Week 14 — Lab / Scientific Inquiry · "Transcribe & Translate a Gene"

Course: Introduction to Biology — General Biology I (BIOL 101) · Silver Oak University (fictional sample) · Prof. Castellano
Objective: Objective 7 — carry a DNA sequence through the central dogma to its protein; interpret molecular data · SLO A (interpret a defined process) · SLO B (connect a sequence to the protein it builds)
Worth 50 points · Labs group = 15% of the grade · Lab 14
Format: a free virtual simulation — you'll decode genes on an online transcribe-and-translate tool, build a data table, and then catch the AI's mistakes when it decodes a sequence.

This is the course's signature weekly component. Every instructional week has one lab. This week's uses a free virtual tool (no equipment, nothing to buy or download); the resource is a link to an external site, verified live.

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Part 1 — The Big Picture

This week you learned the central dogma: a gene's DNA is copied into a messenger RNA (transcription, in the nucleus), and that mRNA is read three letters at a time to build a protein (translation, in the cytoplasm). Now you'll do it — take real DNA sequences and decode them all the way to protein, the exact skill the quiz and assignment test.

The phenomenon: a cell reads a gene by (1) transcribing the template strand into mRNA — pairing A–U, T–A, G–C, C–G, and using uracil (U) in place of thymine (T) — and then (2) translating the mRNA in codons (three bases each), starting at AUG and stopping at a stop codon (UAA, UAG, or UGA). Your job is to run two genes through both steps and record the protein each one makes.

The tool (verified live): Learn.Genetics (University of Utah) — "Transcribe and Translate a Gene": 🔗 https://learn.genetics.utah.edu/content/basics/txtl/
It walks you through transcribing a DNA sequence into RNA (it even reminds you that A in DNA pairs with U in RNA) and then translating it to a protein, one codon at a time. (Tip: it works best in a browser other than Firefox.) You can also do this lab by hand using the codon table in Part 3 — the tool just makes it faster and self-checking.

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Part 2 — Your Scientific Question & Hypothesis

The question: For a given DNA template strand, what protein (chain of amino acids) does the gene encode — and does changing the DNA change the protein?

Before you start, write your hypothesis (an "if… then…" statement is perfect):

If I transcribe a DNA template strand into mRNA and then translate it, then I will get a specific chain of amino acids, and if I change one base in the DNA, then __ (the protein will / will not) change, because ____.

Write it down now — you'll compare it to your results at the end. (A "wrong" prediction is completely fine; the point is to test it.)

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Part 3 — Materials & Procedure

You need: a web browser and the free Learn.Genetics "Transcribe and Translate a Gene" tool above (or just this page + a pencil, using the codon table below).

Codon table for this lab (standard genetic code):

AUG = Methionine (Met), START · GCU = Alanine (Ala) · UAU = Tyrosine (Tyr) · UUU = Phenylalanine (Phe) · CCC = Proline (Pro) · UAA / UAG / UGA = STOP

Transcription pairing rules: DNA A → mRNA U · DNA T → mRNA A · DNA G → mRNA C · DNA C → mRNA G. (Remember: RNA uses U, never T.)

Procedure:
1. Gene 1 — transcribe. Take the DNA template strand 3′-TAC CGA ATA ACT-5′. Transcribe it base-by-base into mRNA (write it 5′→3′). Scan your mRNA for any T — there should be none.
2. Gene 1 — translate. Group your mRNA into codons of three, starting at the AUG. Look up each codon on the table and write the amino acid. Stop at the first stop codon. Record the protein.
3. Gene 2 — a single-base change. Now take the DNA template 3′-TAC AAA GGG ATC-5′ (this is a different gene). Transcribe it, then translate it, the same way. Record its protein.
4. Record everything in the data table (Part 4).
5. Hold these the same every time (your controlled variables): the same codon table, the same reading frame (always start at AUG), the same direction (template read 3′→5′, mRNA written 5′→3′).

Using the virtual tool? Enter each DNA sequence, let it build the RNA, then translate codon by codon, and copy the protein it reports into your table. Either way (tool or by hand), you should get the same answer — that's a built-in check.

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Part 4 — Data Table (fill this in)

Gene	DNA template (3′→5′)	mRNA (5′→3′)	Codons (in threes)	Protein (amino acids)
Gene 1	TAC CGA ATA ACT	_ _	_ / / _ /	____
Gene 2	TAC AAA GGG ATC	_ _	_ / / _ /	____

Show your transcription base-by-base for at least Gene 1 (so a grader can see your work).

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Part 5 — Identify Your Experiment's Parts

Answer in a sentence each:
1. Independent variable (what you changed between Gene 1 and Gene 2): __
2. Dependent variable (what you read out / measured): _
3. Two controlled variables (kept the same):
4. The "control" comparison (which gene is your reference, and why): ___

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Part 6 — Analysis Questions

1. Write out Gene 1's protein and Gene 2's protein. Are they the same or different?
2. In your mRNA, which DNA base became a U? Confirm there is no T anywhere in either mRNA — why not?
3. Gene 1's last codon and Gene 2's last codon are both stop codons but they're different (one is UGA, one is UAG). What do stop codons do, and why don't they add an amino acid?
4. Reading frame: what would happen to Gene 1's protein if you started reading one base after the AUG instead of at it? (You don't have to compute it — just explain the consequence.)
5. Connect it: the central dogma says DNA → RNA → protein. Point to exactly where in your procedure transcription happened and where translation happened, and name the cell location each one occurs in (in a real cell).

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Part 7 — AI-Critique Moment (required — this is the BYOAI step)

Now bring in your approved chatbot (Gemini, Claude, or ChatGPT) and be the scientist who checks its work.

1. Paste this to the chatbot: "Transcribe this DNA template strand to mRNA and then translate it to a protein: 3′-TAC CGA ATA ACT-5′. Show the mRNA and the chain of amino acids."
2. Check everything it says against your own work:
   - Did it use U instead of T in the mRNA — or did it slip a T into the RNA? (Chatbots do this constantly.)
   - Did it read the codons in frame (AUG GCU UAU UGA) — or did it shift the frame and get the wrong amino acids?
   - Did it correctly translate to Met–Ala–Tyr and treat UGA as a stop (not as an amino acid)?
   - If you ask it where translation happens, does it correctly say the cytoplasm — or wrongly say the nucleus?
3. Write 2–3 sentences reporting what the AI got right and at least one thing you had to correct or watch carefully. (If it happened to get everything right, say how you verified each step against your own decode — that's the skill.)

The habit all term: the tool drafts, you judge. A chatbot will confidently put a T in your RNA or shift your reading frame — catching it is the point.

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Part 8 — What to Submit

Submit a single document (or text entry) with: your hypothesis, your completed data table (both genes, mRNA + protein), your Part 5 variable labels, your Part 6 answers, and your Part 7 AI-critique paragraph. Due Sunday, Dec 6, 11:59 p.m. (50 points).

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Instructor answer key & model data — REMOVE BEFORE PUBLISHING TO STUDENTS

Every sequence and amino-acid call below is pre-computed and independently re-verified against the standard genetic code (Python check, 0 errors). Because the sequences are fixed, every student should get exactly these answers — this lab grades the decode, not a student-collected number.

Completed data table:

Gene	DNA template (3′→5′)	mRNA (5′→3′)	Codons	Protein
Gene 1	TAC CGA ATA ACT	AUG GCU UAU UGA	AUG / GCU / UAU / UGA	Met – Ala – Tyr (UGA = stop)
Gene 2	TAC AAA GGG ATC	AUG UUU CCC UAG	AUG / UUU / CCC / UAG	Met – Phe – Pro (UAG = stop)

• Gene 1 transcription (base by base): TAC→AUG, CGA→GCU, ATA→UAU, ACT→UGA. No T in the mRNA. ✓
• Gene 1 translation: AUG=Met (start), GCU=Ala, UAU=Tyr, UGA=STOP → Met–Ala–Tyr. ✓
• Gene 2 transcription (base by base): TAC→AUG, AAA→UUU, GGG→CCC, ATC→UAG. No T. ✓
• Gene 2 translation: AUG=Met (start), UUU=Phe, CCC=Pro, UAG=STOP → Met–Phe–Pro. ✓

Expected answers:
- Part 5: (1) IV = the DNA template sequence (Gene 1 vs. Gene 2 — the bases that differ). (2) DV = the protein produced (the chain of amino acids you read out). (3) two of: same codon table, same reading frame (start at AUG), same direction (template 3′→5′ → mRNA 5′→3′). (4) Gene 1 is the reference/baseline you compare Gene 2 against — changing the DNA is what lets you see whether the protein changes.
- Part 6: (1) Gene 1 = Met–Ala–Tyr; Gene 2 = Met–Phe–Pro — different proteins (different genes → different sequences). (2) Anywhere the DNA template had an A, the mRNA got a U; there is no T in mRNA because RNA uses uracil instead of thymine. (3) A stop codon (UAA/UAG/UGA) signals the ribosome to stop translating and release the finished protein; it codes for no amino acid, so it isn't added to the chain. (4) Starting one base after the AUG shifts the reading frame, so every codon downstream changes and the protein would be completely different (and would have no proper start) — garbage. (5) Transcription = writing the mRNA from the DNA template (Step 1/3) — happens in the nucleus; translation = reading the mRNA codons into amino acids (Step 2/3) — happens in the cytoplasm at the ribosome.
- Part 7 (AI-critique): full credit for a specific catch — most commonly the AI putting a T in the RNA, shifting the reading frame, or placing translation in the nucleus. Full credit also if the student verified each step against their own decode (mRNA AUG GCU UAU UGA → Met–Ala–Tyr, stop = UGA).

Grading rubric — 50 points

Criterion	Full	Partial	None
Hypothesis — a clear, testable "if…then…" prediction with a reason (8)	8	4–6	0–2
Data table — both genes transcribed (U not T) and translated to the correct proteins (15)	15	8–12	0–6
Variables (Part 5) — IV, DV, two constants, and the reference comparison all correct (12)	12	6–10	0–4
Analysis (Part 6) — proteins compared + U-not-T + stop codons + reading-frame + central-dogma locations (10)	10	5–8	0–4
AI-critique (Part 7) — names a specific thing checked/corrected in the AI's decode (5)	5	3	0–2

Quality gate (self-checked): quantitative gate: PASS — every sequence in this lab was re-derived by an independent Python check against the standard genetic code (0 errors): Gene 1 3′-TAC CGA ATA ACT-5′ → mRNA AUG GCU UAU UGA → Met–Ala–Tyr (UGA stop); Gene 2 3′-TAC AAA GGG ATC-5′ → mRNA AUG UUU CCC UAG → Met–Phe–Pro (UAG stop). Transcription uses U not T throughout; the genetic-code calls (AUG=Met, GCU=Ala, UAU=Tyr, UUU=Phe, CCC=Pro; UGA/UAG=STOP) match the standard codon table; the science (read in threes from AUG; translation in the cytoplasm) is correct. No student-collected number is asserted as "the" answer — the sequences are fixed, so the key grades the decode itself.