Week 4 A&P Lab & Inquiry: Decode the Gene

Human Anatomy and Physiology I Free sample edition

Part 1 — The Big Picture

This week you learned that a gene is read into a protein in two ordered, located steps: transcription writes a complementary mRNA in the nucleus, and translation reads it at the ribosome, three bases per codon, until a stop codon ends the chain. You also learned that proteins are the enzymes, channels, pumps, and contractile fibers of every system, so a change in the code can change one amino acid, one shape, and one job. In this lab you decode a lab-built gene codon by codon with a supplied codon table, test what happens to the protein when one template codon changes, and watch the same two steps happen in a free gene-expression simulation. Then you check a chatbot's account of your lab and catch where it mislabels a molecule, swaps a job, miscounts, reorders the steps, reverses a strand's direction, or invents a number.

Time budget: Plan for about 120 minutes.

Part 2 — The Task

Guiding question: In what order, and in which parts of the cell, does a cell turn a gene into a protein, and what happens to the protein when one codon of the template changes?

Before you begin — hypothesis: Before you decode the changed genes, write your hypothesis in the if… then… because… form: if one codon of Gene A's template is changed, then the protein will change in a way you name (a different amino acid, a shorter chain, or no change), because of a reason about codons you can state. Then write the prediction your hypothesis makes for each of the two changed versions.

Workshop data: Gene A, a lab gene built for this activity from the standard codon table, plus your own observations in the free PhET Gene Expression Essentials simulation

Source: Gene A and its two changed versions were constructed for this lab from codons in the standard genetic code; they are not a real human gene. Your simulation observations are your own, recorded with the procedure in Part 3.

Rows: Gene A has 6 codons, shown as 6 rows of the decode table; the hypothesis table has 4 rows, the changed-gene table has 2 rows, and the simulation table has 4 rows
Codon table: Only 8 codons are needed: AUG, GCU, CAU, AAG, GGU, and the stops UAA, UAG, and UGA

Part 3 — Materials & Procedure

Tools and materials

A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet)
A document, notebook, or spreadsheet for your tables and answers

Ways of working

structure-identification-on-a-virtual-atlas
histology-on-a-virtual-microscope
at-home-physiology-measurement-and-data-table

Procedure

Read Gene A's template strand, written 3′ to 5′: TAC TTC GTA CGA CCA ACT. Before decoding anything, write your hypothesis and predictions in the first table, and define the variable so it can be measured: the number of amino acids in the chain, and which amino acid sits at each position. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: Your hypothesis and predictions are written before any changed gene is decoded.
In the decode table, transcribe Gene A one codon at a time with the base pairs A → U, T → A, G → C, C → G, writing the mRNA codon 5′ to 3′ beside each template codon. Check that no T appears in your mRNA. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: Six mRNA codons, each paired base by base from its template codon, with no T anywhere.
Translate each mRNA codon with the supplied codon table only: AUG = Met (start), GCU = Ala, CAU = His, AAG = Lys, GGU = Gly, and UAA, UAG, UGA = stop. Stop the chain at the first stop codon. Then count the mRNA bases (codons × 3) and the amino acids (codons − stop codons), writing each multiplication and subtraction in full. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: An amino-acid name or the word stop beside every codon, and two counts with their arithmetic shown.
Decode the two changed versions in the changed-gene table. Change X replaces Gene A's fourth template codon, CGA, with TTC. Change Y replaces Gene A's third template codon, GTA, with ATC. For each one, write the new mRNA codon, its amino acid or stop, the new chain, and the number of amino acids, then compare the result with your prediction. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: Two rows, each with the new codon, the new chain, a count, and a sentence on whether your prediction held.
Open the free PhET Gene Expression Essentials simulation in a web browser and choose the Expression screen. From the Biomolecule Toolbox, drag a Positive Transcription Factor and then RNA Polymerase onto the gene, watch an mRNA form, then drag a Ribosome onto the mRNA and watch a protein form. In the simulation table, record each step, the molecule that did it, and what you saw happen. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: Four rows recording the order of events in the simulation, with the molecule named for each one.
Answer the analysis questions, then run the AI-critique step in Part 6 or the equivalent route, and assemble everything listed in Part 7. If you like, check your counts in a spreadsheet by multiplying the codon count by three in a cell. Tool: A free virtual anatomy atlas or 3D anatomy viewer (Innerbody, GetBodySmart), a virtual microscope for histology (Histology Guide), free physiology simulations (PhET pH Scale, Membrane Channels, Neuron, Gene Expression Essentials), and a spreadsheet (Google Sheets or any free spreadsheet). Check: Every table is complete, the five questions are answered, and the critique or the marked-up flawed analysis is ready to submit.

Fallback route

When to use it: Use this route if you cannot open the PhET Gene Expression Essentials simulation, or if it will not run on your device.

Use the illustrative fallback observations below, written for this lab, as your simulation table, then complete every scaffold table, analysis question, and the critique step and submit the same items for equal credit.

This route earns the same credit as the primary route.

Illustrative fallback observations, written for this lab, that stand in for your own simulation run.

Fallback model data
Event in the simulation	Molecule that did it	What you saw happen
The gene is switched on	Positive Transcription Factor	It attached near the start of the gene
An mRNA is written from the gene	RNA Polymerase	It moved along the gene and a strand of mRNA grew out behind it
The mRNA is read	Ribosome	It attached to the mRNA and moved along it as a chain of amino acids grew
A protein is finished	Ribosome	The chain was released and folded into a shape that could be dragged to Your Protein Collection

Part 4 — The Scaffold

Name your hypothesis and your measured variable before you decode a changed gene, so the test is fair from the start.

Student scaffold table 1
Part of the test	Your answer
Hypothesis about changing one template codon (if… then… because…)
Prediction for Change X (fourth codon CGA becomes TTC)
Prediction for Change Y (third codon GTA becomes ATC)
The variable you measure, defined so it can be measured

Pair every template base to build the mRNA, then read each codon from the supplied table, one row at a time.

Student scaffold table 2
Codon	Template codon (3′ to 5′)	mRNA codon (5′ to 3′)	Amino acid or stop
1	TAC
2	TTC
3	GTA
4	CGA
5	CCA
6	ACT

Decode each changed version and count its chain, so you can test your prediction against what the code says.

Student scaffold table 3
Changed version	New template codon	New mRNA codon	Amino acid or stop	New chain	Number of amino acids, with arithmetic
Change X (codon 4)	TTC
Change Y (codon 3)	ATC

Record what you watched in the simulation in the order it happened, so you can match each event to its place in the cell.

Student scaffold table 4
Event in the simulation	Molecule that did it	What you saw happen
The gene is switched on
An mRNA is written from the gene
The mRNA is read
A protein is finished

Part 5 — Analysis Questions

Using your decode table, write out both counts for Gene A in full (mRNA bases and amino acids), then give the number of amino acids for Change X and for Change Y with the arithmetic shown. Why does a stop codon change the count but not add to the chain?
In the simulation, which molecule wrote the mRNA and which molecule read it? Put the events in the order you saw them, and name the part of a human cell where each step happens.
Change X kept the chain the same length, but Change Y shortened it. Explain each result codon by codon, then explain how a changed amino acid can change a protein's shape and so its job.
The sodium-potassium pump is a protein that spends ATP. Using your decode, explain how a changed codon in the pump's gene could change its job, then put the three stages of cellular respiration that remake its ATP in order with their places, and name the stage that makes the most.
Choose one of these two reflection options and answer it in 3–4 sentences: (a) Gene A is a lab-built gene read with a short codon table; name one thing this decode shows about real genes and one thing it leaves out; or (b) a simulation is a model, not a cell; name one thing the simulation showed you about transcription and translation and one thing it could not show.

Part 6 — AI-Critique Moment

Choose one equal-credit critique route. Route A: ask an approved AI tool to critique your completed work, then check its response against your own evidence. Route B is the no-AI equivalent printed below.

Approved tools: Claude, Gemini, ChatGPT, Grok, Microsoft Copilot.

Prompt to paste:

I've pasted my completed Decode the Gene tables above. They decode a lab gene called Gene A, whose DNA template strand, read 3' to 5', is TAC TTC GTA CGA CCA ACT, using only this standard codon table: AUG = methionine (Met, start), GCU = alanine (Ala), CAU = histidine (His), AAG = lysine (Lys), GGU = glycine (Gly), and UAA, UAG, UGA = stop. Please do six things, showing your reasoning. First, write the mRNA for Gene A with its 5' and 3' ends labeled. Second, translate it into amino acids and tell me how many bases the mRNA carries and how many amino acids the chain has. Third, say in which part of the cell transcription happens and in which part translation happens, and put the two steps in order. Fourth, say which molecule carries each amino acid to the ribosome and what its three matching bases are called. Fifth, say which stage of cellular respiration makes the most ATP and where in the mitochondrion it sits. Sixth, tell me how many ATP one glucose makes in total.

Test the response for these likely failures:

Chatbots sometimes call the three bases on the tRNA its codon, or place the electron transport chain in the mitochondrial matrix instead of on the inner membrane.
Chatbots sometimes say the ribosome writes the mRNA, or credit glycolysis with most of the cell's ATP.
Chatbots often count the stop codon as an amino acid, reporting 6 amino acids for Gene A, or count one amino acid per base.
Chatbots sometimes describe translation before transcription, or list the respiration stages out of order.
Chatbots sometimes label the mRNA 3' to 5' in the same direction as the template, or write a T into the mRNA where the template has an A.
Chatbots often state one exact, confident total of ATP per glucose, or cite a study that was never given.

Write 3–4 sentences: name at least one thing the chatbot got right, quote at least two of its errors, and correct each one with the codon table, the place in the cell, the order of the steps, the count, or the course's estimate that fixes it.

Equivalent route (no AI required)

No AI account is needed for this lab. Instead of the chatbot, critique this flawed analysis, printed here in full: "Gene A's mRNA starts with ATG, because the copy keeps the template's letters. I read the template 5′ to 3′ and wrote the mRNA 3′ to 5′. The ribosome writes the mRNA in the nucleus, and then RNA polymerase reads it. Translation happens first and transcription second. Gene A's mRNA carries 6 × 3 = 17 bases, and the three bases on each tRNA are its codon. Glycolysis makes most of the cell's ATP, and a study found that every glucose yields exactly 40 ATP." Mark every error you find, write the correction beside it using this week's rules, and add 3–4 sentences on which error you think a student is most likely to miss and why. This route assesses the same objectives as the chatbot critique, 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) and 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), takes comparable effort of about 20 minutes, is scored by the same row of the scoring criteria for the same credit, and its submission artifact is your marked-up flawed analysis with your corrections and sentences, uploaded with the rest of your report.

Part 7 — What to Submit

All four completed scaffold tables, with the simulation table filled from your own run or the illustrative fallback observations
Written answers to all five analysis questions
The chatbot critique report with its share link, or the equivalent route's marked-up flawed analysis

Deliverable:

A short A&P Lab & Inquiry report on decoding a gene: four completed tables (the parts of the test, the codon-by-codon decode of Gene A, the two changed versions, and the simulation observations), written answers to five analysis questions, and a critique of a chatbot's account of your lab, or, on the equivalent route, a marked-up correction of the printed flawed analysis. Submit in any accessible file type or as a link; a recorded response may be submitted as audio or video with a transcript, or as text. Choose a written, recorded, or visual form for your answers; every form is graded by the same scoring criteria.

Rubric

The rubric below shows how each submitted part is evaluated; bands are full, partial, or none.

Workshop evaluation criteria
Criterion	Full	Partial	None
Testable hypothesis and a measurable variable	A falsifiable if… then… because… hypothesis about changing one codon and a prediction for each changed version appear before either is decoded, and the measured variable is named.	A hypothesis appears but names no outcome or reason, or the predictions or the measured variable are missing.	No hypothesis, and no variable named.
Codon-by-codon decode of Gene A	All six template codons are paired into mRNA codons with no T, each codon is read from the supplied table, the chain stops at the stop codon, and both counts show their arithmetic.	Most codons are paired and read correctly, but one or two are wrong, a T appears, or a count is missing its arithmetic.	The decode is missing, invented, or read from memory instead of the table.
Changed genes and the simulation record	Both changed versions are decoded with the new chain and count, each compared with its prediction, and the simulation table names the molecule and the order for all four events.	One changed version is decoded correctly, or both are set up with one slip, or the simulation table is incomplete.	No changed version is decoded and no simulation record appears.
Analysis in words	The answers explain why a stop codon shortens a chain, name where transcription and translation happen and in what order, link a changed codon to a changed job, and give a limitation of the lab.	Two or three of those four pieces are present and accurate.	One or none of those pieces is present, or the places or the order are wrong throughout.
AI-critique or equivalent route	The chatbot report, or the marked-up flawed analysis on the equivalent route, quotes at least two specific errors and corrects each with the course's rule; both routes earn the same credit.	One error is quoted and corrected, or errors are named without a correction, on either route.	No critique on either route, or model output is pasted without any check.

Quality Gate

Every codon call comes from the supplied codon table, never from memory or a chatbot.
No mRNA codon contains a T, and every template base is paired before it is translated.
The hypothesis and predictions were written before either changed gene was decoded and have the if… then… because… form.
The measured variable is defined so it can be measured, and every count shows its multiplication or subtraction.
No ATP total, codon assignment, measurement, or study is invented anywhere in the submission.
The critique quotes the chatbot or the flawed analysis and corrects at least two errors with the course's rules.

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