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by madhadron 2592 days ago
A chromosome is a physical object. You can see them under a microscope. In eukaryotes, they consist of a DNA double helix supercoiled and wrapped around big protein structures called nucleosomes, along with a bunch of chemical modifications of certain bits sticking off the nucleosome and of the DNA structure which are involved in a bunch of different functions in the cell. In bacteria and archaea, it's still supercoiled, and there are some proteins that are similar to nucleosomes in function, but the picture is much more diverse.

Animals tend to have the same number of chromosomes at all times, and they tend to come in pairs that are nearly identical. There are various ways of mapping chromosomes that yield unique fingerprints that are stable under the level of variation we typically see in a species (see restriction mapping for example), so we can take a particular fingerprint and call it chromosome 1 or 2 or whatever. Animals have two copies of chromosome 1 and two copies of chromosome 2, etc. There are individuals who don't, who have a single copy of one or extra copies, and this causes problems, such as Turner syndrome. Similarly, when animals reproduce, each parent produces a germ cell (sperm or egg) that has one of each of the chromosome pairs. One of the reasons that many hybrids like mules are sterile or nearly infertile is that their chromosomes, coming from different species, aren't in pairs, so when they pass on half of them, there may be necessary hunks of DNA that just aren't passed on.

Other species have different numbers of copies of chromosomes, and may vary. Depending on point in lifecycle and conditions, some plants range from two copies to hundreds. Dinoflagellates tend to have four for interesting reasons that I believe are related to the Byzantine generals problem.

There is no XY chromosome. Females in mammals follow the normal pattern with the X chromosome: they have two of them and they are passed on like any other chromosome. Males are weird. They have one copy of X and a copy of a shrunken chromosome called Y. Note that this is only mammals. Birds and reptiles have a totally different set of chromosomes for sex determination, and in some vertebrate orders the chromosomes don't fully determine sex. Incubation temperature often changes it.