Gel electrophoresis lab
Open your materials, follow the steps, then turn in your work.
Run or model gel electrophoresis and interpret band positions to compare DNA fragments.
1. Open your materials
Use the materials named in the first step below. Open lesson resources.
2. Start the work
Load the gel diagram or wet gel with the sample wells and a size ladder labeled.
Show all 5 required steps
- Load the gel diagram or wet gel with the sample wells and a size ladder labeled.
- Record how far each band travels and rank fragments from largest to smallest.
- Use the ladder to estimate the size of two unknown bands in base pairs.
- Write one sentence explaining why smaller fragments travel farther through the gel.
- Submit your banding interpretation with estimated sizes as your lab evidence.
Lost your place? Find your place by step: gel or diagram loaded with wells and ladder labeled, band distances recorded and ranked, two unknown sizes estimated from the ladder, and one sentence on why small fragments run farther. Continue at the first step not finished.
Check your work before submitting
- You'll be able to read band positions on a gel.
- You'll be able to estimate fragment sizes using a ladder.
Before lab work: read the safety rules
- Wear nitrile gloves for the whole lab whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take the gloves off.
- The power supply and the buffer-filled chamber carry a live electrical current. Keep hands, sleeves, and liquids away from the leads, snap the lid on before you switch the power on, and turn the power off before you open the lid or remove the gel.
- Treat the DNA stain (GelRed or SYBR Safe) and used gels as chemical waste. Use only pre-stained or stain-free gels; ethidium bromide is a mutagen and is not used in this class unless your teacher hands it to you directly.
- If your teacher uses a UV transilluminator to photograph the gel, do not look at the UV source and do not stand near it without the UV-blocking shield or UV-rated goggles down. A blue-light box needs the amber filter, not the shield.
- Wipe up any buffer or stain spill right away with paper towels, tell your teacher before you clean a stain spill, and drop spent gels, tips, and gloves in the labeled waste container, not the regular trash. Label every sample and photo with your group code, not your name, and wash your hands before you leave.
3. Turn in your work
DueCheck Schoology- Hand in
- Gel banding data table with migration distances, largest-to-smallest ranking, two size estimates against the ladder, and an explanation of the size-migration relationship.
How to submit and name your file
Use the submission route shown on today's today's page.
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.
Find this lesson's Schoology assignments
These are existing assignments for your section. Follow the directions in the assignment you are working on; this list does not add new work. Check Schoology for each deadline.
Link will not open? Open Schoology, choose your course and section, and find the title shown above.
How this lesson connects
Keep using what you learned last class: Is super hearing, as offered by the Clarity Implant, a net positive for humanity? Today: Agarose acts as a sieve and DNA is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
Optional: listen or watch a unit review▸
Need help? Warm-up, timing, and directions▸
💡 Big idea: acts as a sieve and DNA is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
- 0-8 and equipment orientation; review PCR pre-lab connection
- 8-25Load wells (or annotate gel diagram); identify ladder lane
- 25-45Record distances; rank all bands from largest to smallest
- 45-60Estimate sizes of two unknown bands using ladder; write values in
- 60-72Write explanation sentence for size-vs.- relationship
- 72-80Submit and interpretation; clean up workspace
- • Hook: Show an image of a finished gel and ask: what information is hiding in those faint blue bands?
- • Why it matters: is the standard readout for PCR in forensics, disease diagnosis, and the genetic tests you studied this unit.
- • Today's work: You load, run (or model), and interpret; your is the lab report.
- • Exit goal: Band interpretation with two size estimates submitted before the bell.
- • DNA is negatively charged at neutral pH; an electric field pulls fragments toward the positive pole.
- • acts as a molecular sieve: smaller fragments thread through faster and travel farther.
- • A is a mix of fragments of known size; aligning unknown bands to ladder bands gives a size estimate in .
PLTW connection and today's work
Open Activity 2.1.2 Copying Our Genes in myPLTW and complete the gel electrophoresis activity using your PCR output.
Today's stopping point: PCR diagram should be done (Tuesday); gel banding 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 at the top 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.
Lesson resources: reading, slides, and vocabulary▸
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.
Generated from this lesson's canonical data with a red-team citation check.
Is super hearing, as offered by the Clarity Implant, a net positive for humanity?
acts as a sieve and DNA is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
A library keeps a master plan protected while working copies guide production at different stations.
- Why protect the master copy?
- What information moves?
- Where can an error change the final product?
Stored information can be copied, read, and converted into a functional product.
Genes are regulated biological sequences, not conscious instructions, and one gene rarely determines a whole trait alone.
- • Master plan maps to DNA.
- • Working copy maps to RNA.
- • Production output maps to or a regulated cell function.
Driving question: After PCR, you have a clear tube of DNA fragments you cannot see. How does running them through a gel tell you their sizes in ?
What you already know: Is super hearing, as offered by the Clarity Implant, a net positive for humanity?
New idea: acts as a sieve and DNA is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
Visual or model: F1. F1. A lesson illustration or teaching diagram for Gel electrophoresis lab. Use it with E1-E3; it is a model or context image, not experimental or patient data. What to notice: Trace the labeled testing, treatment, or biological process and identify where evidence limits the decision.
- Observe or measure the relevant feature in lab.
- Organize the observation with a stable evidence ID.
- Apply this rule: Stored information can be copied, read, and converted into a functional product.
- Choose the option the evidence supports and state the limit of the conclusion.
Real biomedical example: After PCR, you have a clear tube of DNA fragments you cannot see. How does running them through a gel tell you their sizes in ?
What the evidence supports: E1-E3 and F1 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 short single strand of DNA that binds to a target sequence and gives DNA polymerase a starting point to build a new strand, as in PCR.
- • : A bacterial that cuts DNA at a specific sequence, leaving clean or sticky ends used to splice genes together.
- • : A lab method that uses an electric field to pull DNA fragments through a gel so they separate by size and show up as bands.
- • : A chip holding thousands of tiny DNA spots that lets scientists measure the activity of many genes at once by detecting which spots light up.
- • : The pairing of two single DNA or RNA strands with matching base sequences into a double strand, used in tests to detect a specific gene.
- • marker: A measurable feature, molecule, or gene used to identify a cell, organism, or condition, like a flag that signals something specific.
Use it now: Choose one decision option. Cite E1 and E3, then explain how the rule connects the evidence to your choice.
Go further, optional: The source links below are optional enrichment. Every fact required for today's local evidence decision appears in this lesson package.
Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, fraction, or remains limited by method resolution and sample quality.
Limit: A band, selected , or fluorescent fraction alone does not prove identity, , correct sequence, biological activity, or clinical suitability.
Stored information can be copied, read, and converted into a functional product.
Limit: Genes are regulated biological sequences, not conscious instructions, and one gene rarely determines a whole trait alone.
You can read band positions on a gel.
Limit: E3 defines the classroom product or success criterion. It is not independent scientific evidence and cannot justify a clinical or causal claim.
PLTW-GEND-2026-10-23 · Simulated classroom evidence scenario
Your role: medical interventions team member
Decision: Your team must decide what the evidence from lab supports before submitting the lab report named on today's page.
- • Check the controls and replicates before calling a bright spot a real expression difference between the supplied conditions.
- • Explain each glowing spot as sample DNA hybridizing to a matching probe, which reports the genes expressed in that sample.
- • Treat the as a faster gel whose colored spots report the size of each DNA fragment in the sample.
Response: State one choice, cite at least two evidence IDs, explain the rule that connects them, and add one limitation. Submit it as the lab report.
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 lab report named on today's page.
Context: sorts DNA by size using charge and a sieve, so band position becomes a readable size measurement in .
- • T1: Load the gel diagram or wet gel with the sample wells and a size ladder labeled.
- • T2: Record how far each band travels and rank fragments from largest to smallest.
- • T3: Use the ladder to estimate the size of two unknown bands in .
- • T4: Write one sentence explaining why smaller fragments travel farther through the gel.
- • T5: Submit your banding interpretation with estimated sizes as your lab evidence.
- • E1: Molecular workflows use controls and complementary separation or detection steps to evaluate a target, while each band, fraction, or remains limited by method resolution and sample quality.
- • E2: Stored information can be copied, read, and converted into a functional product.
- • E3: You can read band positions on a gel.
Measurements: Use only the measurements, units, graph, or counts supplied in today's task. No additional patient measurement is implied.
Figure finding: Teaching diagram for lab. Trace the labeled testing, treatment, or biological process and identify where evidence limits the decision. This is a teaching model, not patient or experimental data.
Uncertainty: This is a composite classroom scenario. Missing history, measurements, or confirmation tests remain unknown and limit the conclusion.
Mean = sum of values / number of values. Median = middle ordered value. Range = maximum - minimum.
For 2, 4, 4, and 10: mean = 20 / 4 = 5, median = 4, and range = 10 - 2 = 8.
Mean, median, and range keep the measurement unit. Order the values before finding the median.
Calculate the requested summary for today's supplied values, then write what it reveals and what it hides.
- • The solution must address the stated need in lab.
- • The decision must be supported by E1-E3.
- • The final product must make the success criteria visible.
- • Complete the work inside the 80-minute block.
- • Use only supplied or teacher-approved materials and evidence.
- • Do not trade , accessibility, or privacy for speed.
- • and evidence quality: must pass before scoring other criteria.
- • User need and effectiveness: highest scored criterion.
- • Time, cost, and ease of use: compare only after and effectiveness pass.
Test evidence: For each option, record the E1-E3 result that supports or fails each criterion. Do not assign a score without a named observation.
- Version or option tested
- Criterion met or missed
- Evidence ID and result
- Revision made
- Reason for the revision
- Need and user
- Criteria and constraints
- Chosen option and evidence
- Test result
- Revision and reason
Students often think Students often think larger DNA fragments travel farther because bigger things seem like they would move faster or push through harder.. The trap: It is the opposite. The is a sieve, so smaller fragments thread through the mesh faster and travel farther, while large fragments get held up near the wells. If you rank size by distance backwards, every size estimate you read off the gel will be wrong.
I recorded how far each band traveled from the well and used the size ladder to estimate the unknown bands.
Ranking, largest to smallest: Band 1 traveled the least (largest), then Band 2, then Band 3 traveled the farthest (smallest).
Size estimates: Unknown Band 2 lined up between the 1000 bp and 750 bp ladder bands, so I estimate about 850 bp. Unknown Band 3 lined up near the 500 bp ladder band, so I estimate about 500 bp.
Why smaller fragments travel farther: DNA is negatively charged, so the electric field pulls all fragments toward the positive end. The agarose acts as a sieve, and smaller fragments thread through the gel's pores more easily, so they move farther in the same time.
| Band | Migration distance | Size estimate |
|---|---|---|
| Ladder 1000 bp | 18 mm | 1000 bp (known) |
| Unknown Band 2 | 21 mm | ~850 bp |
| Ladder 500 bp | 30 mm | 500 bp (known) |
| Unknown Band 3 | 30 mm | ~500 bp |
This model shows the level of evidence and organization needed to complete: Completes the gel lab analysis: a banding data table with migration distances, a largest-to-smallest ranking, two size estimates against the ladder, and an explanation of the size-migration relationship.
- 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 data table and interpretation to Schoology.
- 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 Gel electrophoresis 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.
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.
Placement rationale
Matched PCR, , microarrays by path:Medical-Interventions/Unit-2_How-to-Screen-Your-Genes/2.1_Genetic-Testing-and-Screening; keywords:pcr, gel electrophoresis. Score 142. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Placement rationale
Matched PCR, , microarrays by path:Medical-Interventions/Unit-2_How-to-Screen-Your-Genes/00_Unit-Overview; keywords:pcr, gel electrophoresis. Score 138. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
Use this after the required lesson work when you are ready for a harder application or a deeper connection.
Placement rationale
Matched PCR, , microarrays by path:Medical-Interventions/Unit-2_How-to-Screen-Your-Genes/2.1_Genetic-Testing-and-Screening; keywords:gel electrophoresis. Score 134. Visibility: student-schoology (student-facing resource; link through Schoology rather than local path).
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.
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.
An unknown band sits between the 500 bp and 1000 bp ladder bands, closer to the 500 bp band. Roughly how large is it, and how did size determine its position?
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 name today's hazards and the control for each: Wear nitrile gloves for the whole lab whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take the gloves off. My data table is ready before materials are handled.
Finish the checklist before you handle any material.
- • Wear nitrile gloves for the whole lab whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take the gloves off.
- • The power supply and the buffer-filled chamber carry a live electrical current. Keep hands, sleeves, and liquids away from the leads, snap the lid on before you switch the power on, and turn the power off before you open the lid or remove the gel.
- • Treat the DNA stain (GelRed or SYBR Safe) and used gels as chemical waste. Use only pre-stained or stain-free gels; ethidium bromide is a mutagen and is not used in this class unless your teacher hands it to you directly.
- • If your teacher uses a UV transilluminator to photograph the gel, do not look at the UV source and do not stand near it without the UV-blocking shield or UV-rated goggles down. A blue-light box needs the amber filter, not the shield.
- • Wipe up any buffer or stain spill right away with paper towels, tell your teacher before you clean a stain spill, and drop spent gels, tips, and gloves in the labeled waste container, not the regular trash. Label every sample and photo with your group code, not your name, and wash your hands before you leave.
- 1Before materials are handled, identify the purpose, variables or comparison, controls, measurement units, and stop-work condition.
- 2Frame the question and the model: your task is to figure out how DNA fragment size (the independent variable) controls how far a band travels through the agarose gel (the dependent variable), using the DNA ladder as your known-size reference control.
- 3Design and run the separation: load the size ladder in its own lane and your samples in the remaining wells, close the chamber, run the current at the set voltage until the dye front nears the far end, then stain (or use the pre-stained gel) so bands become visible.
- 4Collect the data: measure each band's migration distance from its well with a ruler in millimeters, rank all bands largest to smallest, and use the ladder bands to estimate the size of your two unknown bands in base pairs.
- 5Build your claim with evidence and reasoning (CER): write a claim answering the question (smaller fragments travel farther), back it with your specific ladder-versus-unknown distances, and reason from the agarose-as-sieve idea for why size sets migration.
- 6Argumentation session: post your claim and estimated band sizes, then walk to another group and question theirs. Ask how they aligned an unknown band to the ladder, whether a band could be two fragments, and how they know their voltage or run time did not distort the result.
- 7Revise and report: use the strongest challenge you heard or gave to revise your claim, size estimates, or explanation, then submit the corrected data table, ladder-based estimates, and final argument as your lab evidence.
- 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.
| Trial or sample ID | Independent condition | Measured result with units | Observation before interpretation | Quality-control note |
|---|---|---|---|---|
Before you load or read the gel, predict the band pattern. Rank a large, a medium, and a small fragment by how FAR you expect each to travel from the wells (which reaches the far end, which stays near the top), sketch where you expect your two unknown bands to land relative to the ladder, and name the size range in base pairs you expect for each unknown. Write it down so it is fixed before you see the run.
After the gel runs and the bands are visible, RECORD the real result: measure each band's migration distance in millimeters from its well, rank all bands largest to smallest, and read your two unknown band sizes off the ladder in base pairs. Then compare to your prediction: Did smaller fragments actually travel farther? Did your unknowns land where you expected against the ladder, and were your predicted size ranges too high, too low, or on target? Name one thing (voltage, run time, well loading, band alignment) that could explain any gap between what you predicted and what you saw.
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.
Use to test how conserved IRF6 is across humans, mice, and zebrafish.
Goes with: BLAST: is IRF6 conserved across species?
Search ClinVar for which IRF6 changes are known to cause disease.
Goes with: ClinVar: which IRF6 changes cause disease?
From home, study the linked Khan PCR and gel resources, then interpret the provided gel image: rank the fragments by size, estimate two unknown bands against the ladder, and explain the pattern.
Khan Academy: gel electrophoresisUse the submission route shown on today's today's page.
Class still runs. Complete the online activity above (it's self-guided). Need the concept taught without a teacher? Use this authoritative explainer:
Genetic Science Learning Center: Gel ElectrophoresisYou've passed Unit 2, so the 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 track- 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. Put your first and last name in the document header. 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.
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