Protein-purification lab
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.
Run a protein-purification procedure and collect fractions to isolate the target protein.
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.
- • Loading the lysate applies all proteins to the resin; only the target binds with high affinity.
- • Wash steps remove loosely bound contaminants before begins.
- • fluorescence under UV is the qualitative signal that confirms the target is in a .
A planned study connects its question to defined variables, controls, sampling, measurement, and analysis so the resulting data can support a bounded and reproducible conclusion.
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: When you actually run the column today, which of your numbered fractions will hold the target , and can you prove it with the green glow under UV?
What you already know: A planned study connects its question to defined variables, controls, sampling, measurement, and analysis so the resulting data can support a bounded and reproducible conclusion.
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 - lab.
- 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 - lab 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 lab technique that separates a mixture into its parts based on how fast each component travels through a material like paper or a gel.
- • : The step in a separation method where a solvent washes the target molecule off a column or material so it can be collected in pure form.
- • : In a separation, one of the numbered portions of liquid collected one after another as it runs off a column. Each tube holds whatever came out at that moment, so the target ends up in some tubes and not others.
- • : How free a sample is from contaminating substances, often given as the percentage of the sample that is the intended compound.
- • : A specific whose presence signals a particular cell type, disease, or biological state, used to identify or track it.
- • : A lab method that uses an electric field to pull fragments through a gel so they separate by size and show up as bands.
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 run a column and collect fractions.
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 - lab supports before submitting the labeled and result claim named on today's page.
- • Collect the later fractions, because the target stays bound to the resin while the wash carries contaminants out first.
- • Watch the first tubes off the column, since the target was loaded first and should drip out early.
- • Run a UV check on the wash fractions too, since we cannot yet prove the target did not leak out early.
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 - lab. 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 - lab supports before submitting the labeled and result claim named on today's page.
Context: Today the medical interventions team uses - lab 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 lab protocol in the PLTW course shell, then open the simulation on this page and set up the column and tubes there.
- • T2: Load the mixture and begin collecting numbered fractions.
- • T3: Add buffer to elute the bound and watch for the green fluorescent protein () signal under ultraviolet (UV) light.
- • T4: Record which fractions glow and label them as your target collection.
- • T5: Note one source of error and how you controlled for it.
- • T6: Submit your -collection data sheet.
- • 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 run a column and collect fractions.
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.
Graph the on x and the measured on y. Slope = change in y / change in x.
A measured value rises from 4 to 10 while x rises from 1 to 3. Slope = (10 - 4) / (3 - 1) = 3 y-units per x-unit.
Label both axes and units. Describe the visible trend before proposing a cause.
Rework the example for a value that rises from 6 to 18 while x rises from 2 to 6. Give the slope with its units, then name one thing a slope cannot tell you about cause.
Students often think a polished answer about - lab 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 Protein-purification lab. 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.
2.2 Start the work
Read the lab protocol in the PLTW course shell, then open the purification simulation on this page and set up the column and tubes there.
Show all 6 required steps
- Read the lab protocol in the PLTW course shell, then open the purification simulation on this page and set up the column and tubes there.
- Load the protein mixture and begin collecting numbered fractions.
- Add buffer to elute the bound protein and watch for the green fluorescent protein (GFP) signal under ultraviolet (UV) light.
- Record which fractions glow and label them as your target collection.
- Note one source of error and how you controlled for it.
- Submit your fraction-collection data sheet.
Lost your place? Reopen today's Protein-purification lab 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.
- 0-10Read protocol; open the simulation, set up the column and label the collection tubes
- 10-25Load mixture; begin collecting fractions as wash proceeds
- 25-45Add buffer; collect elution fractions in order
- 45-58Check fractions under UV; record which fractions glow
- 58-70Label target fractions; note source of error and control
- 70-80Save your simulation run; submit -collection data sheet
- • Today is the - lab, run in the simulation on this page: no cultures were ordered, so there is no lysate to load at the bench.
- • You will run the column in the simulation, collect numbered fractions, and use its UV lamp to find your .
- • Work precisely: order matters, and mislabeling a tube loses data you cannot recover.
- • data collected today feeds directly into the next class's gel interpretation.
PLTW connection and today's work
Open Activity 4.1.3 Protein Purification in myPLTW and run the protein-purification lab protocol to collect and identify your target fractions.
Today's stopping point: Chromatography diagram should be done; fraction-collection data sheet 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.
Course connection
- Activity 4.1.3 Protein Purification
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.
Parallel practice run, not today's column: a red fluorescent protein on a ten-tube column. I loaded the mixture, washed, then eluted while watching for the red glow.
Reading: tubes 1 to 3 were the load flow-through and tubes 4 to 6 the wash, with no glow, so the unbound proteins washed off. Tube 7 glowed faintly, tube 8 glowed strongly, tube 9 faintly, and tube 10 not at all. So tubes 7 to 9 are my target collection, with most of the protein in tube 8.
Error-control note: one source of error is uneven tube volumes, which make a tube look brighter only because it holds more liquid. I controlled for it by collecting the same number of drops in every tube.
| Tube | Buffer applied | Red glow | Label |
|---|---|---|---|
| 1 to 3 | Load flow-through | No | Discard |
| 4 to 6 | Wash | No | Discard |
| 7 | Elution | Faint | Target |
| 8 | Elution | Strong | Target |
| 9 | Elution | Faint | Target |
| 10 | Elution | No | Discard |
This model shows the level of evidence and organization needed to complete: Models the fraction-collection data sheet on a parallel practice column for a different glowing protein: tube number, buffer applied, glow, target labels, and one error-control note.
- Name the variables and include units.
- Enter observations without changing the raw values.
- Check labels, calculations, and patterns before interpreting the data.
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 fraction-collection data sheet in Schoology before leaving lab.
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 run a column purification and collect fractions.
- You'll be able to identify target fractions using the green fluorescent protein (GFP) signal.
Before lab work: read the safety rules
- No bench hazards today: the column runs in a simulation.
- The simulation asks for the rules a real run needs: gloves and goggles, and never look into a UV lamp, because UV light harms eyes and skin.
4.1 Turn in your work
DueCheck the Schoology assignment for this day- Hand in
- Fraction-collection data sheet recording tube number, buffer applied, GFP signal (yes/no), and target-fraction labels plus one error-control note.
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 · Thu 12/10 · Wk16 · Precision medicine and the TPMT enzyme, then align the gene for five patients(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: A planned study connects its question to defined variables, controls, sampling, measurement, and analysis so the resulting data can support a bounded and reproducible conclusion. 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 - lab. It cannot prove causation, diagnose a real patient, or justify action outside this room.
A student treats one classroom result about protein-purification lab as proof. What must the student add before the conclusion is defensible?
Write an answer and pick a confidence to unlock the key.
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 bench hazards today: the column runs in a simulation.
- • The simulation asks for the rules a real run needs: gloves and goggles, and never look into a UV lamp, because UV light harms eyes and skin.
- 1Before materials are handled, identify the purpose, variables or comparison, controls, measurement units, and stop-work condition.
- 2Read the lab protocol in the PLTW course shell, then open the purification simulation on this page and set up the column and tubes there.
- 3Load the protein mixture and begin collecting numbered fractions.
- 4Add buffer to elute the bound protein and watch for the green fluorescent protein (GFP) signal under ultraviolet (UV) light.
- 5Record which fractions glow and label them as your target collection.
- 6Note one source of error and how you controlled for it.
- 7Submit your fraction-collection data sheet.
- 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.
Complete the virtual - run on this page, recording which fractions show the signal under UV, then submit your -collection data sheet.
Learn.Genetics: Gel ElectrophoresisSubmit 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: Genetics basics and proteinsThe 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.
Open this when the class reaches this activity and use it to complete the required lesson artifact.
Open this when the class reaches this activity and use it to complete the required 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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