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Prophase I is the extended first preparatory stage of meiosis I, after DNA replication and before homologous chromosomes separate. Homologues align, the synaptonemal complex can assemble between them, and crossing over exchanges material between nonsister chromatids. These events connect inherited copies while preparing their later segregation.

Suppose a diploid cell has $2n=4$ chromosomes. After DNA replication it still has four chromosomes, each consisting of two chromatids. Pairing the homologues produces two pairs, each containing four chromatids; it does not create eight independent homologous chromosomes. Distinguishing chromosome count from DNA-copy count prevents a common error in following meiosis.

The events are experimentally separable. Yeast lacking normal Zip1 can pair homologues while failing to assemble the usual synaptonemal complex and to progress normally through meiosis.^[ref]

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.