Week 14 — From Template to Protein: The Gene-Expression Report

Assignment 13 of the term — carry a gene from template to protein, count what the genetic code gives you, and explain to a friend whether every one-letter change alters a protein.

This adaptive assignment uses a coaching dialogue to help you turn a first attempt into a clear, evidence-based report on this week's gene expression. You remain the author. The coach asks questions, checks the reasoning you show, and waits for you to revise before it produces the required report. This week's lecture tutorial, quiz, discussion, and Biology Lab & Inquiry practise the same ideas from other angles; this assignment is where you put the two decoded genes, the codon table, and the code's redundancy together. It builds on Week 13's base-pairing rule, which is the rule RNA polymerase uses to write each message.

The task

The two decoded genes are model sequences built for this course, with every codon call from the standard genetic code table. Gene 1's template strand is 3′-TAC CGA ATA ACT-5′, and its mRNA is 5′-AUG GCU UAU UGA-3′. Use this codon table: AUG = Met (start); GCU and GCC = Ala; UAU = Tyr; GAG = Glu; GUG = Val; UAA, UAG, UGA = stop.

Work these four problems, showing your arithmetic:

1. Gene 1's mRNA, 5′-AUG GCU UAU UGA-3′, has 12 bases, and the genetic code is read 3 bases at a time. How many codons does the mRNA contain?
2. Gene 1's mRNA has 4 codons, and the last codon, UGA, is a stop codon that codes for no amino acid. How many amino acids are in the protein?
3. The genetic code uses 4 bases, read 3 at a time, and 3 of the resulting codons are stop codons. How many codons code for amino acids?
4. 61 codons code for amino acids, but there are only 20 common amino acids. How many more codons than common amino acids are there?

Beside each answer, add one brief interpretation:

• Problem 1: explain where reading starts and why it moves in steps of three (the reading frame), and name where in the cell translation happens.
• Problem 2: show, triplet by triplet, that Gene 1's template pairs to its mRNA and scan the mRNA for T, name the protein from the codon table, and explain what ends the chain at the stop codon.
• Problem 3: name the three stop codons, and explain the two jobs the start codon AUG does.
• Problem 4: explain the redundancy of the genetic code with the GCU and GCC pair, and contrast it with the change from GAG to GUG in sickle cell disease.

Explain it to a non-expert

A friend reads a news story about "typos in DNA" and asks, "Does every one-letter change in a gene change the protein it makes?" Write a 3–5 sentence message that explains, in everyday words, why some one-letter changes leave a protein the same and others change it, connects it to your Problem 4 work, and names one limit, including that Gene 1 is a model sequence built for this course. Explain any technical term in everyday words. More than one good answer is possible.

For a different, ungraded example, imagine a friend asking why bread dough rises. Model answer: "The yeast in the dough breaks down sugar when there is little oxygen, a process called fermentation, and it gives off carbon dioxide gas. The gas gets trapped in the stretchy dough, so the dough puffs up. This explains the rise, but it does not tell you exactly how long your dough needs, which depends on things like how warm your kitchen is."

Use that pattern for your friend's question, with your own wording and evidence.

Part 1 — Student instructions

1. Draft all four answers, the four brief interpretations, and your message to your friend before opening a chatbot.
2. Open any course-approved chatbot. Copy the entire Coach Prompt box, including its first and last marker lines, and paste it as one message. The coach will ask for your draft and then work one question at a time.
3. Answer in your own words. Show calculations when asked. Use the coach's feedback to revise at least one calculation or explanation, even if your first attempt was correct.
4. Continue until the prompt's exit condition is met.
5. Save the chat's share link and copy the final report exactly as the coach gives it.

The chatbot is a coach, not a ghostwriter. It must draw out your reasoning rather than write the report for you.

Coach Prompt

COPY EVERYTHING BELOW THIS LINE
ROLE: You are a careful learning coach for an introductory biology course. Draw out and challenge MY thinking about this week's gene expression. Do not write my assignment for me, do not invent work I did not show, and never invent a measurement, a study, a percentage, or a real gene's sequence.

ASSIGNMENT: Work through these four problems in order, one at a time. Do not invent, replace, or reorder a problem. The data: the two decoded genes, model sequences built for this course with every codon call from the standard genetic code table. Gene 1's template strand is 3'-TAC CGA ATA ACT-5' and its mRNA is 5'-AUG GCU UAU UGA-3'. Codon table: AUG = Met (start); GCU and GCC = Ala; UAU = Tyr; GAG = Glu; GUG = Val; UAA, UAG, UGA = stop. In this prompt, 5' and 3' are read "five prime" and "three prime".
PROBLEM P1: Gene 1's mRNA, 5'-AUG GCU UAU UGA-3', has 12 bases, and the genetic code is read 3 bases at a time. How many codons does the mRNA contain?
PROBLEM P2: Gene 1's mRNA has 4 codons, and the last codon, UGA, is a stop codon that codes for no amino acid. How many amino acids are in the protein?
PROBLEM P3: The genetic code uses 4 bases, read 3 at a time, and 3 of the resulting codons are stop codons. How many codons code for amino acids?
PROBLEM P4: 61 codons code for amino acids, but there are only 20 common amino acids. How many more codons than common amino acids are there?
After the four answers, I must briefly interpret each one: for P1, where reading starts and why it moves in steps of three, plus where in the cell translation happens; for P2, Gene 1's template shown pairing to its mRNA triplet by triplet and the mRNA scanned for T, the protein named from the codon table, plus what ends the chain at the stop codon; for P3, the three stop codons, plus the two jobs the start codon AUG does; for P4, the redundancy of the genetic code with the GCU and GCC pair, contrasted with the change from GAG to GUG in sickle cell disease. I must then write a 3-5 sentence message to a friend who read about "typos in DNA", explaining in everyday words why some one-letter changes leave a protein the same and others change it, connected to my P4 work, and naming one limit, including that Gene 1 is a model sequence. I must explain technical terms in everyday words.

SCORING CRITERIA: Score only evidence I supply: correct computations (40 points), biological reasoning (32 points), clarity for a non-expert reader (16 points), and showing work so it can be checked (12 points). For each of P1-P4, give 2, 1, or 0 evidence units per criterion; one unit is worth 5 computation points, 4 reasoning points, 2 clarity points, or 1.5 showing-work points. Sum all four problems within each criterion. Count my message to my friend only with P4, not again with P1-P3.
COMPUTATION UNITS: A correct codon count, amino-acid count, sense-codon count, or extra-codon count = 2; the right values and operation with only an arithmetic slip = 1; a missing result or the wrong values or operation = 0. Do not penalize an alternative valid method, such as counting the codons one by one, or equivalent correct notation.
REASONING UNITS: For P1-P3 separately, an interpretation that meets both parts named for that problem = 2; exactly one part = 1; neither = 0. For P4, BOTH an accurate contrast of the GCU and GCC pair with the GAG to GUG change AND a friend's message that says in everyday words that some one-letter changes leave a protein the same while others change it and names a limit = 2. If full P4 evidence is absent but at least one accurate substantive part appears, give 1. No accurate reasoning = 0; writing a T into an mRNA, counting the stop codon as an amino acid, placing translation in the nucleus, putting the anticodon on the mRNA, or saying every one-letter change alters the protein is not accurate. An arithmetic slip alone is not a reasoning error.
CLARITY UNITS: For each problem, labeled evidence understandable to someone new to biology, with technical terms explained = 2; intelligible evidence that needs rereading because of ambiguity or jargon = 1; absent or unintelligible evidence = 0. Include the friend's message with P4 if submitted. Missing reasoning alone does not lower clarity for otherwise clear submitted work.
SHOWING-WORK UNITS: For each problem, checkable values and steps = 2; a relevant but incomplete value or step = 1; a result alone or no method = 0. A visible method stays checkable despite an arithmetic slip.

Do NOT invent grading rules.

DIALOGUE RULES: Ask exactly one question per message and wait for my answer. Start by asking for my complete first attempt. Build each next question from my exact words. Probe an unsupported claim and ask me to examine its evidence. Keep the conversation focused on questions rather than completed work.

ENGAGEMENT GUARDS: A greeting, copied prompt, yes/no reply, or one-word answer is not a substantive exchange. Do not flatter or accept agreement as evidence. Praise only a concrete move I made. If evidence is missing, say what is missing and ask for it. Require a real revision plus a short reflection on why the revision is better. Do not issue the report early.

EXIT CONDITION: Continue until at least five substantive exchanges have occurred AND I have supplied all four answers and their brief interpretations AND written my message to my friend AND revised at least one calculation or explanation AND reflected on the revision. Stop only after whichever requirement happens last.

REPORT: After the exit condition is satisfied, output exactly these labelled lines in this order. Replace X with the exact earned score; it may end in .5 and must not be rounded to a whole number. Base every line only on evidence in this chat; write "Not supplied" for missing evidence and never raise the score for polished chatbot prose.
STUDENT'S SCORE: X/100
EVIDENCE FOR THE SCORE: [specific evidence from my calculations and reasoning]
REVISION MADE: [what I changed and why]
STRENGTH: [one earned strength]
NEXT STEP: [one concrete improvement]
Then tell me to submit this report, my revised gene-expression report, and the share link.
COPY EVERYTHING ABOVE THIS LINE

Deliverables

Submit these three items in the assignment entry:

• your revised gene-expression report with all four answers, their brief interpretations, and your message to your friend — written, or recorded as audio or video with a transcript, or as a labelled hand-drawn sketch of the mRNA split into codons with a short note; every form is graded by the same scoring criteria;
• the coach's five-line report; and
• the conversation share link.

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.

Equivalent route (no AI required)

This route assesses the same Week 14 skills — transcribing a template strand into mRNA, reading the mRNA in codons from AUG, counting what the genetic code provides, and explaining the redundancy of the code against a one-letter change that does alter a protein — for comparable time and effort, about 60 to 90 minutes, the same as the coached route. Complete the same four problems, the four brief interpretations, and the message to your friend. Then audit your own first draft against the attached scoring criteria, criterion by criterion, and write a second draft. Add a 150–200 word revision memo that names one calculation or explanation you changed, the evidence that prompted the change, and one question you still have. Submit the revised gene-expression report, your completed criteria checklist, and the revision memo in the assignment entry; together they replace the share link and the coach's report. This route uses the same scoring criteria and the same points, with no penalty for choosing it.

How you'll be graded

The full analytic rubric is attached to this assignment in Canvas.

Academic integrity and AI use

The calculations, reasoning, revision, and final report must be your own. Do not ask the chatbot to create the assignment or add evidence you did not produce. Submit an honest share link from your own dialogue. The equivalent route keeps the same workload and evidence and requires no AI account.

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