The synaptonemal complex is an organized protein scaffold assembled between aligned homologous chromosomes during Prophase I of meiosis. Two lateral elements run along the homologues, and transverse components connect them through a central region. Its zipper-like appearance makes chromosome synapsis visible, but the structure itself is not a completed exchange of DNA.
Yeast mutants lacking functional Zip1 helped separate these events. Homologues could pair, yet normal synaptonemal complex assembly failed and meiotic progression was disrupted. The comparison distinguishes initial recognition and alignment from construction of the full scaffold.[ref] This is why a microscopy image showing nearby chromosomes should not automatically be interpreted as evidence for a completed crossing over.

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