed, never made.

3. Sort metabolism: catabolic versus anabolic

Picture a set of toy building bricks. You can pull a finished model apart into single bricks, or you can snap single bricks together into a new model. A cell does both, all day, with molecules.

Metabolism is the whole set of chemical reactions in a cell or organism, both those that break molecules down and those that build them up. It runs in two directions:

A catabolic reaction is a reaction that breaks a larger molecule into smaller ones and releases energy, as in digesting food.
An anabolic reaction is a reaction that builds a larger molecule from smaller ones and requires an input of energy, as in building a protein.

Two more words describe the same split from the energy side:

Exergonic describes a reaction that releases energy overall; breaking-down (catabolic) reactions are exergonic. Think "ex" for exit: energy leaves.
Endergonic describes a reaction that takes in energy overall; building-up (anabolic) reactions are endergonic. Think "end" for enter: energy goes in.

You met both directions in Week 3. Hydrolysis, which breaks a polymer by adding water, is catabolic. Dehydration synthesis, which builds a polymer by removing water, is anabolic.

Worked example — sort four reactions. Label each as catabolic and exergonic, or anabolic and endergonic.

Digesting the starch in a slice of bread into glucose: breaking down, so catabolic and exergonic.
A muscle cell joining amino acids into a new protein after a workout: building up, so anabolic and endergonic.
A liver cell joining glucose units into a long storage chain: building up, so anabolic and endergonic.
A cell breaking glucose down to recharge its ATP: breaking down, so catabolic and exergonic.

In words: breaking down releases energy and building up costs energy, and the cell pays for the building with energy released by the breaking.

Misconception check. Students often swap the two pairs, calling a building reaction exergonic because it "makes something." The slip is tempting because building feels productive. But building a big molecule costs energy, so it is endergonic. Use the "ex for exit, end for enter" hook and ask which way the energy is flowing.

Memory hook: break down, energy out; build up, energy in.

4. Spend and recharge ATP: the cell's energy currency

Think about a phone battery. You charge it at night, spend it all day, and charge it again. The battery is not the power plant and it is not the app; it is the thing in between that carries the charge to where it is needed. ATP plays that role in a cell.

ATP is adenosine triphosphate, the cell's energy currency: adenosine carrying a chain of three phosphates. Picture it as a labeled figure: a base and a sugar together called adenosine at one end, then three phosphate groups in a row like three linked train cars. Removing the outer phosphate releases energy the cell can use for work.

ADP is adenosine diphosphate, the spent form of the energy currency, carrying two phosphates; energy from food adds a phosphate back to make ATP again.

The cycle in one line:

ATP → ADP + phosphate + energy

Read the arrow as "becomes." Spending ATP releases a phosphate and energy. Then the cell uses energy captured from food to put a phosphate back on ADP, and it has ATP again. ATP runs in a cycle, not a one-way street. One glucose recharges roughly thirty ATP, a number you will meet properly in Weeks 6 and 7, when you follow the pathways that do the recharging.

Worked example — count the phosphates. A cell spends one ATP to power a pump.

Start: ATP carries 3 phosphates.
Spend: one phosphate is removed, so 3 − 1 = 2 phosphates remain.
Name it: a molecule with 2 phosphates is ADP, the spent form.
Recharge: energy from food adds a phosphate back, 2 + 1 = 3, and the molecule is ATP again.

In words: three phosphates is charged, two is spent, and food turns two back into three.

You met one ATP customer in Week 4: the sodium-potassium pump, which spends one ATP to move three Na⁺ out of the cell and two K⁺ in. Muscle contraction and building proteins are other customers.

Misconception check. Two slips show up here. First, students blur ATP and DNA because both are built around a base and a sugar. ATP is the energy currency; DNA is the instruction set. They are never the same molecule. Second, students swap ATP and ADP. Count the phosphates: tri means three, which is charged; di means two, which is spent.

Memory hook: ATP is the cash; DNA is the instructions.

5. Lower the hill: how an enzyme works

Picture pushing a cart over a small hill to reach a lower parking lot on the far side. The lot is downhill overall, but you still have to push the cart up the hill first. Many reactions in a cell are like that cart. They would release energy overall, yet they barely start on their own, because of the hill.

Activation energy is the energy that must be put in to get a reaction started, pictured as a hill the reaction has to climb before it can run.

An enzyme is a protein that speeds up a reaction by lowering its activation energy, without changing where the reaction starts or ends; it comes out of the reaction unchanged and is reused. In the cart picture, the enzyme digs a lower pass through the hill. The starting lot and the ending lot stay exactly where they were.

Every enzyme has a working pocket and a partner:

The substrate is the molecule an enzyme acts on; it binds at the enzyme's active site.
The active site is the pocket on an enzyme where the substrate binds and the reaction takes place; its shape decides which substrate fits.

Because the active site has one shape, each enzyme does one job. Lactase acts on lactose, the sugar in milk. Catalase is an enzyme found in potato, liver, and other tissues that splits hydrogen peroxide into water and oxygen gas:

2 H₂O₂ → 2 H₂O + O₂

The oxygen gas is what makes the foam you will measure in this week's lab.

Worked example — follow one catalase molecule. Walk one enzyme through two rounds of work.

Bind: a hydrogen peroxide molecule, the substrate, fits into catalase's active site.
React: with the hill lowered, the substrate is split into water and oxygen far faster than it would split on its own.
Release: the products leave the active site, and the catalase molecule is unchanged.
Repeat: the same catalase grips the next hydrogen peroxide molecule and does it again.

In words: the enzyme lowered the hill, did the job, came out unchanged, and went straight back to work, so a small amount of enzyme can handle a large amount of substrate.

Misconception check. Students often think an enzyme adds energy to a reaction or makes an impossible reaction happen. It does neither. An enzyme only lowers the hill; the start and the end stay where they were. A second common slip is "enzymes get used up." An enzyme is a reusable catalyst: it comes out of each reaction unchanged.

Memory hook: an enzyme lowers the hill; it never moves the start or the end.

6. Compare two models of the active site

Think about a house key and a winter glove. A key either fits a lock or it does not; nothing bends. A glove is different: it is roughly hand-shaped, and it closes snugly around your hand as you pull it on. Biologists use both pictures to describe how an enzyme grips its substrate.

The lock-and-key model is a classroom model of enzyme action in which a rigid active site fits one substrate the way a lock fits one key.
The induced fit model is a classroom model of enzyme action, refining the lock-and-key picture, in which the active site changes shape slightly as the substrate binds, like a glove closing on a hand.

Both are models: simplifications you can hold in one hand, not photographs of every real enzyme. The lock-and-key model explains why each enzyme does one job. The induced fit model keeps that idea and adds that the enzyme's shape is not frozen; the grip tightens as the substrate arrives. Today the induced fit picture is the one biologists prefer, and the lock-and-key picture is kept as the simpler first step.

Worked example — choose the model. Decide which model each observation fits better.

Observation: an enzyme acts on one substrate and ignores molecules of a different shape. Both models explain this, and the lock-and-key model explains it most directly.
Observation: the active site's shape changes a little when the substrate binds. Only the induced fit model explains this, because the lock-and-key model treats the site as rigid.

In words: the lock-and-key model explains why an enzyme is choosy, and the induced fit model adds how its grip moves.

Misconception check. Students often treat a model as a literal description of every enzyme, as if each active site were a rigid keyhole. The idea is tempting because a clear picture feels like a photograph. Caveat: a model is a tool for thinking, and induced fit refines lock-and-key because real active sites flex. Use each model for what it explains.

Memory hook: a key fits; a glove closes.

7. Read what changes an enzyme's rate

Think about an oven that is too cold to bake bread and an oven that burns it. Somewhere between them is the temperature that works best. Enzymes behave the same way, and three conditions change how fast they work: temperature, pH, and the amount of substrate.

An enzyme's optimum is the temperature or pH at which an enzyme works fastest; for most human enzymes the temperature optimum sits near body temperature, about 37 °C.

Temperature: a rise, a peak, and a crash

As an enzyme warms toward its optimum, its rate rises, because molecules move faster and meet the active site more often. Past the optimum, the rate crashes to zero. Heat shakes the enzyme so hard that its shape falls apart, which is denaturation, and the active site is destroyed. A cooked egg does not un-cook: the proteins in the egg white have lost their shape for good.

Cold works differently. Cold only slows an enzyme. The shape survives, so when the enzyme warms up again, the slowing reverses and it works as before.

pH: where each enzyme works

Each enzyme also has a pH optimum. Most human enzymes work best near neutral. Pepsin is the exception worth remembering: pepsin is a protein-digesting enzyme that the stomach's acid activates and that works in the acidic stomach contents, roughly pH 1.5 to 3.5. Move an enzyme far from its pH optimum and its shape is disturbed, so its rate falls.

Substrate: faster until every site is busy

The more substrate there is, the faster the reaction runs, because active sites find partners more often. But the rise stops. Saturation is the point at which every enzyme's active site is busy, so adding more substrate no longer speeds the reaction. Think of a checkout line: once every register has a customer, a longer line does not make checkout faster.

Worked example — read three changes. Predict what happens to the rate in each case.

A human enzyme is warmed from room temperature to about 37 °C: the rate rises toward its peak, because 37 °C is near the optimum.
The same enzyme is boiled and then cooled back down: the rate is zero, because boiling denatured it, and cooling does not rebuild the active site.
Pepsin is moved from the acidic stomach into a neutral solution: the rate falls, because pepsin's optimum is acidic, roughly pH 1.5 to 3.5.

In words: temperature and pH each have a best value, heat far past the optimum can destroy the enzyme for good, and more substrate helps only until every active site is busy.

Misconception check. Students often think "hotter is always faster." The idea is tempting because warming does speed reactions at first. But only up to the optimum; past it, denaturation drops the rate to zero. A second slip is reading denaturation as reversible, like cooling. Cold slows, and the slowing reverses; heat denatures, and a cooked egg does not un-cook.

Memory hook: cold slows; heat destroys.

Pause and reflect. Choose one of these two prompts and think it through, or jot a few sentences in your notes.

(a) A fever raises your body a few degrees above its set point. Using the idea of an enzyme's optimum, explain in your own words why a fever might leave you feeling weak.
(b) Think of something from your own kitchen that changes for good when it is heated. How is that change like an enzyme being denatured?

8. Meet the helpers and the brakes

Think about a power drill that will not run until you snap in its battery pack. The drill is the tool, but it needs a helper part before it can work. Many enzymes are like that drill.

A cofactor is a non-protein helper an enzyme needs in order to work, such as a metal ion like iron or magnesium.
A coenzyme is an organic helper molecule an enzyme needs in order to work; many coenzymes are made from vitamins.

Cells also need brakes. Enzymes often work in chains, where the product of one enzyme becomes the substrate of the next, and the last enzyme makes the end product the cell needs. If the chain ran at full speed forever, the cell would waste energy piling up product it cannot use.

Feedback inhibition is a control in which the end product of a chain of reactions slows an earlier enzyme in that same chain, so the product limits its own production. It works like a home thermostat: when the room reaches the set temperature, the heat turns down, and when the room cools, the heat comes back on.

Worked example — follow the brake. Picture a model three-step chain (illustrative, made up for this chapter): enzyme 1 turns molecule A into B, enzyme 2 turns B into C, and enzyme 3 turns C into the end product, D.

Little D: the chain runs, and D builds up.
Plenty of D: extra D binds to enzyme 1 and slows it.
Chain slows: with less B being made, less C and less D follow.
D used up: as the cell spends D, less of it sits on enzyme 1, and the chain speeds up again.

In words: the end product controls its own supply, which is the reason a pathway is never stuck at full speed.

Misconception check. Students often think feedback inhibition switches a pathway off for good, or that it slows the last enzyme. Both miss the point. The end product slows an earlier enzyme in its own chain, and the slowing lifts as the product is used up. It is a thermostat, not an off switch.

Memory hook: the product sets its own pace.

9. Read the catalase experiment from start to finish

Now you can read a full enzyme experiment, from the reaction to the conclusion. This is the example you will see in the lecture, the slides, the tutorial, the quiz, and this week's Biology Lab & Inquiry. The numbers below are an illustrative dataset constructed for this course, not real data; your own trials at home will land somewhere nearby.

The reaction: catalase splits hydrogen peroxide into water and oxygen, 2 H₂O₂ → 2 H₂O + O₂. The oxygen gas makes the foam, so a taller foam means a faster reaction.

The question: how does temperature change how fast potato catalase works?

The hypothesis: if the potato is warmed toward body temperature, then the foam will rise higher, because the enzyme works faster near its optimum; if it is boiled, then the foam will not rise at all, because heat denatures the enzyme.

Pieces of potato were held at four temperatures, then dropped into hydrogen peroxide, and the foam height was measured after 60 seconds. Each condition was run three times.

Foam height in centimeters after 60 seconds at four temperatures, three trials each (illustrative, constructed for this course, not real data)
Condition	Trial 1	Trial 2	Trial 3
Cold, about 5 °C	1	2	3
Room, about 22 °C	4	5	6
Body, about 37 °C	9	10	11
Boiled, about 100 °C and cooled before testing	0	0	0

Worked example — the catalase data. Work through the steps in order: add the three trials, then divide by three.

Cold average. 1 + 2 + 3 = 6, and 6 ÷ 3 = 2, so the cold average is 2 cm.
Room average. 4 + 5 + 6 = 15, and 15 ÷ 3 = 5, so the room average is 5 cm.
Body average. 9 + 10 + 11 = 30, and 30 ÷ 3 = 10, so the body-temperature average is 10 cm, the peak.
Boiled average. 0 + 0 + 0 = 0, and 0 ÷ 3 = 0, so the boiled average is 0 cm.
Compare. 10 ÷ 2 = 5, so the body-temperature foam is 5 times the cold foam; 10 ÷ 5 = 2, so it is 2 times the room foam.
Range. Cold 3 − 1 = 2 cm; room 6 − 4 = 2 cm; body 11 − 9 = 2 cm; boiled 0 − 0 = 0 cm. Each condition spreads over at most 2 cm, while the averages climb from 2 to 10.

In words: the averages rise from 2 to 5 to 10 and then crash to 0, a rise to a peak and then a crash. The body-temperature foam is 5 times the cold foam versus 2 times the room foam, and the trials in each condition sit close together. The shape and the boiled zero are what matter, never any one centimeter.

Now name the parts, the way Week 1 taught you:

Independent variable: the temperature of the potato.
Dependent variable: the foam height after 60 seconds.
Controlled variables: the same amount of potato, the same hydrogen peroxide, the same container, and the same 60-second timing.
The baseline: the room-temperature sample is the everyday baseline the others are compared with.

Slowed versus denatured. The cold sample is slowed, and the slowing reverses when it warms. The boiled sample is denatured, its active site destroyed for good, so it reads 0.

The conclusion: the evidence supports the hypothesis. It does not prove it; one small experiment supports or fails to support a claim and invites a repeat. Honesty note: real potatoes vary, so your own foam heights will differ from these engineered numbers. The shape of the curve is what you should expect to see again.

In practice (your tools). In a free spreadsheet such as Google Sheets, type the three cold trials into cells B2, C2, and D2, and the other conditions into rows 3, 4, and 5. In cell E2, type =AVERAGE(B2:D2) to get the average, and in cell F2, type =MAX(B2:D2)-MIN(B2:D2) to get the range; copy both down to row 5. To sketch the curve, select the condition names and the averages, then choose Insert and then Chart. Always check the spreadsheet's answers against your own hand calculation.

Misconception check. Students often read the boiled zero as "the enzyme was too cold" or as a failed trial. It is neither. The boiled sample was cooled before testing, so its temperature at the moment of testing was fine; what failed was the enzyme's shape. A zero after boiling is the denaturation result, and it is exactly what the hypothesis predicted.

Memory hook: rise to a peak, then crash.

Key terms

Energy — The capacity to do work, such as moving something, building something, or warming something. (first used: 1. Define energy: kinetic versus potential)
Kinetic energy — The energy of motion, including heat, which is the motion of molecules. (first used: 1. Define energy: kinetic versus potential)
Potential energy — Stored energy that can do work later, such as the energy in a stretched bowstring or in the chemical bonds of food. (first used: 1. Define energy: kinetic versus potential)
First law of thermodynamics — The rule that energy can be transferred and transformed but is never created or destroyed. (first used: 2. Follow the two laws of thermodynamics)
Second law of thermodynamics — The rule that every energy transfer loses some energy as heat that can no longer do work, raising the entropy of the surroundings. (first used: 2. Follow the two laws of thermodynamics)
Entropy — A measure of disorder that rises as energy escapes as unusable heat. (first used: 2. Follow the two laws of thermodynamics)
Metabolism — The whole set of chemical reactions in a cell or organism, both those that break molecules down and those that build them up. (first used: 3. Sort metabolism: catabolic versus anabolic)
Catabolic reaction — A reaction that breaks a larger molecule into smaller ones and releases energy. (first used: 3. Sort metabolism: catabolic versus anabolic)
Anabolic reaction — A reaction that builds a larger molecule from smaller ones and requires an input of energy. (first used: 3. Sort metabolism: catabolic versus anabolic)
Exergonic — Describes a reaction that releases energy overall. (first used: 3. Sort metabolism: catabolic versus anabolic)
Endergonic — Describes a reaction that takes in energy overall. (first used: 3. Sort metabolism: catabolic versus anabolic)
ATP — Adenosine triphosphate, the cell's energy currency, carrying a chain of three phosphates. (first used: 4. Spend and recharge ATP: the cell's energy currency)
ADP — Adenosine diphosphate, the spent form of the energy currency, carrying two phosphates. (first used: 4. Spend and recharge ATP: the cell's energy currency)
Activation energy — The energy that must be put in to get a reaction started, pictured as a hill. (first used: 5. Lower the hill: how an enzyme works)
Enzyme — A protein that speeds up a reaction by lowering its activation energy and comes out unchanged, ready to be reused. (first used: 5. Lower the hill: how an enzyme works)
Substrate — The molecule an enzyme acts on, which binds at the active site. (first used: 5. Lower the hill: how an enzyme works)
Active site — The pocket on an enzyme where the substrate binds and the reaction takes place. (first used: 5. Lower the hill: how an enzyme works)
Catalase — An enzyme in potato, liver, and other tissues that splits hydrogen peroxide into water and oxygen gas. (first used: 5. Lower the hill: how an enzyme works)
Lock-and-key model — A classroom model in which a rigid active site fits one substrate the way a lock fits one key. (first used: 6. Compare two models of the active site)
Induced fit model — A classroom model in which the active site changes shape slightly as the substrate binds, like a glove closing on a hand. (first used: 6. Compare two models of the active site)
Optimum — The temperature or pH at which an enzyme works fastest. (first used: 7. Read what changes an enzyme's rate)
Pepsin — A protein-digesting enzyme that works in the acidic stomach contents, roughly pH 1.5 to 3.5. (first used: 7. Read what changes an enzyme's rate)
Saturation — The point at which every active site is busy, so more substrate no longer speeds the reaction. (first used: 7. Read what changes an enzyme's rate)
Cofactor — A non-protein helper an enzyme needs in order to work, such as an iron or magnesium ion. (first used: 8. Meet the helpers and the brakes)
Coenzyme — An organic helper molecule an enzyme needs in order to work, often made from a vitamin. (first used: 8. Meet the helpers and the brakes)
Feedback inhibition — A control in which the end product of a chain of reactions slows an earlier enzyme in that chain. (first used: 8. Meet the helpers and the brakes)

Summary

Energy is the capacity to do work; kinetic is moving, potential is stored.
Energy is transferred and transformed, never created or destroyed.
Every transfer loses some energy as heat, which raises entropy.
A cell captures and transfers energy; it never makes it.
Catabolic reactions break down and release energy; anabolic reactions build and cost energy.
ATP has three phosphates and is charged; ADP has two and is spent.
ATP is the energy currency; DNA is the instruction set.
An enzyme lowers the activation-energy hill and is reused.
Lock-and-key and induced fit are both models; induced fit is the refined one.
Rate rises to an optimum near 37 °C, then crashes as the enzyme denatures.
Cold slows an enzyme; heat past the optimum destroys it.
Cofactors and coenzymes help; feedback inhibition is the brake.

Check your understanding

Work these before looking at the answers — they are ungraded, and the answers (with reasoning) are at the bottom of the page.

Sort each as kinetic or potential energy: a skateboarder rolling down a ramp, a fully charged phone battery, the warmth coming off a radiator, and a spoonful of honey.
A friend says, "This energy bar creates energy for your muscles." Use the first law of thermodynamics to correct the sentence.
In an illustrative classroom test with made-up numbers, a mystery enzyme makes bubbles at three temperatures, three trials each: 20 °C gives 3, 4, and 5 bubbles per minute; 35 °C gives 7, 8, and 9; 70 °C gives 0, 0, and 0. Find each average, describe the shape, and say what most likely happened at 70 °C.
A model muscle cell (illustrative numbers) holds 10 ATP and spends 4 of them to contract. How many ATP and how many ADP does it hold now, and what must happen before it can contract again?

Answers (worked reasoning — read after attempting)

The skateboarder rolling down the ramp has kinetic energy, because it is motion. The charged phone battery holds potential energy, stored and waiting. The warmth from the radiator is kinetic energy, because heat is the motion of molecules. The honey holds potential energy in the chemical bonds of its sugars.
The first law says energy is never created or destroyed. A better sentence: "Your muscle cells capture energy stored in the bar's chemical bonds and transfer it into ATP, which they spend to contract." The bar supplies stored energy; nothing creates it.
At 20 °C: 3 + 4 + 5 = 12, and 12 ÷ 3 = 4 bubbles per minute. At 35 °C: 7 + 8 + 9 = 24, and 24 ÷ 3 = 8. At 70 °C: 0 + 0 + 0 = 0, and 0 ÷ 3 = 0. The shape rises from 4 to 8 and then crashes to 0, a rise to a peak and then a crash. The zero at 70 °C most likely means the heat denatured the enzyme and destroyed its active site.
Spending 4 ATP leaves 10 − 4 = 6 ATP, and each spent ATP becomes one ADP, so the cell now holds 4 ADP. Before it can spend those 4 again, the cell must use energy captured from food to add a phosphate back to each ADP, turning it into ATP. That is the ATP cycle: spend, then recharge.

Next up in this module: the Readings & Resources page, the lecture tutorial, the practice set, and the quiz — and next week cellular respiration, the enzyme-run mechanism that recharges ATP from glucose, takes the stage.

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