I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (
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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!
Comments
Wouldn't your definition of molecule cover NaCl? I always make sure to stress the necessity of a covalent bond, but I'm mean.
I forgot how small the mitochondrial genome was. It is the size of a large synthetic plasmid, but much smaller than a lot of natural plasmids (as your Agro examples show).
Posted by: Ron | April 4, 2008 2:24 PM
Ron: Good point. I'll add it.
Posted by: Sandra Porter | April 4, 2008 2:29 PM
Posted by: rfguy | April 4, 2008 2:59 PM
oops! you're right. It's fixed now.
Posted by: Sandra Porter | April 4, 2008 3:12 PM
Thanks - it's a great post, sorry for not mentioning that before.
-mark.
(but maybe the wording should be "sperm could have either an X or a Y"?)
Posted by: rfguy | April 4, 2008 3:27 PM
Thanks, it's fixed.
No more editing blog posts during conference calls.
Posted by: Sandra Porter | April 4, 2008 3:32 PM
Recently, my niece, who is an honor student at her high school, refused to eat a hot dog because it had DNA in it. Instead, she just ate the carrots.
Posted by: Will TS | April 4, 2008 5:52 PM
It sounds like she should take biology.
Posted by: Sandra Porter | April 4, 2008 5:55 PM
If you REALY want to have some fun with kids, explain to them that eating raw fruits and vegetables means that they're eating stuff that is still alive! (insert maniacal laugh here)
Sushi or other raw meat would fall into this category, too. Just because it isn't a whole organism doesn't mean it still isn't living. In fact, we tend to avoid non-living (decaying) things.
For extra fun, ask them how many bugs, bacteria, non-mushroom fungi, etc., they've eaten during the day. The amount of "extras" in dry cereal is something you may not want to contemplate too hard.
Posted by: Ron | April 4, 2008 7:32 PM
I didn't follow this during the last five years but there are guys who actually feed mice with purified genomes. Unfortunately, I currently don't have online access to these articles.
Posted by: sparc | April 4, 2008 10:49 PM
I'm thinking of getting a lawn genome. Do they make female lawn genomes?
Posted by: Riesz Fischer | April 5, 2008 11:57 AM
Riesz: Well, of course grasses have genomes.
Perhaps we might rephrase your question to this - do grasses have sex?
I can answer that, but that's another post.
Posted by: Sandra Porter | April 5, 2008 1:07 PM
Hey - I love your blog. I've lurked here and never posted.
LOLZ- I'm so embarassed; I feel very silly - I have a BSc in a biological science (immunology), and I learned something new here. The eggs we eat in the morning are *haploid.* I guess now that I think about it, it makes perfect sense - why exhaust the roosters if you are just going to sell the eggs for human consumption anyway?
But for some reason, since I was a little girl, I had this idea that the eggs would have hatched if it were not for terrible human beings eating them. (One of the reasons I seldom eat eggs).
I guess I can feel less guilty ordering an omelet from now on. thnks ;)
Posted by: kristen in montreal | April 6, 2008 1:48 AM
*embarrassed
:P
sorry
Posted by: kristen in montreal | April 6, 2008 1:50 AM
Welcome Kristen!
And, don't be embarrassed. Professional biologists who study one kind of organism like viruses or humans often forget what happens in the others.
I've known quite famous people who routinely forgot some fundamental things, like that bacteria don't have introns, or red blood cells don't have DNA.
Sometimes biology is like a really long game of trivial pursuit.
Posted by: Sandra Porter | April 6, 2008 11:40 AM
Uh, I am pretty sure that the lawn genome comment by Riesz didn't have anything to do with grass. i.e. lawn genome without the first "e" in genome=gnome.
Posted by: I_like_cows | April 7, 2008 12:20 PM
Only the tiniest part an egg is haploid; the rest comes from the hen that lays the egg. This is common sense for two reasons: the time between ovulation and laying is supposed to be only about 24hr (not enough for all that cell division and protein production), and it is hard to imagine that haploid (unfertilised) eggs could be so similar to diploid (fertilised eggs) given that they would be so different genetically.
It would be difficult for a consumer to tell whether the egg they were eating was fertilised since only a very small amount of embryonic development occurs before laying - the rest happens once the clutch is complete and the hen starts incubation, in common with other birds. The presence (every now and then) of a bloody red speck is no guide - the reason these are seen less in shop eggs than farm ones is that processors shine a bright light through all their eggs and reject those with such imperfections.
So the vast, vast majority of chicken genomes that you could ever eat are diploid.
hope this helps.
Posted by: rory in italy | April 8, 2008 6:59 AM
I think most farms cull the roosters. The eggs can't get fertilized unless there are roosters around.
Posted by: Sandra Porter | April 8, 2008 12:49 PM
Hi, long time lurker, first time poster (I think). Great great great post, but as a microbiologist and accidental intronologist (I found some in the large plasmid I was studying for my thesis work) I have to take a minor exception to that last comment. Contrary to the general misconception, bacteria do so have introns! It's pretty recent stuff, there are several types, and they're a bit "different" in some ways from the classic eukaryotic introns... but there you go, bacteria have introns too. You can Google or Pubmed "bacterial introns" for a deluge of literature. Mobile Type II introns are the coolest; they behave a bit like transposons, you can find them all over the place in bacteria, fungi, eukaryote organelles like chloroplasts and mitochondria, and possibly in archeae; and they're probably the ancestors of eukaryotic introns.
Posted by: Chelonian | April 8, 2008 12:54 PM
Thanks Chelonian,
I know there are some introns. I'm even remember when the first intron was found in one the T phage.
You're right, I really should have written that introns are not as common in bacteria as they are in eucaryotes.
Posted by: Sandra Porter | April 8, 2008 1:03 PM
Oh, okay, thanks for clearing that up. Lots of biologists are still unaware of the existence of bacterial introns, though; and personally I have to say, as an undergrad I was taught that they had none. Imagine my surprise getting an intron-related blast result for a piece of my bacterial plasmid.
Posted by: Chelonian | April 8, 2008 10:29 PM