Week 4 — A&P Lab / Scientific Inquiry · "Decode the Gene"

Course: Anatomy & Physiology I (BIOL 2301 + BIOL 2101) · Silver Oak University (fictional sample) · Prof. Navarro
Objective: Objective 2 — protein synthesis (the central dogma); transcribe and translate a DNA strand · SLO A (relate the code to the protein it builds — structure → function) · SLO B (use the vocabulary of gene expression correctly)
Worth 50 points · Labs group = 15% of the grade · Lab 4
Format: a paper transcribe-and-translate decoding exercise with a codon chart, plus a short exploration of the free PhET Gene Expression Essentials simulation (no download, nothing to buy) — you'll decode a real DNA strand into a protein, then catch the AI's mistakes when it transcribes/translates a strand.

This is the course's signature weekly component. Every instructional week has one A&P lab. This week's is a hands-on decoding exercise (paper + a free simulation); other weeks use a virtual anatomy atlas, a virtual microscope, PhET physiology sims, and simple at-home measurements. All lab resources are links to external sites — nothing to buy or download.

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Part 1 — The Big Picture

This week you learned the central dogma: DNA → (transcription) → mRNA → (translation) → protein. Today you'll run that pathway by hand — take a short DNA strand, transcribe it into mRNA, then translate it into a chain of amino acids using a codon chart. You'll also watch a ribosome do the same thing in a free simulation. Decoding a gene yourself is the clearest way to feel why the order and the three-letter reading frame matter.

The scientific habit this builds: follow a rule-based process exactly, step by step, and check your output against a reference (the codon chart). In molecular physiology, a single misread base changes the protein — so precision is the whole game, and verifying is the skill.

Background (optional, ~10 min): OpenStax A&P §3.4, "Protein Synthesis" — keep it open as your reference for transcription, translation, and the codon: 🔗 https://openstax.org/books/anatomy-and-physiology-2e/pages/3-4-protein-synthesis

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Part 2 — Your Scientific Question & Hypothesis

Molecular labs still start like any inquiry — with a question and a prediction you'll test against evidence (here, the codon chart and the simulation).

The question: Given a DNA strand, can you reliably transcribe it to mRNA and translate it to the correct protein using only the standard genetic code — and can you catch an AI that gets it wrong?

Before you start, write your hypothesis / prediction:

I predict that I can correctly transcribe and translate the DNA strand below into its amino-acid sequence, and that when I ask an AI to do the same (or to decode one codon), it will make at least ______ error(s) I can catch and correct against the codon chart.

(There's no "right" number — you're predicting how reliable the AI will be at decoding, then checking.)

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Part 3 — Materials, the Codon Chart & Procedure

You need (all free, in a browser):
- The codon chart below (the standard genetic code — mRNA codons → amino acids).
- The PhET "Gene Expression Essentials" simulation (free, no download): 🔗 https://phet.colorado.edu/en/simulations/gene-expression-essentials
- Optional reference: OpenStax §3.4 (linked above).
- An approved chatbot (Gemini, Claude, or ChatGPT) for Part 6.

The two rules you'll use:
1. Transcription (DNA template → mRNA): pair each DNA base with its RNA partner — DNA A → U, T → A, C → G, G → C. (RNA uses U instead of T.)
2. Translation (mRNA → amino acids): read the mRNA in three-base codons, left to right, and look up each codon on the chart.

Standard genetic code — mRNA codon → amino acid (read your codon's first base down the left, etc.; STOP ends the chain):

Codon	AA	Codon	AA	Codon	AA	Codon	AA
UUU	Phe	UCU	Ser	UAU	Tyr	UGU	Cys
UUC	Phe	UCC	Ser	UAC	Tyr	UGC	Cys
UUA	Leu	UCA	Ser	UAA	STOP	UGA	STOP
UUG	Leu	UCG	Ser	UAG	STOP	UGG	Trp
CUU	Leu	CCU	Pro	CAU	His	CGU	Arg
CUC	Leu	CCC	Pro	CAC	His	CGC	Arg
CUA	Leu	CCA	Pro	CAA	Gln	CGA	Arg
CUG	Leu	CCG	Pro	CAG	Gln	CGG	Arg
AUU	Ile	ACU	Thr	AAU	Asn	AGU	Ser
AUC	Ile	ACC	Thr	AAC	Asn	AGC	Ser
AUA	Ile	ACA	Thr	AAA	Lys	AGA	Arg
AUG	Met (start)	ACG	Thr	AAG	Lys	AGG	Arg
GUU	Val	GCU	Ala	GAU	Asp	GGU	Gly
GUC	Val	GCC	Ala	GAC	Asp	GGC	Gly
GUA	Val	GCA	Ala	GAA	Glu	GGA	Gly
GUG	Val	GCG	Ala	GAG	Glu	GGG	Gly

Worked example (watch one done first): DNA template strand TAC–GTG–CCT–ACG–TTT–ATT
- Transcribe (A→U, T→A, C→G, G→C): mRNA = AUG–CAC–GGA–UGC–AAA–UAA
- Translate (chart, three at a time): AUG→Met (start), CAC→His, GGA→Gly, UGC→Cys, AAA→Lys, UAA→STOP
- Protein = Met–His–Gly–Cys–Lys (then stop). That's the whole pathway: DNA → mRNA → protein.

Procedure:
1. Decode the strand in the Part 4 table by hand: transcribe the DNA template to mRNA, then translate the mRNA codon-by-codon with the chart.
2. Open the PhET "Gene Expression Essentials" simulation. Build/express a gene and watch the ribosome assemble a protein from mRNA — confirm that transcription happens first, then translation. (You don't have to match the exact strand; the goal is to see the two steps in order.)
3. Note one thing the simulation made click that the paper exercise didn't (or vice versa).

No specific simulation access? Any free transcription/translation animation works (e.g., a Learn.Genetics-style "Build a Protein" activity). The skill — transcribe, translate, verify against the chart — is identical.

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Part 4 — Decoding Table (fill this in)

Your DNA template strand: TAC–CGA–GTA–TTC–CCA–ATT

Step	Codon 1	Codon 2	Codon 3	Codon 4	Codon 5	Codon 6
DNA template	TAC	CGA	GTA	TTC	CCA	ATT
mRNA (transcribe)	______	______	______	______	______	______
Amino acid (translate)	______	______	______	______	______	______

Then write the finished protein (amino-acid chain, stopping at STOP): ____

Reminder: transcribe with A→U, T→A, C→G, G→C; then read the mRNA three bases at a time on the chart. The first codon should come out as the "start," Met.

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Part 5 — Identify the Reasoning

Answer in a sentence each:
1. Your strand began with the DNA template TAC, which transcribes to AUG — the start codon. Why does almost every protein begin with Met, and what does the AUG codon signal?
2. Transcription vs. translation: in your decoding, which step happened in the nucleus and which happened at the ribosome, and what went in and out of each?
3. If you shifted your reading frame by one base (started reading at the 2nd base instead of the 1st), would you get the same protein? Explain what that tells you about why the three-letter codon and the reading frame matter. (This is the structure→function habit: the exact sequence determines the exact protein.)

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Part 6 — AI-Critique Moment (required — this is the BYOAI step)

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

1. Paste this to the chatbot: "Transcribe and translate this DNA template strand into a protein, showing the mRNA and each amino acid: TAC–CGA–GTA–TTC–CCA–ATT. Also, in cellular respiration, put the three stages in order and tell me which one makes the most ATP."
2. Check everything it says against the codon chart and this week's lecture:
   - Did it transcribe correctly (A→U, T→A, C→G, G→C) to get mRNA AUG–GCU–CAU–AAG–GGU–UAA?
   - Did it translate to Met–Ala–His–Lys–Gly–STOP? Chatbots sometimes mis-read a codon (e.g., calling GAA "Asp" when it's Glu) or shift the reading frame.
   - Did it keep transcription and translation straight (not swap them)?
   - Did it put respiration in the right order (glycolysis → Krebs → ETC) and credit the ETC with the most ATP — not glycolysis or the nucleus?
3. Write 2–3 sentences reporting what the AI got right and at least one error you caught and corrected (with the right codon or the right stage). If it happened to get everything right, say how you verified each codon against the chart — that's the skill.

The habit all term: the tool drafts, you judge. A chatbot will confidently mis-read a codon or scramble a pathway — catching it is the point, and in the clinic a confident wrong answer is still wrong.

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Part 7 — What to Submit

Submit a single document (or text entry) with: your hypothesis/prediction, your completed Part 4 decoding table (mRNA + amino acids + the finished protein), your Part 5 answers, and your Part 6 AI-critique paragraph. Due Sunday, Sep 27, 11:59 p.m. (50 points).

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Instructor answer key — REMOVE BEFORE PUBLISHING TO STUDENTS

Every codon below was decoded with the standard genetic code and independently re-verified with a Python script against a standard codon table (transcription A→U/T→A/C→G/G→C, then chart lookup). Both the worked example and the student strand check out exactly.

Part 4 — verified decoding table (student strand TAC–CGA–GTA–TTC–CCA–ATT):

Step	Codon 1	Codon 2	Codon 3	Codon 4	Codon 5	Codon 6
DNA template	TAC	CGA	GTA	TTC	CCA	ATT
mRNA	AUG	GCU	CAU	AAG	GGU	UAA
Amino acid	Met (start)	Ala	His	Lys	Gly	STOP

Finished protein = Met–Ala–His–Lys–Gly (translation stops at UAA). (Worked-example strand for reference: TAC–GTG–CCT–ACG–TTT–ATT → mRNA AUG–CAC–GGA–UGC–AAA–UAA → Met–His–Gly–Cys–Lys–STOP.)

• Part 5: (1) AUG is the start codon and codes for methionine (Met), so the ribosome begins virtually every protein with Met (it's the universal "begin here" signal). (2) Transcription happened in the nucleus (DNA in → mRNA out); translation happened at the ribosome in the cytoplasm (mRNA in → protein out). (3) No — shifting the reading frame by one base regroups every codon and yields a completely different (usually nonsense) amino-acid sequence; this shows the code is read in non-overlapping three-base codons from a fixed start, so the exact sequence and reading frame determine the exact protein (structure → function at the molecular level).
• Part 6 (AI-critique): full credit for a specific catch — most commonly the AI mis-reading a codon (e.g., GAA→"Asp" when GAA is Glu; GAU is Asp), shifting the reading frame, swapping transcription and translation, or mis-ordering respiration / crediting glycolysis with the most ATP (it's the ETC). Full credit also if the student verified each codon against the chart and confirmed the AI was right. The verified target: mRNA AUG–GCU–CAU–AAG–GGU–UAA → Met–Ala–His–Lys–Gly–STOP; respiration order glycolysis → Krebs → ETC, most ATP in the ETC.

Grading rubric — 50 points

Criterion	Full	Partial	None
Hypothesis / prediction — a clear prediction about both the decoding and the AI's reliability (6)	6	3–4	0–2
Decoding table (Part 4) — mRNA transcribed correctly + amino acids translated correctly + finished protein right (18)	18	9–15	0–7
Reasoning (Part 5) — AUG/start logic, transcription-vs-translation (nucleus/ribosome, in/out), and a sound reading-frame/structure→function point (14)	14	7–11	0–5
AI-critique (Part 6) — names a specific decoding or respiration error caught and corrected with the right codon/stage (8)	8	4–6	0–3
Vocabulary — uses transcription, translation, codon, mRNA, amino acid correctly throughout (4)	4	2	0–1

Quality gate (self-checked): Accuracy gate — process ordering: verified. The central dogma order (DNA → transcription → mRNA → translation → protein) and the cellular-respiration order (glycolysis → Krebs → ETC, most ATP in the ETC, O₂ = final electron acceptor) are stated correctly throughout, and transcription (DNA→mRNA, nucleus) vs. translation (mRNA→protein, ribosome) are kept distinct. Quantitative / decoding gate: PASS — every codon in the worked example and the student strand was transcribed and translated with the standard genetic code and re-verified by a Python script (/tmp/codon_chart.py: 64-codon chart confirmed, 3 STOP codons confirmed, student strand → Met–Ala–His–Lys–Gly–STOP, worked example → Met–His–Gly–Cys–Lys–STOP, both 0-error). The embedded codon chart was spot-checked (10 cells) against the standard table. Anatomy-accuracy gate: PASS (no anatomical structures to mislabel this week; the molecular facts and locations are verified). All lab resource links verified live; no license claims.

Provenance: clean-room build from Objective 2 + the standard A&P body of knowledge; codon decoding independently Python-verified; fictional instructor/institution.