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Week 4 · Chapter

Chapter 4 — Cellular Energy & Protein Synthesis (overview)

Human Anatomy and Physiology I Free sample edition

The module's primary reading · ~40–50 minutes · Objective 2 (relate the chemistry of the body to its function — atoms and the three bond types, water's properties, the logarithmic pH scale with the blood's buffered range, and the four classes of organic compounds — and explain the cell's membrane, organelles, and transport (diffusion, osmosis and tonicity, active transport, and bulk transport), the overview of how a cell makes ATP, and how a gene is read into a protein), Objective 1 (use the language of the body correctly — the anatomical position, the directional-term pairs, the three body planes, and the body cavities and abdominal regions — distinguish anatomy from physiology, climb the levels of structural organization, list the functions and requirements of human life, and trace a homeostatic feedback loop through its receptor, control center, and effector, telling negative feedback from positive feedback) · Read it first this week; the lecture, the slides, the tutorial, the quiz, and the lab all build on it.

In plain language

Every cell in your body runs on ATP (a small molecule the cell spends like pocket change whenever it does work). Your cells remake that ATP from food through cellular respiration (a set of steps that burns glucose with oxygen and keeps the energy). The steps happen in a fixed order and in fixed places, and the last step, which needs oxygen, makes most of the ATP. Cells also build proteins (the working molecules that pump, carry, pull, and speed up reactions) by reading a gene (a stretch of DNA that holds the recipe for one protein). This week you follow both stories in order, from the place each step happens to the job its product does.

Why you already care about this

Picture two runs on the same track. In the first, you sprint one lap as hard as you can, and by the last curve your thighs burn. In the second, you jog 4 easy laps and talk the whole way. Both runs spend the same currency, ATP, but they make it in different ways, and the burn of the sprint is the sign of the faster, shortcut route.

Inside each working muscle cell, the first stage of making ATP, glycolysis, nets 2 ATP from one glucose. The full route with oxygen makes far more, about 30 to 32 ATP in current estimates. And while all that energy is being made, the same cell is spending some of it to build proteins: a gene of 6 codons, the one you will decode this week, builds a chain of 5 amino acids. Energy and building are the two halves of a living cell's daily work.

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

  • explain why ATP is spendable currency, not a battery, and write ATP → ADP + phosphate + energy;
  • put the three stages of cellular respiration in order and name the place each one happens;
  • say what oxygen does at the end of the electron transport chain and which stage makes the most ATP;
  • explain why a sprint leans on lactic acid and a jog does not;
  • transcribe a DNA template into mRNA and translate the mRNA into amino acids with a codon table, with every step shown;
  • explain how one changed codon can change one amino acid, one shape, and one job.

Carry this line with you: ATP is pocket change, not a savings account — spend it, then remake it.

Where we are

  • Already covered: Week 1 gave you the levels of organization and homeostasis. Week 2 gave you ATP and proteins built from amino acids. Week 3 gave you the organelles and the pump that spends ATP.
  • This week: how a cell remakes ATP in three ordered, located stages, and how it reads a gene into a protein.
  • How they connect: Week 3 said "mitochondria make ATP" and "ribosomes build proteins"; this week opens those two job descriptions and shows the steps inside them.
  • Where we're going next: Week 5, Tissues, groups cells built from these proteins into the four tissue types.

In Week 2 you met ATP as adenine, ribose, and three phosphate groups, a molecule that releases usable energy when one phosphate group is split off. You also met proteins as chains of amino acids whose shape decides their job. In Week 3 you toured the organelles: the nucleus holds the DNA, ribosomes build proteins, and mitochondria convert the energy in nutrients into ATP. You also watched the sodium-potassium pump spend one ATP to move 3 Na⁺ out and 2 K⁺ in. This chapter picks up exactly there. First you follow the energy; then you follow the code.

1. Spend the currency: ATP is not a battery

Think about the coins in your pocket on a busy day. You hand one over for a bus fare, another for a snack, and you get more from the cash machine when you run low. You never stack the coins in a drawer for next month. ATP works the same way inside a cell.

ATP as currency. ATP is the cell's spendable energy molecule. Cleaving its third phosphate releases energy the cell can use, and what is left is ADP, adenosine diphosphate. Written as a reaction: ATP → ADP + phosphate + energy. The energy in food then adds the phosphate back, so ADP is recharged into ATP. Your cells spend and remake ATP all the time.

Worked example — paying for the pump. In Week 3 the sodium-potassium pump moved 3 Na⁺ out and 2 K⁺ in for each ATP it spent. Follow two turns of the pump:

  1. Each turn spends one ATP: ATP → ADP + phosphate + energy.
  2. Two turns spend two ATP and leave two ADP and two phosphates.
  3. The ions moved: 3 × 2 = 6 Na⁺ out and 2 × 2 = 4 K⁺ in.
  4. Food energy later turns the two ADP back into two ATP.

In words: the pump pays one ATP per turn, and the cell's respiration refills the purse so the pump can keep paying.

Misconception check. Students often think ATP is a battery the body charges up and stores for days, because "energy molecule" sounds like "energy storage." It is not. ATP is spent within moments of being made and is remade from ADP over and over, the way coins pass through your hands. The energy that lasts is in food, which recharges ADP into ATP when the cell needs it.

Memory hook: spend a phosphate, get energy; add it back, get ATP.

2. Start in the cytoplasm: glycolysis

Imagine a long log that is too big for the stove. Before it can burn well, you split it into two halves. Glycolysis is that first split, and it happens before glucose ever reaches the mitochondrion.

Cellular respiration as a whole is written in one line: glucose + oxygen → carbon dioxide + water + ATP. It runs in three stages, always in the same order and always in the same places: glycolysis (cytoplasm) → citric acid cycle (mitochondrial matrix) → electron transport chain (inner mitochondrial membrane).

Glycolysis. Glycolysis is the first stage of cellular respiration. It happens in the cytoplasm, the fluid interior of the cell outside the nucleus. It splits one glucose, a single sugar, into two pyruvate. It uses two ATP and makes four, a net gain of two, and it needs no oxygen.

Worked example — the glycolysis bookkeeping. Follow one glucose through the first stage in your own muscle cell:

  1. Glucose in: 1 glucose.
  2. Products out: 1 glucose → 2 pyruvate.
  3. ATP spent to get started: 2 ATP used.
  4. ATP made: 4 ATP made.
  5. Net gain: 4 ATP made − 2 ATP used = a net 2 ATP.

In words: glycolysis is a small, fast payday. It needs no oxygen, so it can run whenever glucose is present, but two ATP per glucose is a modest return.

Misconception check. Students often credit glycolysis with "4 ATP," because 4 is the number made. That is the gross figure. The cell spent 2 to start the split, so the net gain is 2. A second wrong turn is to think glycolysis makes the most ATP; it nets only 2, and Section 4 shows that the electron transport chain makes the most by far.

Memory hook: one glucose, two pyruvate, net two.

3. Enter the matrix: the citric acid cycle

Picture the pyruvate halves moving from the open floor of a workshop into a back room with its own door. The back room is the inside of a mitochondrion, the organelle Week 3 called the energy transformer.

The citric acid cycle. The citric acid cycle, also called the Krebs cycle, is the second stage of cellular respiration. It runs in the mitochondrial matrix, the fluid-filled space inside the mitochondrion's inner membrane. There, each carbon of pyruvate leaves as CO₂. As the carbons leave, the electron carriers are loaded with electrons for the last stage.

Worked example — order and place. Place the first two stages in order:

  1. Glycolysis runs first, in the cytoplasm, and makes 2 pyruvate from 1 glucose.
  2. The pyruvate moves into the mitochondrion.
  3. The citric acid cycle runs second, in the mitochondrial matrix.
  4. Pyruvate's carbons leave as CO₂, and the electron carriers are loaded.

In words: in your cells, the cycle is where the fuel's carbons are stripped off as carbon dioxide and where the electrons are packed up for delivery.

Misconception check. Students often place the citric acid cycle in the cytoplasm, next to glycolysis, because the two stages run back to back. The cycle runs inside the mitochondrion, in the matrix. Say the place every time you say the stage: glycolysis, cytoplasm; cycle, matrix.

Memory hook: the cycle is inside the room, not on the workshop floor.

4. Finish on the inner membrane: the electron transport chain

Think of a bucket brigade passing water hand to hand toward a fire. Each person passes the bucket on, and the last person throws it. The electron transport chain works like that brigade: a series of proteins set in the inner mitochondrial membrane passes electrons along, and something must be waiting at the end to take them.

The electron transport chain and oxygen. The electron transport chain is the third stage of cellular respiration, on the inner mitochondrial membrane. The electrons the carriers delivered, oxygen, and hydrogen ions combine to form water. Oxygen is the final electron acceptor, the molecule at the end of the chain that takes the electrons. The chain makes the most ATP by far.

Worked example — reading the three stages as one chain. Read the full process in order, as you would say it on a quiz, with each stage's place and its key product:

  1. Glycolysis (cytoplasm): 1 glucose → 2 pyruvate, a net 2 ATP, no oxygen needed.
  2. Citric acid cycle (mitochondrial matrix): pyruvate's carbons leave as CO₂; the carriers are loaded.
  3. Electron transport chain (inner mitochondrial membrane): electrons, O₂, and H⁺ combine to form H₂O; the most ATP is made here.

In words: the overall line glucose + oxygen → carbon dioxide + water + ATP is three stages read in order, and each product appears at a stage you can name.

How many ATP does one glucose make in total? Honesty note: there is no single fixed number. The older theoretical estimate is about 36 ATP per glucose. Current estimates are nearer 30 to 32, because the yield depends on the proton cost of making ATP, on which electron carriers and shuttles are used, and on conditions in the cell. This course teaches the total in words and never asks you to give one exact figure.

Misconception check. Students often say oxygen is "broken down for energy," because we breathe it in and feel energized. Oxygen is not a fuel. It is the final electron acceptor: it takes the electrons at the end of the chain and, with hydrogen ions, becomes water.

Memory hook: oxygen catches the electrons; water is the catch.

5. Compare a sprint and a jog: aerobic versus anaerobic

Go back to the two runs on the track. In the sprint, oxygen falls short of what your working leg muscles need. In the easy jog, oxygen keeps up. The cell's answer to each situation is different, and you can feel the difference.

Aerobic and anaerobic. Aerobic means using oxygen: aerobic respiration runs all three stages and makes far more ATP per glucose. Anaerobic means without oxygen. When oxygen is short, pyruvate is converted to lactic acid so that glycolysis can keep running. That is the fast, low-yield backup behind a sprint's burn.

Worked example — two runs, one rule. Sort each run by asking one question: is oxygen keeping up?

  1. The sprint lap: oxygen falls short of demand, so pyruvate becomes lactic acid and glycolysis keeps going. Yield: the net 2 ATP per glucose from glycolysis. Feel: the burn.
  2. The easy jog: oxygen keeps up, so pyruvate enters the mitochondrion and all three stages run. Yield: far more ATP per glucose, about 30 to 32 in current estimates. Feel: steady.
  3. The trade: the anaerobic route is fast but low-yield; the aerobic route is slower to deliver but far richer.

In words: your sprint buys speed with yield, and your jog buys yield with time. The illustrative runs are made up for this chapter; the rule they show is the pack's.

Misconception check. Students often think lactic acid builds up whenever you exercise, even when oxygen is plentiful. The rule runs the other way: pyruvate becomes lactic acid when oxygen is short. On an easy jog where oxygen keeps up, pyruvate goes on into the mitochondrion instead.

Memory hook: short on oxygen, long on lactic acid.

Caveat: this chapter teaches the two routes as an overview. The step-by-step chemistry inside glycolysis, the cycle, and the chain is beyond this course.

6. Write the copy: transcription in the nucleus

Now switch from energy to building. Picture a rare cookbook that never leaves a locked library. You cannot carry the book to your kitchen, so you copy one recipe onto a card and take the card. The cookbook picture of a gene is a classroom model, a simplification you can hold in one hand, but it fits the first step well.

Gene and transcription. A gene is a functional segment of DNA that carries the information to build a protein. Transcription writes a complementary copy of that gene, an mRNA (messenger RNA), in the nucleus. The protein that does the writing is RNA polymerase. RNA uses uracil in place of thymine, so wherever the DNA template carries A, the mRNA carries U. An mRNA never carries a T.

The base pairs for transcription are fixed: DNA A → mRNA U, T → A, G → C, C → G.

Worked example — transcribing the pinned gene. The template strand of the course's gene, written 3′ to 5′, is TAC CGA GTA TTC CCA ATT. Pair each base, codon by codon:

  1. TAC: T → A, A → U, C → G, so the mRNA codon is AUG.
  2. CGA → GCU.
  3. GTA → CAU.
  4. TTC → AAG.
  5. CCA → GGU.
  6. ATT → UAA.

The mRNA, written 5′ to 3′, is AUG GCU CAU AAG GGU UAA. Check it: it carries U wherever the template carries A, and it carries no T. In words: the recipe card is a faithful copy, written in RNA's alphabet.

Misconception check. Students often write a T into an mRNA, because they copy the template's letters instead of pairing them. Pair each base, and remember that RNA has no thymine: A on the template becomes U in the mRNA. A T in an mRNA is always an error.

Memory hook: transcription writes; it writes in U, never T.

7. Read the code: translation at the ribosome

Take the recipe card to the kitchen. The cook reads it three letters at a time, and each three-letter word names one ingredient. That kitchen is the ribosome, the organelle Week 3 named as the cell's protein builder.

Translation and the codon. Translation reads the mRNA at the ribosome and builds a chain of amino acids. A codon is three mRNA bases for one amino acid. Each tRNA (transfer RNA) carries one amino acid, and its anticodon, three bases of its own, matches the codon on the mRNA. A polypeptide, a chain of amino acids, grows one amino acid at a time. AUG is the start codon for methionine, and UAA, UAG, and UGA are the stop codons. You read every codon from the supplied standard codon table, never from memory.

Worked example — translating the pinned gene. Read the mRNA AUG GCU CAU AAG GGU UAA with the standard table:

  1. Count the bases: 6 codons × 3 bases = 18 mRNA bases.
  2. AUG → Met (start).
  3. GCU → Ala.
  4. CAU → His.
  5. AAG → Lys.
  6. GGU → Gly.
  7. UAA → stop, so translation ends here.
  8. Count the amino acids: 6 codons − 1 stop codon = 5 amino acids.

Your protein is Met–Ala–His–Lys–Gly, then stop. In words: six codons gave five amino acids because the last codon is a stop, not an ingredient.

The pinned gene decoded: DNA template, mRNA, and amino acid for each of the six codons
Step Codon 1 Codon 2 Codon 3 Codon 4 Codon 5 Codon 6
DNA template (3′→5′) TAC CGA GTA TTC CCA ATT
mRNA (5′→3′) AUG GCU CAU AAG GGU UAA
Amino acid Met (start) Ala His Lys Gly stop

Misconception check. Students often swap the two steps, saying translation happens in the nucleus or transcription happens at the ribosome. Keep the verbs and the places together: transcription writes the mRNA in the nucleus; translation reads it at the ribosome. A second slip is reading one base per amino acid. A codon is always three bases, so 18 bases carry 6 codons, not 18.

Memory hook: transcription writes in the nucleus; translation reads at the ribosome.

8. Connect code to job: why physiology cares

Look around a body in motion on a hike: legs pushing uphill, a heart speeding up, sweat on the skin. Each of those jobs is done by proteins. Proteins are the enzymes that speed up reactions, the channels and pumps in every membrane, the contractile fibers that shorten muscle, and the collagen fibers of connective tissue.

Code to shape to job. A protein's amino-acid sequence sets its shape, and its shape sets its job. So a change in the code can change one amino acid, then one shape, then one job. That chain of three is why a physiology course cares about codons.

Worked example — one changed codon (illustrative). Suppose, for this example only, that the third template codon of the pinned gene read CCA instead of GTA:

  1. Transcribe the changed codon: CCA → GGU.
  2. Translate it: GGU → Gly, where the pinned gene had CAU → His.
  3. Read the new chain: Met–Ala–Gly–Lys–Gly.
  4. Compare: the count is still 6 − 1 = 5 amino acids, but the third one changed from His to Gly.

In words: one changed codon swapped one amino acid. If that swap changes the protein's shape, it can change the protein's job. This change is invented for the example; it does not describe any real gene.

Misconception check. Students often think a change in the DNA stays in the DNA and leaves the protein alone. It does not. Transcription copies the change into the mRNA, and translation reads it into the chain. The protein carries whatever the code says.

Limitation: this course stops at the overview. How genes are switched on and off, how mRNA is edited, and how changes in genes are classified belong to later courses.

Memory hook: code, then shape, then job.

Key terms

  • ADP — Adenosine diphosphate, the molecule left when ATP gives up its third phosphate group and releases energy; energy from food adds the phosphate back to remake ATP. (first used: 1. Spend the currency: ATP is not a battery)
  • Cellular respiration — The ordered series of stages by which a cell uses glucose and oxygen to make ATP, releasing carbon dioxide and water. (first used: 2. Start in the cytoplasm: glycolysis)
  • Cytoplasm — The fluid interior of a cell outside the nucleus, together with the organelles suspended in it; glycolysis happens here. (first used: 2. Start in the cytoplasm: glycolysis)
  • Glucose — A single sugar that enters cellular respiration as the fuel the cell breaks down to make ATP. (first used: 2. Start in the cytoplasm: glycolysis)
  • Glycolysis — The first stage of cellular respiration, in the cytoplasm, which splits one glucose into two pyruvate, uses two ATP and makes four for a net gain of two, and needs no oxygen. (first used: 2. Start in the cytoplasm: glycolysis)
  • Pyruvate — The molecule that glycolysis produces, two from each glucose; with oxygen it enters the mitochondrion, and when oxygen is short it is converted to lactic acid. (first used: 2. Start in the cytoplasm: glycolysis)
  • Citric acid cycle — The second stage of cellular respiration, also called the Krebs cycle, which runs in the mitochondrial matrix, releases the carbons of pyruvate as carbon dioxide, and loads the electron carriers. (first used: 3. Enter the matrix: the citric acid cycle)
  • Mitochondrial matrix — The fluid-filled space inside the inner membrane of a mitochondrion, where the citric acid cycle runs. (first used: 3. Enter the matrix: the citric acid cycle)
  • Electron transport chain — The third stage of cellular respiration, a series of proteins on the inner mitochondrial membrane that passes electrons along to oxygen and makes the most ATP of any stage. (first used: 4. Finish on the inner membrane: the electron transport chain)
  • Final electron acceptor — The molecule waiting at the end of the electron transport chain to take the electrons; in human cells it is oxygen, which combines with electrons and hydrogen ions to form water. (first used: 4. Finish on the inner membrane: the electron transport chain)
  • Aerobic — Using oxygen; aerobic respiration runs all three stages and makes far more ATP per glucose than glycolysis alone. (first used: 5. Compare a sprint and a jog: aerobic versus anaerobic)
  • Anaerobic — Without oxygen; anaerobic work relies on glycolysis and converts pyruvate to lactic acid, a fast but low-yield way to make ATP. (first used: 5. Compare a sprint and a jog: aerobic versus anaerobic)
  • Lactic acid — The product pyruvate is converted to when oxygen is short, a step that lets glycolysis keep running and making ATP. (first used: 5. Compare a sprint and a jog: aerobic versus anaerobic)
  • Gene — A functional segment of DNA that carries the information to build a protein. (first used: 6. Write the copy: transcription in the nucleus)
  • Transcription — The writing of a complementary mRNA copy of a gene, carried out in the nucleus by RNA polymerase. (first used: 6. Write the copy: transcription in the nucleus)
  • mRNA — Messenger RNA, the complementary copy of a gene that carries the code from the nucleus to a ribosome. (first used: 6. Write the copy: transcription in the nucleus)
  • RNA polymerase — The protein that reads a gene's DNA template in the nucleus and builds the matching mRNA during transcription. (first used: 6. Write the copy: transcription in the nucleus)
  • Uracil — The RNA base that takes the place of thymine, so adenine in a DNA template pairs with uracil in the mRNA. (first used: 6. Write the copy: transcription in the nucleus)
  • Translation — The reading of an mRNA at a ribosome, codon by codon, to build a chain of amino acids. (first used: 7. Read the code: translation at the ribosome)
  • Codon — A set of three mRNA bases that specifies one amino acid or a stop signal. (first used: 7. Read the code: translation at the ribosome)
  • tRNA — Transfer RNA, a molecule that carries one amino acid to the ribosome and matches its anticodon to the codon on the mRNA. (first used: 7. Read the code: translation at the ribosome)
  • Anticodon — The three bases on a tRNA that pair with a matching codon on the mRNA. (first used: 7. Read the code: translation at the ribosome)
  • Polypeptide — A chain of amino acids built during translation; one or more polypeptides fold into a working protein. (first used: 7. Read the code: translation at the ribosome)
  • Start codon — AUG, the codon for methionine that marks where translation begins. (first used: 7. Read the code: translation at the ribosome)
  • Stop codon — One of UAA, UAG, or UGA, which code for no amino acid and end translation. (first used: 7. Read the code: translation at the ribosome)

Summary

  • ATP is spendable currency: ATP → ADP + phosphate + energy, and food recharges it.
  • Respiration runs in order: glycolysis, then the citric acid cycle, then the electron transport chain.
  • Glycolysis, in the cytoplasm, turns 1 glucose into 2 pyruvate for a net 2 ATP, with no oxygen.
  • The citric acid cycle, also called the Krebs cycle, runs in the mitochondrial matrix and releases CO₂.
  • The electron transport chain, on the inner mitochondrial membrane, makes the most ATP.
  • Oxygen is the final electron acceptor; it becomes water, not fuel.
  • The total ATP per glucose is an estimate: about 36 in the older figure, nearer 30 to 32 now.
  • When oxygen is short, pyruvate becomes lactic acid so glycolysis can keep running.
  • Transcription writes an mRNA in the nucleus, with U in place of T.
  • Translation reads three bases per codon at the ribosome; AUG starts, and UAA, UAG, and UGA stop.
  • One changed codon can change one amino acid, one shape, and one job.

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.

  1. A practice card made up for this question shows a short DNA template, written 3′ to 5′: TAC TTC CGA ACT. Write the mRNA, translate it with the standard table, and count the mRNA bases and the amino acids.
  2. In an illustrative lab-notebook entry, a muscle cell runs glycolysis on 3 glucose. How many pyruvate does it make, and what is its net ATP from glycolysis?
  3. A classmate's study sheet writes an mRNA codon as GCT. What is wrong, and how would you fix it if the template base under the last letter is A?
  4. A workout app's pop-up says: "Your muscles break down oxygen for energy, and glycolysis is where most of your ATP comes from." Correct both halves.

Answers (worked reasoning — read after attempting)

  1. Pair each base: TAC → AUG, TTC → AAG, CGA → GCU, ACT → UGA. The mRNA is AUG AAG GCU UGA. Translate: AUG → Met (start), AAG → Lys, GCU → Ala, UGA → stop. The chain is Met–Lys–Ala. Count the bases: 4 codons × 3 bases = 12 mRNA bases. Count the amino acids: 4 codons − 1 stop codon = 3 amino acids. The stop codon ends the chain and adds no amino acid.
  2. Each glucose gives 2 pyruvate, so 3 × 2 = 6 pyruvate. Each glucose nets 2 ATP from glycolysis (4 made − 2 used), so 3 × 2 = 6 net ATP. Counting 4 per glucose would give the gross figure, not the net.
  3. An mRNA never carries a T, because RNA uses uracil in place of thymine. If the template base is A, it pairs with U in the mRNA, so the codon is GCU. GCU codes for alanine.
  4. Oxygen is not broken down for energy; it is the final electron acceptor at the end of the electron transport chain, where it combines with electrons and hydrogen ions to form water. And glycolysis does not make most of the ATP: it nets only 2 per glucose, while the electron transport chain makes the most by far.

Next up in this module: the lecture, the slides, the Readings & Resources page, the tutorial, the practice set, and the quiz; next week the four-tissue model shows where these proteins go to work.

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