A chromosome is a single long DNA molecule and associated bound proteins—the blobs you see as a chromosome during cell division is way more than half protein. When a cell is not dividing they are decondensed blobs but they fold up neatly into those cords you see in micrographs for segregation during division. A chromosome needs a centromere (point of attachment for fibers to pull it into daughter cells after replication), origins of replication (areas where weak base pairing is pulled apart once per cell division to allow replication to begin), and telomeres (easy-to-rebuild-after-shortening repeats at the ends of chromosomes) if it is a linear chromosome because the ends of linear DNA molecules are difficult to replicate all the way out ot the end.
In a given species the order of genes (and everything else) will be the same on a given chromosome, as within a cell one chromosome is often repaired using the other copy as a template and when generating gametes for sex the two chromosome copies will exchange fragments. Individuals can have differences in the order of genes without having physical problems provided the cut/paste points don’t come in the middle of a functional element, though there might be less efficient reproduction when mating with those with the ‘normal’ arrangement. Over evolutionary time chromosome fragments do break and get shuffled around, but you see between say mice and humans that our chromosomes consist of chunks of an apparent ancestral set of chromosomes that have been differenty cut and pasted back together in the two lineages. Sometimes individual genes move but this is rare.
Asexual species can have their genomes shuffle arond a lot faster because they dont have to stay roughly compatible with their mating partners.
Almost all the time when you have copy number variation of genes, it is due to there being multiple copies of the gene laying right next to each other in tandem. Only a small subset of genes usually have copy number variation, but it CAN exist in a lot of placeswhere it doesn’t TYPICALLY exist. These blocks of tandem gene repeats are usually handed down unchanged, but they do change now and then when gametes are being made for sex. When one chromosome breaks and switches pieces with another, if a breakpoint happens inside one of the repeated genes it could attach itself into any of the multiple repeats with similar sequence, allowing one gamete to gain repeats at the expense of another produced by the same parent cell (2 → 3 + 1, say). As such repeats are unstable and can expand or contract quickly over evolutionary time. I don’t know how much research has been done into genes with multiple copy numbers carrying different versions of the sequence.
To try and really quickly answer some of these:
A chromosome is a single long DNA molecule and associated bound proteins—the blobs you see as a chromosome during cell division is way more than half protein. When a cell is not dividing they are decondensed blobs but they fold up neatly into those cords you see in micrographs for segregation during division. A chromosome needs a centromere (point of attachment for fibers to pull it into daughter cells after replication), origins of replication (areas where weak base pairing is pulled apart once per cell division to allow replication to begin), and telomeres (easy-to-rebuild-after-shortening repeats at the ends of chromosomes) if it is a linear chromosome because the ends of linear DNA molecules are difficult to replicate all the way out ot the end.
In a given species the order of genes (and everything else) will be the same on a given chromosome, as within a cell one chromosome is often repaired using the other copy as a template and when generating gametes for sex the two chromosome copies will exchange fragments. Individuals can have differences in the order of genes without having physical problems provided the cut/paste points don’t come in the middle of a functional element, though there might be less efficient reproduction when mating with those with the ‘normal’ arrangement. Over evolutionary time chromosome fragments do break and get shuffled around, but you see between say mice and humans that our chromosomes consist of chunks of an apparent ancestral set of chromosomes that have been differenty cut and pasted back together in the two lineages. Sometimes individual genes move but this is rare.
Asexual species can have their genomes shuffle arond a lot faster because they dont have to stay roughly compatible with their mating partners.
Almost all the time when you have copy number variation of genes, it is due to there being multiple copies of the gene laying right next to each other in tandem. Only a small subset of genes usually have copy number variation, but it CAN exist in a lot of placeswhere it doesn’t TYPICALLY exist. These blocks of tandem gene repeats are usually handed down unchanged, but they do change now and then when gametes are being made for sex. When one chromosome breaks and switches pieces with another, if a breakpoint happens inside one of the repeated genes it could attach itself into any of the multiple repeats with similar sequence, allowing one gamete to gain repeats at the expense of another produced by the same parent cell (2 → 3 + 1, say). As such repeats are unstable and can expand or contract quickly over evolutionary time. I don’t know how much research has been done into genes with multiple copy numbers carrying different versions of the sequence.