DNA Replication Lab for SBI4U:
Enzymes of the Replication Fork
A free interactive where Grade 12 Biology students watch one fork copy DNA, then switch an enzyme off and see exactly which job stops.
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The quick answerThe Quick Answer
The DNA Replication Lab is a free, browser-based interactive built for Ontario's SBI4U Biology course. Students watch a single replication fork open and copy a stretch of DNA in real time: helicase unzips the helix, topoisomerase relieves the strain ahead of it, SSB proteins hold the strands apart, primase lays down an RNA primer, DNA polymerase III builds the new DNA, polymerase I replaces each primer, and ligase seals the nicks between fragments. Every enzyme is a switch, so students can predict what breaks and then test it. It maps to the Molecular Genetics strand (D2, D3) and it lives in the public library, so any teacher can open it or copy it to their dashboard.
DNA replication is a process, and processes are exactly where diagrams fail. A textbook figure of a replication fork can label every enzyme and still leave students unable to say what happens first, why the lagging strand has to be built in pieces, or what actually goes wrong when one enzyme is missing.
The DNA Replication Lab turns the fork into something students can run. It is a live simulation: the helix spins as it opens, base pairs break and re-form, enzymes sit on the strands doing their jobs, and the two new strands are built in visibly different ways. Because each enzyme is a switch, the lab answers the question students actually ask in this unit: what is each of these proteins for? Turn one off and the fork stops in a specific, diagnosable way.
Open the DNA Replication Lab
The interactive runs in any browser, no login required. Open it now with your students, or sign up free to copy it to your dashboard and share it via QR code.
No credit card required · Free plan · Works on Chromebooks and tablets
What Students Can Do
Watch the fork open
Helicase unzips the double helix, topoisomerase takes the overwinding out ahead of it, and SSB proteins coat the exposed template so it cannot snap shut. Each one is drawn in the picture, not just named in a caption.
Follow both new strands
The leading strand is built continuously toward the fork; the lagging strand is built in Okazaki fragments going away from it, each one starting from a short RNA primer. Arrowheads mark the 3′ ends so students can see the two strands run in opposite directions.
Step through the finishing jobs
DNA polymerase I removes each RNA primer and fills the gap with DNA, then DNA ligase seals the nick between fragments. Switch either one off and the leftover primer or the unsealed nick stays visible on screen.
Take manual control
Pause, step one beat at a time, drop to a quarter speed or run the fork at 3×, and drag the picture to look back over the work already done. Hovering an enzyme name highlights it in the fork.
A Ready-to-Use Investigation Sequence
Hand students these six prompts in order. Each one asks them to predict first, then test the prediction by switching a single enzyme off.
Turn helicase off mid-run. What happens to the fork, and why can neither polymerase copy anything?
Check the science: The helix stays closed, so there is no single-stranded template. Replication stops before it starts.
Leave helicase on and turn topoisomerase off. Watch the fork for ten seconds. Why does it slow down?
Check the science: Unwinding overwinds the helix ahead of the fork. Topoisomerase relieves that strain, so without it helicase fights the tension and the fork crawls.
Turn SSB proteins off. What happens to the single-stranded template just behind the fork?
Check the science: Nothing is holding the strands apart, so complementary bases re-anneal and the fork stalls. SSB proteins exist to keep the template open.
Restart with primase off. Why does synthesis stop at the start of every new piece of DNA?
Check the science: DNA polymerase can only extend an existing 3′ end. It cannot start a chain from nothing, so it needs an RNA primer laid down first.
Restart with DNA ligase off and let the lagging strand reach the end. What is left between the fragments?
Check the science: All the DNA is there, but the sugar-phosphate backbone is not continuous. Those gaps are nicks, and ligase is the enzyme that seals them.
One more: turn DNA polymerase I off. What stays behind in the new strand?
Check the science: The RNA primers stay in place, because polymerase I is the enzyme that removes them and fills the gap with DNA.
Note for the class: the lab shortens each fragment to ten bases so students can see the boundaries. Real Okazaki fragments run about 1000 to 2000 bases in bacteria and 100 to 200 in eukaryotes.
Why an Interactive Beats a Diagram
A replication fork diagram compresses a sequence into a single picture. Students can point at helicase and still not know that it acts first, that the strain it creates is why topoisomerase is there, or that the two new strands cannot be built the same way because DNA polymerase only works in one direction. The order is the content, and a static figure hides it.
The lab makes the sequence run, and it makes each enzyme testable. Turning an enzyme off is a hypothesis: the fork either stalls immediately, keeps going but leaves something behind, or only breaks much later, and the reason is visible in the picture. That is a genuine investigation, and it fits the D2 expectation that students investigate the roles of cell components through lab activity rather than memorize a list.
It also fixes the two ideas students most often carry out of this unit half-formed: that replication is semiconservative, and that the two new strands are antiparallel. When one strand builds smoothly toward the fork while the other is stitched together from fragments running the other way, the lagging strand stops looking arbitrary. Students can see why the fragments exist instead of accepting that they do.
Learning Outcomes
Explain why DNA replication is semiconservative, with each daughter molecule keeping one parental strand and one newly built strand.
Compare leading and lagging strand synthesis and explain why the lagging strand has to be built in Okazaki fragments.
Describe the job of helicase, topoisomerase, SSB proteins, primase, DNA polymerase I and III, and ligase, and predict what stalls when each one is removed.
Use complementary base pairing and the 5′ to 3′ direction of synthesis to explain the antiparallel arrangement of the two new strands.
Ontario Curriculum Alignment
The activity directly supports the Molecular Genetics strand in SBI4U (Grade 12 University Biology).
| Course | Strand | Expectation |
|---|---|---|
| SBI4U | Molecular Genetics · D2 | investigate, through laboratory activities, the structures of cell components and their roles in processes that occur within the cell, including modelling the replication fork and the role of each enzyme in it. |
| SBI4U | Molecular Genetics · D3 | demonstrate an understanding of concepts related to molecular genetics, including semiconservative replication, continuous and discontinuous synthesis, and the enzymes that carry replication out. |
| SBI4U | Scientific Investigation Skills · A1 | demonstrate scientific investigation skills by predicting what happens when one enzyme is removed, testing that prediction in the simulation, and explaining the result with the model. |
| SBI4U | Biochemistry · B3 | demonstrate an understanding of the chemical structures of biochemical compounds, including the sugar-phosphate backbone and complementary base pairing that make accurate copying possible. |
Bring the DNA Replication Lab to Your Students
Open the interactive free in any browser, or sign up to copy it to your dashboard, share it with a QR code, and pair it with your own AI chatbot for a full lesson bundle.