Cloning and purification workflow
This page has four parts, in the order you use them. Part 1 is what you need to know. Part 2 says what to do, in plain English. Part 3 shows the work done once on a case that is not yours. Part 4 is your own work and where to turn it in.
Open your materials, follow the steps, then turn in your work.
Carry out a cloning and protein-purification workflow and record results at each step.
Optional: listen or watch a unit review▸
Part 1 of 4 · Background and definitions▸
💡 Big idea: Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, , or remains limited by method resolution and sample quality.
- • Heat shock or electroporation opens pores in bacterial membranes so can enter.
- • selection kills non-transformed cells; only cells carrying the resistance gene survive.
- • Selection is not instant: a surviving cell has to divide into a visible , which takes 16 to 24 hours, so a plate read too early looks like a failed .
- • The first step separates soluble from cell debris before .
Life-saving biotechnology raises hard questions about access because the same product must pass separate gates of price, patents, and regulation, so who controls those gates decides who the science actually helps.
Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, , or remains limited by method resolution and sample quality.
Driving question: You built recombinant on paper on Dec 1, but how do you force millions of bacteria to actually swallow that , and how do you find the few that did?
What you already know: Life-saving biotechnology raises hard questions about access because the same product must pass separate gates of price, patents, and regulation, so who controls those gates decides who the science actually helps.
New idea: Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, , or remains limited by method resolution and sample quality.
Visual or model: No figure is attached to this lesson. The readings, the worked example and E1 to E3 carry the evidence.
- Observe or measure the relevant feature in today's lesson.
- Organize the observation with a stable evidence ID.
- Apply this rule: Define variables, controls, sampling, units, and the analysis plan before interpreting a result; analysis cannot repair biased or inconsistent measurement.
- Choose the option the evidence supports and state the limit of the conclusion.
Real biomedical example: Today the medical interventions team uses Cloning and to make a bounded evidence decision. A band, selected , or fluorescent alone does not prove identity, , correct sequence, biological activity, or clinical suitability.
What the evidence supports: E1 to E3 support the daily take-home when the response meets the stated success criteria.
What it cannot prove: The package does not support claims beyond this lesson's or any real patient diagnosis.
- • : A small, circular piece of that lives apart from a bacterium's main and is used in the lab to carry a chosen gene into a cell.
- • : An that joins two pieces of together by sealing the gap in their backbone, vital in genetic engineering.
- • : The process by which a bacterial cell takes up foreign , such as a , from its surroundings and begins using those new genes.
- • expression: The process of turning a gene on so its instructions are used to make RNA and , deciding when and where a gene is active.
Use it now: Choose one decision option. Cite E1 and E3, then explain how the rule connects the evidence to your choice. This is thinking practice for the one turn-in named under Turn in, not a second submission.
Go further, optional: The source links below are optional enrichment. Every fact required for today's local evidence decision appears in this lesson package.
National Center for Biotechnology Information is the source this lesson's claim is checked against:
Limit: A band, selected , or fluorescent alone does not prove identity, , correct sequence, biological activity, or clinical suitability.
Define variables, controls, sampling, units, and the analysis plan before interpreting a result; analysis cannot repair biased or inconsistent measurement.
Limit: A well-organized classroom study can still be limited by , measurement quality, confounding, and the population represented.
You can carry out , selection, and steps.
Limit: E3 defines the classroom product or success criterion. It is not independent scientific evidence and cannot justify a clinical or causal claim.
Today's decision · Simulated classroom evidence scenario
Your role: medical interventions team member
Decision: Your team must decide what the evidence from today's lesson supports before submitting the lab report named on today's page.
- • Run first, then plate on so only cells that took the survive to be grown and purified.
- • Plate the cells on plain agar and keep every that grows, since almost all of the bacteria took the .
- • Compare counts on plates with and without first, because we cannot yet tell what of cells transformed.
Response: State one choice, cite at least two evidence IDs, explain the rule that connects them, and add one limitation. Use it inside the one turn-in named under Turn in; it is not a separate submission.
Claim ceiling: Today's evidence supports a classroom claim about today's lesson. It cannot prove causation, diagnose a real patient, or justify action outside this room.
Reason for review: Your team must decide what the evidence from today's lesson supports before submitting the lab report named on today's page.
Context: Today the medical interventions team uses Cloning and to make a bounded evidence decision. A band, selected , or fluorescent alone does not prove identity, , correct sequence, biological activity, or clinical suitability.
- • T1: Read the protocol in the PLTW course shell and gather your materials.
- • T2: Run the in the simulation on this page: introduce the recombinant into host cells.
- • T3: Record the selection counts from the practice plates on this page, which were incubated overnight, and say what the no- control shows.
- • T4: Run the simulated step and note where the target appears.
- • T5: Record yield and one quality observation in your .
- • T6: Submit your cloning and results.
- • E1: National Center for Biotechnology Information is the source this lesson's claim is checked against:
- • E2: Define variables, controls, sampling, units, and the analysis plan before interpreting a result; analysis cannot repair biased or inconsistent measurement.
- • E3: You can carry out , selection, and steps.
Measurements: Use only the measurements, units, graph, or counts supplied in today's task. No additional patient measurement is implied.
Uncertainty: This is a composite classroom scenario. Missing history, measurements, or confirmation tests remain unknown and limit the conclusion.
Students often think a polished answer about cloning and is trustworthy even when its evidence source, comparison, or limitation is missing. The trap: Presentation quality cannot raise the evidence level. A band, selected , or fluorescent alone does not prove identity, , correct sequence, biological activity, or clinical suitability.
- CER:
- Claim, Evidence, Reasoning: make a claim, back it with evidence, explain your reasoning.
- SOP:
- Standard Operating Procedure, the exact steps to follow (especially in a lab).
- Tracker:
- Your PLTW progress log where you record completed evidence.
- myPLTW:
- The PLTW course site where you do the online activities. Find it in Clever with your Microsoft sign-in, right next to Schoology.
Tap the speaker to hear a term. Add two of these to your notebook glossary with a definition and an example in your own words.
Pick just 2 or 3 words from today and make them yours: write what each one means in your own words, name the context clue or evidence that helped, then give one example from what you actually did in Cloning and purification workflow. Try your own words first; the glossary is there if you get stuck. This is voluntary and counts as extra credit, so keep it short.
Saved on this device. Show Mr. Mendoza or add these to your notebook glossary to claim the extra credit.
Part 2 of 4 · Directions in plain English▸
2.1 Open your materials
Use the materials named in the first step below. Open lesson resources.
Practice transformation plates (made-up counts for practice, not from this class)
Four practice plates, incubated overnight (16 to 24 hours) at 37 degrees C
| Plate | Cells spread on it | What the plate contains | What grew |
|---|---|---|---|
| P1 | Cells given the recombinant plasmid | LB with ampicillin | 46 colonies |
| P2 | Cells given no plasmid (control) | LB with ampicillin | 0 colonies |
| P3 | Cells given no plasmid | LB, no antibiotic | A lawn, too many to count |
| P4 | Cells given the recombinant plasmid | LB with ampicillin and arabinose | 44 colonies, glowing green under UV |
- Use these counts for the selection row of your workflow data table.
2.2 Start the work
Read the workflow protocol in the PLTW course shell and gather your materials.
Show all 6 required steps
- Read the workflow protocol in the PLTW course shell and gather your materials.
- Run the transformation in the simulation on this page: introduce the recombinant plasmid into host cells.
- Record the selection counts from the practice plates on this page, which were incubated overnight, and say what the no-plasmid control shows.
- Run the simulated purification step and note where the target protein appears.
- Record yield and one quality observation in your workflow data table.
- Submit your cloning and purification workflow results.
Lost your place? Reopen today's Cloning and purification workflow record. Find the last completed evidence ID, check it against the claim ceiling, and continue with the first unfinished step rather than restarting the whole task.
- 0-10Review protocol; gather materials; confirm lab setup
- 10-30 step: introduce the into host cells in the simulation, following the protocol
- 30-45Selection: read the practice plate counts on this page, incubated 16 to 24 hours, and compare them with the no- control
- 45-60 step: run first ; identify with target
- 60-72Record yield and quality observation in
- 72-80Clean up; submit in Schoology
- • No cultures were ordered, so the runs in the simulation on this page and the step after it is modelled, the way step 4 says.
- • You will introduce recombinant into host bacteria in the simulation, read selection results, and model a first step.
- • Colonies need 16 to 24 hours of to appear, which is why the practice selection counts on this page come from plates incubated overnight at 37 degrees C.
- • Work carefully: at any step ruins results.
- • Lab SOPs and data recording are both scored domains on your end-of-course WebXam for this class.
PLTW connection and today's work
Open Activity 4.1.2 Protein Factories in myPLTW and follow the transformation and selection protocol to model the cloning and purification workflow.
Today's stopping point: The debate should be complete; workflow data table due today.
PLTW activity titles identify the course connection. If your account will not open, use the posted materials for today and tell Mr. Mendoza. Do not mark an online activity complete unless you completed it.
Use the turn-in directions in Part 4 of this page. Do not create a second submission unless your teacher asks for one.
Show another explanation or a smaller first step
Need help? Choose a starting point
Finish the assigned lab safely before starting extra practice.
Part 3 of 4 · Worked example▸
This is a parallel case, not your own. Read it for the order of the work, then do your own in Part 4.
Workflow record:
- Transformation: introduced the recombinant plasmid into host cells using heat shock, which opens pores in the membrane so plasmid DNA can enter.
- Selection: plated cells on antibiotic medium, labelled both plates and incubated them. A surviving cell still has to divide into a visible colony, so I read the plates after their 16 to 24 hours, not at the end of the block: 38 colonies on the plate with my recombinant cells and 0 on the no-plasmid control, which tells me selection worked.
- Purification: ran the first separation step, which split soluble protein away from cell debris. The target protein appeared in the soluble fraction.
- Yield and quality: estimated yield was moderate; one quality note is that the no-plasmid control showed no growth, so the colonies I counted really are transformed cells and not contamination.
| Step | Action | Result |
|---|---|---|
| Transformation | Heat shock plasmid into cells | Cells took up plasmid |
| Selection | Plate on antibiotic, incubate 16 to 24 h | 38 colonies; control 0 |
| Purification | First separation | Target in soluble fraction |
| Quality note | Check control plate | No growth, so no contamination |
This model shows the level of evidence and organization needed to complete: Completes the workflow lab: a data table recording transformation, selection counts, fraction data, yield, and one quality observation across the cloning-to-purification pipeline.
- State the question and method.
- Present the observations and data with units.
- Explain the result, limitations, and next investigation.
Keep the structure. Replace the question, facts, measurements, and evidence. Then recheck units, vocabulary, and whether the conclusion goes beyond the evidence.
Also due today: Submit your cloning and purification workflow data table in Schoology before the end of block.
A research team lays out its question, variables, controls, sampling plan, measurement record, and analysis before deciding what the data support.
- Which variable is changed or compared?
- Which conditions and measurements must stay consistent?
- Which conclusion is inside the study's evidence boundary?
Define variables, controls, sampling, units, and the analysis plan before interpreting a result; analysis cannot repair biased or inconsistent measurement.
A well-organized classroom study can still be limited by , measurement quality, confounding, and the population represented.
- • Question and variable cards map to the study design.
- • Control and measurement cards map to fair, reproducible data collection.
- • The conclusion card maps to a bounded claim supported by the analysis.
Part 4 of 4 · Your work▸
Check your work before submitting
- You'll be able to carry out transformation, selection, and purification steps.
- You'll be able to record yield and a quality note from your workflow.
Before lab work: read the safety rules
- No live cultures today: the transformation runs in a simulation and the plate counts are practice data.
- The simulation still asks for the bench rules a real run needs: gloves and goggles, no mouth contact, biological waste in biohazard bags, and a bleach wipe-down before and after.
4.1 Turn in your work
DueCheck the Schoology assignment for this day- Hand in
- Cloning and purification workflow data table recording transformation results, selection counts, fraction data, yield, and a quality observation.
How to submit and name your file
Submit as one PDF in Schoology.
In Schoology, open your course and the assignment for this lesson. Attach your file, select Submit, and check that it appears in the submission.
PDF upload helpYou get two school days for every day you were absent, so this deadline moves with you.
Today's lesson is in Schoology
Each school day has one lesson page in Schoology that holds everything for the day: the goal, the story so far, every table and data value, the numbered steps, and what to turn in. Open it first and work from it. The other rows for this day, if any, are the score line for a paper quiz or test and the John Carroll debate item; they do not add work. Check Schoology for each deadline.
- Today's Lesson · Mon 12/7 · Wk16 · A stain versus a Western blot, then how to keep and correct a laboratory record(today's lesson page: the goal, the data, the steps, and what to turn in are all on it)
Link will not open? Open Schoology, choose your course and section, and find the title shown above.
- CompleteEvery required part of the artifact is present, nothing left blank.
- AccurateThe science and the data are correct and match the evidence.
- Scientific reasoningYou explain your claim with evidence and reasoning (CER), not just an answer.
- Professional communicationClear, organized, labeled, and written the way a clinician or scientist would.
- SubmittedGo to Schoology to turn this in. Submit one PDF. Schoology attaches your name to your upload; on the page itself, write your period and code. Name the file: FirstName LastName - Assignment Title - YYYY-MM-DD.pdf. If you cannot get in, see Mr. Mendoza. Do not skip the work.
- Error analysis and method · counts doubleName a specific limit of the method and how it moved your result, and compare what you predicted to what happened. "Human error" does not count; say what about the procedure or instrument caused it.
How this lesson connects
Keep using what you learned last class: Life-saving biotechnology raises hard questions about access because the same product must pass separate gates of price, patents, and regulation, so who controls those gates decides who the science actually helps. Today: Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, fraction, or colony remains limited by method resolution and sample quality.
Practice: try a question, then check your answer▸
Claim ceiling for this check: Today's evidence supports a classroom claim about today's lesson. It cannot prove causation, diagnose a real patient, or justify action outside this room.
A student treats one classroom result about cloning and purification workflow as proof. What must the student add before the conclusion is defensible?
Write an answer and pick a confidence to unlock the key.
Fast retrieval with instant answers, not the commit-then-reveal check above. Try each from memory first: write what you remember about the earlier units, then check yourself here.
Missed class or ready for more?▸
Run this before you touch the bench. It is built from the real lab procedure, so the decisions you make here are the ones you will make with the equipment in your hands.
I can name the procedure's purpose and the evidence I will record. I can state today's specific hazards and the control for each. If this deck does not name them, I ask Mr. Mendoza before I touch anything. My data table is ready before materials are handled.
Finish the checklist before you handle any material.
- • No live cultures today: the transformation runs in a simulation and the plate counts are practice data.
- • The simulation still asks for the bench rules a real run needs: gloves and goggles, no mouth contact, biological waste in biohazard bags, and a bleach wipe-down before and after.
- 1Before materials are handled, identify the purpose, variables or comparison, controls, measurement units, and stop-work condition.
- 2Read the workflow protocol in the PLTW course shell and gather your materials.
- 3Run the transformation in the simulation on this page: introduce the recombinant plasmid into host cells.
- 4Record the selection counts from the practice plates on this page, which were incubated overnight, and say what the no-plasmid control shows.
- 5Run the simulated purification step and note where the target protein appears.
- 6Record yield and one quality observation in your workflow data table.
- 7Submit your cloning and purification workflow results.
- 8Record each result in the prepared table before interpreting it. Mark missing, repeated, or invalid results truthfully.
- 9Complete the named cleanup and waste route, remove PPE safely, wash hands when required, and confirm the station is ready for the next group.
| Which trial or sample this row is | What you changed on purpose | What you measured, with units | What you saw, before you explain it | Anything that could make this reading wrong |
|---|---|---|---|---|
Before the procedure, predict the result and cite the rule behind the prediction.
After the procedure, compare the result with the prediction and name one limitation or source of uncertainty.
What today's skills lead to. These are real health-science careers this course builds toward. Tap one to see, on the US Department of Labor's O*NET site, what the job actually involves, what it pays, and how fast it is growing.
Run the simulation on this page, record the selection counts from the practice plates on this page, then submit your . is its own lab later this unit, so the half comes with it.
Learn.Genetics: Bacterial TransformationSubmit as one PDF in Schoology.
Class still runs. Complete today's work as this page describes (it is self-guided). Need the concept taught without a teacher? Use this authoritative explainer:
Genetic Science Learning Center: CloningThe optional extra-credit track is open. Complete reserved-unit work from home, including virtual labs, for extra credit. Each item shows its correct submission route.
Open the extra-credit trackSources: slides, readings, and resources▸
The deck carries the prior idea forward, lets you inspect an analogy, maps the rule to biology, and ends with the same evidence decision and exit ticket used on this page.
Classroom documents for this lesson are posted in Schoology. Open Clever, then Schoology, and find each one by the name shown on its card.
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Sign in to Clever with your district Microsoft account to open Schoology or myPLTW. Follow today's posted steps. If myPLTW will not open, use the posted alternative and tell Mr. Mendoza. Turn in your completed work through the Schoology assignment.
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