Biotech Virtual Lab: Transformation and Gel Electrophoresis

Updated 2026-10-07

This biotech virtual lab covers two AP Biology investigations on one bench: bacterial transformation and restriction enzyme analysis of DNA. In the first tab, students transform E. coli with a plasmid that carries an ampicillin-resistance gene and a GFP gene switched on by arabinose. They read six plates under room and UV light and calculate the transformation efficiency. In the second tab, they cut DNA with EcoRI, BamHI and HindIII, run an agarose gel and size the fragments from a ladder's standard curve. Every number below was read from the simulation.

Biotech bench – transformation, restriction digest and gel

Curriculum links

AP Biology: Unit 6 (Gene Expression and Regulation), topic 6.8 Biotechnology (IST-1.P), with the arabinose switch as an example of gene regulation (topic 6.5). It matches the AP bacterial transformation and restriction enzyme analysis investigations (Labs 8 and 9).
Simulic is not affiliated with or endorsed by the College Board or AQA.

Before the lab (5 min)

Ask: "E. coli from the + plasmid and − plasmid tubes is spread on LB, LB/amp and LB/amp/ara plates. Which plates will have colonies that glow green under UV light?" Students give one reason. On a class link this is question 1; the simulation unlocks after they answer.

Method in the simulation

Part A: transformation. Keep the starting values: plasmid 0.08 µg/µL, heat shock 50 s, 100 µL per plate.

In 1. Transformation, press each step button in order, from Add CaCl₂ to Incubate at 37 °C. Read the message after each step.
Drag Incubation time to 24 h.
Record the growth on all six plates. Press UV light and record which plates glow.
Tap the + plasmid LB/amp/ara plate, then tap each colony to count it, or press Count for me. Press Back to 6 plates and count the + plasmid LB/amp plate too.
Read the efficiency under Transformation efficiency, from the LB/amp/ara plate.

Plate	Growth	Under UV	Colonies counted
+ plasmid, LB
+ plasmid, LB/amp
+ plasmid, LB/amp/ara
− plasmid, LB
− plasmid, LB/amp
− plasmid, LB/amp/ara

Part B: digest and gel. Keep 100 V, 40 min and phage DNA. Lane 1 holds the ladder; lanes 2–6 hold phage DNA uncut, + EcoRI, + BamHI, + HindIII, + EcoRI + BamHI.

In 2. Digest and gel, press Digest at 37 °C, Load wells, Run gel, then Stain and view.
Press Measure the ladder for me to plot the standard curve.
Tap each band in lanes 3–5. The sample table shows its distance d and its size from the curve.

Lane	Enzyme	Number of bands	d (mm)	Size from curve (bp)
3	EcoRI
4	BamHI
5	HindIII

the stained gel with lane 3 selected and the standard curve below it

Expected results

Transformation. Both LB plates grow a lawn, and both − plasmid ampicillin plates stay empty. The + plasmid LB/amp and LB/amp/ara plates grow separate colonies in similar numbers. Under UV, only the LB/amp/ara colonies glow green. One test run gave 67 and 70 colonies.

The calculation: 0.80 µg of plasmid in 510 µL, 100 µL spread, so the plate received 0.157 µg. Then 70 ÷ 0.157 ≈ 450 transformants/µg. Counts vary at random around 73 per plate, so most runs give 300 to 650 transformants/µg. Skipping the heat shock leaves about a tenth of the colonies.

Gel. The ladder runs from 17.0 mm (10,000 bp) to 54.0 mm (250 bp). The curve is log₁₀(bp) = 4.695 − 0.0411·d (R² = 0.996, 13 points). EcoRI cuts the phage twice, giving 3 bands at 18.5, 20.0 and 25.5 mm. The curve reads them as 8,590, 7,450 and 4,430 bp; the actual sizes are 8,700, 7,100 and 4,200 bp. BamHI (3 sites) gives 4 bands and HindIII (4 sites) gives 5. The 250 bp point lies below the straight line: like a real gel, the curve bends at both ends, so read sizes from its straight middle part.

Questions for students

Prediction: which plates will have colonies that glow green under UV light?
Which plate shows that ampicillin kills cells without the plasmid?
Count the + plasmid LB/amp/ara plate. What is the transformation efficiency?
Phage DNA + EcoRI: what is the size of the band farthest from the well?
Explain why DNA moves towards the positive electrode, and why smaller fragments travel farther.

Answers for teachers:

Only the + plasmid LB/amp/ara plate.
− plasmid, LB/amp.
About 450 transformants/µg; any answer from 250 to 700 is accepted.
About 4,400 bp (actual 4,200); 3,900 to 4,700 bp is accepted.
Phosphate groups make DNA negative, so it moves to the positive electrode. The agarose gel is a mesh of pores: small fragments slip through more easily, so they travel farther in the same time.

Common misconceptions

"The arabinose made the bacteria resistant." Resistance comes from the bla gene on the plasmid. Arabinose only switches on the GFP gene.
"No glow on LB/amp means the cells have no GFP gene." The gene is there but not expressed without arabinose.
"Three cuts always give three pieces." Linear DNA cut at n sites gives n + 1 fragments; a circular plasmid gives n.
"Bigger fragments are darker because they are bigger molecules." Band darkness follows the mass of DNA, so a small fragment carries less DNA and looks fainter.

Extension

Optimise the heat shock. Run New experiment with heat shock times from 0 to 120 s and plot the colony count. It peaks near 50 s.
Map the plasmid. Set a lane to GFP plasmid + BamHI. Two sites give 2 fragments, 1,800 and 3,600 bp. Ask why the uncut plasmid gives two bands that cannot be sized from the ladder.

FAQ

Does this replace the wet lab?

It replaces the parts schools often cannot do: no genetically modified bacteria, no UV light and no DNA stain. Use it to plan, to practise the calculations, or in place of a lab you cannot run. See virtual labs vs physical labs.

Why do students get different colony counts?

Which cells take up the plasmid is random, as in a real lab. Pool the class results and calculate a mean efficiency.

Can I pin the settings for my class?

Yes. On the Share page, create a link and set the plasmid concentration, heat shock time, volume, DNA sample, voltage and run time in the starting values.