Why does DNA move toward the positive electrode in gel electrophoresis?

In IB Biology, the simplest explanation is also the correct one: DNA is negatively charged. The phosphate groups in the sugar-phosphate backbone carry negative charges at typical buffer pH. When an electric field is applied, negatively charged molecules are attracted to the positive electrode (anode). That attraction creates a consistent direction of movement for all fragments. Because every fragment is pulled the same way, the gel can then separate them based on how easily they pass through the agarose mesh. In exam answers, explicitly linking “negative phosphate backbone” to “movement toward positive electrode” usually earns the mark.

Does gel electrophoresis separate DNA by charge or by size?

For IB Biology, you should say it separates DNA primarily by size. Although charge is what makes DNA move in the first place, different DNA fragments have similar charge-to-mass ratios. That means charge differences do not meaningfully sort fragments from each other. The gel acts as the discriminating factor, slowing larger fragments more than smaller ones. So the observable pattern (how far bands travel) corresponds to fragment length. If you are asked to justify this, mention that the agarose gel functions like a sieve and that smaller fragments experience less resistance.

What is a DNA ladder and how do you use it to estimate fragment length?

A DNA ladder is a mixture of DNA fragments with known sizes that runs in a separate lane. In IB Biology questions, it is your reference scale. After electrophoresis, you compare the position of an unknown band to the ladder bands at known base-pair lengths. If an unknown band aligns closest to the 500 bp marker, you estimate it is roughly 500 base pairs. You can also interpolate if it sits between two ladder bands, giving an approximate size range. The ladder is crucial because distance traveled depends on gel conditions, so you need an internal standard for that specific run.