PCR & Gel Electrophoresis

Compare an unknown lane with a ladder

Predict which of two fragments will travel farther before loading the samples. Keep voltage and run time fixed, check electrode orientation, and run the size ladder beside the comparison lanes. Record lane identity, migration distance in centimeters, and the ladder-based size estimate in base pairs. Compare the complete pattern rather than selecting one matching band.

For a controlled first comparison, the ideal references below hold voltage at 135 V and compare the same 4361 bp fragment after 2700 s and 3600 s. Ask whether its farther position indicates a different fragment or simply a longer run. At the PCR station, vary cycle count and relate amplification to visibility; copying a target and separating fragments answer different questions. A matching band pattern supports consistency under these conditions, not a unique identity claim.

The poster above is a course preview; the access button states the current start condition. This lab is outside the three flagship trial courses, so read its access state before expecting to run it. For related preparation, use the AP Biology practice paths.

What you will investigate

This gel electrophoresis virtual lab combines DNA separation with a PCR amplification investigation. Load samples into lanes, compare the direction and distance of migration, use a ladder to estimate fragment size, and evaluate whether band patterns are consistent. The PCR station asks why a small starting sample may need amplification before a band can be seen.

DNA's phosphate backbone gives it a negative charge in the course model. In the electric field, fragments migrate toward the positive electrode. The wells and electrode connections are therefore part of the experimental setup. Reversing the connections does not create an ordinary size comparison with the same useful outcome.

Size, voltage, time, and a reference band

Shorter DNA fragments move farther in the modeled agarose separation under matching run conditions. Use the ladder to relate migration distance to the logarithm of fragment length, rather than assuming a direct linear relation between distance and the number of base pairs.

Ideal 4361 bp fragment comparison	Model center distance
135 V for 2700 s	3.7427 cm
135 V for 3600 s	4.9902 cm
50 V for 2700 s	1.3862 cm

These values are continuous model centers from the prompt's validation cases. Ruler readings are rounded separately. A displayed distance should not be expected to preserve every digit of the underlying center position. Keep voltage and run time attached to each measurement before comparing samples from different runs.

Increasing run duration can improve separation for some bands, but continuing indefinitely is not a solution. A fragment can move beyond the gel or become unsuitable for the intended comparison. The dye front provides another visible reference for deciding when to stop. A band that is absent from a displayed lane needs interpretation: low visibility, merging, and leaving the useful region are different explanations.

Matching patterns and acknowledging resolution

Compare a sample's collection of bands with the reference lanes. Nearby fragments can merge into a single visible band, so the number of visible bands need not equal the number of distinct fragments originally present. Mass from merged components is combined in the model; the image is therefore not a perfect one-symbol-per-fragment list.

A pattern consistent with an evidence lane supports a comparison under the selected model and procedure. It is not sufficient to identify a person with certainty or establish guilt. The course's forensic context asks for a claim supported by band evidence and a statement of limitations. Avoid replacing that reasoning with an absolute conclusion based only on a visual resemblance.

PCR and visibility

PCR cycles include denaturation, annealing, and extension. The course connects those stages with strand separation, primer binding, and copying by a heat-tolerant polymerase. Early growth can be approximately doubling per cycle in an ideal comparison, which explains why repeated cycles can turn a small input into a much larger sample.

The modeled amplification and visibility account also distinguishes copy number, DNA mass in the tube, and the amount loaded onto the gel. A large total tube amount is not necessarily the same as the loaded dose. Real-mode efficiency changes the growth comparison, so the ideal early-cycle relationship should not be applied unchanged to every run or extended indefinitely without the model's limits.

Standards and classroom use

The principal catalog connection is AP Biology Unit 6 and the gel-electrophoresis investigation. Ask students to interpret a ladder graph, compare a controlled voltage–time pair, and explain how amplification affects detection. A complete explanation separates fragment identity, migration, and visibility. Continue with population genetics or diffusion and osmosis to investigate another biological model.

Build an explanation from your records

Make a prediction before changing the conditions, then record a comparison that actually tests it. Keep the conditions attached to each row: a number without its setup can be misleading even when the arithmetic is correct. Explain what changed, what stayed fixed, and which observation supports your conclusion. If the result differs from your prediction, revise the explanation using the evidence rather than choosing a new answer without a reason.

The reference examples on this page describe the course model or its stated source data. They are not measurements collected from a physical laboratory by the reader. Compare like conditions, keep units visible, and distinguish rounded instrument displays from underlying model quantities. Use the investigation's stated limits when deciding whether a result can be generalized beyond the simulated setup. This guide supports preparation and interpretation; practical laboratory technique and safety training remain separate learning activities.