Gel electrophoresis 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 or model gel electrophoresis and interpret band positions to compare DNA fragments.
Optional: listen or watch a unit review▸
Part 1 of 4 · Background and definitions▸
💡 Big idea: acts as a sieve and is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
- • 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 .
- • Read the control lanes before any sample: the must show the target band and the no-template control must be blank, or the run cannot be interpreted.
Is super hearing, as offered by the Clarity Implant, a net positive for humanity?
acts as a sieve and is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
Driving question: After , you have a clear tube of fragments you cannot see. How does running them through a gel tell you their sizes in ?
What you already know: From the class before the John Carroll debate: Genetic results can be uncertain and easy to misread, so who controls access to them is an ethical decision that can protect or harm a patient.
New idea: acts as a sieve and is pulled by charge, so smaller fragments travel farther and band position becomes a readable size map.
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: 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 , you have a clear tube of fragments you cannot see. How does running them through a gel tell you their sizes in ?
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 short single strand of that binds to a target sequence and gives DNA polymerase a starting point to build a new strand, as in .
- • : A bacterial that cuts at a specific sequence, leaving clean or sticky ends used to splice genes together.
- • : A lab method that uses an electric field to pull fragments through a gel so they separate by size and show up as bands.
- • : A chip holding thousands of tiny spots that lets scientists measure the activity of many genes at once by detecting which spots light up.
- • : The pairing of two single 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. 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.
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.
Limit: A band, selected , or fluorescent 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.
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 lab report named on today's page.
- • Send the sample for sequencing before naming which fragment a band is, since a gel reports size and never identity.
- • Read the farthest traveling bands as the smallest fragments, because the sieve holds larger near the wells.
- • Assign the biggest sizes to the bands farthest from the wells, since larger fragments push through the gel harder.
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 lab report named on today's page.
Context: sorts 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. If you were absent or your class models the gel, use this practice gel (a drawn teaching example, not a real run): the ladder lane has bands at 1,500 bp (12 mm from the well), 1,000 bp (17 mm), 500 bp (28 mm) and 250 bp (38 mm); the sample lane has unknown band A at 22 mm and unknown band B at 33 mm.
- • 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, , 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.
Uncertainty: This is a composite classroom scenario. Missing history, measurements, or confirmation tests remain unknown and limit the conclusion.
Students often think larger 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.
- 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.
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.
PCR controls: read the control lanes before any sample
What each control lane is for
| Lane | What went into the tube | What you should see | If you see something else |
|---|---|---|---|
| DNA ladder | Fragments of known sizes | A row of bands you can label in base pairs | You cannot estimate sizes; do not report any band size |
| Positive control | DNA known to contain the target | One band at the target size | No band: the PCR failed, so a blank sample lane could be a false negative. Repeat the run |
| No-template control (negative control) | Every reagent, but water instead of DNA | No band at the target size | A band at the target size: something is contaminated, so a sample band could be a false positive. Repeat with fresh reagents |
- A PCR run is only as trustworthy as its controls. Check these lanes first, every time, before you say anything about a sample.
One rule, then read your samples
- Read the sample lanes only when the positive control shows the target band AND the no-template control is blank at the target size.
- A faint, fuzzy band near the very bottom of a lane (under about 100 base pairs) is usually primer dimer: primers stuck to each other. It is not the target and does not mean contamination.
- The samples you run today were amplified before class. The practice gels below show what the control lanes of a run like theirs tell you.
Control check: three practice gels (target size 500 bp)
| Gel | Positive control lane | No-template control lane | Your call: valid, failed, or contaminated |
|---|---|---|---|
| 1 | One band at 500 bp | Blank | ? |
| 2 | Blank | Blank | ? |
| 3 | One band at 500 bp | One band at 500 bp | ? |
- For each gel, write one line in your data table: valid, failed, or contaminated, and the lane that tells you.
2.2 Start the work
Load the gel diagram or wet gel with the sample wells and a size ladder labeled. If you were absent or your class models the gel, use this practice gel (a drawn teaching example, not a real run): the ladder lane has bands at 1,500 bp (12 mm from the well), 1,000 bp (17 mm), 500 bp (28 mm) and 250 bp (38 mm); the sample lane has unknown band A at 22 mm and unknown band B at 33 mm.
Show all 5 required steps
- Load the gel diagram or wet gel with the sample wells and a size ladder labeled. If you were absent or your class models the gel, use this practice gel (a drawn teaching example, not a real run): the ladder lane has bands at 1,500 bp (12 mm from the well), 1,000 bp (17 mm), 500 bp (28 mm) and 250 bp (38 mm); the sample lane has unknown band A at 22 mm and unknown band B at 33 mm.
- 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.
- 0-8 and equipment orientation; five-minute review, including what the positive and no-template control lanes are for (the samples come already amplified)
- 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 the size-vs.- sentence and the three-line control check for the practice gels
- 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 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.
PLTW connection and today's work
Open Activity 2.1.2 Copying Our Genes in myPLTW and complete the gel electrophoresis activity using the pre-amplified PCR products provided (the PCR day is not on this calendar).
Today's stopping point: Your PCR review from the debate day's before-next-class block should be done; 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 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.
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 750 bp | 23 mm | 750 bp (known) |
| 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 as one PDF to Schoology assignment Wk9 Lab report: Gel electrophoresis lab.
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 .
- • Working copy maps to RNA.
- • Production output maps to or a regulated cell function.
Part 4 of 4 · Your work▸
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 safety goggles and nitrile gloves for the whole lab. Keep the gloves on whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take them 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. This class uses only pre-stained gels or those safer stains. Students never handle ethidium bromide; if it is ever used, only the teacher handles it.
- If your teacher uses an ultraviolet (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.
4.1 Turn in your work
DueCheck the Schoology assignment for this day- Hand in
- Gel banding data table with migration distances, largest-to-smallest ranking, two size estimates against the ladder, an explanation of the size-migration relationship, and a three-line control check (valid, failed, or contaminated) for the practice gels.
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 · Fri 10/23 · Wk9 · Plan the gene test, then isolate DNA from cheek cells(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: 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.
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 safety goggles and nitrile gloves for the whole lab. Keep the gloves on whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take them off. My data table is ready before materials are handled.
Finish the checklist before you handle any material.
- • Wear safety goggles and nitrile gloves for the whole lab. Keep the gloves on whenever you touch the gel, loading dye, buffer, or stain, and wash your hands with soap after you take them 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. This class uses only pre-stained gels or those safer stains. Students never handle ethidium bromide; if it is ever used, only the teacher handles it.
- • If your teacher uses an ultraviolet (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.
| 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 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 is across humans, mice, and zebrafish.
Goes with: BLAST: is IRF6 conserved across species?
Search ClinVar for which changes are known to cause disease.
Goes with: ClinVar: which IRF6 changes cause disease?
From home, study the linked Khan and gel resources, then use the practice gel in step 1 on this page: rank the fragments by size, estimate the two unknown bands against the ladder, and explain the pattern.
Khan Academy: 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: Gel ElectrophoresisThe 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.
Use this if you were absent, got stuck, or need another pass before you submit the lesson artifact.
Use this after the required lesson work when you are ready for a harder application or a deeper connection.
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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