Unfortunately, the article handwaves the one thing I’ve been struggling with the most: chromosomes.
What is the relationship between chromosomes and the human genome?
I somewhat get that a chromosome is somewhat of a partition of the genome, but how does the „two copies“ phenomenon of the human genome and the „two copies“ thing of chromosomes fit together? Are those one and the same concept?
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.
This is a movie of a human kidney cell dividing [1].
The red chunks are its DNA. But they're 'chunky' because the 'whole genome' is partitioned into 23 chunk - each chunk is a 'chromosome'. And each chromosome comes as a pair. And in the movie you can see the cell split the pairs, where one set goes to one cell, and the other set goes to the other.
If you notice, in the cells just prior to 'condensing', the nuclei (red stuff) looks kind of brain-like in its topology. Those are the chromosomes as well, just relaxed and spread out.
You have 46 chromosomes. Each chromosome is one massive contiguous molecule of DNA, which can be represented as a string of (up to) 150 million letters ("nucleotides") drawn from {A, C, G, T}. Together, the whole human genome is roughly 3 billion nucleotides. Since you have two copies in each cell, you have 6 billion nucleotides in total.
Each chromosome is either an autosome or sex chromosome. The autosomes are chr1 to chr22. All people (excepting those with chromosomal disorders, like trisomy 21) have two copies of each autosome, with one copy coming from each parent. Then, for the sex chromosomes:
* If you're male, you get an X chromosome from your mom and a Y chromosome from your dad.
* If you're female, you get an X chromosome from your mom and another X chromosome from your dad.
So, yes, "two copies of each chromosome" and "two copies of the genome" are the same concept, since the genome consists of chromosomes.
> how does the „two copies“ phenomenon of the human genome and the „two copies“ thing of chromosomes fit together? Are those one and the same concept?
Which phenomena are you referring to exactly? That we have two copies of each chromosome and if they mean we have two copies of the human genome?
> Are there two copies of the XY chromosome, too?
Each of our non-sex cells[1] contain two sex chromosomes: one from our father and one from our mother. Since your mother always inherits her X chromosome, your sex is determined by which sex chromosome you got from your father. If you are a female (XX), your father passed on his X chromosome. If you are a male (XY), your father passed on his Y chromosome.
This rule makes for some interesting inferences. For example, your father in turn got his X chromosome from your grandmother and his Y chromosome from your grandfather (both on your father side, of course). Your mother, on the other hand, got his X chromsome from both your grandparents on her side.
So if you're a male, your Y chromosome was passed on from your grandfather on your father's side. If you're a female, one of your X chromosome comes from your grandmother on father's side, but your other X chromosome may come from either of your grandparents on your mother's side.
You can trace this Y-chromosome lineage back to what's called the Y-Chromosomal Adam, which is the last universal common ancestor of all currently living human males[2]. You can make a similar inference using your mitochondrial genome[3] and arrive at what we call the Mitochondrial Eve[4].
Our sex cells[5] are different, since they only have one copy of our chromosome set. The number of the chromosome set we have is called ploidy[6] and so our sex cells are haploid cells, as opposed to our non-sex cells, which are called diploid.
If you're a male, a single mature sperm cell in your body contains either the X or Y chromosome. For females it's different, since they only have the X chromosome, all their mature cells contain only one copy of the X chromosome.
What is the relationship between chromosomes and the human genome?
I somewhat get that a chromosome is somewhat of a partition of the genome, but how does the „two copies“ phenomenon of the human genome and the „two copies“ thing of chromosomes fit together? Are those one and the same concept?
Are there two copies of the XY chromosome, too?