Friday, April 4, 2008 - 05:45
This morning I had a banana genome, an orange genome, two chicken genomes (haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit of coffee DNA too, but didn't consume a complete coffee genome since my grinder isn't that powerful and much of the DNA would be trapped inside the ground up beans. Of course, microbes have genomes, too. But I do my best to cook those first. So, what is a genome? Is it a chromosome? Is it one of those DNA fragments or sequences that people are always writing about? A genome is a concept that's kind of like the idea of a molecule in chemistry. The best definition of a molecule that I found on the web for molecule was this:
The smallest particle of a compound that has all the chemical properties of that compound. Molecules are made up of two or more atoms ...from amfar.org Note: the atoms in a molecule are joined together by covalent bonds. A genome is a similar kind of thing. A genome is the smallest amount of DNA that's needed to make an organism what it is. Some definitions will also tell you that a genome only contains chromosomes, but that's not exactly true. Bacterial genomes can also include plasmids (yikes! Another new term!). What's a plasmid? And what's the difference between a plasmid and a chromosome and a genome? How are they alike? How are they different? Let's start with two genomes, one human and one bacterial. A genome can contain one or more molecules of DNA. We call the large molecules chromosomes and the smaller molecules, that aren't always required, plasmids. The human genome (in an unfertilized egg) has 23 chromosomes, of varying size, and several copies of identical mitochondrial chromosomes (which are about the size of large bacterial plasmids). I said "unfertilized egg" because fertilized eggs and humans have two copies of each of the 23 chromosomes and several copies of mitochondrial chromosomes. Each of the chicken eggs that I ate this morning contained 39 chromosomes and some mitochondria. If those eggs had been fertilized, I would have eaten 78 chromosomes in each egg. We measure the size of any DNA molecule, be it a small chunk that we made in a test tube or a large human chromosome, by the number of bases it contains. I made this picture in Cn3D and colored each base differently to show that this bit of DNA is three bases long. It also has a direction. Just like the letters we read on the screen, the bases are read in a left to right direction in the picture (the 5' phosphate is shown on the left side of the image and we read the sequence from 5' end to the 3' end). When we talk about sequencing DNA, we're referring to the methods we use for identifying the bases and their order.
In the human genome, the largest chromosome, number 1, contains about 247 million bases. The mitochondrial chromosome is much smaller with about 16,600 bases. Note - this picture shows 2 sex chromosomes (X and Y), 22 other chromosomes, and one mitochondria. Normally, a human genome from an unfertilized egg would only have one sex chromosome (eggs would have an X, a sperm could have an X or a Y chromosome).
A bacterial genome on the other hand, usually contains only one chromosome and one or more plasmids. But, there are exceptions. Agrobacterium tumefaciens, for example has two chromosomes (one circular and one linear) and two large plasmids. The Agrobacterium chromosomes range between 2.1 to 2.8 million bases in size and the plasmids contain between 200,000 to 540,000 bases.
To summarize, a genome contains all the DNA that's needed to make an organism what it is. A genome can have big pieces of DNA with millions of bases (the chromosomes) and smaller pieces (plasmids). And, the DNA molecules can have different shapes, too, either circular or linear. Oh yeah, I'm cooking scrambled chicken genomes for breakfast. Yum!