They do, but they don't have the endoplasmic reticulum mitochondria choroplasts. So, what do all organisms have, including prokaryotes? I just said ribosomes.
What are some of those features of life that absolutely everything has and is part of the evidence for the common ancestor theory of evolution? Rhytosomes? DNA?
Yeah. So the fact that DNA and RNA are the genetic material, there's no other type of molecule that's passed down. If you came in late, just sign this on your way out.
So everything uses DNA, everything has radisomes. What's one of the other things that defines living things? cell membrane yeah gotta have a cell membrane um thank you okay so you came in late this would be up here and um before i get too much further providence Providence is our ATP, our assistant, teacher, peer, mentor.
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Alright, so, all organisms have cell membranes and ribosomes. Common set of metabolic pathways. Cellular respiration is cellular respiration is cellular respiration.
Semi-conservative DNA replication. All that means is remember how when DNA replicates it splits the two strands and then each strand acts as a template. So in the two new stretches of DNA, half of each of them is from the original.
So it's conserved from the original to the new one. So that's what we mean. That's the semi-conservant part of that.
And DNA. And this PowerPoint is posted. Should be there. There are practice questions interspersed.
All right, so pro-periodic cells. So all are unicellular. They divide by binary vision. Vision splitting binary into two. DNA is circular and not in the nucleus, and no membrane-closed organelles, which we mentioned before.
So the basic structure of a bacteria is that there's going to be the... Plasma membrane may or may not be a cell wall, may or may not be a capsule. Some of them have flagellum, but they all have ribosomes and DNA. Now when we think about what are the three domains of life?
Three domains. Archaea, bacteria, eukarya. Right? So, what you see here is that from that original origin, first it split into bacteria and archaea.
Both bacteria and archaea are prokaryotes. And then from the, within the arcadia is where you carry us to. I'm going to talk more later. about endosymbiosis, but basically this one large arcadia, unicellular, no nucleus, swallowed a bacteria that became the mitochondria, and swallowed another bacteria that became the chloroplast.
So eukaryotes share a more recent common ancestor with Archaea. And, in chloroplasts, we're from an early cell swallowing a little bacteria, and now there's mitochondria in chloroplasts. And so some eukaryotic genes are going to be most closely related to that ancient Archaea cell.
Some of them are going to be more closely related to this bacteria that turned into a mitochondria and this bacteria that turned into a chloroplast. Of course, we couldn't study any of this until microscopes were invented. And before we had DNA sequencing, all we knew was basically shape, color, motility, if they could move or not. So bacteria tend to be shaped, one of these three things.
We're going to observe these in the lab this week. Also nutritional requirements, whether they use glucose, lactose, sucrose. Sensitivity to antibiotics.
and the structure of the cell wall, which we'll get to. So this is how we characterize and describe bacteria and Archaea. Sorry, prokaryotes and gel. So this cell wall. Most bacterial cell walls contain a molecule called peptidoglycemic.
I have trouble saying this every time. Peptidyl glycan. Okay.
Peptidyl, yeah, that molecule stains differently depending on how thick it is and where it is in the So we've got gram-positive bacteria appear blue or purple, a gram-negative appear pink or red. Gram is the type of stain we're using. And what we have is in...
the cell wall, so this one's purple, so that's gram positive. See how thick the peptidoglycan is? And it's on the outside of the cell membrane, and then this is inside the cell. So gram positive stains purple, picks up more of the stain with this thick wall of peptidoglycan. Gram-negative stains pink, picks up less of the stain, the peptidoglycan layer is much thinner, and it's in between two plasma membranes.
So there's an outer membrane and an inner membrane. So not only is there less of it, but it's sandwiched between two membranes. So usually if we're trying to identify... We don't know what it is. This is one of the first things that we'll do is stain it, see if it's gram positive or gram negative, and then into one of those two classes.
Then we look at the shape. And try to grow it with different food sources. So the shapes are either spherical, like this one in the middle, which is called coccyx or cocci. And these can be individual or they can be...
Chains or clusters. And then the rod shaped ones are bacillus or bacilli. They can also be in chains. And the most common one is a spiral shape.
Spirulum or spirula. And again, conform. Chains or clusters.
So those are the three basic shapes. Hopefully we'll see all the three of those in lab. Other bacteria are filamentous. They just look like threads. Or there are some other less common ones.
Various bizarre looking shapes and if they have a bunch of, they can have several flagella or just one little whip tail. But these three are the most common. As far as the art video, we don't know that much about them.
Many of them have never been seen and we only know about them because we find their DNA in the environment. So we find their DNA in water samples or soil samples. We haven't actually seen a whole thing. So we know that there are some poxibacilli and some are shaped like triangles and some are square. Some have little reddy-like hair.
Some are flat and grow on surfaces and look like sheets of slime. So there's a lot of variation in the Arcadia. So we said that all living things have ribosomes. All pre-living organisms have ribosomes. So sequencing the ribosomal RNA, remember that ribosomes are the thing that's going to read the...
Messenger, I'm sorry, read the transfer RNA and spit and hook up the amino acids. That ribosome has RNA. So the ribosomal RNA was present in the common ancestor of all life. It's in everything.
And we get lateral transfer of pieces of ribosomal RNA even among things that are not closely related. And so this ribosomal RNA has evolved relatively slowly compared to DNA. And so in terms of building a phylogeny, phylogenetic tree of prokaryotes, we tend to use the RNA. And now we can do whole genome sequencing and we can see that even things that are not close related sometimes exchange DNA as well. And so we call this lateral gene transfer when something moves sideways.
from one species to another and so it makes it basically confuses us in doing the phylogenetic trees but how how does this stuff move there's three ways that genetic material can move from one individual to another and it's conjugation transformation and transduction We talked about this a little bit in Bio 1. Conjugation is like bacteria sex. The two cells actually are linked by like a little bridge of cell membrane called the pylos and then directly exchange genetic material maybe the whole plasmid maybe just a gene so that's conjugation in think um a conjugal visit transformation is when one Bacteria cell dies and so as its cell membrane breaks down DNA fragments, it's spit into the environment and then a recipient cell, a living cell, picks up some of those fragments of DNA and then they get incorporated into that chromosome. So it is a transformed cell.
And then transduction is specifically with a virus that attacks bacteria. A virus that attacks bacteria is called a bacterial phase, and we'll look at some examples of that in a second. And so this is a little virus that attacks this bacteria, spits in some viral DNA, and then once it replicates and kills this bacteria, it might be carrying some of the bacterial DNA to its... Next victim, so a virus transfers is transduction.
Okay, so what does this do to us when we're trying to make these biogenetic trees and figure out how things are related? Well, if we're looking at a piece of DNA, we might say, well... If we're looking at the DNA, it looks like C and D are most closely related because they share a gene. But really, B and C are most closely related and a piece of DNA just transferred.
They don't actually have the common ancestor. So this is one of the reasons that particularly with prokaryotes where this lateral gene transfer happens, we use several genes or several locations on the genome plus morphology-like shape, and we get consensus among... Many different trees to come up with the correct one. Now these transfer genes, right, can then, of course, evolve.
Maybe they confer new adaptations and higher fitness for wherever they ended up. Genes for antibiotic, antibiotic resistance are often transferred. So this is just a reminder of how antibiotic resistance works, right? If you've got a bacteria, they're all the same species, but one of them, the pink one, Just happens to not die with that.
There has some mutation that says that antibiotic doesn't kill it. So then you killed all the green ones, but the pink one's still there. Now as the pink one replicates, now we have a whole plate of bacteria that the antibiotic doesn't work on.
This is why whenever you prescribe antibiotics, you take them for the whole five days. And then through that conjugation, transformation, or transduction, we can get lateral transfer of that resistant D, resistant G, lower muscle. And so when we're talking about the prokaryotes, many of them, maybe whole clades, we've never seen them.
They've never been described by biologists, and we can't really grow them. So the only way that we know... is through environmental genomics because we've picked up pieces of their DNA in soil or water or environmental samples and so there are probably thousands of prokaryotic species that we've never actually seen or been able to describe.
So the diversity of prokaryotes is huge. I mean they think 3.8 billion years ago was the first prokaryote. There are still prokaryotes here. They exist in massive numbers.
In terms of number of individuals, prokaryotes outnumber all eukaryotes combined. And they are pretty much everywhere. The thing to keep in mind about prokaryotes is when you think bacteria, 90% of almost most bacteria that exist in the world are beneficial.
Relatively few are actually harmful and cause disease. It's just that the ones that do cause disease, we talk about a lot because we're selfish and want to know about the ones that do. of bacteria several lineages of bacteria are what we call extremophiles phyle meaning lights so they like extreme conditions so for instance thermophiles Like heat. Magobacteria are an example of that. There are some that are even resistant to radiation and can break down nuclear waste and toxins.
So we use them to clean up contaminated sites. This image is showing the hot springs out in Yellowstone. Where we get Thermus Aquaticus, TAC.
Thermus Aquaticus was the source of the thermally stable DNA polymerase that we use in PCR. So remember we've got to have a source of polymerase for PCR, but when we're doing PCR, we're heating it up. So we had to have a polymerase that won't break down when we heat it up. So instead of using polymerase from humans, which would break down, we used polymerase from this heat-resistant bacteria. So it's called TAP because it's T.
aquaticus. Thermophilic. It's really hot. Like this thing is called Thermotoga, live in underground oil reservoirs and high temperature environments. When we take a look at this and when we think that this in particular may be related to ancient prokaryotes because when life originated 3.8 billion years ago, the planet was much hotter.
And some of the conserved gene sequences, the ancestral gene sequences, work best at high temperatures. So the gene sequences that are in just about everything work best at high temperatures. Okay, some bacteria called Firmicutes Sandvests are heat resistant because, in part because they have these endospores. So this little endospore is basically a way of it going dormant. So that it can survive unfavorable conditions like overheating, like too much salt in the water, like the pond drying out.
It just leaves this endospore behind, which has the chromosome, and can survive as long as a thousand years. Until things cool down, or the pond refills, or whatever. Some examples of that are Clostridium and Bacillus. Okay.
Another one that you've probably heard of and can be a really nasty infection is staphylococcus. People get staph infections, can be super dangerous, often end up in the hospital. If it's real bad.
So staphylococcus are abundant in the skin and they cause oils and other skin problems. This one, Staph aureus, can also cause respiratory, intestinal, and wound infections. So Staph is kind of a nasty one.
Mycoplasma, these are unique because they have no cell wall. They have a cell membrane, no cell wall. And they're very small and have a very small genome. Less than half as much DNA as other prokaryotes.
So we think that this might be the minimum amount that you need to be a living thing. is represented in these microplastics. In terms of what I'll expect you to know, I won't expect you to know specific species like Staphylococcus sporeus, but You should know what an endospore is and that they're in permacutes, that mycoplasmas have no cell wall, so the larger categories.
And one of the nasty mycoplasmas is what can cause pneumonia. So it gets into your lungs and fluid builds up and can... Kill part of your lung tissue. Yes. In terms of the anode part of the, is that the only thing you really need to know is that the heat resistant part?
It's basically a way of like a dormancy. So it can, it's not just heat resistant, it can survive for a long time and get a lot of. Peptinobacteria are what we call high GC.
They have a lot of G's and C's in their DNA. So high GC, gram positive, they have thick peptidoglycan layers. And some of them can form reproductive spores at these filament tips.
So in addition to binary fission, they also produce these spores that once released can develop into a new bacterial cell. A lot of these we get antibiotics from. So thinking about what an antibiotic is, antibiotics kill bacteria.
So actinobacteria have genes that produce proteins that can kill other bacteria. And then we harvest those and use them and now we make a lot of them in the lab. That's basically where they originated. One of them, though, is a nasty one and it does cause tuberculosis.
This is the oldest known human pathogen is tuberculosis. That's the one that will get cough and respiratory distress and can be deadly. Okay.
Like I said, vocabulary and list. Right? Business is part of the job.
Alright, so cyanobacteria. Now cyanobacteria is in particular special because we think that it was an ancient cyanobacteria that was swallowed up and became a chloroplast in E. pyridose.
So it is photosynthetic. It's photosynthetic. Does it have chloroplasts?
Chloroplasts in the right area have organs. So it does photosynthesis, but it does not have a chloroplast. It does not have a membrane-bound chloroplast. It has similar things called thylakoid that we find inside chloroplasts, but they're just in there free, naked.
So they have blue and green pigments that absorb light's energy. and can then produce carbohydrates. A lot of them can fix nitrogen, so they can take that atmospheric nitrogen and add hydrogen so that plants can take it up. So the photosynthesis is carried out on internal membrane system called photosynthetic lamellae. Alright, so here's the bacteria.
And here's these little photosynthetic lamellae, these kind of little fragments, and that's what's going to give pigment and do photosynthesis. When we look at a plant cell, inside the chloroplast, these thylakoid membranes, basically... The big eukaryotic cell swallowed up a cyanobacterium and that became the chloroplast. And that's endosymbiosis.
Oh, I had that picture bigger. So here's the thylakoid in the bacteria and here are the thylakoids in the chloroplast. This cyanobacteria, it can be free- Living in single cells, but it also forms colonies. And some of these colonies can differentiate into vegetative cells.
Vegetative meaning they don't reproduce. They just replicate. Spores.
That it's kind of like that endospore, right? The endospore was on the inside of the bacteria. This has spores that are on the outside and they can resist harsh conditions and then grow into a new cell once the conditions are right.
And heterocysts that are the nitrogen fixants. So basically what we have within this colony is we have... Cell differentiation.
That is maybe a precursor to the cell differentiation that we see in eukaryotes. Spiral keeps. So spiral keeps are gram-negative and they're modal. They can swim. They have axial filaments which are modified flagella that length of it and give them their shape and motility.
A lot of them are parasites to humans, some are pathogens. So what's the difference between a parasite and a pathogen? What's the definition of a parasite?
It needs a host. It needs a host, feeds off something else, lives inside or off of something else. So what's the definition of a pathogen? Causes disease. So a parasite doesn't necessarily cause disease.
So a parasite that causes disease is a parasitic pathogen. So, I'm sorry? So, spirochetes cause syphilis and Lyme disease and others are free-living medicines. Then we've got chlamydias. Can live only as parasites.
So from all communities are parasites. They're gram negative, they're super small. What they do is they take up ATP from the host using an enzyme called translimase.
And they have, I'm not going to go into the details of it, but they do have a complex life cycle with two different forms. Can cause eye infections, STDs, pneumonia. They're nasty.
And they do not always produce symptoms. So this is the public service announcement of the day. The thing is that... You can have pneumonia and not know and transmitted and it's much more common for it to be asymptomatic in men. So, be careful.
Pneumons are your friend. And don't believe them when he says, no baby, it's not true. So chlamydia, the way it works is, so this is the one that causes pneumonia. It's got these little elementary bodies that get taken into a cell, swallowed in by the cell, and then it differentiates into a replicating body.
And then it basically flusses out of the cell and spreads to other cells. So it's using the cell's machinery and enzymes and everything to replicate. Okay. Proteobacteria are the biggest group. And this is where we believe the mitochondria of eukaryotes were derived from.
So proteobacterium are the ones that were swallowed up and proteobacterium can do cellular work. They can take oxygen and water and CO2 and make up the CO2. So if these are doing cellular respiration, what are the other ones doing with their energy?
They're absorbing nutrients from the environment. And they have a mechanism for producing energy that just doesn't use oxygen. Doesn't follow all those steps of the Krebs cycle.
But these guys are mitochondrial-like and in part just like the thylakoids in the chloroplasts we can see in the cyanobacteria, in these proteobacteria they have membrane pieces on the inside that is where cellular respiration is happening. Some are photoautotrophs. So, autotroph makes its own food. Photo does it with light, as opposed to a chemical that it just absorbs from the environment. Some are nitrogen fixing.
So remember, nitrogen fixing is taking that atmospheric nitrogen and turning it into something that a plant can take up. One example is Escherichia coli. E.
coli, one of the most studied organisms on earth, can make humans really sick. It's one of the contaminants you sometimes hear about in the news that there's an E. coli. You can sell in a restaurant or recall a food. Some of the pathogens in this fruit cause bubonic plague, cholera, salmonella, nasty, nasty blobs.
Okay. That was a lot of bacteria. Alright, so prokaryotes are bacteria and archaea.
We've got the commonalities. They all have ribosomes. They all have a cell membrane. Some have a cell wall. They all are unicellular.
And we did examples of bacteria. Now we'll do examples of archaea. So So the separation of Arcadia from Bacteria, so back in the day my parents never learned about Arcadia. We didn't know what it was.
Thought everything that was unicellular was Bacteria. Then once we got to the point of being able to sequence DNA and RNA, differences in the RNA is what separated archaea from bacteria. And similarities in the RNA of archaea and eukarya are what told us that evolutionary institution.
And then complete genome sequencing, you know, gave us more details, which in about half the genes in archaea are unique from bacteria. So there's a lot of difference. A lot of them live in extreme habitats, like high temperatures, low oxygen, high salinity.
So a lot of them are extremophiles. One of the reasons why they weren't found for a while is... They're in these extreme environments, but there's also some common in soil and the oceans and all that stuff.
So there are five Archaea lineages. So remember, so bacteria split into these and then Archaea split into these and Eukarya branched off of this last one listed here, Loki Archaeota. So we've got Yuri Archeota, Thalma Archeota, and Loki Archeota.
All of them lack of peptidyl-like acid. So none of them have the peptidoglycan that bacteria do. That's one of the things that makes them different. They also have unique lipids in the cell membranes.
So one of the ways that makes a difference is both bacteria and eukaryotic membranes have lipids where the fatty acid is connected to the glycerol by... ester linkage which is like this and in archaea it's with an ether linkage so this is one of the things that separates archaea from everything else so the long chain lipids of archaea are branched and This glycerol at both ends of the hydrocarbons that form a lipid monolayer. So some archaea have these things in a lipid monolayer instead of a lipid bilayer, right? So here's everything else with its phospholipid bilayer. We've got two fatty acids on the inside.
This one, it's just one fatty acid with glycerol on both ends. Okay, some of them are methanogens, meaning that instead of using oxygen for respiration, they're obligate anaerobes. So they're going to be deep in water. deep in the soil where there's no oxygen or inside of other cells and they produce methane as a byproduct of their respiration a lot of them live in the guts of ruminants termites and cockroaches so think about i'm sure you've heard like at the end of the world the only thing left is going to be cockroaches and keith richards anybody know who keith richards is He's a member of the Rolling Stones who did a lot of drugs so he's well preserved. So there's a lot of cockroaches on the planet.
There's a lot of cows on the planet because we like to eat them. So these bacteria in the guts of cows are producing methane. Cow farts are methane. Anaerobic bacteria in your gut are releasing methane.
That's why your farts stank. It's the methane. Methane is a greenhouse gas. So, one of the things that we've learned is that