

Biology: Three-Domain System



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  • Type: Video Tutorial
  • Length: 12:26
  • Media: Video/mp4
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  • Size: 133 MB
  • Posted: 07/01/2009

This lesson is part of the following series:

Biology Course (390 lessons, $198.00)
Biology: Classifying Earth's Organisms (4 lessons, $8.91)



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So now that you guys are experts-I mean, absolute experts on how we systematize things, particularly molecularly, we can start to talk about why we're messing with a system that's been in place since the days of Linnaeus. You know, some times we biologists just yearn for the good old days when you would just look at something and say, "bacteria," "plant," "animal." Well, we don't really yearn for those good old days because then we'd have nothing to do sometimes. But you see, the point is because of this whole idea of molecular systematics now, we have really had to relook at the entire way we break up organisms-the entire phylogeny, not just of the animal kingdom, not just of the fungus, not just of the protusts-we have to look at everything, because we are finding out that using these concepts of molecular clocks and DNA mutation, and mutation rate, and the fact that some molecules change faster than others-all of these things have literally opened up our eyes.
And so you probably have heard somewhere before that we're actually moving out of a five kingdom system and into a three-domain system and why. What's wrong with just plain old monera? There's the big one. That was the biggest change that everybody got all upset about, the fact that we have taken what used to be called the monera and literally made them illegal. No more monera. Well, where did they go? We have found out some startling things, and in essence have found out that with our three-domain system of bacteria, archaea, eukaryota, that there are as many similarities between eukaryotes and archaea, what used to be called bacteria, as there are between archaea and bacteria. Pah! You say. I'm sure you don't believe that for a moment, do you? Well, let's see if we can change that around.
What I'm going to show you right now-we're going to build a little cladogram. Remember cladograms? Cladograms are pretty cool. What we've done is we have taken-we, meaning the scientific community-not like me and my buddies-we have other things to do. What I'm going to show you, this is going to be some of them. We've taken some of the attributes of the three groupings. Let's just say I have a critter, and I say, "All right, do I want it to be a bacteria? Do I want it to be an archaea? Do I want it to be a eukaryote?" How am I going to determine it? I'm going to take you through, and I'm going to review some things because maybe it's been awhile since you saw some of those earlier lectures about cell biology and molecular biology. I'm going to take you through and I'm going to show you how and why we've decided to take these things and literally separate them. This is going to be kind of fun, I hope.
Here's what we're going to do. I'm going to take you through the chart and I'm going to make a column for bacteria, a column for archaea, and a column for eukarya, and we're going to go through one thing at a time. So the first thing we want to look at is ribosomes. Remember what a ribosome is? This is a picture from the Thinkwell archives. You remember that ribosomes are structures that are made out of RNA and protein and they're instrumental in protein synthesis and they're literally involved in the whole idea of ruling the cell. DNA makes RNA, RNA makes protein, and we always used to say that prokaryotes had different ribosomes than eukaryotes. Well, we've actually been able to look at sequences of these things now. One of the things we find is that when we look at just the size-we're not even going to mess around with sequencing here. That's another whole story. But just the size-the Svedburg unit, we find out that the bacteria and the archaea have 70S ribosomes and the eukarya has an 80S ribosome. Look what I'm going to do here. I'm going to make a check mark for bacteria and archaea. So far bacteria and archaea are winning over anybody being related to the eukaryotes. Get it? This is what we're doing. We're going to build a little cladogram here.
Now let's move down. Initiator TRNA. What do you remember about protein synthesis? Do you remember about protein synthesis that first we have transcription, where you're making MRNA, and then we have these TRNAs, and I'll just draw one for lack of a picture. And you'll remember that there was an anti-codon on the TRNA and that that anti-codon actually coded for a codon on the MRNA, and the very first amino acid that I taught you about usually carried methianine. Well, the very first TRNA was methianine. Well, look at this. Initiator TRNA for bacteria for one group of these things, these prokaryotes, has formal methianine, and these two have methianine. So look at that. They have something in common. Let's keep going.
Introns-remember what introns are? Remember that DNA has pieces of junk-hunks of DNA that are pretty meaningless, and what happens is they are edited out after transcription. So MRNA, you're going to edit out introns and you're going to leave exons-intervening sequences. Well, guess what? Introns-and I skipped RNA polymerases, but we'll come back to that one. See, I gave one away. I'm so disappointed. So introns in the TRNA, let's take a look at this. Introns are very rare in bacteria, but things that we call archaea and eukarya, both have those things. So I'm going to put a little checkmark here and here for that.
Now, let me go back, because I did skip RNA polymerases. RNA polymerases-remember, these are the enzymes that make RNA. Well, bacteria has one, archaea has several different types, and eukarya has three-I think we say several because we know it's more than one, but we're not exactly sure how many. So we're going to give this one to archaea and eukarya. You see what we're building here? This is a case for evolutionary ancestry here.
Capping in the poly (A) tail of MRNA. What do you remember about that? Remember that once messenger RNA is edited and the introns are cut out that we cap it. We put a methylated cap on it, and we actually put a big poly (A) tail on the end of it. And golly, gee, whiz-you and I do that, eukarya does that, but bacteria and archaea don't. So we're going to do a boom, boom right there.
I've got another chart. We've got about 11 of these things that we've kind of just put together, and remember, there's many more. Do you remember an operon is? Here's your worst nightmare. This is our Thinkwell archived lacoperon. You remember that the lacoperon was the lactose operon. I told you back then it was in prokaryotes, and it's simply a way to read along our RNA strand so that-or how to turn on RNA polymerase so that literally the RNA is going to be made on a gene in-and I said back then-in prokaryotes. Well, let's take a look. Who has operons? You and I don't. Operons have not been found in eukaryotic cells, but they have been found in prokaryotic cells, so we've got to give bacteria and archaea two yeses.
Plasmids. Remember what a plasmid is? A plasmid is an extra-chromosomal piece of DNA that expresses-and we use them for vectors in bioengineering and in biotechnology, but mostly these things are found in bacteria and they're transferred during bacterial conjugation. So let's see where we're going to find those things. Plasmids are rare in eukarya. They're very rare in eukarya so we really can't say yes for that, but they're in bacteria and archaea, so we're going to do this in on our cladogram-yes for that.
Oh, here's a big one. Membrane-enclosed nucleus. Boy, that was the central difference between the eukaryotes and the prokaryotes, was the fact that membrane-bound organelles. Remember that? And we saw that in this prototypical eukaryotic cell that there was a membrane-bound nucleus, and indeed, membrane-bound organelles. Well, that kind of covers our next two parts, because let's take a look here. A membrane-enclosed nucleus is absent in bacteria and archaea, so we have to give them two checks for that, and membrane-bound organelles are both absent in bacteria and archaea.
Peptidoglycan in the cell wall. What's up with that? Well, this is very, very interesting. You know, in our bacteria lectures we talk about Graham's staining, and this whole idea of peptidoglycan is really important in the structure of a bacteria of a prokaryotic cell wall, because it turns out that bacteria have it, but archaea and eukaryotes don't. Check, check.
And last, but not least, membrane lipids. Remember membrane lipids? Remember that the typical plasma membrane had a lipid bi-layer. Let's take a look at these membrane lipids. Well, for you molecular chemists and biochemists in the audience, we see that the membrane lipids in the bacteria have ester-linked and unbranched lipids. The eukaryotes have ester-linked and unbranched, and these don't. So we even have one that goes like this.
I think it's time to tally up, and I think you're going to see something here. Let's give a count and let's do this-let's link bacteria, archaea, archaea, eukaryotes, and bacteria, eukaryotes. And you're going to see why we've had to rethink everything. Okay, bacteria and archaea. One, two, three, four, five, six. All right. So there are six linkages; six things that link together to put bacteria and archaea together. Archaea and eukarya. One, two, three, four. And one bacteria, eukarya.
Take a look at this. We're one away from 50/50. I feel like a lawyer arguing a case here, but I rest my case. You can't tell me that you can't put archaea and bacteria as a completely separate group with good conscious. You have to realize-we have to realize-we have been forced to realize as systematists, that the archaea and the eukarya and the bacteria have to be literally three different groups because of the numbers of similarities between these two. This is exciting stuff. You are lucky to be a biologist in the new millennium because these are new things. Stay tuned.
The Evolution of Life on Earth
Classifying Earth's Organisms
A Phylogenetic Tree of Organisms: A Three Domain System

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